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Are juveniles as tolerant to salinity stress as adults?: A case study of Northern European, Ponto-Caspian and North American species

Aim: Global biodiversity and ecosystems are highly impacted by anthropogenic activities, such as climate change and introduction of non-indigenous species. As numerous species from the Ponto-Caspian region have established in the North and Baltic Seas, as well as in the Laurentian Great Lakes, there have been large number of studies examining environmental tolerance of these species to determine their future potential to spread. However, many of those studies were conducted only on adult stages, while neglecting the possibility that early life history stages might not be equally resilient. Location: Northern European, Ponto‐Caspian and North American regions. Methods: To determine if juveniles would demonstrate the same environmental tolerance as their parents, we examined the salinity tolerance of adults and juveniles of one Northern European (Gammarus salinus), one Ponto-Caspian (Pontogammarus maeoticus) and one North American species (Gammarus tigrinus). Additionally, we compared our study to that of Paiva et al. (2018), who tested the salinity tolerance of the same species using only adults. Results: Our study determined that both adults and juveniles of all three species tolerated wide ranges of salinity, with juveniles of G. salinus tolerating only slightly narrower salinity range than their parents, while those of P. maeoticus and G. tigrinus much narrower range. Additionally, we determined better survival and higher growth rates of juveniles of G. salinus in higher salinities, and better survival of P. maeoticus in lower salinities. Main conclusions: Based on juvenile salinity tolerance, our study further supported findings of Paiva et al. (2018), where Northern European species may be adapted to marine, while Ponto-Caspian to lower saline and freshwater environments. The North American species is probably adapted to intermediate salinities. As juveniles do not tolerate the same salinity stress as adults, we emphasize the importance of testing all life-history stages when predicting species resilience to environmental stressors.

Data from: Osteosarcopenia in reproductive-aged women with polycystic ovary syndrome: a multicenter case-control study

Context: Osteosarcopenia (loss of skeletal muscle and bone mass and/or function usually associated with aging) shares pathophysiological mechanisms with polycystic ovary syndrome (PCOS). However, the relationship between osteosarcopenia and PCOS remains unclear. Objective: We evaluated skeletal muscle index% (SMI%=[appendicular muscle mass/weight {kg}]×100) and bone mineral density (BMD) in PCOS <a name="_Hlk36059693">(hyperandrogenism+oligoamenorrhea), and contrasted these musculoskeletal markers against 3 reproductive phenotypes: (1) HA (hyperandrogenism+eumenorrhea); (2) OA (normoandrogenic+oligoamenorrhea) and, (3) controls (normoandrogenic+eumenorrhea). </a>Endocrine predictors of SMI% and BMD were evaluated across groups. Design, Setting, Participants: Multicenter case-control study of 203 women (18–48y) in New York State. <a name="_Hlk36062204">Results:</a> PCOS group exhibited reduced SMI% (<a name="_Hlk35952064">mean [95%CI]; 26.2% [25.1,27.3] vs. 28.8% [27.7,29.8])</a>, lower-extremity SMI% (57.6% [56.7,60.0] vs. 62.5% [60.3,64.6]), and BMD (1.11 [1.08,1.14] vs. 1.17 [1.14,1.20] g/cm2) compared to controls. PCOS group also had decreased upper (0.72 [0.70,0.74] vs. 0.73 [0.71,0.76] g/cm2) and lower (1.13 [1.10,1.16] vs. 1.15 [1.12,1.18] g/cm2) limb BMD compared to HA. Matsuda index was lower in PCOS vs. controls and positively associated with SMI% in all groups (All:P≤0.05). Only controls showed associations between insulin-like-growth-factor-1 (IGF-1) and upper (r=0.84) and lower (r=0.72) limb BMD (All:P<0.01). Unlike in PCOS, IGF binding-protein-2 was associated with SMI% in controls (r=0.45) and HA (r=0.67), and with upper limb BMD (r=0.98) in HA (All:P<0.05). Conclusions: Women with PCOS exhibit early signs of osteosarcopenia compared to controls likely attributed to disrupted insulin function. Understanding the degree of musculoskeletal deterioration in PCOS is critical for implementing targeted interventions that prevent and delay osteosarcopenia in this clinical population.

opencc-by-4.0Aug 2020View details →

GPS 50 Hz data set for the case study. Part 2 (Version sbf)

GPS 50 Hz data set for the case study entitled "Comparison of TEC calculations based on Trimble, Javad, Leica and Septentrio GNSS receiver data". Part 2 (Septentrio dataset).

