pinecone/core-2020-05-10-deduplication huggingface dataset:
Evaluating the potential of photo-identification as a monitoring tool for flapper skate (Dipturus intermedius)

Financial support for this study was received from SNH through the SNH‐COSPIDS grant. This study received additional funding from the SIORC (Sharks, skates and rays In the Offshore Region and Coastal Zone of Scotland community project) from the MASTS (Marine Alliance for Science and Technology for Scotland) pooling initiative, and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.1. Flapper skates (Dipturus intermedius) were once widespread in European shelf waters but are currently classified as critically endangered by the International Union for Conservation of Nature due to historical overexploitation. Novel monitoring approaches are needed to assess the efficacy of management measures, such as dedicated marine protected areas, for the conservation of relict skate populations. 2. Flapper skates possess distinctive dorsal spot patterns, which could potentially be used for individual recognition using photo‐identification (photo‐ID) approaches. This study assessed the potential of photo‐ID as a method for individual recognition of a relict population of skates within a dedicated marine protected area in western Scotland (UK), which has long been targeted by directed recreational angling. A collection of 486 photographs of 373 separate skate capture events from 2011 to 2016, taken with standard mobile phones and compact cameras, was studied using visual pairwise comparison methods to determine number of individuals and recapture rates. 3. Results indicated that adult flapper skates were individually recognizable with a high degree of certainty through comparison of spot patterns, assuming appropriate lighting conditions. A total of 226 individuals were identified, of which 77 (34%) were recaptured at least once. The average recapture interval was 308 days (SE: 29.4 days), with the longest recapture interval to date being 4.4 years. Spot patterns among recaptured tagged or otherwise uniquely identifiable skates were found to remain stable over timescales of months to >1 year. 4. Results indicate that photo‐ID, based on photographs sourced through citizen science approaches, can provide a low‐cost alternative means of monitoring flapper skate presence and distribution for the purposes of underpinning management decisions.Publisher PDFPeer reviewe
Response of benthic cave invertebrates to organic pollution events

This is the pre-peer reviewed version of the article which has been published in final form at: http://dx.doi.org/10.1002/aqc.9331.	Even though the fragility and vulnerability of subterranean ecosystems (caves, groundwater and hyporheic habitats) is widely acknowledged, the impacts of anthropogenic disturbances have been poorly quantified when compared to surface waters. In particular, limited data exist regarding the impact of organic pollution upon aquatic cave invertebrate communities.  \ud
2.	The Peak-Speedwell Cavern system (Derbyshire, UK) was affected by two organic pollution events, during a 7–year study (1997-2003), originating from the same source in the surface catchment but resulting in markedly different ecological responses. The first event led to the elimination of most taxa from affected sites while the second resulted in an increase in abundance of organisms within the cave associated with the increased availability of trophic resources. The second event also coincided with the invasion of the stygophilic amphipod, Gammarus pulex, at a site where it had not previously been recorded.\ud
3.	Recovery of the invertebrate community following both organic pollution events occurred within 12-months. Recolonisation of the affected sites was facilitated by annual flooding of the cave and by the presence of refugia on unaffected subterranean tributaries. \ud
4.	The data highlight the problems associated with the conservation and management of subterranean ecosystems where impacts in distant surface catchments may have unseen repercussions for the subterranean environment. Aquatic subterranean habitats are not widely monitored and the impacts of pollution/disturbance may not be detected in surface waters for some time, if at all, due to dilution effects. Caves supporting obligate subterreanean organisms (stygobites) are particularly vulnerable to these pressures and require clear management strategies to protect both the subterranean and surface catchments which support them
Comparison of loss on ignition and thermal analysis stepwise methods for determination of sedimentary organic matter

