Modeling Skin Mark Temporal Variations to Estimate the Sex of Delphinids with Low Sexual Dimorphism: Implications for Management and Conservation.

Skin marks occur frequently in many cetacean species across the globe revealing a broad spectrum of causes, including social interactions, infectious diseases and injuries produced by anthropogenic factors. The current study used photo-id data from 2005–2014 to estimate the skin mark pattern on resident bottlenose dolphins (Tursiops truncatus) from the Aeolian Archipelago (Italy). Thirteen skin mark types were identified and their origin, prevalence and permanence time were examined. The pattern of skin marks was assessed for the abundance, richness, distribution and severity in six body regions and compared among age classes, sex and degree of dolphins’ interaction with trammel nets (DIN). Our results showed higher prevalence, abundance, richness and distribution of skin marks in adults than in the younger age classes, with the exception of black marks and white ring lesions. The prevalence and abundance of skin marks were higher in males than females, with the exception of scratches and white patches. Moreover, gunshot wounds, mutilations and irregular dorsal fin edges were found only on adult males. Since males showed higher DIN than females and, in dolphins with higher DIN, skin marks were more abundant and frequently distributed in different body regions, the skin mark pattern in regard to DIN seems to be sex-related. The more severe marks were observed on adults, males and dolphins with higher DIN, namely skin disorder, tooth rake marks, small shallow indentations, deep indentations and mutilations. On the contrary, the severity of scratches, white patches and dark ring lesions was higher in females than males, but not significantly related to DIN and age of the individuals. Our results showed that photo-id data provide an efficient and cost-effective approach to document the occurrence of skin marks in free-ranging bottlenose dolphin populations, a critical step toward understanding the cause and supporting the conservation strategies.

Some Thoughts About Data Type, Distribution, and Statistical Significance

An Institutional Review Board-approved protocol was used to quantify breast tissue inclusion in 52 women, under conditions simulating both craniocaudal (CC) and mediolateral oblique (MLO) views in mammography, dedicated breast CT in the upright subject position, and dedicated breast CT in the prone subject position. Using skin as a surrogate for the underlying breast tissue, the posterior aspect of the breast that is aligned with the chest-wall edge of the breast support in a screen-film mammography system was marked with the study participants positioned for CC and MLO views. The union of skin marks with the study participants positioned for CC and MLO views was considered to represent chest-wall tissue available for imaging with mammography and served as the reference standard. For breast CT, a prone stereotactic breast biopsy unit and a custom-fabricated barrier were used to simulate conditions during prone and upright breast CT, respectively. For the same breast marked on the mammography system, skin marks were made along the breast periphery that was just anterior to the apertures of the prone biopsy unit and the upright barrier. The differences in skin marks between subject positioning simulating breast CT (prone, upright) and mammography were quantified at six anatomic locations. For each location, at least one study participant had a skin mark from breast CT (prone, upright) posterior to mammography. However for all study participants, there was at least one anatomic location where the skin mark from mammography was posterior to that from breast CT (prone, upright) positioning. The maximum amount by which the skin mark from mammography was posterior to breast CT (prone and upright) over all six locations was quantified for each study participant and pair-wise comparison did not exhibit statistically significant difference between prone and upright breast CT (paired t- test, p = 0.4). Quantitatively, for 95% of the study participants the skin mark from mammography was posterior to breast CT (prone or upright) by at the most 9 mm over all six locations. Based on the study observations, geometric design considerations targeting chest-wall coverage with breast CT equivalent to mammography, wherein part of the x-ray beam images through the swale during breast CT are provided. Assuming subjects can extend their chest in to a swale, the optimal swale-depth required to achieve equivalent coverage with breast CT images as mammograms for 95% of the subjects varies in the range of ∼30–50 mm for clinical prototypes and was dependent on the system geometry.

