keyword
https://read.qxmd.com/read/38493170/fungal-community-composition-predicts-forest-carbon-storage-at-a-continental-scale
#1
JOURNAL ARTICLE
Mark A Anthony, Leho Tedersoo, Bruno De Vos, Luc Croisé, Henning Meesenburg, Markus Wagner, Henning Andreae, Frank Jacob, Paweł Lech, Anna Kowalska, Martin Greve, Genoveva Popova, Beat Frey, Arthur Gessler, Marcus Schaub, Marco Ferretti, Peter Waldner, Vicent Calatayud, Roberto Canullo, Giancarlo Papitto, Aleksander Marinšek, Morten Ingerslev, Lars Vesterdal, Pasi Rautio, Helge Meissner, Volkmar Timmermann, Mike Dettwiler, Nadine Eickenscheidt, Andreas Schmitz, Nina Van Tiel, Thomas W Crowther, Colin Averill
Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors...
March 16, 2024: Nature Communications
https://read.qxmd.com/read/38493130/infrared-a-declarative-tree-decomposition-powered-framework-for-bioinformatics
#2
JOURNAL ARTICLE
Hua-Ting Yao, Bertrand Marchand, Sarah J Berkemer, Yann Ponty, Sebastian Will
MOTIVATION: Many bioinformatics problems can be approached as optimization or controlled sampling tasks, and solved exactly and efficiently using Dynamic Programming (DP). However, such exact methods are typically tailored towards specific settings, complex to develop, and hard to implement and adapt to problem variations. METHODS: We introduce the Infrared framework to overcome such hindrances for a large class of problems. Its underlying paradigm is tailored toward problems that can be declaratively formalized as sparse feature networks, a generalization of constraint networks...
March 16, 2024: Algorithms for Molecular Biology: AMB
https://read.qxmd.com/read/38493117/the-utilization-of-decision-trees-on-orthopantomographic-and-lateral-panoramic-graphs-for-the-diagnosis-of-unilateral-anterior-disc-displacement-of-the-temporomandibular-joint
#3
JOURNAL ARTICLE
Muhammed Enes Naralan, Binali Cakir, Kaan Orhan
BACKGROUND: Investigation is to utilize decision trees in conjunction with orthopantomography (OPT) and lateral panoramic graphy (LPG) to diagnose unilateral anterior disc displacement (ADD) of the temporomandibular joint. METHODS: In this study, 161 patients with images obtained through all three imaging methods, MRI, OPT, and LPG, were selected from the archives. The participants were categorized into two groups: the study group, comprising 89 patients with unilateral anterior disc displacement, and the control group, consisting of 72 healthy individuals...
March 16, 2024: BMC Oral Health
https://read.qxmd.com/read/38493056/a-sweet-tooth-makes-a-fly-a-pest
#4
JOURNAL ARTICLE
Nicolas O Rode, Camille Meslin
The major insect pest of soft and stone fruits, the spotted-wing drosophila, Drosophila suzukii, has evolved a greater preference for laying eggs on ripe fruits over fermented ones. In a recent study, Cavey et al. found that higher responsiveness to low sugar concentrations has had an important role in this evolutionary shift in egg-laying behavior.
March 15, 2024: Trends in Ecology & Evolution
https://read.qxmd.com/read/38492590/prediction-of-adsorption-of-metal-cations-by-clay-minerals-using-machine-learning
#5
JOURNAL ARTICLE
Shoushi Zhao, Kai Chen, Beiyi Xiong, Chuling Guo, Zhi Dang
Adsorption of heavy metals by clay minerals occurs widely at the solid-liquid interface in natural environments, and in this paper, the phenomenon of adsorption of Cd2+ , Cu2+ , Pb2+ , Zn2+ , Ni2+ and Co2+ by montmorillonite, kaolinite and illite was simulated using machine learning. We firstly used six machine learning models including Random Forest(R), Extremely Forest(E), Gradient Boosting Decision Tree(G), Extreme Gradient Boosting(X), Light Gradient Boosting(LGB) and Category Boosting(CAT) to feature engineer the metal cations and the parameters of the minerals, and based on the feature engineering results, we determined the first order hydrolysis constant(log K), solubility product constant(SPC), and higher hydrolysis constant (HHC) as the descriptors of the metal cations, and site density(SD) and cation exchange capacity(CEC) as the descriptors of the clay minerals...