1. Loss on ignition (LOI) is a widely used method to estimate organic matter (OM) in the sediment of marine and freshwater ecosystems. Thermogravimetric-differential thermal analysis (TG-DTA) of organic species provides information on thermal reactions, the amount and properties of clay structural water, organic species and carbonates. 2. The accuracy of LOI compared with that of TG-DTA was evaluated in 33 sediment samples from the Lagoon of Venice (Italy). 3. In all tests conducted with TG-DTA the mass loss of OM and the loss of clay structural water (LCSW) from oxidized samples were measured. The mass loss of OM at 3508C (TG-DTA 350 OM) and the total extraction of organic matter at 5678C (TEOM) calculated from the difference between natural state samples and oxidized samples highlight the presence of both thermally labile and thermally stable substances. 4. The grain size data of sediment samples from the Lagoon shows a variable distribution between slightly muddy sand and mud. Loss of clay structural water at 3508C (LCSW 350) and total extraction of clay structural water at 5678C (TECSW) both estimated by TG-DTA on oxidized samples, were found to correspond approximately to 6% and 10%, respectively of the clay fraction (54 mm). This percentage may be used to correct LOI measurements of OM in sediments with high clay content. 5. LOI 350 (loss on ignition at 3508C) and LOI 550 (loss on ignition at 5508C) proved to be 80% and 200%, respectively, of total extraction of mass loss at 3508C (TG-DTA 350 tot) and at 5678C (TEML) estimated by TG-DTA on natural samples, meaning that the LOI 550 value represents a significant overestimate. The difference between the LOI 550 and TEML values indicates that the mass loss excess (MLE) may be accounted for by losses due to breakdown of carbonates
The reproductive ecology of exotic Trachemys scripta elegans in an invaded area of southern Europe

1. The main reproductive parameters of exotic Trachemys scripta elegans in established populations from two ponds in southern Spain are described. 2. Females were found to reproduce at 5 years of age, although sexually mature individuals of 4 and 3 years of age were also detected. Annual reproductive frequency was estimated to be 80-86% of reproductive females. Mean clutch size was 11.5 eggs and was not correlated with maternal body size. 3. The number of follicles of different size in ovaries suggested that four or more clutches could be laid per season. Eggs were laid from April to June (inclusive) mainly during morning hours, when females were easily detected during nesting trips. 79.5% of eggs were fertile. 4. Reproductive parameters of this species in southern Spain were of similar or even higher values than in native areas, thus placing them among chelonian species of earlier maturity. 5. Although chelonians might never be considered explosive breeders, the number of T. s. elegans individuals could surpass that of native aquatic chelonians in southern Spain, where T. s. elegans reach maturity earlier, are more fecund and their eggs are more fertile. Copyright © 2008 John Wiley & Sons, Ltd.Peer Reviewe
Differentially localized incorporation of amino acids in relation to epidermal keratinization in the newborn rat

Incorporation of tritiated methionine, phenylalanine, leucine, glycine and histidine into protein in the epidermis of the newborn rat was studied by autoradiography.Methionine, phenylalanine and leucine behaved similarly. Thirty minutes after injection, radioactivity was detected in both nucleus and cytoplasm of the basal, spinous and granular cells with a greater intensity over the cells of the lower layer as compared with that observed over the upper layer. The label appeared over the cornified cells at 24 hours after injection probably as a result of the migration of cells into the cornified layer. In the case of glycine and histidine, the label was detected in eachof the three layers at 30 minutes after injection but the labeling was higher in the upper part of the epidermis as compared with the lower part. The label appeared in the cornified layer six hours after injection. Processes possibly involved in formation of the cornified layer are discussed
Middle Cranial Fossa Anatomy and the Origin of Modern Humans

