Local extinctions of birds in forest fragments in the Santa Elena region, Central Andes, Colombia

Los registros históricos de la avifauna de la región de Santa Elena (Andes centrales colombianos), realizados entre 1879 y 1952, fueron comparados con los de las aves presentes actualmente en tres fragmentos remanentes de bosque de 41, 129 y 136 ha. De las 132 especies presentes originalmente solo se conservan 64 en los tres fragmentos. En los tres fragmentos han desaparecido el 78%, el 66% y el 63% de sus especies. Las especies con alta especificidad de hábitat, con peso corporal de 51–100 g, las que se alimentan en el estrato arbóreo y las que lo hacen en troncos tendieron a presentar una proporción de extinción mayor a lo esperado. Sin embargo, no hubo diferencias estadísticamente significativas entre la proporción de especies extintas observada y esperada para ninguna de las categorías (gremio trófico, estrato de alimentación, tamaño corporal y especificidad de hábitat), lo que indica que todos los grupos presentaron la misma vulnerabilidad a la extinción. El peso promedio de las aves extintas fue similar al de las aves aún presentes en los tres fragmentos. Las especies de las familias Grallaridae, Cotingidae, Thraupidae, Trogonidae y de la subfamilia Dendrocolaptinae fueron las más afectadas. Se discute por qué las características ecológicas evaluadas pueden no estar relacionadas con la extinción local de aves en estos fragmentos de bosque.We compared historic records from 1879 until 1952 of birds of Santa Elena region (Colombian central Andes) with those from a recent survey in three forest fragments of 41, 129 and 136 ha. Only 64 out of the 132 original species still remain in the three fragments; 78%, 66% and 63% of the original species have disappeared from the fragments. Species with high habitat specificity, those with body mass of 51–100 g, those which forage in the arboreal stratum, and those which forage on trunks showed a tendency to suffer more extinctions than expected. However, there were no statistical differences between observed and expected proportions of extinctions in any of the categories (trophic guild, foraging stratum, body mass and habitat specificity), indicating that all the bird groups presented the same vulnerability to extinction. Mean body mass of extinct birds was similar to that of the birds still remaining in the fragments. Species from the families Grallaridae, Cotingidae, Thraupidae, Trogonidae and from the subfamily Dendrocolaptinae were the most affected. We discuss why the evaluated ecological features could not be related with local extinction of bird species in these forest fragments

A Mainly Circum-Mediterranean Origin for West Eurasian and North African mtDNAs in Puerto Rico with Strong Contributions from the Canary Islands and West Africa

Maternal lineages of West Eurasian and North African origin account for 11.5% of total mitochondrial ancestry in Puerto Rico. Historical sources suggest that this ancestry arrived mostly from European migrations that took place during the four centuries of the Spanish colonization of Puerto Rico. This study analyzed 101 mitochondrial control region sequences and diagnostic coding region variants from a sample set randomly and systematically selected using a census-based sampling frame to be representative of the Puerto Rican population, with the goal of defining West Eurasian-North African maternal clades and estimating their possible geographical origin. Median-joining haplotype networks were constructed using HVR-I and –II sequences from various reference populations in search of shared haplotypes. A posterior probability analysis was performed to estimate the percentage of possible origins across wide geographic regions for the entire sample set and for the most common haplogroups on the island. Principal component analyses were conducted to place the Puerto Rican mtDNA set within the variation present amongst all reference populations. Our study shows that up to 38% of West Eurasian and North African mitochondrial ancestry in Puerto Rico most likely migrated from the Canary Islands. However, most of those haplotypes had previously migrated to the Canary Islands from elsewhere, and there are substantial contributions from various populations across the circum-Mediterranean region and from West African populations related to the modern Wolof and Serer peoples from Senegal and the nomad Fulani who extend up to Cameroon. In conclusion, the West Eurasian mitochondrial ancestry in Puerto Ricans is geographically diverse. However, haplotype diversity seems to be low and frequencies have been shaped by population bottlenecks, migration waves, and random genetic drift. Consequently, approximately 47% of mtDNAs of West Eurasian and North African ancestry in Puerto Rico probably arrived early in its colonial history