March 14, 2024: Science of the Total Environment
https://read.qxmd.com/read/38492585/wet-events-increase-tree-growth-recovery-after-different-drought-intensities
#6
JOURNAL ARTICLE
Peng Zhang, Liang Jiao, Ruhong Xue, Mengyuan Wei, Xuge Wang, Qian Li
Understanding the dynamics of tree recovery after drought is critical for predicting the state of tree growth in the context of future climate change. While there has been a great deal of researches showing that drought events can cause numerous significant negative effects on tree growth, the positive effects of post-drought wetting events on tree growth remain unclear. Therefore, we analyzed the effect of wet and dry events on the radial growth of trees in Central Asia using data on the width of tree rings...
March 14, 2024: Science of the Total Environment
https://read.qxmd.com/read/38492424/monitoring-tree-canopy-dynamics-across-heterogeneous-urban-habitats-a-longitudinal-study-using-multi-source-remote-sensing-data
#7
JOURNAL ARTICLE
Yasong Guo, Wendy Y Chen
Urban trees have attracted increasing attention to serve as a green prescription for addressing various challenges facing human society like climate change and environmental deterioration. However, without healthy growth of urban trees, they cannot service any environmental, social, and economic benefits in a sustainable manner. By monitoring the canopy development, the tree growth dynamics in different urban habitats can be detected and appropriate management approaches can be executed. Using the Kowloon Peninsula, Hong Kong, as a case, this study explores how remote sensing data can help monitor and understand the impacts of heterogeneous urban habitats on tree canopy dynamics...
March 15, 2024: Journal of Environmental Management
https://read.qxmd.com/read/38492397/experimental-analysis-and-prediction-of-radionuclide-solubility-using-machine-learning-models-effects-of-organic-complexing-agents
#8
JOURNAL ARTICLE
Bolam Kim, Amaranadha Reddy Manchuri, Gi-Taek Oh, Youngsu Lim, Yuhwa Son, Seho Choi, Myunggoo Kang, Jiseon Jang, Jaechul Ha, Chun-Hyung Cho, Min-Woo Lee, Dae Sung Lee
Radioactive wastes contain organic complexing agents that can form complexes with radionuclides and enhance the solubility of these radionuclides, increasing the mobility of radionuclides over great distances from a radioactive waste repository. In this study, four radionuclides (cobalt, strontium, iodine, and uranium) and three organic complexing agents (ethylenediaminetetraacetic acid, nitrilotriacetic acid, and iso-saccharic acid) were selected, and the solubility of these radionuclides was assessed under realistic environmental conditions such as different pHs (7, 9, 11, and 13), temperatures (10 °C, 20 °C, and 40 °C), and organic complexing agent concentrations (10-5 -10-2 M)...
March 12, 2024: Journal of Hazardous Materials
https://read.qxmd.com/read/38492213/pagargos-promotes-low-lignin-wood-formation-in-poplar
#9
JOURNAL ARTICLE
Xiaomin Yao, Guifang Zhang, Geng Zhang, Qian Sun, Cuimei Liu, Jinfang Chu, Yanping Jing, Shihui Niu, Chunxiang Fu, Tedrick Thomas Salim Lew, Jinxing Lin, Xiaojuan Li
Wood formation, which occurs mainly through secondary xylem development, is important not only for supplying raw material for the 'ligno-chemical' industry but also for driving the storage of carbon. However, the complex mechanisms underlying the promotion of xylem formation remain to be elucidated. Here, we found that overexpression of Auxin-Regulated Gene involved in Organ Size (ARGOS) in hybrid poplar 84 K (Populus alba × Populus tremula var. glandulosa) enlarged organ size. In particular, PagARGOS promoted secondary growth of stems with increased xylem formation...
March 16, 2024: Plant Biotechnology Journal
https://read.qxmd.com/read/38492188/choice-of-metric-divergence-in-genome-sequence-comparison
#10
JOURNAL ARTICLE
Soumen Ghosh, Jayanta Pal, Bansibadan Maji, Carlo Cattani, Dilip Kumar Bhattacharya
The paper introduces a novel probability descriptor for genome sequence comparison, employing a generalized form of Jensen-Shannon divergence. This divergence metric stems from a one-parameter family, comprising fractions up to a maximum value of half. Utilizing this metric as a distance measure, a distance matrix is computed for the new probability descriptor, shaping Phylogenetic trees via the neighbor-joining method. Initial exploration involves setting the parameter at half for various species. Assessing the impact of parameter variation, trees drawn at different parameter values (half, one-fourth, one-eighth)...
