scholarly journals Comparing shade tolerance measures of woody forest species

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5736 ◽  
Author(s):  
Jiayi Feng ◽  
Kangning Zhao ◽  
Dong He ◽  
Suqin Fang ◽  
TienMing Lee ◽  
...  
Keyword(s):  
Wood Species ◽  
Tree Species ◽  
Shade Tolerance ◽  
Life History Traits ◽  
Niche Differentiation ◽  
Low Light ◽  
Large Dataset ◽  
Future Studies ◽  
Tolerance Indices

Shade tolerance, the minimum light requirement for plant survival, is a key trait for understanding community assembly and forest dynamics. However, it is poorly defined for tree species to date. Current methods of measuring shade tolerance vary considerably in their performance. For instance, some measures of shade tolerance are unreliable except under some specific conditions. Therefore, it is necessary to compare the performance of these methods to provide guidance of choosing appropriate shade tolerance measures in future studies. We collected a large dataset of light traits and other life history traits for 137 understory wood species in a subtropical forest and tested the performance of five commonly used shade-tolerance indices. Results showed that all the shade-tolerance measures, except the low-light abundance index, performed poorly in distinguishing and ranking shade tolerance of the tested species. The shade tolerance quantified by the low-light abundance was consistent with empirical classification of shade-tolerance/intolerance groups and successional seral stages of species. Comparison of the shade tolerance between trees of different diameter at breast height (DBH) or height classes further confirmed the reliability of low-light abundance. We conclude that low-light abundance is the most objective and practical of the five most commonly-used methods for measuring and ranking shade tolerance of understory wood species in our study forest, and likely in other forests as well. The simplicity of the method should greatly facilitate the assessment of light niche differentiation between species and thus contribute to understanding coexistence of tree species in forests.

scholarly journals Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems

2020 ◽  
Vol 48 (22) ◽  
pp. 12632-12647
Author(s):  
Mario Rodríguez Mestre ◽  
Alejandro González-Delgado ◽  
Luis I Gutiérrez-Rus ◽  
Francisco Martínez-Abarca ◽  
Nicolás Toro
Keyword(s):  
Biological Function ◽  
Open Reading Frames ◽  
Computational Pipeline ◽  
Ncrna Gene ◽  
Large Dataset ◽  
Future Studies ◽  
Non Coding Rna ◽  
Additional Protein ◽  
Reading Frames

Abstract Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.

scholarly journals Close association of RGR, leaf and root morphology, seed mass and shade tolerance in seedlings of nine boreal tree species grown in high and low light

1998 ◽  
Vol 12 (3) ◽  
pp. 327-338 ◽  
Author(s):  
P. B. Reich ◽  
M. G. Tjoelker ◽  
M. B. Walters ◽  
D. W. Vanderklein ◽  
C. Buschena
Keyword(s):  
Root Morphology ◽  
Tree Species ◽  
Shade Tolerance ◽  
Close Association ◽  
Seed Mass ◽  
Low Light

A test of the accuracy of shade-tolerance classifications based on physiognomic and reproductive traits

1983 ◽  
Vol 61 (6) ◽  
pp. 1595-1598 ◽  
Author(s):  
Craig G. Lorimer
Keyword(s):  
Growth Rates ◽  
Tree Species ◽  
Shade Tolerance ◽  
Reproductive Traits ◽  
Permanent Plot ◽  
Oak Forest ◽  
Tolerance Index ◽  
Stem Density ◽  
Survival And Growth ◽  
Tolerance Indices

Traits such as live crown ratio and understory stem density are often used subjectively as a guide to grouping tree species into shade tolerance classes. The accuracy of this approach was tested on nine species in an upland oak forest by comparing a tolerance index based on measurements of live crown ratio and understory stem density with observed survival and growth rates of suppressed trees obtained from 19-year permanent plot records. A high correlation (r = 0.93) was found between predicted and observed tolerance indices. The observed tolerance of several species differs from traditional classifications but was correctly predicted by the tolerance index.

Growth and phenotypic plasticity of two tropical tree species under low light availability

2020 ◽  
Author(s):  
Marúcia da Cunha Fagundes ◽  
Ândrea Carla Dalmolin ◽  
Luciana Santos Lobo ◽  
Ana Cristina Schilling ◽  
Martielly Santana dos Santos ◽  
...  
Keyword(s):  
Phenotypic Plasticity ◽  
Growth Rates ◽  
Tree Species ◽  
Shade Tolerance ◽  
Carbon Allocation ◽  
Secondary Forest ◽  
Light Availability ◽  
Tropical Tree ◽  
Low Light ◽  
Tropical Tree Species

