Article
Forestry
Stefan Kaufmann, Sarah-Katharina Funck, Franziska Paintner, Thomas Asbeck, Markus Hauck
Summary: Retention forestry is an effective method to create structurally more diverse forests, which can have a positive impact on epiphytic bryophytes and lichens. In continuous-cover forests, retained trees, especially habitat trees, have shown to support higher species richness and diversity of lichens. Species diversity of tree species may play a more important role in protecting epiphytic bryophytes and lichens than stem diameter.
FOREST ECOLOGY AND MANAGEMENT
(2021)
Article
Biochemical Research Methods
Tao Cui, Tingting Wang
Summary: Researchers developed a Python-based package (TensorZINB) using the TensorFlow deep learning framework to solve the zero-inflated negative binomial (ZINB) model for single cell RNA sequencing data analysis. They also proposed a hybrid model to further improve performance and systematically evaluated seven different statistical models. The study showed that TensorZINB outperformed existing ZINB solvers in terms of stability, computing speed, and performance.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Health Care Sciences & Services
T. Baghfalaki, M. Ganjali
Summary: The study utilized the INLA approach for joint modeling of zero-inflated count and time-to-event data, introducing zero-inflated hurdle and Weibull models as sub-models, as well as a joint partially linear model. The method's performance was assessed through simulation studies and compared with MCMC approach, and applied to analyze two real datasets on pregnancy and HIV research.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2021)
Article
Computer Science, Interdisciplinary Applications
Niloufar Dousti Mousavi, Hani Aldirawi, Jie Yang
Summary: AZIAD is a newly developed R package for analyzing zero-inflated or zero-altered data, covering a larger class of models with more accurate parameter estimates and greater power for model identification and selection.
JOURNAL OF STATISTICAL COMPUTATION AND SIMULATION
(2021)
Article
Forestry
Vasilije Trifkovic, Andrej Boncina, Andrej Ficko
Summary: In this study, the influences of various stand, site, and climatic factors on tree recruitment in uneven-aged forests were explored. It was found that stand structure, including stand basal area and the proportion of tree species, was the most important factor affecting recruitment. Soil pH and rockiness were important for fir recruitment, while decadal precipitation and temperature played significant roles in beech and spruce recruitment. Furthermore, the optimal and critical ranges of these factors differed among the species.
FOREST ECOLOGY AND MANAGEMENT
(2023)
Article
Economics
Pengcheng Zhang, David Pitt, Xueyuan Wu
Summary: The article emphasizes the importance of zero-inflated count models in analyzing the frequency of insurance claims. While there is a vast literature on univariate models, the research on multivariate models is relatively less advanced. The article proposes a multivariate zero-inflated hurdle model and applies the expectation-maximization algorithm for parameter estimation. The results demonstrate the superior performance of the model in multivariate claim count modeling.
ASTIN BULLETIN-THE JOURNAL OF THE INTERNATIONAL ACTUARIAL ASSOCIATION
(2022)
Article
Forestry
Julia C. Haas, Alexander Vergara, Alonso R. Serrano, Sanatkumar Mishra, Vaughan Hurry, Nathaniel R. Street
Summary: Drought stress has significant impacts on seedling establishment, survival, and productivity of plants, particularly coniferous tree species. Norway spruce seedlings show reversible physiological plasticity in response to drought, with changes in shoot water potential and ABA levels. Root and needle transcriptional responses to drought differ, with roots showing more down-regulation of growth-related genes. Comparison with previously studied drought-response genes in Arabidopsis thaliana shows both conservation and divergence in transcriptional response in P. abies, highlighting the importance of profiling both above- and belowground tissues to understand drought response mechanisms in coniferous species.