Anatomically, modern humans differ from archaic forms in possessing
a globular neurocranium and a retracted face and in cognitive functions,
many of which are associated with the temporal lobes. The middle cranial
fossa (MCF) interacts during growth and development with the temporal
lobes, the midface, and the mandible. It has been proposed that evolutionary transformations of the MCF (perhaps from modification of the temporal lobes) can have substantial influences on craniofacial morphology.  Here, we use three-dimensional (3D) geometric morphometrics and computer reconstructions of computed tomography-scanned fossil hominids, fossil and recent modern humans and chimpanzees to address this issue further. Mean comparisons and permutation analyses of scaled 3D basicranial landmarks confirm that the MCF of Homo sapiens is highly significantly different (P < 0.001) from H. neanderthalensis, H. heidelbergensis, and Pan troglodytes. Modern humans have a unique configuration with relatively more anterolateral projection of the MCF pole relative to the optic chiasm and the foramen rotundum. These findings are discussed in the context of evolutionary changes in craniofacial morphology and the origins of modern human autapomorphies. In particular, the findings of this study point to variations in the temporal lobe, which, through effects on the MCF and face, are central to the evolution of modern human facial form.Anthropolog
3D computerized model for measuring strain and displacement of the brachial plexus following placement of reverse shoulder prosthesis

The aim of the present study was to develop a method for three-dimensional (3D) reconstruction of the brachial plexus to study its morphology and to calculate strain and displacement in relation to changed nerve position. The brachial plexus was finely dissected and injected with contrast medium and leaden markers were implanted into the nerves at predefined places. A reverse shoulder prosthesis was inserted in a cadaveric specimen what induced positional change in the upper limb nerves. Computed tomography (CT) was performed before and after this surgical intervention. The computer assisted image processing package Mimics (R) was used to reconstruct the pre- and postoperative brachial plexus in 3D. The results show that the current interactive model is a realistic and detailed representation of the specimen used, which allows 3D study of the brachial plexus in different configurations. The model estimated strains up to 15.3% and 19.3% for the lateral and the medial root of the median nerve as a consequence of placing a reverse shoulder prosthesis. Furthermore, the model succeeded in calculating the displacement of the brachial plexus by tracking each implanted lead marker. The presented brachial plexus 3D model currently can be used in vitro for cadaver biomechanical analyses of nerve movement to improve diagnosis and treatment of peripheral neuropathies. The model can also be applied to study the exact location of the plexus in unusual upper limb positions like during axillary radiation therapy and it is a potential tool to optimize the approaches of brachial plexus anesthetic blocks
New insights into mid-late Pleistocene fossil hominin paranasal sinus morphology

Mid-late Pleistocene fossil hominins such as Homo neanderthalensis and H. heidelbergensis are often described as having extensively pneumatized crania compared with modern humans. However, the significance of pneumatization in recognizing patterns of phyletic diversification and/or functional specialization has remained controversial. Here, we test the null hypothesis that the paranasal sinuses of fossil and extant humans and great apes can be understood as biological spandrels, i.e., their morphology reflects evolutionary, developmental, and functional constraints imposed onto the surrounding bones. Morphological description of well-preserved mid-late Pleistocene hominin specimens are contrasted with our comparative sample of modern humans and great apes. Results from a geometric morphometric analysis of the correlation between paranasal sinus and cranial dimensions show that the spandrel hypothesis cannot be refuted. However, visualizing specific features of the paranasal sinus system with methods of biomedical imaging and computer graphics reveals new aspects of patterns of growth and development of fossil hominins
A morphogenetic model of cranial pneumatization based on the invasive tissue hypothesis

The interpretation of patterns of cranial pneumatization in terms of evolution, development, and function is controversial, because these structures exhibit extreme diversity and variability among and within taxa. However, there is general consensus that air-filled spaces are \ud
formed by invasion of mucous epithelial tissue from the nasopharyngeal cavity into the surrounding cranial bones. This investigation presents a morphogenetic model of pneumatization, which combines empirical data about epithelial growth with physical concepts of surface growth. The study develops a minimum model that defines growth equations with a minimum number of system parameters to model the invasion of mucous tissue and air-filled spaces into the cancellous compartment of cranial bones. Computer simulations show that tuning a small set of model parameters permits generation of a wide diversity of morphologies mimicking natural air-filled spaces. Comparison of virtual with actual morphologies yields new insights into possible factors controlling the process of cranial pneumatization
Three-dimensional structure of the nasal passageway of a hagfish and its implications for olfaction