March 16, 2024: Protein Journal
https://read.qxmd.com/read/38492096/diffusion-weighted-imaging-based-radiomics-model-using-automatic-machine-learning-to-differentiate-cerebral-cystic-metastases-from-brain-abscesses
#11
JOURNAL ARTICLE
Linyang Cui, Zheng Qin, Siyuan Sun, Weihua Feng, Mingyuan Hou, Dexin Yu
OBJECTIVES: To develop a radiomics model based on diffusion-weighted imaging (DWI) utilizing automated machine learning method to differentiate cerebral cystic metastases from brain abscesses. MATERIALS AND METHODS: A total of 186 patients with cerebral cystic metastases (n = 98) and brain abscesses (n = 88) from two clinical institutions were retrospectively included. The datasets (129 from institution A) were randomly portioned into separate 75% training and 25% internal testing sets...
March 16, 2024: Journal of Cancer Research and Clinical Oncology
https://read.qxmd.com/read/38491994/cascading-impacts-of-overstory-structure-in-managed-forests-on-understory-structure-microclimate-conditions-and-ixodes-scapularis-acari-ixodidae-densities
#12
JOURNAL ARTICLE
Stephanie N Hurd, Laura S Kenefic, Jessica E Leahy, Carly C Sponarski, Allison M Gardner
Forest management practices designed to meet varied landowner objectives affect wildlife habitat and may interrupt the life-cycle stages of disease vectors, including the black-legged tick, Ixodes scapularis Say (Acari: Ixodidae). Ixodes scapularis transmits multiple pathogens including Borrelia burgdorferi, the causative agent of Lyme disease, which is the most common tick-borne disease in the United States. There is evidence that a range of active forest management practices (e.g., invasive plant removal, prescribed burning) can alter tick densities and pathogen transmission...
March 16, 2024: Journal of Medical Entomology
https://read.qxmd.com/read/38491985/an-efficient-genetic-transformation-system-mediated-by-rhizobium-rhizogenes-in-fruit-trees-based-on-the-transgenic-hairy-root-to-shoot-conversion
#13
JOURNAL ARTICLE
Lin Liu, Jinghua Qu, Chunyan Wang, Miao Liu, Chunmeng Zhang, Xinyue Zhang, Cheng Guo, Changai Wu, Guodong Yang, Jinguang Huang, Kang Yan, Huairui Shu, Chengchao Zheng, Shizhong Zhang
Genetic transformation is a critical tool for gene editing and genetic improvement of plants. Although many model plants and crops can be genetically manipulated, genetic transformation systems for fruit trees are either lacking or perform poorly. We used Rhizobium rhizogenes to transfer the target gene into the hairy roots of Malus domestica and Actinidia chinensis. Transgenic roots were generated within 3 weeks, with a transgenic efficiency of 78.8%. Root to shoot conversion of transgenic hairy roots was achieved within 11 weeks, with a regeneration efficiency of 3...
March 16, 2024: Plant Biotechnology Journal
https://read.qxmd.com/read/38491950/susceptibility-of-mangifera-indica-sapindales-anacardiaceae-cultivars-to-fruit-flies-diptera-tephritidae-in-2-agroecological-zones-of-cameroon
#14
JOURNAL ARTICLE
Didi Gaëlle Mokam, Ndakabo Atougour, Zephirin Tadu, Désirée Chantal Aléné, Ezechiel Awono, Serge Lontsi Tapeo, Leonard Simon Ngamo Tinkeu, Champlain Djieto-Lordon
The Sudano-Sahelian and the high Guinea savannahs agroecological zones of Cameroon are suitable for the full development of tree crops, including mango. Unfortunately, fresh fruits exported to local and international markets are frequently rejected due to the presence of fruit fly larvae (Diptera: Tephritidae), resulting in drastic income losses and overuse of chemical control products. To promote sustainable management strategies, a 2-yr study (2020-2021) was conducted in 4 and 3 mixed orchards, respectively...
March 1, 2024: Journal of Insect Science
https://read.qxmd.com/read/38491818/contemporary-trends-in-choledochal-cyst-excision-an-analysis-of-the-pediatric-national-surgical-quality-improvement-program
#15
JOURNAL ARTICLE
Thomas Clark Howell, Catherine B Beckhorn, Ryan M Antiel, Tamara N Fitzgerald, Henry E Rice, Alisha Mavis, Kadiyala Ravindra, Elisabeth T Tracy
BACKGROUND: Choledochal cysts are rare congenital anomalies of the biliary tree that may lead to obstruction, chronic inflammation, infection, and malignancy. There is wide variation in the timing of resection, operative approach, and reconstructive techniques. Outcomes have rarely been compared on a national level. METHODS: We queried the Pediatric National Surgical Quality Improvement Program (NSQIP) to identify patients who underwent choledochal cyst excision from 2015 to 2020...