Article
Multidisciplinary Sciences
Beatrice Franzolini, Andrea Cremaschi, Willem van den Boom, Maria De Iorio
Summary: This article introduces a novel Bayesian approach for analyzing and clustering multiple, possibly related, zero-inflated processes. By introducing a joint model for zero-inflated counts, the number of parameters is reduced and the probabilities of zero-inflation and the parameters of the sampling distribution are flexibly modeled. The proposed approach is demonstrated on an application involving the use of the messaging service WhatsApp.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2023)
Article
Multidisciplinary Sciences
Madiha Liaqat, Shahid Kamal, Florian Fischer, Nadeem Zia
Summary: This study aims to explore factors influencing the number of axillary lymph nodes in women diagnosed with primary breast cancer. The zero-inflated negative binomial model is found to be the best model for predicting and describing the number of involved nodes. Tumor size and grade contribute to a higher number of lymph nodes, while women's age does not have a significant influence.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2022)
Article
Forestry
Clement Fritsch, Stephane Dumarcay, Francis Colin, Philippe Gerardin
Summary: In the context of global warning, sustainable development, bioeconomy and circular economy, this study aims to explore better utilization of by-products in the wood processing industry. The effects of longitudinal position and silviculture on the chemical composition of bark in three softwood species were investigated. The results showed that the content of different polymers generally decreased slightly with tree height, while extractives content increased. The chemical composition of bark also varied slightly according to the position along the trunk and the silvicultural treatment.
SCANDINAVIAN JOURNAL OF FOREST RESEARCH
(2022)
Article
Mathematics
Dongyang Yang, Wei Xu
Summary: The use of mediation analysis in studying cause-and-effect relationships through mediators has become increasingly popular. The human microbiome can play a role in the development of complex diseases by mediating disease-causing pathways. However, standard mediation analysis is not suitable for microbiome data due to excessive zero values and over-dispersion in sequencing reads. To address these challenges, a novel mediation analysis algorithm was developed under the potential-outcome framework. This algorithm estimates the mediation effect of the microbiome by decomposing indirect effects based on zero-inflated distributions. Extensive simulations showed that the proposed model performed well compared to alternative approaches. The algorithm was applied to a real human microbiome study investigating the relationship between LACTIN-V treatment and immune response mediated by certain taxa.
Article
Forestry
Cecilia Laurell, Torkel Berglund, Anna B. Ohlsson
Summary: In this study, RNA-seq technology was used to study the effects of nicotinamide treatment on gene expression in the roots of spruce seedlings. The results showed that stress response genes and epigenetic-related genes were differentially expressed, supporting the hypothesis of nicotinamide as a potential defense-signal mediator.
JOURNAL OF FORESTRY RESEARCH
(2022)
Article
Multidisciplinary Sciences
Ewa Blonska, Jaroslaw Lasota, Marta Kempf, Ivika Ostonen
Summary: This study aimed to compare the effects of soil and deadwood substrates on the regeneration of silver fir seedlings. The results showed that heavily decomposed fir logs provided a favorable substrate for seedling growth, and the type of substrate had an impact on root morphology.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Sangsung Park, Sunghae Jun
Summary: A large part of big data is made up of text documents, and analyzing this data requires preprocessing and building a structured document-word matrix. This matrix represents the frequency of words in each document and helps to improve predictive model performance. This paper proposes a method to solve the sparsity problem caused by the abundance of zero values in the matrix, and uses compound Poisson linear modeling. By comparing the Akaike information criterion (AIC) values of the proposed model with traditional models, the validity and effectiveness of the method are verified.
APPLIED SCIENCES-BASEL
(2023)
Article
Mathematical & Computational Biology
Tong Kang, Jeremy Gaskins, Steven Levy, Somnath Datta
Summary: We propose a Bayesian hurdle mixed-effects model for analyzing longitudinal ordinal data with a complex multilevel structure. The model is applied to the dataset from the Iowa Fluoride Study (IFS) to examine the relationships between fluorosis status and potential risk/protective factors. The complex hierarchical structure of the data and the presence of a large proportion of zero values that follow different statistical patterns from non-zero categories are addressed by the use of a hurdle model. The accuracy and effectiveness of the proposed methodology are evaluated through simulation studies.
STATISTICS IN MEDICINE
(2023)
Article
Agronomy
B. Bordron, A. Germon, J-P Laclau, I. R. Oliveira, A. Robin, C. Jourdan, R. R. Paula, R. C. Pinheiro, J. Guillemot, J. L. M. Goncalves, J-P Bouillet
Summary: In mixed species forests, the effects of soil fertility on belowground processes were investigated. Fertilization increased competition between species, leading to partial exclusion of Acacia fine roots from nutrient-rich topsoil. Eucalyptus roots explored soil near Acacia trees more in unfertilized stands, indicating facilitation through higher soil N availability and direct N transfer from Acacia trees.
