-
American Journal of Botany Feb 2023Riparian plants can exhibit intraspecific phenotypic variability across the landscape related to temperature and flooding gradients. Phenotypes that vary across a...
PREMISE
Riparian plants can exhibit intraspecific phenotypic variability across the landscape related to temperature and flooding gradients. Phenotypes that vary across a climate gradient are often partly genetically determined and may differ in their response to inundation. Changes to inundation patterns across a climate gradient could thus result in site-specific inundation responses. Phenotypic variability is more often studied in riparian trees, yet riparian shrubs are key elements of riparian systems and may differ from trees in phenotypic variability and environmental responses.
METHODS
We tested whether individuals of a clonal, riparian shrub, Pluchea sericea, collected from provenances spanning a temperature gradient differed in their phenotypes and responses to inundation and to what degree any differences were related to genotype. Plants were subjected to different inundation depths and a subset genotyped. Variables related to growth and resource acquisition were measured and analyzed using hierarchical, multivariate Bayesian linear regressions.
RESULTS
Individuals from different provenances differed in their phenotypes, but not in their response to inundation. Phenotypes were not related to provenance temperature but were partially governed by genotype. Growth was more strongly influenced by inundation, while resource acquisition was more strongly controlled by genotype.
CONCLUSIONS
Growth and resource acquisition responses in a clonal, riparian shrub are affected by changes to inundation and plant demographics in unique ways. Shrubs appear to differ from trees in their responses to environmental change. Understanding environmental effects on shrubs separately from those of trees will be a key part of evaluating impacts of environmental change on riparian ecosystems.
Topics: Ecosystem; Bayes Theorem; Floods; Climate; Genotype; Rivers
PubMed: 36462152
DOI: 10.1002/ajb2.16115 -
Ying Yong Sheng Tai Xue Bao = the... Jul 2023For exploring the difference of root stoichiometric characteristics among diameter classes and provenances, we examined the contents and stoichiometric ratios of carbon...
For exploring the difference of root stoichiometric characteristics among diameter classes and provenances, we examined the contents and stoichiometric ratios of carbon (C), nitrogen (N), phosphorus (P), and potassium (K) in three diameter classes of roots (0-1, 1-2 and 2-5 mm, respectively) of 39-year-old grown in a common garden. The results showed that root element contents and their stoichiometric ratios had significant difference among three diameter classes of roots. C content, C:N, C:P, C:K were the lowest, and N, P, K contents, N:P, and N:K were the highest in 0-1 mm diameter class roots. Compared with the 1-2 and 2-5 mm diameter class roots, 0-1 mm diameter class roots had different seasonal dynamics, which might be caused by the fact that 0-1 mm diameter class roots are absorptive roots and the other diameter class roots are transport roots. There was no provenance difference in C content among all diameter class roots, while significant provenance differences were found in N, K contents, C:N, and C:K in 0-1 mm diameter class roots, and great provenance differences for in P content, C:P, N:P, and N:K in 0-1 and 1-2 mm diameter class roots. N content, K content, C:P, N:P, and N:K in 0-1 mm diameter class roots had positive correlation with the aridity index of seed-source sites, while the P content, C:N and C:K had negative correlations. The stoichiometric characteristics were related with the diameter (or function) of roots, and had significant provenance differences in 0-1 mm (absorptive root) and 1-2 mm diameter class roots, which might be attributed to their genotypic adaptation to the environment of seed-source sites.
Topics: Larix; Acclimatization; Carbon; Genotype; Nitrogen
PubMed: 37694463
DOI: 10.13287/j.1001-9332.202307.005 -
Frontiers in Genetics 2022Currently, most of the personal health data (PHD) are managed and stored separately by individual medical institutions. When these data need to be shared, they must be...
