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FIGURE 1 in The Cainozoic to present-day record of Circum-Mediterranean, NE Atlantic and North Sea Cantharidinae and Trochinae (Trochoidea, Gastropoda)-a synopsis

FIGURE 1. Chronostratigraphy after Gradstein et al. (2012) with regional Paratethys stages after Popov et al. (2004)

FIGURE 4 in The Cainozoic to present-day record of Circum-Mediterranean, NE Atlantic and North Sea Cantharidinae and Trochinae (Trochoidea, Gastropoda)-a synopsis

FIGURE 4. Comparison of the molecular phylogeny of Uribe et al. (2017a) (grey bars are 95% confidence intervals) and assumed serigraphic distributions based on the fossil record (in orange).

FIGURE 7 in The Cainozoic to present-day record of Circum-Mediterranean, NE Atlantic and North Sea Cantharidinae and Trochinae (Trochoidea, Gastropoda)-a synopsis

FIGURE 7. Eocene to present-day Cantharidinae: 7A1–A2. Amonilea parnensis (Bayan, 1870), Eocene, Lutetian, FontenaySaint-Père (France), MNHN.F.J02025; 7B1–B2. Anceps anceps (Eichwald, 1850), late Miocene, Bessarabian, Kertsch (Russia), NHMW 2020/0050/0001; 7C1–C2. Anceps papilla (Eichwald, 1850), late Miocene, Bessarabian, Jenikale Kertsch (Russia), NHMW 2020/0050/0004; 7D1–D2. Callumbonella suturalis (Philippi, 1836), present-day, Alboran Sea, reproduced from Go-

FIGURE 6 in The Cainozoic to present-day record of Circum-Mediterranean, NE Atlantic and North Sea Cantharidinae and Trochinae (Trochoidea, Gastropoda)-a synopsis

FIGURE 6. Fossil record of extant species; only a small number of the 85 extant Cantharidinae and 9 Trochinae species can be traced back to the late Miocene.

opencc-zeroJan 2021View details →

Neutrophil extracellular traps are present in the airways of ENaC-overexpressing mice with cystic fibrosis-like lung disease

Background: Neutrophils are key components of the exacerbated inflammation and tissue damage in cystic fibrosis (CF) airways. Neutrophil extracellular traps (NETs) trap and kill extracellular pathogens. While NETs are abundant in the airways of CF patients and have been hypothesized to contribute to lung damage in CF, the in vivo role of NETs remains controversial, partially due to lack of appropriate animal models. The goal of this study was to detect NETs and to further characterize neutrophilmediated inflammation in the airways of mice overexpressing the epithelial sodium channel (βENaC-Tg mice on C57BL/6 background) in their lung with CF-like airway disease, in the absence of any apparent bacterial infections. Methods: Histology scoring of lung tissues, flow cytometry, multiplex ELISA, immunohistochemistry and immunofluorescence were used to characterize NETs and the airway environment in uninfected, βENaC-Tg mice at 6 and 8 weeks of age, the most chronic time points so far studied in this model. Results: Excessive neutrophilic infiltration characterized the lungs of uninfected, βENaC-Tg mice at 6 and 8 weeks of age. The bronchoalveolar lavage fluid (BALF) of βENaC-Tg mice contains increased levels of CF-associated cytokines and chemokines: KC, MIP-1α/β, MCP-1, G-CSF, IL-5, and IL-6. The BALF of βENaC-Tg mice contain MPO-DNA complexes, indicative of the presence of NETs. Immunofluorescence and flow cytometry of BALF neutrophils and lung tissues demonstrated increased histone citrullination, a NET-specific marker, in βENaC-Tg mice. Conclusions: NETs are detected in the airways of βENaC-Tg mice, in the absence of bacterial infections. These data demonstrate the usefulness of the βENaC-Tg mouse to serve as a model for studying the role of NETs in chronic CF airway inflammation. Keywords Cystic fibrosis; neutrophil extracellular traps; NET; ENaC, neutrophil.