The Guadiaro-Baños contourite drifts (SW Mediterranean). A geotechnical approach to stability analysis

Two Quaternary plastered contourite drifts, with terraced and low-mounded morphologies, make up the continental slope and base-of-slope in the northwestern Alboran Sea, respectively, between the Guadiaro and Baños turbidite systems, close to the Strait of Gibraltar. Considering their significant lateral extent, the link between the contourite drift deposits and landslides may be particularly important for hazard assessment. The physical properties, composition and geometry of contourite drifts have been proposed as key factors in slope stability, although this relationship still needs to be better constrained. In this work, new in-situ geotechnical data (cone penetration tests; CPTu) has been combined with morphostratigraphic, sedimentological, and (laboratory) geotechnical properties to determine the stability of the Guadiaro-Baños drifts. For the depositional domains of both drifts, the resulting sedimentary and geotechnical model describes low-plasticity granular and silty sands on the erosive terraced domain that evolve seawards to silty and silty-clay deposits with a higher plasticity and uniform geomechanical properties. For the shallower coarse-grained contourite sediments, the cohesion (c') and internal friction angle (ϕ') values are 0–9 kPa and 46–30°, respectively, whereas for the distal fine contourites the undrained shear strength gradient (∇Su) is 2 kPa/m. These properties allow us to establish high factors of safety for all the scenarios considered, including seismic loading. Slope failure may be triggered in the unlikely event that there is seismic acceleration of PGA > 0.19, although no potential glide planes have been observed within the first 20 m below the seafloor. This suggests that the contourite drifts studied tend to resist failure better than others with similar sedimentary characteristics. The interplay of several processes is proposed to explain the enhanced undrained shear strength: 1) the geometry of the drifts, defined by an upper contouritic terrace and lower low-mounded shapes; 2) recurrent low-intensity earthquakes with insufficient energy to trigger landslides, favouring increased strength due to dynamic compaction; and 3) cyclic loading induced by solitons/internal waves acting on the sediment.En prens

Understanding the complex geomorphology of a deep sea area affected by continental tectonic indentation: The case of the Gulf of Vera (Western Mediterranean)

19 pages, 11 figures, 1 table, supplementary data https://doi.org/10.1016/j.geomorph.2022.108126.-- Data availability: Casas, D., & UTM-CSIC. (2018). FAUCES-1 Cruise, RV Sarmiento de Gamboa [Data set]. UTM-CSIC. doi: 10.20351/29SG20170925 Comas, M. & UTM-CSIC. TOPOMED-GASBATS. Cruise, RV Sarmiento de Gamboa [Data set]. UTM-CSIC.doi: 10.20351/29SG20120517We present a multidisciplinary study of morphology, stratigraphy, sedimentology, tectonic structure, and physical oceanography to report that the complex geomorphology of the Palomares continental margin and adjacent Algerian abyssal plain (i.e., Gulf of Vera, Western Mediterranean), is the result of the sedimentary response to the Aguilas Arc continental tectonic indentation in the Eurasian–Africa plate collision. The indentation is imprinted on the basement of the margin with elongated metamorphic antiforms that are pierced by igneous bodies, and synforms that accommodate the deformation and create a complex physiography. The basement is partially covered by Upper Miocene deposits sealed by the regional Messinian Erosive Surface characterized by palaeocanyons that carve the modern margin. These deposits and outcropping basement highs are then covered and shaped by Plio-Quaternary contourites formed under the action of the Light Intermediate and Dense Deep Mediterranean bottom currents. Even though bottom currents are responsible for the primary sedimentation that shapes the margin, 97% of this region's seafloor is affected by mass-movements that modified contourite sediments by eroding, deforming, faulting, sliding, and depositing sediments. Mass-movement processes have resulted in the formation of recurrent mass-flow deposits, an enlargement of the submarine canyons and gully incisions, and basin-scale gravitational slides spreading above the Messinian Salinity Crisis salt layer. The Polopo, Aguilas and Gata slides are characterized by an extensional upslope domain that shapes the continental margin, and by a downslope contractional domain that shapes the abyssal plain with diapirs piercing (hemi)pelagites/sheet-like turbidites creating a seafloor dotted by numerous crests. The mass movements were mostly triggered by the interplay of the continental tectonic indentation of the Aguilas Arc with sedimentological factors over time. The indentation, which involves the progressively southeastward tectonic tilting of the whole land-sea region, likely generated a quasi-continuous oversteepening of the entire margin, thus reducing the stability of the contourites. In addition, tectonic tilting and subsidence of the abyssal plain favoured the flow of the underlying Messinian Salinity Crisis salt layer, contributing to the gravitational instability of the overlying sediments over large areas of the margin and abyssal plainThis research has been funding by the Spanish projects: DAMAGE (CGL2016-80687-RAEI/FEDER) and FAUCES (CTM2015-65461-C2-1-R); and the Junta de Andalucía projects: RNM-148 (AGORA) P18-RT-3275 and PAPEL (B-RNM-301-UGR18). [...] This work acknowledges to IGCP 640 - S4LIDE (Significance of Modern and Ancient Submarine Slope LandSLIDEs), and to the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S

