scholarly journals zetadiv: an R package for computing compositional change across multiple sites, assemblages or cases

2018 ◽  
Author(s):  
Guillaume Latombe ◽  
Melodie A. McGeoch ◽  
David A. Nipperess ◽  
Cang Hui
Keyword(s):  
Species Turnover ◽  
R Package ◽  
Common Species ◽  
Distance Decay ◽  
Space Environment ◽  
List Type ◽  
Compositional Change ◽  
Number Of Species ◽  
The Mean ◽  
Compositional Diversity

AbstractSpatial variation in compositional diversity, or species turnover, is necessary for capturing the components of heterogeneity that constitute biodiversity. However, no incidence-based metric of pairwise species turnover can calculate all components of diversity partitioning. Zeta (ζ) diversity, the mean number of species shared by any given number of sites or assemblages, captures all diversity components produced by assemblage partitioning. zetadiv is an R package for analysing and measuring compositional change for occurrence data using zeta diversity. Four types of analyses are performed on bird composition data in Australia: (i) decline in zeta diversity; (ii) distance decay; (iii) multi-site generalised dissimilarity modelling; and (iv) hierarchical scaling. Some analyses, such as the zeta decline, are specific to zeta diversity, whereas others, such as distance decay, are commonly applied to beta diversity, and have been adapted using zeta diversity to differentiate the contribution of common and rare species to compositional change.HighlightsAn R package to analyse compositional change using zeta diversity is presented.Zeta diversity is the mean number of species shared by any number of assemblagesZeta diversity captures all diversity components produced by assemblage partitioningAnalyses relate zeta diversity to space, environment and spatial scaleAnalyses differentiate the contribution of rare and common species to biodiversity

Sampling Emerging Chironomidae (Diptera) with Submerged Funnel Traps in a New Northern Canadian Reservoir, Southern Indian Lake, Manitoba

1980 ◽  
Vol 37 (6) ◽  
pp. 927-936 ◽  
Author(s):  
David M. Rosenberg ◽  
Allen P. Wiens ◽  
Bohdan Bilyj
Keyword(s):  
Sampling Strategy ◽  
Common Species ◽  
Optimal Sampling ◽  
Trapping Time ◽  
Number Of Species ◽  
Emergence Patterns ◽  
The Mean ◽  
Water Trapping

We examined sampling characteristics of submerged funnel traps which were used to study emergence of Chironomidae in a large boreal riverine reservoir. Clay, bedrock, and marsh shorelines were sampled at 1.0-, 2.0-, 3.5-, and 4.5-m depths with four replicate traps at each depth. Numbers∙m−2 emerging from the three shorelines were similar but differences among depths were significant. The most common species emerging offshore (3.5 and 4.5 m) differed from those emerging inshore (1.0 and 2.0 m). Species emerging from all three shorelines were similar offshore. Inshore, clay and bedrock shorelines were similar but differed from the marsh shoreline. Twelve traps for each depth and 16 traps for each shoreline usually gave a ± 30% precision of the mean no.∙m−2 emerging. Single traps collected [Formula: see text] the number of species collected by 16 traps. All of the more abundant (≥ 1% of the total numbers caught) species in Southern Indian Lake were caught in two to four traps. A minimum of four traps was required to interpret emergence patterns of the most common species with one emergence peak; 16 for the most common species with two emergence peaks. Discontinuous trapping (48 h∙wk−1) gave similar results to continuous trapping (168 h∙wk−1). Our studies in Southern Indian Lake suggest that an optimal sampling strategy for mesotrophic lakes would be to trap discontinuously and use high numbers of traps.Key words: Chironomidae, sampling (biological), submerged funnel traps, reservoirs (water), trapping time, shorelines, depths, replicates, precision

Lichens on Picea abies and Pinus sylvestris – from tree bottom to the top

2013 ◽  
Vol 45 (1) ◽  
pp. 51-63 ◽  
Author(s):  
Liis MARMOR ◽  
Tiiu TÕRRA ◽  
Lauri SAAG ◽  
Ede LEPPIK ◽  
Tiina RANDLANE
Keyword(s):  
Vertical Gradient ◽  
Common Species ◽  
Lichen Species ◽  
Coniferous Forests ◽  
Epiphytic Lichens ◽  
Forest Canopies ◽  
Number Of Species ◽  
Lichen Diversity ◽  
The Mean ◽  
One New Species

