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PloS One 2024The study of spatial (paleo)ecology in mammals is critical to understand how animals adapt to and exploit their environment. In this work we analysed the 87Sr/86Sr,...
The study of spatial (paleo)ecology in mammals is critical to understand how animals adapt to and exploit their environment. In this work we analysed the 87Sr/86Sr, δ18O and δ13C isotope composition of 65 moose bone and antler samples from Sweden from wild-shot individuals dated between 1800 and 1994 to study moose mobility and feeding behaviour for (paleo)ecological applications. Sr data were compared with isoscapes of the Scandinavian region, built ad-hoc during this study, to understand how moose utilise the landscape in Northern Europe. The 87Sr/86Sr isoscape was developed using a machine-learning approach with external geo-environmental predictors and literature data. Similarly, a δ18O isoscape, obtained from average annual precipitation δ18O values, was employed to highlight differences in the isotope composition of the local environment vs. bone/antler. Overall, 82% of the moose samples were compatible with the likely local isotope composition (n = 53), suggesting that they were shot not far from their year-round dwelling area. 'Local' samples were used to calibrate the two isoscapes, to improve the prediction of provenance for the presumably 'non-local' individuals. For the latter (n = 12, of which two are antlers and ten are bones), the probability of geographic origin was estimated using a Bayesian approach by combining the two isoscapes. Interestingly, two of these samples (one antler and one bone) seem to come from areas more than 250 km away from the place where the animals were hunted, indicating a possible remarkable intra-annual mobility. Finally, the δ13C data were compared with the forest cover of Sweden and ultimately used to understand the dietary preference of moose. We interpreted a difference in δ13C values of antlers (13C-enriched) and bones (13C-depleted) as a joint effect of seasonal variations in moose diet and, possibly, physiological stresses during winter-time, i.e., increased consumption of endogenous 13C-depleted lipids.
Topics: Humans; Animals; Strontium Isotopes; Sweden; Antlers; Bayes Theorem; Isotopes; Deer
PubMed: 38598461
DOI: 10.1371/journal.pone.0300867 -
IUCrJ May 2024The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of...
RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures.
The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.
Topics: Databases, Protein; SARS-CoV-2; COVID-19; Protein Conformation; Humans; Computational Biology; Proteins
PubMed: 38597878
DOI: 10.1107/S2052252524002604 -
PloS One 2024Morphological variation in modern human dentition is still an open field of study. The understanding of dental shape and metrics is relevant for the advancement of human...
Morphological variation in modern human dentition is still an open field of study. The understanding of dental shape and metrics is relevant for the advancement of human biology and evolution and is thus of interest in the fields of dental anthropology, as well as human anatomy and medicine. Of concern is also the variation of the inner aspects of the crown which can be investigated using the tools and methods of virtual anthropology. In this study, we explored inter- and intra-population morphometric variation of modern humans' upper third and fourth premolars (P3s and P4s, respectively) considering both the inner and outer aspects of the crown, and discrete traits. We worked by means of geometric morphometrics on 3D image data from a geographically balanced sample of human populations from five continents, to analyse the shape of the dentinal crown, and the crown outline in 78 P3s and 76 P4s from 85 individuals. For the study of dental traits, we referred to the Arizona State University Dental Anthropology System integrated with more recent classification systems. The 3D shape variation of upper premolar crowns varied between short and mesio-distally broad, and tall and mesio-distally narrow. The observed shape variation was independent from the geographical origin of the populations, and resulted in extensive overlap. We noted a high pairwise correlation (r1 = 0.83) between upper P3s and P4s. We did not find any significant geographic differences in the analysed non-metric traits. Our outcomes thus suggest that geographical provenance does not play a determinant role in the shaping of the dental crown, whose genesis is under strict genetic control.
Topics: Animals; Humans; Bicuspid; Anthropology, Physical; Hominidae; Anthropology; Tooth Crown
PubMed: 38593117
DOI: 10.1371/journal.pone.0301482 -
Plants (Basel, Switzerland) Mar 2024The accumulation of crystal calcium oxalate (CaOx) in plants is linked to a type of stress-induced photosynthesis termed 'alarm photosynthesis', serving as a carbon...
The accumulation of crystal calcium oxalate (CaOx) in plants is linked to a type of stress-induced photosynthesis termed 'alarm photosynthesis', serving as a carbon reservoir when carbon dioxide (CO) exchange is constrained. is an extremophyte found from southern Mexico to Antarctica, which thrives in high-altitude Andean regions. Growing under common garden conditions, from different latitudinal provenances display significant variations in CaOx crystal accumulation. This raises the following questions: are these differences maintained under natural conditions? And is the CaOx accumulation related to mesophyll conductance (g) and net photosynthesis (A) performed in situ? It is hypothesized that in provenances with lower g, will exhibit an increase in the use of CaOx crystals, resulting in reduced crystal leaf abundance. Plants from Central Chile (33°), Patagonia (51°), and Antarctica (62°) were measured in situ and sampled to determine gas exchange and CaOx crystal accumulation, respectively. Both A and g decrease towards higher latitudes, correlating with increases in leaf mass area and leaf density. The crystal accumulation decreases at higher latitudes, correlating positively with A and g. Thus, in provenances where environmental conditions induce more xeric traits, the CO availability for photosynthesis decreases, making the activation of alarm photosynthesis feasible as an internal source of CO.
