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BMC Genomic Data Jun 2024Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported...
Implications of accounting for marker-based population structure in the quantitative genetic evaluation of genetic parameters related to growth and wood properties in Norway spruce.
BACKGROUND
Forest geneticists typically use provenances to account for population differences in their improvement schemes; however, the historical records of the imported materials might not be very precise or well-aligned with the genetic clusters derived from advanced molecular techniques. The main objective of this study was to assess the impact of marker-based population structure on genetic parameter estimates related to growth and wood properties and their trade-offs in Norway spruce, by either incorporating it as a fixed effect (model-A) or excluding it entirely from the analysis (model-B).
RESULTS
Our results indicate that models incorporating population structure significantly reduce estimates of additive genetic variance, resulting in substantial reduction of narrow-sense heritability. However, these models considerably improve prediction accuracies. This was particularly significant for growth and solid-wood properties, which showed to have the highest population genetic differentiation (Q) among the studied traits. Additionally, although the pattern of correlations remained similar across the models, their magnitude was slightly lower for models that included population structure as a fixed effect. This suggests that selection, consistently performed within populations, might be less affected by unfavourable genetic correlations compared to mass selection conducted without pedigree restrictions.
CONCLUSION
We conclude that the results of models properly accounting for population structure are more accurate and less biased compared to those neglecting this effect. This might have practical implications for breeders and forest managers where, decisions based on imprecise selections can pose a high risk to economic efficiency.
Topics: Picea; Wood; Genetic Markers; Models, Genetic; Genetics, Population; Genetic Variation
PubMed: 38877416
DOI: 10.1186/s12863-024-01241-x -
BMJ (Clinical Research Ed.) Jun 2024call for greater use of this inexpensive generic drug that can improve surgical outcomes, avoid unnecessary blood transfusion, and conserve blood stocks
call for greater use of this inexpensive generic drug that can improve surgical outcomes, avoid unnecessary blood transfusion, and conserve blood stocks
Topics: Tranexamic Acid; Humans; Antifibrinolytic Agents; Blood Loss, Surgical
PubMed: 38866414
DOI: 10.1136/bmj-2024-079444 -
PeerJ. Computer Science 2024The availability of drugs across the country is a direct measure for fairer public health. Several issues have been reported drastically related to various organizations...
The availability of drugs across the country is a direct measure for fairer public health. Several issues have been reported drastically related to various organizations that fail to provide quality medicines on time. There has been a consistent increase in cases where the treatment, as well as exempted drugs, were supplied due to the unavailability of proper traceability of the supply chain. Several parties are involved in the supply and have similar interests that may defer the adequate shareability of the drugs. The existing system for managing the drug supply chain suffers from several backlogs. The loss of information, unavailability of resources to track the proper medicinal storage, transparency of information sharing between various stakeholders and sequential access. The applicability of the decentralized model emerging from the blockchain can apply to one of the perfect solutions in this case. The drug traceability chain can be deployed to a Ledger-based blockchain that may result in decentralized information. Continuous supply from the Internet of Things (IoT) based devices might be handy as the middleware for providing a trustworthy, safe, and proper transaction-oriented system. The data integrity, along with the provenance resulting from the IoT-connected devices, is an effective solution towards managing the supply chain and drug traceability. This study presents a model that can provide a token-based blockchain that will help provide a cost-efficient and secure system for a reliable drug supply chain.
PubMed: 38855238
DOI: 10.7717/peerj-cs.2072 -
European Journal of Cancer (Oxford,... May 2024Providing patient access to precision oncology (PO) is a major challenge of clinical oncologists. Here, we provide an easily transferable model from strategic management...
PURPOSE
Providing patient access to precision oncology (PO) is a major challenge of clinical oncologists. Here, we provide an easily transferable model from strategic management science to assess the outreach of a cancer center.
METHODS
As members of the German WERA alliance, the cancer centers in Würzburg, Erlangen, Regensburg and Augsburg merged care data regarding their geographical impact. Specifically, we examined the provenance of patients from WERA´s molecular tumor boards (MTBs) between 2020 and 2022 (n = 2243). As second dimension, we added the provenance of patients receiving general cancer care by WERA. Clustering our catchment area along these two dimensions set up a four-quadrant matrix consisting of postal code areas with referrals towards WERA. These areas were re-identified on a map of the Federal State of Bavaria.
