An abundance- and morphology-based similarity index

Paleobiology ◽  
2021 ◽  
pp. 1-18
Author(s):  
Daniel G. Dick ◽  
Marc Laflamme
Keyword(s):  
River Flow ◽  
Similarity Index ◽  
Ecological Gradients ◽  
Jaccard Similarity ◽  
Real World Data ◽  
Large Component ◽  
Morphological Gradient ◽  
Random Samples ◽  
Similarity Indices ◽  
General Method

Abstract Classic similarity indices measure community resemblance in terms of incidence (the number of shared species) and abundance (the extent to which the shared species are an equivalently large component of the ecosystem). Here we describe a general method for increasing the amount of information contained in the output of these indices and describe a new “soft” ecological similarity measure (here called “soft Chao-Jaccard similarity”). The new measure quantifies community resemblance in terms of shared species, while accounting for intraspecific variation in abundance and morphology between samples. We demonstrate how our proposed measure can reconstruct short ecological gradients using random samples of taxa, recognizing patterns that are completely missed by classic measures of similarity. To demonstrate the utility of our new index, we reconstruct a morphological gradient driven by river flow velocity using random samples drawn from simulated and real-world data. Results suggest that the new index can be used to recognize complex short ecological gradients in settings where only information about specimens is available. We include open-source R code for calculating the proposed index.

New similarity index for crystal structure determination from X-ray powder diagrams

2005 ◽  
Vol 38 (6) ◽  
pp. 861-866 ◽  
Author(s):  
Detlef Walter Maria Hofmann ◽  
Ludmila Kuleshova
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Similarity Index ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Organic Pigments ◽  
Structure Solution ◽  
Similarity Indices

A new similarity index for automated comparison of powder diagrams is proposed. In contrast to traditionally used similarity indices, the proposed method is valid in cases of large deviations in the cell constants. The refinement according to this index closes the gap between crystal structure prediction and automated crystal structure determination. The opportunities of the new procedure have been demonstrated by crystal structure solution of un-indexed powder diagrams of some organic pigments (PY111, PR181 and Me-PR170).

scholarly journals Genetic structure and gene flow of Eugenia dysenterica natural populations

2005 ◽  
Vol 40 (10) ◽  
pp. 975-980 ◽  
Author(s):  
Maria Imaculada Zucchi ◽  
José Baldin Pinheiro ◽  
Lázaro José Chaves ◽  
Alexandre Siqueira Guedes Coelho ◽  
Mansuêmia Alves Couto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Variability ◽  
Pearson Correlation ◽  
Natural Populations ◽  
Similarity Index ◽  
Genetic Distances ◽  
Strong Positive Correlation ◽  
Randomly Amplified Polymorphic Dna ◽  
Jaccard Similarity ◽  
Eugenia Dysenterica

This study was carried out to assess the genetic variability of ten "cagaita" tree (Eugenia dysenterica) populations in Southeastern Goiás. Fifty-four randomly amplified polymorphic DNA (RAPD) loci were used to characterize the population genetic variability, using the analysis of molecular variance (AMOVA). A phiST value of 0.2703 was obtained, showing that 27.03% and 72.97% of the genetic variability is present among and within populations, respectively. The Pearson correlation coefficient (r) among the genetic distances matrix (1 - Jaccard similarity index) and the geographic distances were estimated, and a strong positive correlation was detected. Results suggest that these populations are differentiating through a stochastic process, with restricted and geographic distribution dependent gene flow.

scholarly journals Genetic Variation among and within United States Collard Cultivars and Landraces as Determined by Randomly Amplified Polymorphic DNA Markers

1996 ◽  
Vol 121 (3) ◽  
pp. 374-379 ◽  
Author(s):  
Mark W. Farnham
Keyword(s):  
Genetic Variation ◽  
Dna Markers ◽  
Crop Improvement ◽  
Similarity Index ◽  
Randomly Amplified Polymorphic Dna ◽  
Brussels Sprouts ◽  
Breeding Lines ◽  
Intrapopulation Variation ◽  
Similarity Indices ◽  
Systematic Collection