Data from: Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models

The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. Our results show that the subset of genes chosen for manual annotation by a research community (3.5-7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species' gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.

Supporting fisheries management with genomic tools: a case study of kingklip (Genypterus capensis) off southern Africa

Kingklip, Genypterus capensis, is a valuable fish resource in southern African waters, with a wide geographic distribution spanning South Africa and Namibia. Previous studies have provided evidence for multiple stocks in South Africa, but the extent of stock structuring across the Southern African region remains unclear. In this study, we genotyped over 40 000 SNPs to characterise the spatial distribution of genomic variation for G. capensis throughout its core distribution. Results suggest that fish sampled at the northernmost range (off central Namibia) are characterised by lower genomic diversity, although the region exhibited the highest number of private SNPs, suggesting some degree of geographic isolation. Using neutral and putative outlier loci independently, we show that kingklip exhibits three population clusters, "northern Benguela", "southern Benguela" and South African "South Coast". Population differentiation was observed only using "outlier" loci, suggesting that local adaptation might be one of the main drivers of the observed differentiation. Overall, our research provides novel insights into the regional dynamics that can support the sustainable long-term exploitation of this valuable fisheries resource.

Supplementary material 1 from: Di Cecco V, Di Santo M, Di Musciano M, Manzi A, Di Cecco M, Ciaschetti G, Marcantonio G, Di Martino L (2020) The Majella National Park: a case study for the conservation of plant biodiversity in the Italian Apennines. Italian Botanist 10: 1-24. https://doi.org/10.3897/italianbotanist.10.52952

Complete list of taxa stored at the MSB

opencc-zeroSep 2020View details →

Supplementary material 1 from: Snyder MR, Stepien CA (2020) Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River. Metabarcoding and Metagenomics 4: e53455. https://doi.org/10.3897/mbmg.4.53455

Supplementary material: Additional methods, results, figures, and tables

opencc-zeroOct 2020View details →

Mind the outgroup and bare branches in total-evidence dating: a case study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: "bare-branch attraction", namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

opencc-by-4.0Oct 2020View details →

What drives residents' intentions to adopt e-commerce in rural regions of western China? A case study in Chongqing municipality

Research data

opencc-by-4.0Nov 2020View details →

On the Importance and Shortcomings of Code Readability Metrics: A Case Study on Reactive Programming - replication package

This is the replication package for the conference paper submission "On the Importance and Shortcomings of Code Readability Metrics: A Case Study on Reactive Programming" Contents: <ul> <li>measurements.zip <ul> <li>DATASET_ORIGINAL.csv</li> <li>DATASET_REACTIVE.csv</li> </ul> </li> <li>source_code.zip <ul> <li> source_code_orig <ul> <li>Client.java</li> <li>Connection.java</li> <li>Server.java</li> <li>TcpConnection.java</li> <li>UdpConnection.java</li> </ul> </li> <li> source_code_rx <ul> <li>Client.java</li> <li>Connection.java</li> <li>Server.java</li> <li>TcpConnection.java</li> <li>UdpConnection.java</li> </ul> </li> </ul> </li> </ul>

opencc-zeroDec 2020View details →

Data from: Estimating population density of insectivorous bats based on stationary acoustic detectors: a case study