March 16, 2024: World Journal of Surgery
https://read.qxmd.com/read/38491535/explainable-artificial-intelligence-in-the-design-of-selective-carbonic-anhydrase-i-ii-inhibitors-via-molecular-fingerprinting
#16
JOURNAL ARTICLE
Kevser Kübra Kırboğa, Mesut Işık
Inhibiting the enzymes carbonic anhydrase I (CA I) and carbonic anhydrase II (CA II) presents a potential avenue for addressing nervous system ailments such as glaucoma and Alzheimer's disease. Our study explored harnessing explainable artificial intelligence (XAI) to unveil the molecular traits inherent in CA I and CA II inhibitors. The PubChem molecular fingerprints of these inhibitors, sourced from the ChEMBL database, were subjected to detailed XAI analysis. The study encompassed training 10 regression models using IC50 values, and their efficacy was gauged using metrics including R2 , RMSE, and time taken...
March 15, 2024: Journal of Computational Chemistry
https://read.qxmd.com/read/38491515/pitting-the-olive-seed-microbiome
#17
JOURNAL ARTICLE
Nuria M Wentzien, Antonio J Fernández-González, Antonio Valverde-Corredor, Ana V Lasa, Pablo J Villadas, Wisnu Adi Wicaksono, Tomislav Cernava, Gabriele Berg, Manuel Fernández-López, Jesús Mercado-Blanco
BACKGROUND: The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter...
March 15, 2024: Environmental microbiome
https://read.qxmd.com/read/38491403/a-cyst-forming-coccidian-with-large-geographical-range-infecting-forest-and-commensal-rodents-sarcocystis-muricoelognathis-sp-nov
#18
JOURNAL ARTICLE
Tao Qin, Paula Ortega-Perez, Gudrun Wibbelt, Maklarin B Lakim, Sulaiman Ginting, Yuvaluk Khoprasert, Konstans Wells, Junjie Hu, Thomas Jäkel
BACKGROUND: The geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known. METHODS: Experimental infections, morphological and molecular characterizations were used for discrimination of a new Sarcocystis species isolated from colubrid snakes and small mammals collected in Thailand, Borneo and China. RESULTS: We identified a new species, Sarcocystis muricoelognathis sp...
March 15, 2024: Parasites & Vectors
https://read.qxmd.com/read/38491375/identifying-a-survival-associated-cell-type-based-on-multi-level-transcriptome-analysis-in-idiopathic-pulmonary-fibrosis
#19
JOURNAL ARTICLE
Fei Xu, Yun Tong, Wenjun Yang, Yiyang Cai, Meini Yu, Lei Liu, Qingkang Meng
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive disease with a five-year survival rate of less than 40%. There is significant variability in survival time among IPF patients, but the underlying mechanisms for this are not clear yet. METHODS AND RESULTS: We collected single-cell RNA sequence data of 13,223 epithelial cells taken from 32 IPF patients and bulk RNA sequence data from 456 IPF patients in GEO. Based on unsupervised clustering analysis at the single-cell level and deconvolution algorithm at bulk RNA sequence data, we discovered a special alveolar type 2 cell subtype characterized by high expression of CCL20 (referred to as ATII-CCL20), and found that IPF patients with a higher proportion of ATII-CCL20 had worse prognoses...
March 15, 2024: Respiratory Research
https://read.qxmd.com/read/38491333/machine-learning-approach-using-18-f-fdg-pet-radiomic-features-and-the-visibility-of-right-ventricle-18-f-fdg-uptake-for-predicting-clinical-events-in-patients-with-cardiac-sarcoidosis
#20
JOURNAL ARTICLE
Masatoyo Nakajo, Daisuke Hirahara, Megumi Jinguji, Satoko Ojima, Mitsuho Hirahara, Atsushi Tani, Koji Takumi, Kiyohisa Kamimura, Mitsuru Ohishi, Takashi Yoshiura
OBJECTIVES: To investigate the usefulness of machine learning (ML) models using pretreatment 18 F-FDG-PET-based radiomic features for predicting adverse clinical events (ACEs) in patients with cardiac sarcoidosis (CS). MATERIALS AND METHODS: This retrospective study included 47 patients with CS who underwent 18 F-FDG-PET/CT scan before treatment. The lesions were assigned to the training (n = 38) and testing (n = 9) cohorts. In total, 49 18 F-FDG-PET-based radiomic features and the visibility of right ventricle 18 F-FDG uptake were used to predict ACEs using seven different ML algorithms (namely, decision tree, random forest [RF], neural network, k-nearest neighbors, Naïve Bayes, logistic regression, and support vector machine [SVM]) with tenfold cross-validation and the synthetic minority over-sampling technique...
March 16, 2024: Japanese Journal of Radiology
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