A collection of collard (Brassica oleracea L., Acephala group) germplasm, including 13 cultivars or breeding lines and 5 landraces, was evaluated using randomly amplified polymorphic DNA (RAPD) markers and compared to representatives of kale (Acephala group), cabbage (Capitata group), broccoli (Italica group), Brussels sprouts (Gemmifera group), and cauliflower (Botrytis group). Objectives were to assess genetic variation and relationships among collard and other crop entries, evaluate intrapopulation variation of open-pollinated (OP) collard lines, and determine the potential of collard landraces to provide new B. oleracea genes. Two hundred nine RAPD bands were scored from 18 oligonucleotide decamer primers when collard and other B. oleracea entries were compared. Of these, 147 (70%) were polymorphic and 29 were specific to collard. Similarity indices between collard entries were computed from RAPD data and these ranged from 0.75 to 0.99 with an average of 0.83. Collard entries were most closely related to cabbage (similarity index = 0.83) and Brussels sprouts entries (index = 0.80). Analysis of individuals of an OP cultivar and landrace indicated that intrapopulation genetic variance accounts for as much variation as that observed between populations. RAPD analysis identified collard landraces as unique genotypes and showed them to be sources of unique DNA markers. The systematic collection of collard landraces should enhance diversity of the B. oleracea germplasm pool and provide genes for future crop improvement.

An Attempt to Estimate the Noises in Homeopathic Pathogenetic Trials by Employing the Jaccard Similarity Index and Noise Index

Homeopathy ◽  
2021 ◽  
Author(s):  
Kurian Poruthukaren
Keyword(s):  
Placebo Group ◽  
Hepatitis C ◽  
Intervention Group ◽  
Similarity Index ◽  
Signs And Symptoms ◽  
Piper Methysticum ◽  
Common Elements ◽  
Jaccard Similarity ◽  
Noise Index ◽  
Trial Drug

Abstract Background The critical task of researchers conducting double-blinded, randomized, placebo-controlled homeopathic pathogenetic trials is to segregate the signals from the noises. The noises are signs and symptoms due to factors other than the trial drug; signals are signs and symptoms due to the trial drug. Unfortunately, the existing tools (criteria for a causal association of symptoms only with the tested medicine, qualitative pathogenetic index, quantitative pathogenetic index, pathogenic index) have limitations in analyzing the symptoms of the placebo group as a comparator, resulting in inadequate segregation of the noises. Hence, the Jaccard similarity index and the Noise index are proposed for analyzing the symptoms of the placebo group as a comparator. Methods The Jaccard similarity index is the ratio of the number of common elements among the placebo and intervention groups to the aggregated number of elements in these groups. The Noise index is the ratio of common elements among the placebo and intervention group to the total elements of the intervention group. Homeopathic pathogenetic trials of Plumbum metallicum, Piper methysticum and Hepatitis C nosode were selected for experimenting with the computation of the Jaccard similarity index and the Noise index. Results Jaccard similarity index calculations show that 8% of Plumbum metallicum's elements, 10.7% of Piper methysticum's elements, and 19.3% of Hepatitis C nosode's elements were similar to the placebo group when elements of both the groups (intervention and placebo) were aggregated. Noise index calculations show that 10.7% of Plumbum metallicum's elements, 13.9% of Piper methysticum's elements and 25.7% of Hepatitis C nosode's elements were similar to those of the placebo group. Conclusion The Jaccard similarity index and the Noise index might be considered an additional approach for analyzing the symptoms of the placebo group as a comparator, resulting in better noise segregation in homeopathic pathogenetic trials.

scholarly journals Evaluation of Automatic Facial Wrinkle Detection Algorithms

2020 ◽  
Vol 6 (4) ◽  
pp. 17
Author(s):  
Remah Mutasim Elbashir ◽  
Moi Hoon Yap
Keyword(s):  
Gabor Filter ◽  
Ground Truth ◽  
Jaccard Similarity ◽  
Skin Changes ◽  
Detection Algorithms ◽  
New Methods ◽  
Facial Wrinkle ◽  
Similarity Indices ◽  
The Face ◽  
Enhancement Method