Currently, most of the personal health data (PHD) are managed and stored separately by individual medical institutions. When these data need to be shared, they must be transferred to a trusted management center and approved by data owners through the third-party endorsement technology. Therefore, it is difficult for personal health data to be shared and circulated over multiple medical institutions. On the other hand, the use of directly exchanging and sharing the original data has become inconsistent with the data rapid growth of medical institutions because of the need of massive data transferring across agencies. In order to secure sharing and managing the mass personal health data generated by various medical institutions, a federal personal health data management framework (PHDMF, https://hvic.biosino.org/PHDMF) has been developed, which had the following advantages: 1) the blockchain technology was used to establish a data consortium over multiple medical institutions, which could provide a flexible and scalable technical solution for member extension and solve the problem of third-party endorsement during data sharing; 2) using data distributed storage technology, personal health data could be majorly stored in their original medical institutions, and the massive data transferring process was of no further use, which could match up with the data rapid growth of these institutions; 3) the distributed ledger technology was utilized to record the hash value of data, given the anti-tampering feature of the technology, malicious modification of data could be identified by comparing the hash value; 4) the smart contract technology was introduced to manage users' access and operation of data, which made the data transaction process traceable and solved the problem of data provenance; and 5) a trusted computing environment was provided for meta-analysis with statistic information instead of original data, the trusted computing environment could be further applied to more health data, such as genome sequencing data, protein expression data, and metabolic profile data through combining the federated learning and blockchain technology. In summary, the framework provides a convenient, secure, and trusted environment for health data supervision and circulation, which facilitate the consortium establish over medical institutions and help achieve the value of data sharing and mining.
PubMed: 35495148
DOI: 10.3389/fgene.2022.877870 -
National Science Review Feb 2023This paper reviews published and presents new data on U-Pb detrital zircon ages, and petrographic, geochemical and isotope (Sm-Nd, Lu-Hf) compositions obtained from... (Review)
Review
This paper reviews published and presents new data on U-Pb detrital zircon ages, and petrographic, geochemical and isotope (Sm-Nd, Lu-Hf) compositions obtained from greywacke sandstones of Kazakhstan in order to reconstruct fossil intra-oceanic arcs that once existed at Pacific-type convergent margins of the Paleo-Asian Ocean (PAO) in Paleozoic time. We focus on orogenic belts of central Kazakhstan (Itmurundy and Tekturmas) and eastern Kazakhstan (Zharma and Char) in the western Central Asian Orogenic belt. These orogenic belts host accretionary complexes with greywacke sandstones of early Paleozoic (central Kazakhstan) and middle-late Paleozoic (eastern Kazakhstan) ages. First, we evaluate general perspectives for studying sandstones to reconstruct survived and disappeared magmatic arcs, taking into account episodes of subduction erosion. Then we discuss the analytical data from sandstones to make conclusions about the ages and formation settings of their igneous protoliths and define maximum deposition ages. Finally, we discuss the role of serpentinite mélanges in tectonic reconstructions. We argue that sandstones hosted by accretionary complexes are typically greywackes deposited close to their igneous sources and buried rapidly. The provenances of the studied greywacke sandstones of central and eastern Kazakhstan were dominated by mafic to andesitic igneous protoliths derived from juvenile mantle sources. The igneous rocks in the provenances were emplaced in an intra-oceanic arc setting. The sandstones were deposited in fore-arc/trench basins or, to a lesser degree, in back-arc basins. The data from both sandstones and serpentinite mélanges reconstruct middle-late-Cambrian, Ordovician, late-Devonian and Carboniferous arcs of the western PAO. The middle-late Cambrian arcs were fully destroyed by subduction erosion, whereas the Ordovician and Carboniferous arcs survived. The late-Devonian arcs were also eroded, but partly. Both the early and late Paleozoic active margins of the PAO were characterized by alternating periods of accretionary growth and subduction erosion.
PubMed: 36817843
DOI: 10.1093/nsr/nwac215 -
IEEE Computer Graphics and Applications 2019Data quality management and assessment play a vital role for ensuring the trust in the data and its fitness-of-use for subsequent analysis. The transformation history of...
Data quality management and assessment play a vital role for ensuring the trust in the data and its fitness-of-use for subsequent analysis. The transformation history of a data wrangling system is often insufficient for determining the usability of a dataset, lacking information how changes affected the dataset. Capturing workflow provenance along the wrangling process and combining it with descriptive information as data provenance can enable users to comprehend how these changes affected the dataset, and if they benefited data quality. We present DQProv Explorer, a system that captures and visualizes provenance from data wrangling operations. It features three visualization components: allowing the user to explore the provenance graph of operations and the data stream, the development of quality over time for a sequence of wrangling operations applied to the dataset, and the distribution of issues across the entirety of the dataset to determine error patterns.