FIG. 4A–L in Review of Reuteria Puton, 1875 (Heteroptera: Miridae) species present in Lodos Entomological Museum, Turkey (LEMT)

FIG. 4A–L. Reuteria atalayi sp. n. A—Habitus of female (Scale bar = 1 mm), B—Left paramere, C, D—Right paramere from different perspectives, E–H—vesica, from different perspectives, I–L, idem, outline of vesical processes (Scale bars = 0,1 mm) (Numbers in the figures from E to L mark the distinct vesical processes, letters mark the branches of a process, e.g. 2c indicates the third branch of second vesical process).

FIG. 3A–G. Reuteria winkelmanni. A in Review of Reuteria Puton, 1875 (Heteroptera: Miridae) species present in Lodos Entomological Museum, Turkey (LEMT)

FIG. 3A–G. Reuteria winkelmanni. A—Habitus of male (Scale bar = 1 mm), B—Habitus of female (Scale bar = 1 mm), C—Left paramere, D–E—Right paramere, F—vesica, G—idem, outline of vesical processes (Scale bars = 0,1 mm).

FIG. 2A–E in Review of Reuteria Puton, 1875 (Heteroptera: Miridae) species present in Lodos Entomological Museum, Turkey (LEMT)

FIG. 2A–E. Reuteria serratis sp. n. A—Habitus of male (Scale bar = 1 mm), B—Left paramere, C—Right paramere, D—vesica, E—idem, outline of vesical processes (Scales bar = 0,1 mm).

FIG. 1A–H. Reuteria riegeri. A—R. riegeri torosensis ssp. n in Review of Reuteria Puton, 1875 (Heteroptera: Miridae) species present in Lodos Entomological Museum, Turkey (LEMT)

FIG. 1A–H. Reuteria riegeri. A—R. riegeri torosensis ssp. n., habitus of male (Scale bar = 1 mm), B—idem, left paramere, C—idem, right paramere, D—idem, right paramere of a different specimen, E—R. reigeri riegeri, right paramere, F—idem, vesica, theca removed, G—R. riegeri torosensis ssp.n., vesica, theca removed, H—idem, aedeagus, theca intact (Scale bars = 0,1 mm). (Numbers indicate each distinct vesical process; in G, vesical processes 2 and 3 are separately illustrated from different views) [A–D, G–H, original, E–F, from Strauss & Simon (2014)].

opencc-zeroDec 2016View details →

Data from: The present and future effects of land use on ecological assemblages in tropical grasslands and savannas in Africa

The world is currently experiencing a period of rapid, human-driven biodiversity loss. Over the past decade, numerous metrics for biodiversity have been used to create indicators to track change in biodiversity. However, our ability to predict future changes has been limited. In this study, we use two very different models to predict the status and possible futures for the composition and diversity of ecological assemblages in African tropical grasslands and savannas under land-use change. We show that ecological assemblages are affected more by land use in African grasslands and savannas than in other biomes. We estimate that average losses of assemblage composition and diversity are already between 9.7 and 42.0%, depending on the model and measure used. If current socio-economic trajectories continue ('business-as-usual'), the likely associated land-use changes are predicted to lead to a further 5.6–12.3% loss of assemblage composition and diversity. In contrast, a scenario that assumes more efficient use of agricultural areas (thus requiring a smaller total area) could be associated with a partial reversal ‒ of as much as 3.2% ‒ of past losses. While the agriculture that causes the majority of land-use change is an important source of economic growth, projections of the effects of land use on ecological assemblages can allow for more informed decisions.

opencc-zeroDec 2011View details →

Data from: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (1) in silico PCRs using all standard sequences in the EMBL public database as templates, (2) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway, and (3) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~ 16 000–50 000 yr BP) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a paleoecological tool.