Facial wrinkles (considered to be natural features) appear as people get older. Wrinkle detection is an important aspect of applications that depend on facial skin changes, such as face age estimation and soft biometrics. While existing wrinkle detection algorithms focus on forehead horizontal lines, it is necessary to develop new methods to detect all wrinkles (vertical and horizontal) on whole face. Therefore, we evaluated the performance of wrinkle detection algorithms on the whole face and proposed an enhancement technique to improve the performance. More specifically, we used 45 images of the Face Recognition Technology dataset (FERET) and 25 images of the Sudanese dataset. For ground truth annotations, the selected images were manually annotated by the researcher. The experiments showed that the method with enhancement performed better at detecting facial wrinkles when compared to the state-of-the-art methods. When evaluated on FERET, the average Jaccard similarity indices were 56.17%, 31.69% and 15.87% for the enhancement method, Hybrid Hessian Filter and Gabor Filter, respectively.

scholarly journals What Interferes with the Similarity Between Free Lists Applied at Different Times?

2020 ◽  
Author(s):  
Melise Pessôa Araujo Meireles ◽  
Ulysses Paulino de Albuquerque ◽  
Patrícia Muniz de Medeiros
Keyword(s):  
Rural Community ◽  
Generalized Linear Model ◽  
Similarity Index ◽  
Third Parties ◽  
Jaccard Similarity ◽  
Stepwise Approach ◽  
Individual Knowledge ◽  
Cultural Domain ◽  
The Individual ◽  
External Stimuli

Abstract AbstractBackground: The free list is an ethnographic method that characterizes the local knowledge of a population about a given cultural domain. However, there is still much to be elucidated about the variables that can influence the number of plants cited by the participants with the use of this technique. This study analyzed whether age and external stimuli influence the similarity of free lists applied at different times.Methods: Data was collected from 103 farmers from the rural community Alto dos Canutos, in the municipality of Picos, PI. For that purpose, two free lists were applied at two different times, with an interval of three months between them. Subsequently, the similarity between the first and second free lists of each participant was calculated using the Jaccard Similarity Index. The Generalized Linear Model (GLM) with binomial errors and stepwise approach was also used to analyze how age and external stimuli affect the collection of information when comparing the free lists applied at different times.Results: The age of the participants influenced the information collected in the free lists, demonstrating that the older the participants, the lower the similarity among the free lists. Among the external stimuli analyzed, only the presence of third parties influenced the content of the free lists at the time of the interview. However, contrary to expectations, it positively influenced the similarity of the lists. Conclusion: The results show that the studied variables can influence the capture of knowledge if the objective of the research is to influence the individual knowledge of the participants.

scholarly journals Ethno-Veterinary Survey and Quantitative Study of Medicinal Plants with Anthelmintic Potential Used by Sheep and Goat Breeders in the Cotton Zone of Central Benin (West Africa)

J ◽  
2021 ◽  
Vol 4 (4) ◽  
pp. 544-563
Author(s):  
Christian Cocou Dansou ◽  
Pascal Abiodoun Olounladé ◽  
Basile Saka Boni Konmy ◽  
Oriane Songbé ◽  
Kisito Babatoundé Arigbo ◽  
...  
Keyword(s):  
Similarity Index ◽  
Gastrointestinal Parasites ◽  
Vernonia Amygdalina ◽  
Jaccard Similarity ◽  
Medicinal Species ◽  
Agreement Rate ◽  
Pearson’S Correlation ◽  
Face To Face ◽  
Level Of Use ◽  
Pearson's Correlation