PubMed: 38592779
DOI: 10.3390/plants13060769 -
Data in Brief Jun 2024This paper provides comprehensive and systematized lists of names of 'moko' drums from Alor Island, in Southeast Indonesia. 'Moko' drums are unique cultural objects from...
This paper provides comprehensive and systematized lists of names of 'moko' drums from Alor Island, in Southeast Indonesia. 'Moko' drums are unique cultural objects from the Alor-Pantar Archipelago and, besides their ancient function of ritual instruments used mainly for religious purposes and in public events by the indigenous peoples of the islands, they represented and still are considered a very valuable local 'currency' for trade and for specific social interactions rooted in aboriginal culture, like bride price negotiations. Despite the fact that they are extremely popular and widespread among Papuan peoples in Alor and Pantar, the origins of these drums are still relatively obscure. The native speakers, indeed, cannot explain the name 'moko' in itself, at the etymological and semantic level, and, despite the fact that they agree upon non-local origins of the instruments, they do not know where the instruments themselves were produced and from where they came to the islands. Our paper provides the readers with comprehensive lists that systematically collect the names of the drums, with the related glosses and basic additional information, from three representative Papuan languages of Alor Island, namely Abui, Sawila, and Kula. Configured as potentially indispensable tools to develop further research, these lists enhance our knowledge and understanding of the culture of the 'moko' drums in the Alor-Pantar Archipelago, at the linguistic (etymology of the names), anthropological (social value of the drums), and archeological (typology and provenance of the instruments) levels. This cataloguing operation is also part of the effort of documentation of the languages and cultures, still scarcely documented and definitely endangered, of the native peoples of the Alor-Pantar Archipelago.
PubMed: 38590619
DOI: 10.1016/j.dib.2024.110354 -
Food Chemistry Aug 2024Hazelnuts' features and price are influenced by their geographical origin, making them susceptible to fraud, especially counterfeit claims regarding their provenance....
Hazelnuts' features and price are influenced by their geographical origin, making them susceptible to fraud, especially counterfeit claims regarding their provenance. Stable isotope analysis is a recognised approach to establish the geographical origin of foods, yet its potential in hazelnut authentication remains unexplored. In this prospective study, we assessed multiple isotopic markers in hazelnuts from different origins and evaluated the most promising variables for geographical authentication by chemometric tools. Our findings indicate that bulk δO, along with δH and δC in the main fatty acid methyl esters, exhibit significant potential in discriminating geographical origins, and Sr/Sr analysis could serve as a proficient confirmatory tool. Though no single marker alone can differentiate between all the studied origins, employing a multi-isotopic approach based on PLS-DA models achieved up to 92.5 % accuracy in leave-10 %-out cross-validation. These findings will probably lay the groundwork for developing robust models for hazelnut geographical authentication based on larger datasets.
Topics: Corylus; Nuts; Carbon Isotopes; Geography; Oxygen Isotopes; Fatty Acids; Discriminant Analysis
PubMed: 38581795
DOI: 10.1016/j.foodchem.2024.139083 -
Database : the Journal of Biological... Apr 2024When the scientific dataset evolves or is reused in workflows creating derived datasets, the integrity of the dataset with its metadata information, including...
When the scientific dataset evolves or is reused in workflows creating derived datasets, the integrity of the dataset with its metadata information, including provenance, needs to be securely preserved while providing assurances that they are not accidentally or maliciously altered during the process. Providing a secure method to efficiently share and verify the data as well as metadata is essential for the reuse of the scientific data. The National Science Foundation (NSF) funded Open Science Chain (OSC) utilizes consortium blockchain to provide a cyberinfrastructure solution to maintain integrity of the provenance metadata for published datasets and provides a way to perform independent verification of the dataset while promoting reuse and reproducibility. The NSF- and National Institutes of Health (NIH)-funded Neuroscience Gateway (NSG) provides a freely available web portal that allows neuroscience researchers to execute computational data analysis pipeline on high performance computing resources. Combined, the OSC and NSG platforms form an efficient, integrated framework to automatically and securely preserve and verify the integrity of the artifacts used in research workflows while using the NSG platform. This paper presents the results of the first study that integrates OSC-NSG frameworks to track the provenance of neurophysiological signal data analysis to study brain network dynamics using the Neuro-Integrative Connectivity tool, which is deployed in the NSG platform. Database URL: https://www.opensciencechain.org.