From high-resolution (65 mu m) data acquired by magnetic resonance imaging, we have reconstructed the nasal passageway of a single adult hagfish specimen (probably Eptatretus stoutii). We have used this reconstruction to investigate how the anatomy and morphometry of the nasal passageway influence the olfactory ability of the hagfish. We found that the long, broad section of the passageway preceding the nasal chamber will delay the response to an odor by 1-2 s. Diffusion of odorant to the olfactory epithelium, on which the olfactory sensitivity of an animal depends, will be favored by the relatively large surface area of the olfactory epithelium (similar to 140 mm(2)) and a modest expansion in the nasal chamber. Oscillating flow (0.3-0.4 Hz) within the narrow (65-130 mu m) sensory channels of the nasal chamber is laminar (Reynolds number similar to 5) and quasi-steady (Womersley number generally less than one). Distribution of flow over the olfactory epithelium may be aided by: (a) a narrowing before the nasal chamber; (b) partial blockage of the nasal passageway by a protrusion on the central olfactory lamella; and (c) the inward inclination of the olfactory lamellae
Histology‐Based Morphology of the Neurocentral Synchondrosis in  Alligator Mississippiensis  (Archosauria, Crocodylia)

Morphology of the neurocentral synchondroses—thin cartilaginous layers between centra and neural arches—are documented in the extant crocodilian,  Alligator mississippiensis  (Archosauria, Crocodylia). Examination of dry skeletons demonstrates that neurocentral suture closure occurs in very late postnatal ontogeny (after reaching sexual maturity and/or body size ca. 40% from the upper range). Before sexual maturity (body length (BL) ≥ ca. 1.80 m), completely fused centra and neural arches are restricted to the caudal vertebral series. In contrast, the presacral vertebrae often remain unfused throughout postnatal ontogeny, retaining open sutures in very mature individuals (BL ≥ 2.80 m). These unfused centra and neural arches are structurally supported by the relatively large surface area of the neurocentral junctions, which results from primarily horizontal (mediolateral) increases with strong positive allometry. Cleared and stained specimens show that the cartilaginous neurocentral synchondrosis starts to form after approximately 40 embryonic days. Histological examination of the neurocentral junction in dorsal and anterior caudal vertebrae of six individuals (BL = 0.28–3.12 m) shows : (1) neurocentral fusion is the result of endochondral ossification of the neurocentral synchondrosis, (2) the neurocentral synchondrosis exhibits bipolar organization of three types of cartilaginous cells, and (3) complex neurocentral sutures (i.e., curved, zigzagged, and/or interdigitated boundaries) come from clumping of bone cells of the neural arches and centra into the neurocentral synchondrosis. The last two morphological features can be advantageous for delaying neurocentral fusion, which seems to be unique in crocodilians and possibly their close relatives, including nonavian dinosaurs and other Mesozoic archosaurs. Anat Rec, 2012. © 2011 Wiley Periodicals, Inc
The Auditory Anatomy of the Minke Whale (Balaenoptera acutorostrata): A Potential Fatty Sound Reception Pathway in a Baleen Whale

Cetaceans possess highly derived auditory systems adapted for underwater hearing. Odontoceti (toothed whales) are thought to receive sound through specialized fat bodies that contact the tympanoperiotic complex, the bones housing the middle and inner ears. However, sound reception pathways remain unknown in Mysticeti (baleen whales), which have very different cranial anatomies compared to odontocetes. Here, we report a potential fatty sound reception pathway in the minke whale (Balaenoptera acutorostrata), a mysticete of the balaenopterid family. The cephalic anatomy of seven minke whales was investigated using computerized tomography and magnetic resonance imaging, verified through dissections. Findings include a large, well-formed fat body lateral, dorsal, and posterior to the mandibular ramus and lateral to the tympanoperiotic complex. This fat body inserts into the tympanoperiotic complex at the lateral aperture between the tympanic and periotic bones and is in contact with the ossicles. There is also a second, smaller body of fat found within the tympanic bone, which contacts the ossicles as well. This is the first analysis of these fatty tissues' association with the auditory structures in a mysticete, providing anatomical evidence that fatty sound reception pathways may not be a unique feature of odontocete cetaceans
Ultrastructural and spectrophotometric study on the effects of putative triggers on aortic valve interstitial cells in in vitro models simulating metastatic calcification.