AbstractThe vertical gradient of the community structure of epiphytic lichens in forest canopies was studied in southern Estonian coniferous forests. All lichen species on 15 Norway spruces and 15 Scots pines were recorded; age of trees ≥100 years. Species were sampled in height ranges on entire trees from the bottom to the top. The number of lichen species on pine trunks decreased with height from the ground, whereas the number of species on branches increased. There was no significant vertical change in the number of lichen species on spruce trunks; number of species on spruce branches was highest in mid canopy. The mean number of lichen species on a tree was 41 in spruces and 34 in pines; the mean number of species on the first 2 m was 14 in spruces and 12 in pines. According to the results, about two thirds of a tree's lichen species remain unrecorded if only the first 2 m near the ground are surveyed. Many lichen species were found only higher than 2 m, including several common species (e.g. Buellia griseovirens, Lecanora pulicaris, and Melanohalea exasperatula), but also some locally rather rare (Fellhanera subtilis, Micarea nitschkeana, Rinodina efflorescens) or red-listed ones (Evernia mesomorpha, Usnea barbata, U. fulvoreagens, U. substerilis, U. wasmuthii) and one new species for Estonia, Lecanora farinaria. There were also some species, such as Chaenotheca stemonea, Cladonia cenotea and C. norvegica, that were restricted to the lowest 2 m. The results indicate that canopy lichens form a significant part of lichen diversity in coniferous forests, and could add valuable information when estimating forest lichen diversity for conservation and other purposes.

scholarly journals The application of zeta diversity as a continuous measure of compositional change in ecology

2017 ◽  
Author(s):  
Melodie A. Mcgeoch ◽  
Guillaume Latombe ◽  
Nigel R. Andrew ◽  
Shinichi Nakagawa ◽  
David A. Nipperess ◽  
...  
Keyword(s):  
Original Data ◽  
Common Species ◽  
Continuous Measure ◽  
Data Sets ◽  
Compositional Change ◽  
Data Types ◽  
Sampling Schemes ◽  
Operational Taxonomic Units ◽  
Compositional Diversity ◽  
Biological Organisation

AbstractZeta diversity provides the average number of shared species acrossnsites (or shared operational taxonomic units (OTUs) acrossncases). It quantifies the variation in species composition of multiple assemblages in space and time to capture the contribution of the full suite of narrow, intermediate and wide-ranging species to biotic heterogeneity. Zeta diversity was proposed for measuring compositional turnover in plant and animal assemblages, but is equally relevant for application to any biological system that can be characterised by a row by column incidence matrix. Here we illustrate the application of zeta diversity to explore compositional change in empirical data, and how observed patterns may be interpreted. We use 10 datasets from a broad range of scales and levels of biological organisation – from DNA molecules to microbes, plants and birds – including one of the original data sets used by R.H. Whittaker in the 1960’s to express compositional change and distance decay using beta diversity. The applications show (i) how different sampling schemes used during the calculation of zeta diversity may be appropriate for different data types and ecological questions, (ii) how higher orders of zeta may in some cases better detect shifts, transitions or periodicity, and importantly (iii) the relative roles of rare versus common species in driving patterns of compositional change. By exploring the application of zeta diversity across this broad range of contexts, our goal is to demonstrate its value as a tool for understanding continuous biodiversity turnover and as a metric for filling the empirical gap that exists on spatial or temporal change in compositional diversity.

THE EXTRACTION OF PROLACTIN FROM HUMAN PITUITARY GLANDS

1965 ◽  
Vol 49 (1) ◽  
pp. 1-16 ◽  
Author(s):  
M. Apostolakis
Keyword(s):  
Growth Hormone ◽  
Pituitary Gland ◽  
List Type ◽  
Distilled Water ◽  
Hormone Activity ◽  
Isoelectric Precipitation ◽  
Human Pituitary ◽  
Pituitary Glands ◽  
Prolactin Content ◽  
The Mean

ABSTRACT A method for the extraction of prolactin from human pituitary glands is described. It is based on acetone drying, distilled water extraction, acetone and isoelectric precipitation. Two main products are obtained: Fraction R8 with a mean prolactin activity of 12.2 IU/mg and fraction U8 with a mean prolactin activity of 8.6 IU/mg. The former fraction does not contain any significant gonadotrophin activity and the latter contains on an average 50 HMG U/mg. In both cases contamination with ACTH and MSH is minimal. The growth hormone activity of both these fractions is low. It is postulated that in man too, prolactin and growth hormone are two distinct hormones. A total of 1250 human pituitary glands have been processed by this method. The mean prolactin content per pituitary gland has been found to be 73 IU.