Article
Agronomy
Olivier Dassou, Leifi Nodichao, Herve Aholoukpe, Yves Cakpo, Christophe Jourdan
Summary: This study compared three methods for estimating root biomass of young and adult oil palm trees in commercial plantations. The simplified Voronoi trench method required twice as much labor time as the auger method but was the most efficient way to estimate oil palm total root biomass.
Article
Agronomy
Amaury Frankl, Olivier Evrard, Erik Cammeraat, Bjorn Tytgat, Elie Verleyen, Alexia Stokes
Summary: High mountain environments are fragile and subject to accelerated soil erosion due to human disturbances and extreme weather events. Identifying erosion hotspots is crucial for effective mitigation strategies. While sediment source fingerprinting using geochemical properties has limitations in complex lithologies or shallow soils, environmental DNA (eDNA) from plant litter fixed onto fine soil particles shows promise as a targeted sediment fingerprinting method. Pioneering studies indicate that eDNA can detect vegetation communities and individual plant species, making it a valuable tool for identifying erosion hotspots and prioritizing ecological restoration efforts in high mountain environments.
Article
Plant Sciences
Guangqi Zhang, Zhun Mao, Claire Fortunel, Jordi Martinez-Vilalta, Gaelle Viennois, Pascale Maillard, Alexia Stokes
Summary: Nonstructural carbohydrates are mainly stored in the radial parenchyma of tree stems, which has a larger surface area in warmer climates. The content of nonstructural carbohydrates in radial parenchyma is positively correlated with wood density, but not with axial parenchyma. Tree height is not related to nonstructural carbohydrates.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Ecology
Lorene Siegwart, Isabelle Bertrand, Olivier Roupsard, Maxime Duthoit, Christophe Jourdan
Summary: In agroforestry systems, the decomposition rate of root litter is mainly impacted by soil moisture and depth, with Faidherbia roots decomposing more slowly than cowpea and pearl millet roots. Pearl millet aboveground biomass is higher under trees compared to farther away, while Faidherbia fine roots contribute slightly to higher carbon stocks under trees.
JOURNAL OF ARID ENVIRONMENTS
(2022)
Article
Soil Science
Yali Yang, Hongtu Xie, Zhun Mao, Xuelian Bao, Hongbo He, Xudong Zhang, Chao Liang
Summary: No-till with medium and high amounts of stover mulching can increase SOC stocks in croplands, and fungal necromass C plays a significant role in the storage of SOC.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Review
Ecology
Ilenia Murgia, Filippo Giadrossich, Zhun Mao, Denis Cohen, Gian Franco Capra, Massimiliano Schwarz
Summary: Slope Stability Models (SSMs) are valuable tools in land management to mitigate the effects of shallow landslides caused by rainfall. They consider vegetation to evaluate the influence of trees on slope stability and the strategies for root reinforcement.
ECOLOGICAL ENGINEERING
(2022)
Editorial Material
Agronomy
Timothy S. George, Ismail Cakmak, Richard J. Simpson, Alexia Stokes, Philip J. White
Summary: This special issue commemorates Hans Lambers' 30 years as Editor in Chief of Plant and Soil, reflecting on the impact and highlights of the journal during his tenure. The issue includes 44 papers, covering a wide range of topics and showcasing the depth and breadth of scientific research in Plant and Soil. Special attention is given to the Marschner reviews and past Special Issues, as well as the most impactful papers published under Hans Lambers' editorship. The editorial also provides insights into the changes from the perspective of the Editor in Chief.
Article
Biology
Guangqi Zhang, Pascale Maillard, Zhun Mao, Loic Brancheriau, Julien Engel, Bastien Gerard, Claire Fortunel, Jean-Luc Maeght, Jordi Martinez-Vilalta, Merlin Ramel, Sophie Nourissier-Mountou, Stephane Fourtier, Alexia Stokes
Summary: This study describes the functional traits in leaves, stems, and roots, including NSC, carbon, nitrogen, specific leaf area, stem and root wood density, and xylem traits. Data from up to 90 angiosperm species from temperate, Mediterranean, and tropical climates are provided. These data are useful for understanding the trade-offs in resource allocation from a whole-plant perspective and to better quantify xylem structure and function related to water transportation, mechanical support, and storage. The data also provide researchers with insights into how trees can adapt to a changing climate.