Abstract Aims Screening tree species in tropical rainforest according to their shade tolerance is important to efficiently manage the native trees of economic significance in secondary forest enrichment regimes. The objective of this study was to determine the whole-plant light compensation point (WPLCP) and compare the phenotypic plasticity in relation to growth and carbon allocation of Cariniana legalis and Gallesia integrifolia seedlings under low light availability. Methods Seedlings were cultivated for 77 days under conditions of five photosynthetically active radiation (PAR) (0.02, 1.1, 2.3, 4.5 and 5.9 mol photons m -2 day -1) in three replicates. Growth and carbon allocation variables were determined. Important Findings Growth rates of C. legalis were higher and lower than those of G. integrifolia under 1.1 and 5.9 mol photons m -2 day -1, respectively. The WPLCP differed significantly between the two species. In accordance with the criteria of the shade tolerance classification for these two tropical tree species, our results showed that C. legalis had lower WPLCP and phenotypic plasticity in terms of higher growth rates and greater shade tolerance than G. integrifolia. From a practical point of view, we demonstrated that the differential linkage between growth and changing PAR between the two species can become a useful tool for comparing and selecting tree species in forest enrichment projects.

Values in Action Inventory of Strengths (VIA-IS): Translation and Validation in Urdu Language

2020 ◽  
Vol 35 (1) ◽  
pp. 163-189
Author(s):  
Afifa Anjum ◽  
Naumana Amjad
Keyword(s):  
Factor Structure ◽  
Convergent Validity ◽  
Character Strengths ◽  
Future Studies ◽  
Structure Factors ◽  
Adult Participants ◽  
Positive Correlations ◽  
Cross Language ◽  
Translation And Validation

Values in Action is a classification of 24 character strengths grouped under six virtue categories. This classification is claimed to be universal across cultures and religions (Peterson & Seligman, 2004) and its measure that is, Values in Action Inventory of Strengths (VIA-IS) has been translated and validated in many languages. The present study aimed at its Urdu translation and validation on Pakistani adults taken from different educational institutes and workplaces. Study comprised two parts. Part I dealt with the translation and cross-language validation while in Part II, Construct validation on a sample of 542 adults and convergent validity on a sample of 210 adult participants were determined. Findings revealed satisfactory alpha coefficients for Urdu version. Significant positive correlations with positive affect and life satisfaction and negative correlations with negative affect were indicators of its convergent validity. Age was negatively associated with five strengths whereas significant gender differences were found on seven strengths. Social desirability effects were nonsignificant. Strength-to-virtue level factor structure exploration resulted in a theoretically meaningful four factor structure. Factors were named as Interpersonal, Cognitive, Vitality, and Transcendence and were comparable to factor structures proposed in studies on VIA-IS from a few other cultures. The study offers a valid Urdu translation for use in future studies with adult Urdu speaking population.

scholarly journals A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium

2021 ◽  
Vol 9 (5) ◽  
pp. 1034
Author(s):  
Carlos Sabater ◽  
Lorena Ruiz ◽  
Abelardo Margolles
Keyword(s):  
Machine Learning ◽  
Supervised Classification ◽  
Machine Learning Algorithms ◽  
Learning Approach ◽  
Human Milk Oligosaccharides ◽  
Future Studies ◽  
High Fiber ◽  
Machine Learning Approach ◽  
Prebiotic Oligosaccharides

This study aimed to recover metagenome-assembled genomes (MAGs) from human fecal samples to characterize the glycosidase profiles of Bifidobacterium species exposed to different prebiotic oligosaccharides (galacto-oligosaccharides, fructo-oligosaccharides and human milk oligosaccharides, HMOs) as well as high-fiber diets. A total of 1806 MAGs were recovered from 487 infant and adult metagenomes. Unsupervised and supervised classification of glycosidases codified in MAGs using machine-learning algorithms allowed establishing characteristic hydrolytic profiles for B. adolescentis, B. bifidum, B. breve, B. longum and B. pseudocatenulatum, yielding classification rates above 90%. Glycosidase families GH5 44, GH32, and GH110 were characteristic of B. bifidum. The presence or absence of GH1, GH2, GH5 and GH20 was characteristic of B. adolescentis, B. breve and B. pseudocatenulatum, while families GH1 and GH30 were relevant in MAGs from B. longum. These characteristic profiles allowed discriminating bifidobacteria regardless of prebiotic exposure. Correlation analysis of glycosidase activities suggests strong associations between glycosidase families comprising HMOs-degrading enzymes, which are often found in MAGs from the same species. Mathematical models here proposed may contribute to a better understanding of the carbohydrate metabolism of some common bifidobacteria species and could be extrapolated to other microorganisms of interest in future studies.

scholarly journals Minimization of the Line Resistance Impact on Memdiode-Based Simulations of Multilayer Perceptron Arrays Applied to Pattern Recognition