Bio[statistics]philia

ABSTRACTThe analysis of skin marks and lesions is used for many cetacean species to assess the general health status of the populations with the purpose of developing effective conservation strategies. This study applies mark analysis to characterise common bottlenose dolphin (Tursiops truncatus) skin marks and lesions, and their variation at the individual level across years, in the Tiber River Estuary area (Mediterranean Sea, Italy), to test their efficacy as proxies of individual or population health. Using high‐quality photographic data collected between 2016 and 2023 during 205 sightings, marks were identified, classified, counted and measured on 39 individuals photographed on multiple occasions. Marks related to intraspecific interactions (e.g. tooth‐rakes), anthropogenic activities (e.g. signs of interaction with fishery) and health conditions (e.g. skin diseases and emaciation) were selected as indicators, and five indices were applied to estimate their extension and progression through time. Prevalent marks in all individuals were of social origin and aggressive nature. Marks related to skin diseases and emaciation were present in 97% and 70% of individuals, respectively. Almost half of the individuals showed physical signs of interaction with fishing gears. No significant temporal trends were observed. These results highlight that the local population is under the pressure of multiple stressors, mostly related to human activities, both directly (fishing) and indirectly (malnutrition, aggression). The consequences of stressor interactions may be complex to predict and raise challenges for the conservation of this protected species—and of the ecosystem it belongs to—in a highly anthropised and currently unmanaged area.

Statistical errors in immunologic research

Nonparametric vs Parametric Tests of Location in Biomedical Research

Inferential Statistics

A fine-mesh seine net was used at regular intervals to collect fishes from theentrance channel and basin of the Blackwood River Estuary (south-western Australia), from Deadwater Lagoon, which is joined to the entrance channel by a narrow and shallow watercourse and thus constitutes part of this estuary, and from Flinders Bay into which the estuary discharges. Sampling was at six-weekly intervals between February and December 1994. The juveniles of some marine species, such as Pelates sexlineatus, Rhabdosargus sarba and Aldrichetta forsteri, were either found only in the estuary or were in far higher densities in the estuary than in Flinders Bay. In contrast, the juveniles of some other marine species, such as Sillago schomburgkii, were relatively abundant in both environments, while others such as S. bassensis, Pelsartia humeralis, Lesueurina platycephala and Spratelloides robustus were either far more abundant in Flinders Bay or entirely restricted to this marine embayment. The various marine species found in inshore waters thus apparently vary considerably in their 'preference' for estuaries as nursery areas. Although some marine species were abundant in the shallows of the estuary, the fish fauna of these waters was dominated by the estuarine-spawning species Leptatherina wallacei, Favonigobius lateralis, L. presbyteroides and Atherinosoma elongata. The above regional differences help account for the very marked difference that was found between the compositions of the shallow-water ichthyofaunas of Flinders Bay and each of the three estuarine regions. The ichthyofaunal compositions of the basin and channel underwent pronounced changes during winter, when freshwater discharge increased markedly and salinities in the estuary thus declined precipitously. This faunal change was mainly attributable to the emigration of marine stragglers, a reduction in the densities of marine estuarine-opportunist species such as Pelates sexlineatus and R. sarba, and the immigration of large numbers of both young 0+ Aldrichetti forsteri from the sea and of L. wallacei from the river. Although most of the above species were also abundant in Deadwater Lagoon, the ichthyofaunal composition of this region did not undergo the same seasonal changes, presumably due to the lack of riverine input and thus the maintenance of relatively high salinities throughout the year. The number of marine straggler species was much lower in Deadwater Lagoon than in the estuary basin, reflecting a far more restricted tidal exchange with the entrance channel. However, the overall density of fishes was far higher in Deadwater Lagoon than in the estuary basin or entrance channel, due mainly to the far higher densities of the estuarine species Atherinosoma elongata and L. wallacei and of the 0+ age class of the marine species R. sarba. The high densities of certain species in Deadwater Lagoon are assumed to be related, at least in part, to the high level of productivity and protection that is provided by the presence of patches of Ruppia megacarpa, an aquatic angiosperm that was not present in the estuary basin or entrance channel.