RESULTS
The WERA matrix overlooked an active screening area of 821 postal code areas - representing about 50 % of Bavaria´s spatial expansion and more than six million inhabitants. The WERA matrix identified regions successfully connected to our outreach structures in terms of subsidiarity - with general cancer care mainly performed locally but PO performed in collaboration with WERA. We also detected postal code areas with a potential PO backlog - characterized by high levels of cancer care performed by WERA and low levels or no MTB representation.
CONCLUSIONS
The WERA matrix provided a transparent portfolio of postal code areas, which helped assessing the geographical impact of our PO program. We believe that its intuitive principle can easily be transferred to other cancer centers.
PubMed: 38852290
DOI: 10.1016/j.ejca.2024.114144 -
Acta Crystallographica. Section D,... Jun 2024The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining...
The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields.
Topics: Software; Computational Biology
PubMed: 38832828
DOI: 10.1107/S2059798324004881 -
Heliyon Jun 2024The rise in the cost of essentials affects every nation around the world, but it has become a major concern for developing nations. It is getting increasingly difficult... (Review)
Review
The rise in the cost of essentials affects every nation around the world, but it has become a major concern for developing nations. It is getting increasingly difficult to keep up with rising prices for everyday items in these countries, where the majority of the population is from the middle class or lower middle class. Inflation, pandemics, wars, and other important variables all contribute to price increases. There may be another significant factor at play, which is supply-chain corruption. The supply chain's unreliable, chaotic, and opaque nature is to blame for this corruption. We are concentrating on the agri-food supply chain in our study. Because many of the current agri-food supply chains are intricate and challenging to monitor, dishonest parties can exploit the situation. Therefore, we suggested a thorough blockchain-based agri-food supply chain to identify the source of price increases. The private Ethereum blockchain was used in the suggested system. Since the private Ethereum blockchain is more efficient, safe, and fast, it was chosen. Smart contracts were created to describe the system and its underlying rules and laws. Furthermore, in order to showcase the usefulness of our smart contracts, we exhibited a sample decentralized application to support our hypothesis. We also gave the system a complete security and vulnerability assessment to make sure it is operating properly and is protected from threats and attacks. Due to the use of blockchain, the system is immutable, transparent, and simple to track and monitor. The proposed system has demonstrated greater transparency, traceability, reliability, speed, security, and cost-efficiency compared to conventional systems. It effectively traces the origin of corruption in the supply chain, providing a more straightforward means to tackle concerns related to price hikes.
PubMed: 38832272
DOI: 10.1016/j.heliyon.2024.e30972 -
Nature Communications May 2024Selection causes local adaptation across populations within species and simultaneously divergence between species. However, it is unclear if either the force of or the...
Selection causes local adaptation across populations within species and simultaneously divergence between species. However, it is unclear if either the force of or the response to selection is similar across these scales. We show that natural selection drives divergence between closely related species in a pattern that is distinct from local adaptation within species. We use reciprocal transplant experiments across three species of Phlox wildflowers to characterize widespread adaptive divergence. Using provenance trials, we also find strong local adaptation between populations within a species. Comparing divergence and selection between these two scales of diversity we discover that one suite of traits predicts fitness differences between species and that an independent suite of traits predicts fitness variation within species. Selection drives divergence between species, contributing to speciation, while simultaneously favoring extensive diversity that is maintained across populations within a species. Our work demonstrates how the selection landscape is complex and multidimensional.
Topics: Selection, Genetic; Adaptation, Physiological; Species Specificity; Genetic Speciation; Genetic Fitness
PubMed: 38821972
DOI: 10.1038/s41467-024-49075-6 -
Scientific Reports May 2024Stress drop is an earthquake property indicative for the characteristic relation of slip to fault dimension. It is furthermore affected by fault strength, fault...