1. Automated recording units are commonly used by consultants to assess environmental impacts and to monitor animal populations. Although estimating population density of bats using stationary acoustic detectors is key for evaluating environmental impacts, estimating densities from call activity data is only possible through recently developed numerical methods, as the recognition of calling individuals is impossible. 2. We tested the applicability of generalized random encounter models (gREMs) for determining population densities of three bat species (Common pipistrelle Pipistrellus pipistrellus, Northern bat Eptesicus nilssonii,, and Natterer's bat Myotis nattereri) based on passively collected acoustical data. To validate the results, we compared them to (i) density estimates from the literature and to (ii) Royle-Nichols (RN) models of detection/non-detection data. 3. Our estimates for M. nattereri matched both the published data and RN-model results. For E. nilssonii, the gREM yielded similar estimates to the RN-models, but the published estimates were more than twice as high. This discrepancy might be because the high-altitude flight of E. nilssonii is not accounted for in gREMs. Results of gREMs for P. pipistrellus were supported by published data but were approximately 10 times higher than those of RN-models. RN-models use detection/non-detection data and this loss of information probably affected population estimates of very active species like P. pipistrellus. 4. gREM models provided realistic estimates of bat population densities based on automatically recorded call activity data. However, the average flight altitude of species should be accounted for in future analyses. We suggest including flight altitude in the calculation of the detection range to assess the detection sphere more accurately and to obtain more precise density estimates.

opencc-by-4.0Dec 2016View details →

Fig. 1 in A case of intersex occurrence in Steindachneridion parahybae (Steindachner, 1877) (Siluriformes: Pimelodidae) under captivity condition: a cytogenetic and morphological study

Fig. 1. Micrographs of the ovaries of Steindachneridion parahybae juveniles in captivity showing different germ cell types. a) scattered oogonia (arrow) within the germinal epithelium surrounded by prefollicle cells (arrowhead); b) proliferation of the oogonium gives rise to cell cluster that appears as small nests (delimited by the arrows), and are also surrounded by prefollicle cells (arrowhead); c) inside this nests, oogonia (arrow) enter into meiosis and progressively individualized by cells derived from the epithelium (prefollicle cells), and they become separated from nests, originating the oocytes (arrowhead); d) following the ovarian development, early primary growth or perinucleolar oocyte (arrowhead) is characterized by an enhancement of cytoplasm basophilia; e) Perinucleolar oocyte (asterisk) showing the thin follicular layer (arrow) and multiple nucleoli displaced in a perinuclear position (arrowhead); f) Perinucleolar stage in different size, showing in an initial (arrowhead) and advanced stage (arrow). Periodic-Acid-Schiff (PAS)/Weigert's Haematoxylin/Metanil Yellow staining. Scale bars: 10 µm (a); 30 µm (b,c,d,e); 400 µm (f).

opencc-zeroDec 2011View details →

Data from: Testing for ecological limitation of diversification: a case study using parasitic plants

Imbalances in phylogenetic diversity could be the result of variable unbounded diversification rates, differing limits on diversity, or a combination of the two. We propose an approach to distinguish between rates and limits as the primary cause of phylogenetic imbalance, using parasitic plants as a model. With sister-taxon comparisons, we show that parasitic plant lineages are typically much less diverse than their autotrophic sisters. We then use age estimates for taxa used in the sister-taxon comparisons to test for correlations between clade age and diversity. We find that parasitic plant diversity is not significantly correlated with the age of the lineage, whereas there is a strong positive correlation between the age and diversity of autotrophic sister lineages. The Ericaceae sister-pair Monotropoideae (parasitic) and Arbutoideae (autotrophic) are sufficiently well samples at the species level to allow more parametric comparisons of diversification patterns. Model-fitting for this group supports ecological limitation in Monotropoideae and unconstrained diversification in Arbutoideae. Thus, differences in diversity between parasitic plants and their autotrophic sisters might be caused by a mixture of ecological limitation and unbounded diversification. A combination of sister-taxon comparisons of diversity and age, coupled with model-fitting of well-sampled phylogenies of focal taxa, provides a powerful test of likely causes of asymmetry in the diversity of lineages.

opencc-zeroDec 2015View details →

Data from: Divergence maintained by climatic selection despite recurrent gene flow: a case study of Castanopsis carlesii (Fagaceae)