Understanding the complex geomorphology of a deep sea area affected by continental tectonic indentation: the case of the Gulf of Vera (Western Mediterranean)

We present a multidisciplinary study of morphology, stratigraphy, sedimentology, tectonic structure, and physical oceanography to report that the complex geomorphology of the Palomares continental margin and adjacent Algerian abyssal plain (i.e., Gulf of Vera, Western Mediterranean), is the result of the sedimentary response to the Aguilas Arc continental tectonic indentation in the Eurasian–Africa plate collision. The inden tation is imprinted on the basement of the margin with elongated metamorphic antiforms that are pierced by igneous bodies, and synforms that accommodate the deformation and create a complex physiography. The basement is partially covered by Upper Miocene deposits sealed by the regional Messinian Erosive Surface characterized by palaeocanyons that carve the modern margin. These deposits and outcropping basement highs are then covered and shaped by Plio-Quaternary contourites formed under the action of the Light Intermediate and Dense Deep Mediterranean bottom currents. Even though bottom currents are responsible for the primary sedimentation that shapes the margin, 97% of this region's seafloor is affected by mass-movements that modified contourite sediments by eroding, deforming, faulting, sliding, and depositing sediments. Mass-movement processes have resulted in the formation of recurrent mass-flow deposits, an enlargement of the submarine canyons and gully incisions, and basin-scale gravitational slides spreading above the Messinian Salinity Crisis salt layer. The Polopo, Aguilas and Gata slides are characterized by an extensional upslope domain that shapes the continental margin, and by a downslope contractional domain that shapes the abyssal plain with diapirs piercing (hemi)pelagites/sheet-like turbidites creating a seafloor dotted by numerous crests. The mass movements were mostly triggered by the interplay of the continental tectonic indentation of the Aguilas Arc with sedimentological factors over time. The indentation, which involves the progressively southeastward tectonic tilting of the whole land-sea region, likely generated a quasi-continuous oversteepening of the entire margin, thus reducing the stability of the contourites. In addition, tectonic tilting and subsidence of the abyssal plain favoured the flow of the underlying Messinian Salinity Crisis salt layer, contributing to the gravitational instability of the overlying sediments over large areas of the margin and abyssal plain

Opposite cannabis-cognition associations in psychotic patients depending on family history

The objective of this study is to investigate cognitive performance in a first-episode psychosis sample, when stratifying the interaction by cannabis use and familial or non-familial psychosis. Hierarchical-regression models were used to analyse this association in a sample of 268 first-episode psychosis patients and 237 controls. We found that cannabis use was associated with worse working memory, regardless of family history. However, cannabis use was clearly associated with worse cognitive performance in patients with no family history of psychosis, in cognitive domains including verbal memory, executive function and global cognitive index, whereas cannabis users with a family history of psychosis performed better in these domains. The main finding of the study is that there is an interaction between cannabis use and a family history of psychosis in the areas of verbal memory, executive function and global cognition: that is, cannabis use is associated with a better performance in patients with a family history of psychosis and a worse performance in those with no family history of psychosis. In order to confirm this hypothesis, future research should explore the actual expression of the endocannabinoid system in patients with and without a family history of psychosis