PubMed: 31581076
DOI: 10.1109/MCG.2019.2941856 -
Ecological Applications : a Publication... Jan 2022Restoration in this era of climate change comes with a new challenge: anticipating how best to restore populations to persist under future climate conditions....
Restoration in this era of climate change comes with a new challenge: anticipating how best to restore populations to persist under future climate conditions. Specifically, it remains unknown whether locally adapted or warm-adapted seeds best promote native plant community restoration in the warmer conditions predicted in the future and whether local or warm-adapted soil microbial communities could mitigate plant responses to warming. This may be especially relevant for biomes spanning large climatic gradients, such as the North American tallgrass prairie. Here, we used a short-term mesocosm experiment to evaluate how seed provenances (Local Northern region, Non-local Northern region, Non-local Southern region) of 10 native tallgrass prairie plants (four forbs, two legumes, and four grasses) responded to warmer conditions predicted in the future and how soil microbial communities from those three regions influenced these responses. Warming and seed provenance affected plant community composition and warming decreased plant diversity for all three seed provenances. Plant species varied in their individual responses to warming, and across species, we detected no consistent differences among the three provenances in terms of biomass response to warming and few strong effects of soil provenance. Our work provides evidence that warming, in part, may reduce plant diversity and affect restored prairie composition. Because the southern provenance did not consistently outperform others under warming and we found little support for the "local is best" paradigm currently dominating restoration practice, identifying appropriate seed provenances to promote restoration success both now and in future warmer environments may be challenging. Due to the idiosyncratic responses across species, we recommend that land managers compare seeds from different regions for each species to determine which seed provenance performs best under warming and in restoration for tallgrass prairies.
Topics: Ecosystem; Grassland; Plants; Seeds; Soil
PubMed: 34679217
DOI: 10.1002/eap.2487 -
Bioinformatics (Oxford, England) Jun 2021Reproducibility is of central importance to the scientific process. The difficulty of consistently replicating and verifying experimental results is magnified in the era...
MOTIVATION
Reproducibility is of central importance to the scientific process. The difficulty of consistently replicating and verifying experimental results is magnified in the era of big data, in which bioinformatics analysis often involves complex multi-application pipelines operating on terabytes of data. These processes result in thousands of possible permutations of data preparation steps, software versions and command-line arguments. Existing reproducibility frameworks are cumbersome and involve redesigning computational methods. To address these issues, we developed RepeatFS, a file system that records, replicates and verifies informatics workflows with no alteration to the original methods. RepeatFS also provides several other features to help promote analytical transparency and reproducibility, including provenance visualization and task automation.
RESULTS
We used RepeatFS to successfully visualize and replicate a variety of bioinformatics tasks consisting of over a million operations with no alteration to the original methods. RepeatFS correctly identified all software inconsistencies that resulted in replication differences.
AVAILABILITYAND IMPLEMENTATION
RepeatFS is implemented in Python 3. Its source code and documentation are available at https://github.com/ToniWestbrook/repeatfs.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Automation; Computational Biology; Reproducibility of Results; Software; Workflow
PubMed: 33230554
DOI: 10.1093/bioinformatics/btaa950 -
ACS Omega Feb 2022Organic matter (OM) is the material basis for hydrocarbon generation. Its type and abundance determine the hydrocarbon generation ability of source rocks, which is...
Organic matter (OM) is the material basis for hydrocarbon generation. Its type and abundance determine the hydrocarbon generation ability of source rocks, which is closely related to the provenance and sedimentary environment of source rocks. The tectonic backgrounds of the eastern and western subsags (ESS and WSS) of the Lishui Sag in the East China Sea Shelf Basin are significantly different and their influence on the OM in the source rocks is worthy of attention. This paper comprehensively analyzes the provenance and environmental characteristics and their influence on the features of the OM of Paleocene source rocks in the ESS and WSS. The study finds that the source rocks in the ESS have multiple sources. During the deposition period, as the salinity and paleoproductivity of the water column increased, the proportion of OM in the autochthonous components of the water column continued to increase, but the overall water column was in an oxidizing environment, resulting in a generally low abundance of OM. The provenance of the source rocks in the WSS was relatively simple and terrestrial. Also, the sedimentary environment had little effect on the type of OM. However, the whole water column of the WSS was in an anoxic environment, so the OM was better preserved, resulting in a higher abundance. Due to the influence of provenance and the sedimentary environment in different areas of the sag, the characteristics of OM in the source rocks are different, so relevant exploration strategies need to be adopted in actual exploration.