Local adaptation to different environments has the potential to maintain divergence between populations despite recurrent gene flow and is an important driver for generating biological diversity. In this study, we investigate the role of adaptation in the maintenance of two parapatric varieties of a forest tree. We used sequence variation of chloroplastic DNA and restriction site-associated DNA to investigate the genetic structure of two varieties of Castanopsis carlesii in subtropical China and relate it to climatic variation. We used niche reconstruction methods to investigate niche differentiation between the two varieties and to estimate the past distribution of this species. A deep divergence was observed between the two varieties, but evidence of introgression and genetic admixture was detected in two phenotypically and geographically intermediate populations. Niche reconstruction suggests that the distribution of the two varieties was disjunct during periods of global cooling and that the two varieties occupy significantly different niches. The genetic structure was mainly driven by environmental factors, and 13 outlier loci under divergent selection were correlated with climatic variation. These results suggest that the two varieties evolved in allopatry and came back into secondary contact after the last glacial maximum and that they are an evolutionary example of divergence maintained by climatic selection despite recurrent gene flow.

opencc-zeroDec 2017View details →

Data from: Numerical simulation of the free surface and water inflow of a slope, considering the nonlinear flow properties of gravel layers: a case study

Groundwater is an important factor of slope stability, and ninety percent of slope failures are related to the influence of groundwater. In the past, free surface calculations and the prediction of water inflow were based on Darcy's law. However, Darcy's law for steady fluid flow is a special case of non-Darcy flow, and many types of non-Darcy flows occur in practical engineering applications. In this paper, based on the experimental results of laboratory water seepage tests, the seepage state of each soil layer in the open-pit slope of the Yanshan Iron Mine, China, were determined, and the seepage parameters were obtained. The seepage behaviour in the silt layer, fine sand layer, silty clay layer, and gravelly clay layer followed the traditional Darcy law, while the gravel layers showed clear nonlinear characteristics. The relation among the permeability, the porosity and the non-Darcy coefficient is investigated. A coupled mathematical model is established for two flow fields, on the basis of Darcy flow in the low-permeability layers and Forchheimer flow in the high-permeability layers. In addition, we considered the effect of the seepage in the slope on the transition from Darcy flow to Forchheimer flow. Then, a numerical simulation was conducted by using finite element software (LELAC 2.2). The results indicate that the free surface calculated by the Darcy-Forchheimer model is in good agreement with the in situ measurements; however, there is an evident deviation of the simulation results from the measured data when the Darcy model is used. Through a parameter sensitivity analysis of the gravel layers, we found that the height of the overflow point and the water inflow calculated by the Darcy-Forchheimer model are consistently less than those of the Darcy model, and the discrepancy between these two models increase as the permeability increases. The necessity of adopting the Darcy-Forchheimer model was explained.

opencc-zeroDec 2015View details →

Data from: Three-dimensional reconstruction on cell level: case study elucidates the ultrastructure of the spinning apparatus of Embia sp. (Insecta: Embioptera)

Spinning is a phenomenon not only present in spiders, but also in many other arthropods. The functional morphology and complexity of spinning organs is often poorly understood. Their elements are minute and studying them poses substantial methodological difficulties. This study presents a three-dimensional reconstruction of a silk gland of Embia sp. on cellular level, based on serial sections acquired with serial block-face scanning electron microscopy (SBFSEM) to showcase the power of this method. Previous studies achieved either high resolution to elucidate the ultrastructure or satisfying three-dimensional representations. The high-resolution achieved by SBFSEM can be easily used to reconstruct the three-dimensional ultrastructural organization of cellular structures. The herein investigated spinning apparatus of Embioptera can be taken as an example demonstrating the potential of this method. It was possible to reconstruct a multinucleated silk gland containing 63 nuclei. We focused on the applicability of this method in the field of morphological research and provide a step-by-step guide to the methodology. This will help in applying the method to other arthropod taxa and will help significantly in adapting the method to other animals, animal parts and tissues.

opencc-zeroDec 2017View details →

Data from: QuLinePlus: extending plant breeding strategy and genetic model simulation to cross-pollinated populations – case studies in forage breeding