2021 ◽  
Vol 11 (1) ◽  
pp. 9
Author(s):  
Fernando Leonel Aguirre ◽  
Nicolás M. Gomez ◽  
Sebastián Matías Pazos ◽  
Félix Palumbo ◽  
Jordi Suñé ◽  
...  
Keyword(s):  
Pattern Recognition ◽  
Ex Situ ◽  
Multilayer Perceptrons ◽  
Spice Simulation ◽  
Large Dataset ◽  
High Line ◽  
Calibration Algorithm ◽  
The Impact ◽  
Line Resistance

In this paper, we extend the application of the Quasi-Static Memdiode model to the realistic SPICE simulation of memristor-based single (SLPs) and multilayer perceptrons (MLPs) intended for large dataset pattern recognition. By considering ex-situ training and the classification of the hand-written characters of the MNIST database, we evaluate the degradation of the inference accuracy due to the interconnection resistances for MLPs involving up to three hidden neural layers. Two approaches to reduce the impact of the line resistance are considered and implemented in our simulations, they are the inclusion of an iterative calibration algorithm and the partitioning of the synaptic layers into smaller blocks. The obtained results indicate that MLPs are more sensitive to the line resistance effect than SLPs and that partitioning is the most effective way to minimize the impact of high line resistance values.

scholarly journals Geometric and Topological Bases of a New Classification of Wood Vascular Tissues Part 1: Shape and Arrangement Classifications of Vessels

2021 ◽  
Vol 13 (14) ◽  
pp. 7545
Author(s):  
Nikolai Bardarov ◽  
Vladislav Todorov ◽  
Nicole Christoff
Keyword(s):  
Computer Vision ◽  
Detailed Analysis ◽  
Tree Species ◽  
Complete Solution ◽  
New Classification ◽  
Topological Characteristics ◽  
Definition Of ◽  
Wood Science ◽  
Quantitative Indicators

The need to identify wood by its anatomical features requires a detailed analysis of all the elements that make it up. This is a significant problem of structural wood science, the most general and complete solution of which is yet to be sought. In recent years, increasing attention has been paid to the use of computer vision methods to automate processes such as the detection, identification, and classification of different tissues and different tree species. The more successful use of these methods in wood anatomy requires a more precise and comprehensive definition of the anatomical elements, according to their geometric and topological characteristics. In this article, we conduct a detailed analysis of the limits of variation of the location and grouping of vessels in the observed microscopic samples. The present development offers criteria and quantitative indicators for defining the terms shape, location, and group of wood tissues. It is proposed to differentiate the quantitative indicators of the vessels depending on their geometric and topological characteristics. Thus, with the help of computer vision technics, it will be possible to establish topological characteristics of wood vessels, the extraction of which would be used to develop an algorithm for the automatic classification of tree species.

scholarly journals Fluctuating Asymmetry and Sexual Dimorphism in Human Facial Morphology: A Multi-Variate Study

Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 304
Author(s):  
Omid Ekrami ◽  
Peter Claes ◽  
Ellen Van Assche ◽  
Mark D. Shriver ◽  
Seth M. Weinberg ◽  
...  
Keyword(s):  
Fluctuating Asymmetry ◽  
Life History Traits ◽  
Principal Component ◽  
Underlying Mechanism ◽  
High Density ◽  
Direct Result ◽  
Facial Morphology ◽  
Strongly Correlated ◽  
Large Dataset ◽  
Genetic Quality

(1) Background: Fluctuating asymmetry is often used as an indicator of developmental instability, and is proposed as a signal of genetic quality. The display of prominent masculine phenotypic features, which are a direct result of high androgen levels, is also believed to be a sign of genetic quality, as these hormones may act as immunosuppressants. Fluctuating asymmetry and masculinity are therefore expected to covary. However, there is lack of strong evidence in the literature regarding this hypothesis. (2) Materials and methods: In this study, we examined a large dataset of high-density 3D facial scans of 1260 adults (630 males and 630 females). We mapped a high-density 3D facial mask onto the facial scans in order to obtain a high number of quasi-landmarks on the faces. Multi-dimensional measures of fluctuating asymmetry were extracted from the landmarks using Principal Component Analysis, and masculinity/femininity scores were obtained for each face using Partial Least Squares. The possible correlation between these two qualities was then examined using Pearson’s coefficient and Canonical Correlation Analysis. (3) Results: We found no correlation between fluctuating asymmetry and masculinity in men. However, a weak but significant correlation was found between average fluctuating asymmetry and masculinity in women, in which feminine faces had higher levels of fluctuating asymmetry on average. This correlation could possibly point to genetic quality as an underlying mechanism for both asymmetry and masculinity; however, it might also be driven by other fitness or life history traits, such as fertility. (4) Conclusions: Our results question the idea that fluctuating asymmetry and masculinity should be (more strongly) correlated in men, which is in line with the recent literature. Future studies should possibly focus more on the evolutionary relevance of the observed correlation in women.

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