opencc-zeroDec 2012View details →

Data from: Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata Née

Phylogeography and ecological niche models (ENMs) suggest that late Quaternary glacial cycles have played a prominent role in shaping present population genetic structure and diversity, but have not applied quantitative methods to dissect the relative contribution of past and present climate vs. other forces. We integrate multilocus phylogeography, climate-based ENMs and multivariate statistical approaches to infer the effects of late Quaternary climate change on contemporary genetic variation of valley oak (Quercus lobata Née). ENMs indicated that valley oak maintained a stable distribution with local migration from the last interglacial period (~120 ka) to the Last Glacial Maximum (~21 ka, LGM) to the present compared with large-scale range shifts for an eastern North American white oak (Quercus alba L.). Coast Range and Sierra Nevada foothill populations diverged in the late Pleistocene before the LGM [104 ka (28–1622)] and have occupied somewhat distinct climate niches, according to ENMs and coalescent analyses of divergence time. In accordance with neutral expectations for stable populations, nuclear microsatellite diversity positively correlated with niche stability from the LGM to present. Most strikingly, nuclear and chloroplast microsatellite variation significantly correlated with LGM climate, even after controlling for associations with geographic location and present climate using partial redundancy analyses. Variance partitioning showed that LGM climate uniquely explains a similar proportion of genetic variance as present climate (16% vs. 11–18%), and together, past and present climate explains more than geography (19%). Climate can influence local expansion–contraction dynamics, flowering phenology and thus gene flow, and/or impose selective pressures. These results highlight the lingering effect of past climate on genetic variation in species with stable distributions.

opencc-zeroDec 2012View details →

Data from: Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation

Determining the timing, extent, and underlying causes of inter-specific gene exchange during or following speciation is central to understanding species' evolution. Antarctic notothenioid fish, thanks to the acquisition of antifreeze glycoproteins during Oligocene transition to polar conditions, experienced a spectacular radiation to >100 species during Late Miocene cooling events. The impact of recent glacial cycles on this group is poorly known, but alternating warming and cooling periods may have affected species' distributions, promoted ecological divergence into recurrently opening niches, and/or possibly brought allopatric species into contact. Using microsatellite markers and statistical methods including Approximate Bayesian Computation, we investigated genetic differentiation, hybridization and the possible influence of the last glaciation/deglaciation events in three icefish species of the genus Chionodraco. Our results provide strong evidence of contemporary and past introgression by showing that: i) a substantial fraction of contemporary individuals in each species has mixed ancestry; ii) evolutionary scenarios excluding hybridization or including it only in ancient times have small or zero posterior probabilities; iii) the data support a scenario of interspecific gene flow associated with the two most recent interglacial periods. Glacial cycles might therefore have had a profound impact on the genetic composition of Antarctic fauna, as newly available shelf areas during the warmer intervals might have favoured secondary contacts and hybridization between diversified groups. If our findings are confirmed in other notothenioids, they offer new perspectives for understanding evolutionary dynamics of Antarctic fish, and suggest a need for new predictions on the effects of global warming in this group.

opencc-zeroDec 2016View details →

Data from: Are patients with cancer with sepsis and bacteraemia at a higher risk of mortality? A retrospective chart review of patients presenting to a tertiary care centre in Lebanon

Objective: Most sepsis studies have looked at the general population. The aim of this study is to report on the characteristics, treatment and hospital mortality of patients with cancer diagnosed with sepsis or septic shock. Setting: A single-centre retrospective study at a tertiary care centre looking at patients with cancer who presented to our tertiary hospital with sepsis, septic shock or bacteraemia between 2010 and 2015. Participants: 176 patients with cancer were compared with 176 cancer-free controls. Primary and secondary outcomes: The primary outcome of this study was the in hospital mortality in both cohorts. Secondary outcomes included patient demographics, emergency department (ED) vital signs and parameters of resuscitation along with laboratory work. Results: A total of 352 patients were analysed. The mean age at presentation for the cancer group was 65.39±15.04 years, whereas the mean age for the control group was 74.68±14.04 years (p<0.001). In the cancer cohort the respiratory system was the most common site of infection (37.5%) followed by the urinary system (26.7%), while in the cancer-free arm, the urinary system was the most common site of infection (40.9%). intravenous fluid replacement for the first 24 hours was higher in the cancer cohort. ED, intensive care unit and general practice unit length of stay were comparable in both the groups. 95 (54%) patients with cancer died compared with 75 (42.6%) in the cancer-free group. The 28-day hospital mortality in the cancer cohort was 87 (49.4%) vs 46 (26.1%) in the cancer-free cohort (p=0.009). Patients with cancer had a 2.320 (CI 95% 1.225 to 4.395, p=0.010) odds of dying compared with patients without cancer in the setting of sepsis. Conclusions: This is the first study looking at an in-depth analysis of sepsis in the specific oncology population. Despite aggressive care, patients with cancer have higher hospital mortality than their cancer-free counterparts while adjusting for all other variables.