This study presents the diversity of anthelmintic plants in the cotton zone of Central Benin. The aim was to identify the medicinal anthelmintic plants used by small ruminant breeders in cotton zone of Central Benin to treat gastrointestinal parasites. Three hundred and sixty breeders were selected during individual semi-structured face-to-face interviews. Different quantitative indices of cultural importance were calculated in order to determine the level of use of plant species. Jaccard similarity index (JI) was calculated and Pearson’s correlation was determined for Use Value (UV) and Relative Frequency of Citation (RFC). In this study, a total of 99 medicinal species, of which 63 have anthelmintic potential, were listed, including Khaya senegalensis, Launaea taraxacifolia, Napoleonaea vogelii, Momordica charantia and Vernonia amygdalina, which all had UV and RFC above 20%. Each of them had a Fidelity Level above 50% and an Informant Agreement Rate (IAR) value close to one. Pearson’s correlation showed a significant correlation between RFC and UV with r = 0.94, and the studies were clearly independent (IJ < 50%). This study showed that the cotton zone of Central Benin represents 4% of the total flora of Benin, with many anthelmintic plants such as Launaea taraxacifolia and Napoleonaea vogelii that require further investigation.

scholarly journals What interferes with conducting free lists? A comparative ethnobotanical experiment

2020 ◽  
Author(s):  
Melise Pessôa Araujo Meireles ◽  
Ulysses Paulino de Albuquerque ◽  
Patrícia Muniz de Medeiros
Keyword(s):  
Rural Community ◽  
Generalized Linear Model ◽  
Similarity Index ◽  
Third Party ◽  
Information Collection ◽  
Future Research ◽  
Jaccard Similarity ◽  
Stepwise Approach ◽  
Cultural Domain ◽  
External Stimuli

Abstract Background: The free list, also written “freelist”, or “free recall”, is an ethnographic method that characterizes the local knowledge of a population about a given cultural domain. However, there is still much to elucidate about the variables that can influence the number of items that participants cite using this technique. This study applied a casual-comparative experiemental design to analyze whether three months’ time, age and external stimuli influence the similarity of plant free lists applied at different times.Methods: Data was collected from 103 farmers from the rural community Alto dos Canutos, in the municipality of Picos, Piauí state, Brazil.Two free lists were conducted at two different times, with an interval of three months between them. Subsequently, the similarity between the first and second free lists of each participant was calculated using the Jaccard Similarity Index. The Generalized Linear Model (GLM) with binomial errors and stepwise approach was used to analyze the effects of age and external stimuli on information collection when comparing free lists applied at different times.Results: Participants’ age influenced the information that the free lists collected, demonstrating that the older the participants, the lower the similarity among the free lists. Among the external stimuli analyzed, only the presence of third parties influenced the content of the free lists at the time of the interview. However, contrary to expectations, third-party presence positively influenced the similarity of the lists. Conclusion: The results show that the studied variables age and third-party presence can influence the capture of knowledge. These findings warrant future research into the influences' causes and their potential mitigation, e.g., by isolation or by breaking the medicinal plant domain into focused sub-domains and conducting simpler, successive free-lists, which can mitigate memory issues.

Fabrication of Robust Nano-Signatures for Identification of Authentic Electronic Components and Counterfeit Avoidance

2017 ◽  
Vol 26 (03) ◽  
pp. 1740006 ◽  
Author(s):  
Kiarash Ahi ◽  
Abdiel Rivera ◽  
Anas Mazadi ◽  
Mehdi Anwar
Keyword(s):  
Supply Chain ◽  
Integrated Circuit ◽  
Similarity Index ◽  
Structural Similarity ◽  
Global Supply Chain ◽  
Electronic Components ◽  
Structural Similarity Index ◽  
Novel Approach ◽  
Similarity Indices ◽  
Processing Techniques

In this paper, a novel approach for marking integrated circuit packages with authentication nanosignatures is introduced. In this work, the signatures patterns are fabricated using electron beam lithography. Moreover, the robustness of these signatures against aging and humidity is investigated. A recipe comprising image processing techniques and measurement of similarity indices has been developed. These signatures are proposed to be fabricated at the manufacturer side of the supply chain. Then, they are decoded at the consumer end. Thus, robustness against ambient environment and aging is a requirement for these signatures to survive in the global supply chain. Calculated Mean Square Error and Structural SIMilarity Index confirmed that the reflected patterns of the signatures remain unchanged against aging and humidity.

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