IMMUNOREACTIVE GROWTH HORMONE IN PLASMA AND URINE IN JUVENILE DIABETICS BEFORE AND DURING INITIAL INSULIN TREATMENT

1974 ◽  
Vol 75 (1) ◽  
pp. 50-63 ◽  
Author(s):  
Kristian F. Hanssen
Keyword(s):  
Growth Hormone ◽  
Insulin Treatment ◽  
Juvenile Diabetes ◽  
Control Group ◽  
List Type ◽  
Newly Diagnosed ◽  
Renal Tubular Reabsorption ◽  
Juvenile Diabetics ◽  
The Mean ◽  
Renal Tubular

ABSTRACT Twenty newly diagnosed, but as yet untreated patients of both sexes with classical juvenile diabetes were investigated by determining the mean plasma immunoreactive growth hormone (IRHGH) and urinary IRHGH for a 24 hour period before and during initial insulin treatment. The plasma IRHGH was significantly higher (0.05 > P > 0.01) before than during initial insulin treatment. During initial insulin treatment, the mean plasma IRHGH was significantly higher (0.01 > P > 0.001) than in a control group. The urinary IRHGH was significantly higher (0.01 > P > 0.001) before than during insulin treatment. The increased urinary IRHGH observed before insulin treatment is thought to be partly due to a defective renal tubular reabsorption of growth hormone. No significant correlation was found between the mean blood sugar and plasma or urinary IRHGH either before or during insulin treatment.

CHROMATOGRAPHY OF THE 17-KETOGENIC STEROIDS IN THE DIAGNOSIS AND CONTROL OF CONGENITAL ADRENAL HYPERPLASIA

1960 ◽  
Vol XXXIII (II) ◽  
pp. 230-250 ◽  
Author(s):  
Eileen E. Hill
Keyword(s):  
Congenital Adrenal Hyperplasia ◽  
List Type ◽  
Adrenal Hyperplasia ◽  
Normal Children ◽  
Paediatric Practice ◽  
The Mean ◽  
Cortisone Therapy ◽  
And Control ◽  
Clinical Problems ◽  
Stimulation Of

ABSTRACT A method for the fractionation of the urinary 17-ketogenic steroids with no oxygen grouping at C11 and those oxygenated at C11, is applied to the clinical problems of congenital adrenal hyperplasia. In normal children the mean ratio of the non-oxygenated to oxygenated steroids is 0.24. In childrern with congenital adrenal hyperplasia the ratio is 2.3. The reason for this difference in ratio is discussed. The changes in ratio found under stimulation of the adrenal gland with exogenous or endogenous corticotrophin and the suppression with cortisone therapy are studied. This test can be applied to isolated samples of urine, a major advantage in paediatric practice, and can be carried out in routine laboratories. It is found to be reliable in the diagnosis and sensitive in the control of congenital adrenal hyperplasia.

Abstract 3016: Spirituality and Medication Adherence in Older African American Adults Diagnosed with Hypertension: A Qualitative Study

Circulation ◽  
2007 ◽  
Vol 116 (suppl_16) ◽  
Author(s):  
Lisa M Lewis
Keyword(s):  
African American ◽  
Medication Adherence ◽  
Qualitative Study ◽  
Antihypertensive Medication ◽  
Demographic Data ◽  
Patient Treatment ◽  
List Type ◽  
Medication Regimen ◽  
Antihypertensive Medications ◽  
The Mean

Background : Medication adherence (ADH) is key to decreasing hypertension (HTN)-related morbidity and mortality in older African-American (AA) adults. However, older AA adults have poorer ADH to prescribed antihypertensive medications when compared to their younger and Caucasian-American counterparts. Patient beliefs and cultural concepts about their medications influence their medication ADH. An important cultural concept in this regards is spirituality, which is a significant resource in the AA community. Thus, the purpose of this qualitative study was to explore the role of spirituality in ADH to antihypertensive medications for older AA adults. Methods: Older AA adults who were members of a Program of All Inclusive Care for the Elderly (PACE) and who were (a) diagnosed with HTN; (b) prescribed at least one antihypertensive medication; (c) self-identified as African-American or Black; and (d) self-identified as spiritual completed one in-depth individual face-to-face in this qualitative descriptive study informed by grounded theory. Demographic data were also collected. Results : Twenty-one PACE members completed the study. All of the participants were female. The mean age of participants was 73 years with most completing high school (67%). The mean HTN diagnosis was16.7 years and mean number of prescriptions for antihypertensives was 3.3. Participants indicated that their spirituality was used in a collaborative process with formal health care to manage their ADH to antihypertensive medications. This process was identified as Partnering with God to Manage My Medications. Partnering with God to Manage My Medications indicated that the PACE members acknowledged personal responsibility for adhering to their antihypertensive medication regimen but used their spirituality as a resource for making decisions to remain adherent; coping with medication side effects; and increasing their self-efficacy to deal with barriers to ADH . Conclusions : Spirituality played a positive role in medication adherence for the PACE members. Incorporating individual beliefs, such as spirituality, into patient treatment for HTN may capitalize on their inner resources for medication ADH and demonstrates culturally appropriate care.