opencc-zeroDec 2012View details →

Data from: Visual phenotype matching: cues to paternity are present in rhesus macaque faces

The ability to recognize kin and thus behaviourally discriminate between conspecifics based on genetic relatedness is of importance both in acquiring inclusive fitness benefits and to enable optimal inbreeding. In primates, mechanisms allowing recognition of paternal relatives are of particular interest, given that in these mating systems patrilineal information is unlikely to be available via social familiarity. Humans use visual phenotype matching based on facial features to identify their own and other's close relatives, and recent studies suggest similar abilities may be present in other species. However it is unclear to what extent familial resemblances remain detectable against the background levels of relatedness typically found within demes in the wild – a necessary condition if facial cues are to function in kin recognition under natural conditions. Here, we experimentally investigate whether parent-offspring relationships are discernible in rhesus macaque (Macaca mulatta) faces drawn from a large free-ranging population more representative of the latter scenario, and in which genetic relatedness has been well quantified from pedigrees determined via molecular markers. We used the human visual system as a means of integrating multiple types of facial cue simultaneously, and demonstrate that paternal, as well as maternal, resemblance to both sons and daughters can be detected even by human observers. Experts performed better than participants who lacked previous experience working with nonhuman primates. However the finding that even naïve individuals succeeded at the task underlines the strength of the phenotypic cues present in faces.

opencc-zeroDec 2017View details →

Data from: Missed opportunities for HIV testing among patients newly presenting for HIV care at a Swiss university hospital: a retrospective analysis

Objectives: To determine the frequency of missed opportunities (MOs) among patients newly-diagnosed with HIV, risk factors for presenting MOs, and the association between MOs and late presentation to care. Design: Retrospective analysis Setting: HIV outpatient clinic at a Swiss tertiary hospital Participants: Patients aged ≥18 years old newly presenting for HIV care between 2010 and 2015 Measures: Number of medical visits, up to five years preceding HIV diagnosis, at which HIV testing had been indicated, according to Swiss HIV testing recommendations. A visit at which testing was indicated but not performed was considered a MO for HIV testing. Results: Complete records were available for all 201 new patients of whom 51% were male and 33% from sub-Saharan Africa. Thirty patients (15%) presented with acute HIV infection while 119 patients (59%) were late presenters (LPs) (CD4 counts <350 cells/mm3 at diagnosis). Ninety-four patients (47%) had presented at least one MO, of whom 44 (47%) had multiple MOs. MOs were more frequent among individuals from sub-Saharan Africa, men who have sex with men, and patients under follow-up for chronic disease. MOs were less frequent in LPs than non-LPs (42.5% versus 57.5%, P = 0.03). Conclusions: At our centre, 47% of patients presented at least one MO. Whilst our late presentation rate is higher than the national figure of 49.8%, LPs were less likely to experience MOs, suggesting that these patients were diagnosed late through presenting late, rather than through being failed by our hospital. We conclude that, in addition to optimising physician-initiated testing, access to testing must be improved among patients unaware they are at HIV risk and who do not seek health care.

opencc-zeroDec 2014View details →

Data from: Land-use legacies and present fire regimes interact to mediate herbivory by altering the neighboring plant community