BMC RESEARCH NOTES
(2022)
Article
Ecology
Zhun Mao, Catherine Roumet, Lorenzo M. W. Rossi, Luis Merino-Martin, Jerome Nespoulous, Olivier Taugourdeau, Hassan Boukcim, Stephane Fourtier, Maria Del Rey-Granado, Merlin Ramel, Kang Ji, Juan Zuo, Nathalie Fromin, Alexia Stokes, Florian Fort
Summary: This study characterizes the mechanical traits of plant roots and explores their relationship with the root economics space. The results show that transport roots tend to be stronger and tougher than absorptive roots, and their mechanical traits are positively correlated with specific root length and negatively correlated with root diameter and tissue density. Moreover, the taxonomical subgroup and root type also play a significant role in shaping root mechanical variation.
Article
Agronomy
Lorene Siegwart, Christophe Jourdan, Gabin Piton, Soh Sugihara, Karel Van den Meersche, Isabelle Bertrand
Summary: This study aimed to evaluate the contribution of understory vegetation strip and crop roots to soil C stocks in a young agroforestry system. The results showed heterogeneous root biomass and properties in the system, and no horizontal variation in soil microbiological properties and organic C stocks at this stage.
Article
Agronomy
Fatou Gning, Christophe Jourdan, Diatta Marone, Daouda Ngom, Anders Raebild
Summary: Understanding the root distribution of sub-Sahelian tree species is crucial for comprehending their ecophysiology and optimizing their use in agroforestry. This study investigated the root distribution of three sub-Sahelian tree species, Adansonia digitata, Faidherbia albida, and Borassus akeassii, across three sites with different precipitation and soil conditions in Senegal. The results showed that root density varied significantly among sites, with the highest density observed in the humid site for all tree species. B. akeassii had the highest root density compared to the other two species. Fine root biomass was concentrated at different soil depths for different species. Understanding the root distribution of sub-Sahelian tree species can help mitigate competition between crops and perennials in agroforestry parklands.
AGROFORESTRY SYSTEMS
(2023)
Article
Water Resources
Djim M. L. Diongue, Olivier Roupsard, Frederic C. C. Do, Christine Stumpp, Didier Orange, Sidy Sow, Christophe Jourdan, Serigne Faye
Summary: This study aims to evaluate the ability of different pedotransfer functions (PTFs) in simulating soil hydraulic parameters (SHPs) in Sahelian regions, particularly in terms of water fluxes in Senegal's Groundnut basin. The study found that inverse modeling methods can accurately simulate soil water dynamics compared to traditional PTFs.
HYDROLOGICAL SCIENCES JOURNAL
(2022)
Article
Engineering, Civil
Djim M. L. Diongue, Giuseppe Brunetti, Christine Stumpp, Frederic C. Do, Olivier Roupsard, Didier Orange, Waly Faye, Sidy Sow, Christophe Jourdan, Serigne Faye
Summary: The Faidherbia tree is commonly used as an intercrop in the Sahelian agroforestry parklands, but its effect on the water balance is not well understood. In this study, a low-fidelity hydrological model was combined with a correction function to emulate a high-fidelity description of the system. The results show that the model can accurately reproduce observations and indicate a positive effect of Faidherbia on the water balance in arid areas.
JOURNAL OF HYDROLOGY
(2023)
Article
Forestry
Nicolas Bilot, Christine Deleuze, Laurent Saint-Andre, Yann Rogaume, Meriem Fournier, Holger Wernsdoerfer
Summary: Bioenergy from wood can contribute to energy-transition policies, and using low-quality wood as fuel is important. The study aims to develop a model that links management decisions with indicators of wood fuel production and supply chain, and test it in a case study. Management decisions greatly influence efficiency indicators and its relevance for energy-transition policies.
ANNALS OF FOREST SCIENCE
(2023)