Lack of variation in voltage-gated sodium channels of common bottlenose dolphins (Tursiops truncatus) exposed to neurotoxic algal blooms

The Adriatic Sea is one of the Mediterranean areas most heavily impacted by fishing and other human stressors. The northern part of the basin has been certified as an Important Marine Mammal Area because of the regular occurrence of common bottlenose dolphins, Tursiops truncatus. Boat surveys, totalling 76 days at sea and 10,711 km of navigation, were conducted between April 2018 and October 2019 to assess cetacean abundance within a 3,000‐km2 area off Veneto, Italy. Bottlenose dolphins – the only marine mammal species observed – were encountered on 52 days and were tracked for 81 h and 26 min, resulting in 15,066 dorsal fin photographs of high quality and resolution. Various capture–recapture models were applied on individual photo‐identification datasets. Model‐based estimates indicate that approximately 600 individuals occurred within the study area during the sampling period in both years. Abundance varied monthly: minimum estimates were obtained in May 2018 (291 individuals; 95% CI 134–630) and May 2019 (121; 95% CI 20–721), whereas maximum estimates were obtained in September 2018 (385; 95% CI 310–477) and October 2019 (494; 95% CI 378–645). Evidence provided by this study can be used to complement and validate coarse ‘snapshot’ information from recent aerial surveys of the entire Adriatic Sea, and to enforce management action mandated by the European Community (EC) Habitats Directive and Marine Strategy Framework Directive, as well as guiding the EC’s Maritime Spatial Planning.

This article reviews and compares different existing statistical tests utilized in significance analysis of gene expression from DNA microarray data. Microarray gene expression study facilitates the investigation of genes that are differentially expressed with respect to different classes of samples. Many gene expression studies also aim to find groups of genes that do something together, or to find out molecular similarities among a group of samples. In all respects, it is very important to know whether there is a difference between two sets of results, and whether that difference is likely to occur due to random variations of the datasets. Hence instead of simple data analysis, statistical tests are the proper way to check statistical relevance. Basically, the statistical significance test is compulsory for yielding an ordered list of relevant genes in terms of differential expression to the investigator. This article surveys a few important statistical tests which include both parametric and nonparametric tests and compares those statistical tests with respect to different performance metrics. The statistical tests have been applied on several artificial and real-life microarray gene expression datasets. Most of the time, real-life datasets contain noise and noisy data can have undesirable effect on the results of any data mining analysis. Therefore, performance analysis on noisy datasets for different statistical tests has also been performed to facilitate the comparative study. Furthermore, correlation analysis of the resultant genes from different statistical methods has been accomplished. Keywords: Analysis, correlation analysis, eigenvector, nonparametric tests, P-value, parametric tests, principal component, statistical tests.

Simple SummaryThe gastrointestinal tract of the bottlenose dolphin (Tursiops truncatus) differs structurally and functionally from that of terrestrial mammals. In particular, the intestine does not show any macroscopic subdivision and lacks a caecum. In addition, the histological aspect of the intestine is relatively constant, without marked differences between the anterior and posterior parts. Although the intestine of these cetaceans presents differences in comparison with terrestrial mammals, little information is currently available on their enteric nervous system. The aim of the present study was to investigate the morphological and quantitative aspects of neurons immunoreactive (IR) for the neuronal nitric oxide synthase (nNOS) and Substance P (SP) in the intestine of bottlenose dolphins (Tursiops truncatus). In these dolphin specimens, a smaller number of nNOS-IR neurons in the submucosal plexus and a larger number of SP-IR neurons in the myenteric plexus were observed compared to other mammals. Interestingly, no co-localization between nNOS- and SP-IR neurons was detected in either of the plexuses, suggesting the existence of two completely distinct functional classes of neurons in the intestine of the bottlenose dolphin.Compared with other mammals, the digestive system of cetaceans presents some remarkable anatomical and physiological differences. However, the neurochemical features of the enteric nervous system (ENS) in these animals have only been described in part. The present study gives a description of the nitrergic and selected peptidergic systems in the myenteric plexus (MP) and submucosal plexus (SMP) of the intestine of the bottlenose dolphin (Tursiops truncatus). The distribution and morphology of neurons immunoreactive (IR) for the neuronal nitric oxide synthase (nNOS) and Substance P (SP) were immunohistochemically studied in formalin-fixed specimens from the healthy intestine of three animals, and the data were compared with those described in the literature on other mammals (human and non-human). In bottlenose dolphins, the percentages of nitrergic neurons (expressed as median and interquartile range—IQR) were 28% (IQR = 19–29) in the MP and 1% (IQR = 0–2) in the SMP, while the percentages of SP-IR neurons were 31% (IQR = 22–37) in the MP and 41% (IQR = 24–63) in the SMP. Although morphological features of nNOS- and SP-IR neurons were similar to those reported in other mammals, we found some noticeable differences in the percentages of enteric neurons. In fact, we detected a lower proportion of nNOS-IR neurons in the SMP and a higher proportion of SP-IR neurons in the MP compared to other mammals. To the best of the authors’ knowledge, this study represents the first description and quantification of nNOS-IR neurons and the first quantification of SP-IR neurons in the intestine of a cetacean species. As nNOS and SP are important mediators of intestinal functions and the nitrergic population is an important target for many neuroenteropathies, data obtained from a healthy intestine provide a necessary basis to further investigate and understand possible functional differences and motor intestinal dysfunctions/alterations in these special mammals.