Topics: Reproducibility of Results; Databases, Factual; Publications; Neurosciences; Metadata
PubMed: 38581360
DOI: 10.1093/database/baae023 -
Heliyon Apr 2024This research investigates the physico-chemical, mineralogical and geochemical attributes of alluvial clayey sediments in the Nkoteng-Mbandjock regions of the Sanaga...
Mineralogical and geochemical characteristics of the Nkoteng-Mbandjock alluvial clays from Sanaga valley deposits (Cameroon, Central Africa): Implications for source weathering and provenance.
This research investigates the physico-chemical, mineralogical and geochemical attributes of alluvial clayey sediments in the Nkoteng-Mbandjock regions of the Sanaga valley, Cameroon. The primary objective is to elucidate the source area-weathering and provenance of these sediments. Grain size distribution analyses were conducted using the Robinson-Kӧln's pipetting method. The physico-chemical parameters were evaluated by an HACH-HQ11d brand electric pH meter, while the mineralogical compositions were determined by X-ray Diffraction. Major and trace element concentrations were measured employing X-ray Fluorescence and Inductively Coupled Plasmas-Mass Spectrometry. Textural classification identified the Sanaga valley alluvial clay deposits as predominantly silty clayey and clayey muddy. Geochemical classification diagram positioned them in the shale and Fe-shale fields. Weathering indices of alteration exhibited a consistent trend indicating a high degree of weathering in the source rock. A low NaO/KO ratio (average 0.18) and a high Index of Compositional Variability (ICV; average 2.29) suggested immature sediments. Additionally, low SiO/AlO ratio (average 3.93) implied an origin from stable settings with recycled inputs. These characteristics were further supported by elemental ratios such as Zr/Sc (average 47.12), U/Th (average 0.24) and Th/Sc (average 1.48). Furthermore, indicators like V/Cr (average 1.17), U/Th (average 0.24) and authigenic U (average -1.67) values suggested the deposition of the Sanaga valley alluvial clay under oxic conditions. The collective analysis of major and trace element distribution revealed felsic sources with minimal contributions from mafic rocks. These findings contribute to a comprehensive understanding of the geological processes and conditions influencing the composition and characteristics of the studied alluvial clay deposits in the Sanaga valley.
PubMed: 38560138
DOI: 10.1016/j.heliyon.2024.e28395 -
Scientific Reports Mar 2024Unraveling the Paleo-Kuril Arc's origins is key to understanding northwest Pacific tectonics. The Paleo-Kuril Arc is viewed as an intraoceanic arc from trench subduction...
Unraveling the Paleo-Kuril Arc's origins is key to understanding northwest Pacific tectonics. The Paleo-Kuril Arc is viewed as an intraoceanic arc from trench subduction between the Izanagi and Pacific Plates. Alternatively, several studies suggest the Paleo-Kuril Arc as a continental magmatic arc, hypothesizing the existence of a mid-oceanic ridge and Paleogene subduction, placing the Paleo-Kuril Arc near the Okhotsk Block's southern edge. This study clarifies these hypotheses, previously clouded by limited geochronological data on deposits in the Paleo-Kuril Arc. We conducted U-Pb dating to examine the origins of detrital zircons from the Cretaceous-Paleogene Tokoro and Nemuro Belts of the Paleo-Kuril Arc. Cluster analysis, merging new and existing data, identified two unique detrital zircon age clusters. The abundance of Precambrian zircons in Cretaceous-Paleocene Paleo-Kuril Arc sandstones (Type 1 Cluster) suggests a continental magmatic origin, supporting the ridge subduction model. However, an early Eocene shift to a consistent local volcanic source (Type 2 Cluster) highlights a significant provenance change. This geochronological evidence, indicating a separation from continental sources, calls for further research to decode the simultaneous development of sediment sources in different geological belts, potentially tied to the ridge subduction event.
PubMed: 38538604
DOI: 10.1038/s41598-024-55471-1 -
ChemElectroChem Dec 2023Insert A multiple-scan voltammetry strategy is described and applied to a set of 107 Bronze Age and later copper/bronze objects, mainly from sites in Central Europe....
Insert A multiple-scan voltammetry strategy is described and applied to a set of 107 Bronze Age and later copper/bronze objects, mainly from sites in Central Europe. This methodology allows the study of the compositional and textural properties (compactness, crystallinity, degree of hydration) of the patina to be studied from the accumulated peak current values for the characteristic signals corresponding to the reduction of cuprite and tenorite to metallic copper. A new model for the relationship between peak current and the depth reached in successive scans is presented and used to discriminate samples of different provenance and manufacturing technique, as well as their ascription to different Bronze Age periods.
PubMed: 38529335
DOI: 10.1002/celc.202300405