Plant breeders are supported by a range of tools that assist them to make decisions about the conduct or design of plant breeding programs. Simulations are a strategic tool that enable the breeder to integrate the multiple components of a breeding program into a number of proposed scenarios that are compared by a range of statistics measuring the efficiency of the proposed systems. A simulation study for the trait growth score compared two major strategies for breeding forage species, among half-sib family selection and among and within half-sib family selection. These scenarios highlighted new features of the QuLine program, now called QuLinePlus, incorporated to enable the software platform to be used to simulate breeding programs for cross pollinated species. Each strategy was compared across three levels of HS family mean heritability (0.1, 0.5 and 0.9), across three sizes of the initial parental population (10, 50, and 100), and across three genetic effects models (fully additive model, a mixture of additive, partial and over dominance model, and a mixture of partial dominance and over dominance model). Among and within half-sib selection performed better than among half-sib selection for all scenarios. The new tools introduced into QuLinePlus should serve to accurately compare among methods and provide direction on how to achieve specific goals in the improvement of plant breeding programs for cross breeding species.

opencc-zeroDec 2017View details →

Data from: Venom gland size and venom complexity – essential trophic adaptations of venomous predators: a case study using spiders

Specialised predators possess variety of adaptations. In the venomous predators this may include size of the venom gland and venom composition. It is expected that due to different foraging strategies predators with a wide trophic niche (generalists) should possess larger venom glands that contain more diversified components than species with a narrow niche (specialists). We focused on spiders, as the most diversified group of venomous predators, in which a wide variety of trophic strategies has evolved. We conducted a comparative analysis using 40 spider species, in which we measured the size of their venom gland and its complexity using proteome profiling methods. The species were classified into three trophic groups: generalists, facultative specialists, and obligatory specialists. We found that the venom glands of generalists are larger than those of obligatory specialists, which is presumably due to more frequent prey capture by the former. The complexity of venom, of peptides (2-15 kDa) and proteins (15-250 kDa), was more diverse in generalists than in specialists. Multivariate analysis of venom revealed significant differences among the three trophic categories only in the complexity of peptides. Our study thus shows that venom gland size and its content have taken different pathways during the evolution of trophic strategies in spiders. Generalists evolved larger venom glands with more complex composition, whereas obligatory specialists possess smaller glands with less diverse chemical structures, presumably containing prey-specific toxins.

opencc-zeroSep 2019View details →

Data from: Modified antibiotic adjuvant ratios can slow and steer the evolution of resistance: Co-amoxiclav as a case study

As antibiotic resistance spreads, developing sustainable methods to restore the efficacy of existing antibiotics is increasingly important. One widespread method is to combine antibiotics with synergistically acting adjuvants that inhibit resistance mechanisms, allowing drug killing. Here we use co-amoxiclav (a clinically important combination of the -lactam antibiotic amoxicillin and the -lactamase inhibitor clavulanate) to ask whether treatment efficacy and resistance evolution can be decoupled via component dosing modifications. A simple mathematical model predicts that different ratios of these two drug components can produce distinct evolutionary responses irrespective of initial efficacy. We test this hypothesis by selecting Escherichia coli with a plasmid encoded -lactamase (CTX-M-14), against different compositions of amoxicillin and clavulanate. Consistent with our theory, we found that while resistance evolved under all conditions, the component ratio influenced both the rate and mechanism of resistance evolution. Specifically, we found that the current clinical practice of high amoxicillin to clavulanate ratios resulted in the most rapid adaptation to antibiotics via gene dosing responses. Increased plasmid copy number allowed E. coli to increase -lactamase dosing and effectively titrate out low quantities of clavulanate, restoring amoxicillin resistance. In contrast, high clavulanate ratios were more robust - plasmid copy number did not increase, although porin or efflux resistance mechanisms were found, as in all drug ratios. Our results indicate that by changing the ratio of adjuvant to antibiotic we can slow and steer the path of resistance evolution. We therefore suggest using increased adjuvant dosing regimens to slow the rate of resistance evolution.