The Natura 2000 (N2k) network is an important site-based protection tool for the protection of biodiversity in Europe. However, for highly mobile and adaptable marine species, such a tool might not be the most effective way to achieve conservation objectives, unless this includes a broader consideration of the direct threats to these species throughout their range. Considering that the N2k network requires that a ‘significant proportion’ of 60% of the population be under protection, this creates a challenge for the conservation of these wide-ranging species. This paper reviews the efficacy of the N2k network as it is presently implemented within the Adriatic Sea for the conservation of two highly mobile marine species - the common bottlenose dolphin and the loggerhead turtle. In particular, it considers the appropriateness of the current Sites of Community Importance (SCIs) in the region and the relevance of the existing marine N2k network for the conservation of these species. It provides new insights on the approach used to evaluate SCI designations highlighting important weaknesses in the system, including threat identification after SCI designation, and the relevance of SCI size in relation to management commitments. Data from two basin-wide aerial surveys were used to define areas of relative high density of these species, in comparison to other areas in the basin. Given the ambitious 60% conservation target of the N2k network, analysis shows that site-based protection tools are unlikely to be sufficient to protect a ‘significant proportion’ of either species, unless very large areas are designated as SCIs. However, given that the main threats known to affect these species in this region (i.e. fishery bycatch and seismic surveys) are present throughout the basin, these large SCIs would still have limited conservation success without implementing other wide-scale mitigation measures. For these two species, the Member States and the European Union authorities should give higher priority to the implementation of another pillar of the Habitats Directive, mitigating accidental catches in fishing gear and other human-induced mortalities. This should take into consideration the full effects of these mortalities on the populations of these two species through regular transboundary monitoring programs.

To prove that a certain algorithm is superior to the benchmark algorithms, the statistical hypothesis tests are commonly adopted with experimental results on a number of datasets. Some statistical hypothesis tests draw statistical test results more conservative than the others, while it is not yet possible to characterize quantitatively the degree of conservativeness of such a statistical test. On the basis of the existing nonparametric statistical tests, this paper proposes a new statistical test for multiple comparison which is named as t-Friedman test. T-Friedman test combines t test with Friedman test for multiple comparison. The confidence level of the t test is adopted as a measure of conservativeness of the proposed t-Friedman test. A bigger confidence level infers a higher degree of conservativeness, and vice versa. Based on the synthetic results generated by Monte Carlo simulations with predefined distributions, the performance of several state-of-the-art multiple comparison tests and post hoc procedures are first qualitatively analyzed. The influences of the type of predefined distribution, the number of benchmark algorithms and the number of datasets are explored in the experiments. The conservativeness measure of the proposed method is also validated and verified in the experiments. Finally, some suggestions for the application of these nonparametric statistical tests are provided.