Past and present human activities, such as historic agriculture and fire suppression, are widespread and can create depauperate plant communities. Although many studies show that herbivory on focal plants depends on the density of herbivores or the composition of the surrounding plant community, it is unclear whether anthropogenic changes to plant communities alter herbivory. We tested the hypothesis that human activities that alter the plant community lead to subsequent changes in herbivory. At 20 sites distributed across 80 300 hectares, we conducted a field experiment that manipulated insect herbivore access (full exclosures and pseudo-exclosures) to four focal plant species in longleaf pine woodlands with different land-use histories (post-agricultural sites or non-agricultural sites) and degrees of fire frequency (frequent and infrequent). Plant cover, particularly herbaceous cover, was lower in post-agricultural and fire suppressed woodlands. Density of the dominant insect herbivore at our site (grasshoppers) was positively related to plant cover. Herbivore access reduced biomass of the palatable forb Solidago odora in frequently burned post-agricultural sites and in infrequently burned non-agricultural woodlands and increased mortality of another forb (Pityopsis graminifolia), but did not affect two other less palatable species (Schizachyrium scoparium and Tephrosia virginiana). Herbivory on S. odora exhibited a hump-shaped response to plant cover, with low herbivory at low and high levels of plant cover. Herbivore density had a weak negative effect on herbivory. These findings suggest that changes in plant cover related to past and present human activities can modify damage rates on focal S. odora plants by altering grasshopper foraging behavior rather than by altering local grasshopper density. The resulting changes in herbivory may have the potential to limit natural recovery or restoration efforts by reducing the establishment or performance of palatable plant species.

opencc-zeroDec 2016View details →

Data from: Present conditions may mediate the legacy effect of past land-use changes on species richness and composition of above- and below-ground assemblages

1. In forest ecosystems, the influence of landscape history on contemporary biodiversity patterns has been shown to provide a convenient framework to explain shifts in plant assemblages. However, very few studies have controlled for present human-induced activities when analyzing the effect of forest continuity on community structures. By cutting and removing trees, foresters substantially change stand ecological conditions, with consequences on biodiversity patterns. Disentangling the effect of past and present human activities on biodiversity is thus crucial for ecosystem management and conservation. 2. We explored the response of plant and springtail species richness and composition to forest continuity (ancient vs recent) in montane forests, while controlling for stand maturity (mature vs overmature). We established 70 sites in landscapes dominated by unfragmented ancient forests where we surveyed plants and assessed springtails by analyzing environmental DNA. 3. Neither plant nor springtail species richness was influenced by forest continuity or by stand maturity. Instead, site-specific characteristics, especially soil properties and canopy openness, were of major importance in shaping above- and below-ground richness. 4. For plant and springtail species composition, the effect of forest continuity was mediated by stand maturity. Thus, both plants and springtails showed a convergence in assemblage patterns with the increasing availability of overmature stand attributes. Moreover, soil and stand-scale factors were evidently more important than landscape-scale factors in shaping above- and below-ground species composition. 5. Synthesis. We clearly demonstrated that biodiversity patterns are more strongly influenced by present human-induced activities than by past human-induced activities. In the Northern Alps where our study sites were located, the colonization credit of most species has been paid off and the transient biodiversity deficit usually related to forest continuity has moved toward equilibrium. These findings emphasize the necessity to better control for local-scale factors when analyzing the response of biodiversity to forest continuity; we call for more research into the effects of forest continuity in unfragmented mountain forests.

opennotspecifiedDec 2023View details →

FIGURE 4 in Is the North Atlantic Geodia barretti (Porifera, Tetractinellida, Geodiidae) present on the Southwest Indian Ridge?

FIGURE 4. Maximum likelihood (ML) COI phylogenetic tree of the Depressiogeodia clade. ML bootstrap supports (1,000 bootstrap replicates)> 70 are indicated. Numbers refer to NCBI Genbank accession numbers.