Metastatic calcification of cardiac valves is a common complication in patients affected by chronic renal failure. In this study, primary bovine aortic valve interstitial cells (AVICs) were subjected to pro-calcific treatments consisting in cell stimulation with (i) elevated inorganic phosphate (Pi = 3mM), in order to simulate hyperphosphatemic conditions; (ii) bacterial endotoxin lipopolysaccharide (LPS), simulating direct effects by microbial agents; and (iii) conditioned media (CM) derived from cultures of either LPS-stimulated heterogenic macrophages (commercial murine RAW264.7 cells) or LPS-stimulated fresh allogeneic monocytes/macrophages (bCM), simulating consequent inflammatory responses, alone or combined. Compared to control cultures, spectrophotometric assays revealed shared treatment-dependent higher values of both calcium amounts and alkaline phosphatase activity for cultures involving the presence of elevated Pi. Ultrastructurally, shared peculiar pro-calcific degeneration patterns were exhibited by AVICs from the same cultures irrespectively of the applied treatment. Disappearance of all cytomembranes and concurrent formation of material showing positivity to Cuprolinic Blue and co-localizing with silver precipitation were followed by the outcropping of such a material, which transformed in layers outlining the dead cells. Subsequent budding of these layers resulted in the formation of bubbling bodies and concentrically laminated calcospherulae mirroring those in actual soft tissue calcification. In conclusion, the in vitro models employed appear to be reliable tools for simulating metastatic calcification and indicate that hyperphosphatemic-like conditions could trigger valve calcification per se, with LPS and allogeneic macrophage-derived secretory products acting as possible calcific enhancers via inflammatory responses
Mitochondrial Swelling and Incipient Outer Membrane Rupture in Preapoptotic and Apoptotic Cells

Outer mitochondrial membrane (OMM) rupture was first noted in isolated mitochondria in which the inner mitochondrial membrane (IMM) had lost its selective permeability. This phenomenon referred to as mitochondrial permeability transition (MPT) refers to a permeabilized inner membrane that originates a large swelling in the mitochondrial matrix, which distends the outer membrane until it ruptures. Here, we have expanded previous electron microscopic observations that in apoptotic cells, OMM rupture is not caused by a membrane stretching promoted by a markedly swollen matrix. It is shown that the widths of the ruptured regions of the OMM vary from 6 to 250 nm. Independent of the perforation size, herniation of the mitochondrial matrix appeared to have resulted in pushing the IMM through the perforation. A large, long focal herniation of the mitochondrial matrix, covered with the IMM, was associated with a rupture of the OMM that was as small as 6 nm. Contextually, the collapse of the selective permeability of the IMM may precede or follow the release of the mitochondrial proteins of the intermembrane space into the cytoplasm. When the MPT is a late event, exit of the intermembrane space proteins to the cytoplasm is unimpeded and occurs through channels that transverse the outer membrane, because so far, the inner membrane is impermeable. No channel within the outer membrane can expose to the cytoplasm a permeable inner membrane, because it would serve as a conduit for local herniation of the mitochondrial matrix. Anat Rec, 2012. (c) 2012 Wiley Periodicals, Inc.Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo, FAPESP [00/06648-2]Conselho Nacional de Pesquisas (CNPq)Conselho Nacional de Pesquisas, CNPq [Processo 520359/1996-8 e, Processo 472208/2004-7