Stress drop is an earthquake property indicative for the characteristic relation of slip to fault dimension. It is furthermore affected by fault strength, fault topography, the presence of fluids, rupture size, slip, and velocity. In this article, the stress drop image of an entire subduction zone, namely for the seismically highly active northernmost part of Chile, is combined with mapped b-values and their corresponding magnitude distribution in order to better constrain the conditions under which earthquakes of different provenances may nucleate. The underlying recent earthquake catalog contains over 180,000 events, covering 15 years of seismicity, from which more than 50,000 stress drop estimates were computed. Their spatial average segments the subduction zone into different parts, i.e., average stress drop between seismotectonic areas is different, although this difference is small compared to the natural scatter of stress drop values. By considering stress drop variations, b-value map, magnitude distribution, and thermal models, candidate earthquake nucleation mechanisms are identified which can explain the observed distributions. This is done for two exemplary regions: (1) The plate interface, where principally lower stress drop events are found, while at the same time a high spatial heterogeneity of stress drop values is observed. This indicates relatively smooth or lubricated rupture surfaces, and locally it suggests the existence of alternating regions controlled by strong asperities, weaker material, or creep. (2) The highly active intermediate depth (ID) seismicity region, where the variation of stress drop and b-value point to a gradual change of nucleation mechanism from dehydration embrittlement at the top of the ID cloud, over dehydration driven stress transfer in its central part, to thermal runaway shear mechanisms at its bottom. In both cases, the combination of stress drop and b-value distribution helps to better understand the origin and the differences of the observed seismicity.
PubMed: 38806618
DOI: 10.1038/s41598-024-63015-w -
PloS One 2024Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and...
Engineered plasmids have been workhorses of recombinant DNA technology for nearly half a century. Plasmids are used to clone DNA sequences encoding new genetic parts and to reprogram cells by combining these parts in new ways. Historically, many genetic parts on plasmids were copied and reused without routinely checking their DNA sequences. With the widespread use of high-throughput DNA sequencing technologies, we now know that plasmids often contain variants of common genetic parts that differ slightly from their canonical sequences. Because the exact provenance of a genetic part on a particular plasmid is usually unknown, it is difficult to determine whether these differences arose due to mutations during plasmid construction and propagation or due to intentional editing by researchers. In either case, it is important to understand how the sequence changes alter the properties of the genetic part. We analyzed the sequences of over 50,000 engineered plasmids using depositor metadata and a metric inspired by the natural language processing field. We detected 217 uncatalogued genetic part variants that were especially widespread or were likely the result of convergent evolution or engineering. Several of these uncatalogued variants are known mutants of plasmid origins of replication or antibiotic resistance genes that are missing from current annotation databases. However, most are uncharacterized, and 3/5 of the plasmids we analyzed contained at least one of the uncatalogued variants. Our results include a list of genetic parts to prioritize for refining engineered plasmid annotation pipelines, highlight widespread variants of parts that warrant further investigation to see whether they have altered characteristics, and suggest cases where unintentional evolution of plasmid parts may be affecting the reliability and reproducibility of science.
Topics: Plasmids; Genetic Engineering; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Mutation; Base Sequence; Sequence Analysis, DNA
PubMed: 38805426
DOI: 10.1371/journal.pone.0304164 -
Plants (Basel, Switzerland) May 2024The Asian chestnut gall wasp (ACGW) (Hymenoptera Yasumatsu) is a severe pest of sweet chestnut ( Mill.) with a strong impact on growth and nut production. A comparative...
The Asian chestnut gall wasp (ACGW) (Hymenoptera Yasumatsu) is a severe pest of sweet chestnut ( Mill.) with a strong impact on growth and nut production. A comparative field trial in Central Italy, including provenances from Spain, Italy, and Greece, was screened for ACGW infestation over consecutive years. The Greek provenance Hortiatis expressed a high proportion of immune plants and was used to perform a genome-wide association study based on DNA pool sequencing (Pool-GWAS) by comparing two DNA pools from 25 susceptible and 25 resistant plants. DNA pools were sequenced with 50X coverage depth. Sequence reads were aligned to a reference genome and the pools were compared to identify SNPs associated with resistance. Twenty-one significant SNPs were identified and highlighted a small genomic region on pseudochromosome 3 (Chr 3), containing 12 candidate genes of three gene families: , , and . Functional analyses revealed a putative metabolic gene cluster related to saccharide biosynthesis in the genomic regions associated with resistance that could be involved in the production of a toxic metabolite against parasites. The comparison with previous genetic studies confirmed the involvement of Chr 3 in the control of resistance to ACGW.
PubMed: 38794426
DOI: 10.3390/plants13101355