Clinical validation of risk scoring systems to predict risk of delayed bleeding after EMR of large colorectal lesions

[Background and Aims]: The Endoscopic Resection Group of the Spanish Society of Endoscopy (GSEED-RE) model and the Australian Colonic Endoscopic Resection (ACER) model were proposed to predict delayed bleeding (DB) after EMR of large superficial colorectal lesions, but neither has been validated. We validated and updated these models.[Methods]: A multicenter cohort study was performed in patients with nonpedunculated lesions ≥20 mm removed by EMR. We assessed the discrimination and calibration of the GSEED-RE and ACER models. Difficulty performing EMR was subjectively categorized as low, medium, or high. We created a new model, including factors associated with DB in 3 cohort studies.[Results]: DB occurred in 45 of 1034 EMRs (4.5%); it was associated with proximal location (odds ratio [OR], 2.84; 95% confidence interval [CI], 1.31-6.16), antiplatelet agents (OR, 2.51; 95% CI, .99-6.34) or anticoagulants (OR, 4.54; 95% CI, 2.14-9.63), difficulty of EMR (OR, 3.23; 95% CI, 1.41-7.40), and comorbidity (OR, 2.11; 95% CI, .99-4.47). The GSEED-RE and ACER models did not accurately predict DB. Re-estimation and recalibration yielded acceptable results (GSEED-RE area under the curve [AUC], .64 [95% CI, .54-.74]; ACER AUC, .65 [95% CI, .57-.73]). We used lesion size, proximal location, comorbidity, and antiplatelet or anticoagulant therapy to generate a new model, the GSEED-RE2, which achieved higher AUC values (.69-.73; 95% CI, .59-.80) and exhibited lower susceptibility to changes among datasets.[Conclusions]: The updated GSEED-RE and ACER models achieved acceptable prediction levels of DB. The GSEED-RE2 model may achieve better prediction results and could be used to guide the management of patients after validation by other external groups. (Clinical trial registration number: NCT 03050333.)Research support for this study was received from “La Caixa/Caja Navarra” Foundation (ID 100010434;project PR15/11100006)

Structure and non-structure of centrosomal proteins

Here we perform a large-scale study of the structural properties and the expression of proteins that constitute the human Centrosome. Centrosomal proteins tend to be larger than generic human proteins (control set), since their genes contain in average more exons (20.3 versus 14.6). They are rich in predicted disordered regions, which cover 57% of their length, compared to 39% in the general human proteome. They also contain several regions that are dually predicted to be disordered and coiled-coil at the same time: 55 proteins (15%) contain disordered and coiled-coil fragments that cover more than 20% of their length. Helices prevail over strands in regions homologous to known structures (47% predicted helical residues against 17% predicted as strands), and even more in the whole centrosomal proteome (52% against 7%), while for control human proteins 34.5% of the residues are predicted as helical and 12.8% are predicted as strands. This difference is mainly due to residues predicted as disordered and helical (30% in centrosomal and 9.4% in control proteins), which may correspond to alpha-helix forming molecular recognition features (α-MoRFs). We performed expression assays for 120 full-length centrosomal proteins and 72 domain constructs that we have predicted to be globular. These full-length proteins are often insoluble: Only 39 out of 120 expressed proteins (32%) and 19 out of 72 domains (26%) were soluble. We built or retrieved structural models for 277 out of 361 human proteins whose centrosomal localization has been experimentally verified. We could not find any suitable structural template with more than 20% sequence identity for 84 centrosomal proteins (23%), for which around 74% of the residues are predicted to be disordered or coiled-coils. The three-dimensional models that we built are available at http://ub.cbm.uam.es/centrosome/models/index.php

Tau Structures

Tau is a microtubule-associated protein that plays an important role in axonal stabilization, neuronal development, and neuronal polarity. In this review, we focus on the primary, secondary, tertiary, and quaternary tau structures. We describe the structure of tau from its specific residues until its conformation in dimers, oligomers, and larger polymers in physiological and pathological situations