scholarly journals FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

2019 ◽  
Author(s):  
Cheynna Crowley ◽  
Yuchen Yang ◽  
Yunjiang Qiu ◽  
Benxia Hu ◽  
Armen Abnousi ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Spatial Organization ◽  
R Package ◽  
Specific Gene ◽  
List Type ◽  
Cell Type ◽  
R Software ◽  
Computational Tools ◽  
Cell Type Specific ◽  
User Friendly

AbstractHi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller.Highlights– Frequently Interacting Regions (FIREs) can be used to identify tissue and cell-type-specific cis-regulatory regions.– An R software, FIREcaller, has been developed to identify FIREs and clustered FIREs into super-FIREs.

scholarly journals Standardizing carabid pitfall catches for trapping effort; a meta-analysis

2020 ◽  
Author(s):  
Pavel Saska ◽  
David Makowski ◽  
David Bohan ◽  
Wopke van der Werf
Keyword(s):  
Meta Analysis ◽  
Carabid Beetles ◽  
Published Data ◽  
Power Exponent ◽  
List Type ◽  
Catch Per Unit Effort ◽  
Pitfall Trapping ◽  
Number Of Species ◽  
Activity Density ◽  
Abundance And Diversity

AbstractCarabid beetles (Coleoptera: Carabidae) provide important ecological services and are frequently used as a bio-indicator in monitoring environmental quality. The abundance and diversity of carabids is usually determined using pitfall trapping, but trap catches are difficult to compare between studies due to variation in trapping effort. The standardization of the catch for trapping effort has not been previously addressed in a global analysis of studies in the literature.The aims of this study are (i) to define a method for estimating the effect of trapping effort on the size of the pitfall catch, and (ii) to explore factors related to study designs, sampling method, study origin, and level of data aggregation to determine how these factors affect the catch per unit effort in pitfall trapping.We conducted a meta-analysis on the activity-density and diversity of carabids across studies, based on published data from Europe and North-America to analyse whether standardization of catch measurements might be possible. Data were extracted from 104 publications, spanning a period of 42 years.The total catch was proportional to the number of trap days, and ranged from 0.19-9.53 beetles/(trap day) across studies (95% range), with a mean of 1.33 beetles/(trap day). The number of species was allometrically related to the trapping effort defined as the product of the number of traps, their perimeter and the time of exposure in the field, and characterized by a power exponent of 0.25. Species richness ranged across studies from 2.30-13.18 species/(m day)0.25 (95% range) with a mean of 7.15 species/(m day)0.25. The size of the catch and the number of species were higher in crops with narrow as compared to wide rows. There was no significant change in abundance or diversity of carabids in arable land over the 42 years covered. We also found that increasing trapping effort may not yield more accurate results.The results show that it is possible to standardize activity-density-based catches and species diversity for trapping effort across studies using a power transformation, allowing meta-analysis of such data, e.g. to elucidate factors affecting abundance and diversity of the focal taxa.

scholarly journals Hierarchical correction of p-values via an ultrametric tree running Ornstein-Uhlenbeck process

2021 ◽  
Author(s):  
Antoine Bichat ◽  
Christophe Ambroise ◽  
Mahendra Mariadassou
Keyword(s):  
Multiple Testing ◽  
R Package ◽  
Statistical Testing ◽  
Uhlenbeck Process ◽  
Explanatory Variables ◽  
New Associations ◽  
Penalized Estimation ◽  
Ultrametric Tree ◽  
Ornstein Uhlenbeck Process ◽  
The Mean

AbstractStatistical testing is classically used as an exploratory tool to search for association between a phenotype and many possible explanatory variables. This approach often leads to multiple testing under dependence. We assume a hierarchical structure between tests via an Ornstein-Uhlenbeck process on a tree. The process correlation structure is used for smoothing the p-values. We design a penalized estimation of the mean of the Ornstein-Uhlenbeck process for p-value computation. The performances of the algorithm are assessed via simulations. Its ability to discover new associations is demonstrated on a metagenomic dataset. The corresponding R package is available from https://github.com/abichat/zazou.

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