PubMed: 35224339
DOI: 10.1021/acsomega.1c05764 -
Frontiers in Plant Science 2023is an orchid with medicinal and nutritional properties that has received increasing attention because of its health benefits; however, there is limited information...
is an orchid with medicinal and nutritional properties that has received increasing attention because of its health benefits; however, there is limited information about the metabolic basis of these properties. In this report, secondary metabolites and the antioxidant activity of stem samples from three provenances were analyzed, using a UHPLC-QqQ-MS/MS-based metabolomics approach. In total, 411 metabolites were identified including 8 categories such as flavonoids and phenolic acids, 136 of which were differential metabolites. These differentially accumulated metabolites (DAMs) were mainly enriched in secondary metabolic pathways such as flavone, flavonol, tropane, piperidine, pyridine, isoquinoline alkaloid biosynthesis and tyrosine metabolism. The metabolomic profiling suggested that the quantity and content of flavonoid compounds accounted for the highest proportion of total metabolites. Hierarchical cluster analysis (HCA) showed that the marker metabolites of from the three provenances were mainly flavonoids, alkaloids and phenolic acids. Correlation analysis identified that 48 differential metabolites showed a significant positive correlation with antioxidant capacity (r ³ 0.8 and p < 0.0092), and flavonoids were the main factors affecting the different antioxidant activities. It is worth noting that quercetin-3-O-sophoroside-7-O-rhamnoside and dihydropinosylvin methyl ether might be the main compounds causing the differences in antioxidant capacity of Yunnan provenance (YN), Zhejiang provenance (ZJ), and Guizhou provenance (GZ). These finding provides valuable information for screening varieties, quality control and product development of .
PubMed: 36760636
DOI: 10.3389/fpls.2023.1060242 -
JAMA Internal Medicine Jan 2024Both the commercial sector and academia play a vital role in medicine development. Ongoing debates exist on their contribution and the value of medicinal products...
IMPORTANCE
Both the commercial sector and academia play a vital role in medicine development. Ongoing debates exist on their contribution and the value of medicinal products entering the market.
OBJECTIVE
To identify the provenance and clinical benefit of medicines that entered the French market between 2008 and 2018.
DESIGN AND SETTING
In this cross-sectional study, the provenance of each medicine in the French market was established via a review of multiple sources documenting at least 2 matching findings per product. The clinical benefit was assigned using the matched scale developed from the Prescrire and Haute Autorité de Santé (HAS) gradings. The χ2 test was used to analyze the proportions and frequencies of medicines graded by Prescrire and HAS by origin, therapeutic category, and clinical benefit.
MAIN OUTCOMES AND MEASURES
The origins and therapeutic categories of medicines. Clinical benefit based on Prescrire and HAS grading. Concordance of Prescrire and HAS grading.
RESULTS
Of the 632 medicines that entered the French market between 2008 and 2018, 464 originated (73%) in the commercial sector, and 168 originated (27%) in the academic setting or in collaboration with commercial enterprises. Prescrire graded psychotropic agents (13/14 [93%]), whereas HAS graded respiratory agents (24/25 [96%]) as the highest percentage of medicines that provided no added benefit. Prescrire graded 360 medicines (77.6%) that originated in the industry and 108 medicines (64.3%) that originated in the academic setting (P = .001) to have no added clinical benefit. HAS assigned such grading to 331 ([71.3%] industry) vs 104 ([61.9%] academia) (P = .02). Based on the Prescrire grading, academia invented more medicines delivering some added benefit 57 (33.9%) vs 98 (21.1%) invented by industry (P = .001). HAS grading on some added benefit 51 ([30.4%] academia) vs 121 ([26.1%] industry) did not reach statistical significance (P = .29). However, HAS grading on substantial added clinical benefit reached statistical significance in favor of academia (13 [7.7%] vs 12 [2.6%] in the industry; P = .003), whereas Prescrire grading did not (1.8% academia vs 1.3% industry; P = .64).
CONCLUSIONS AND RELEVANCE
More than 70% of medicines that entered the French market during the 10-year period originated in the commercial sector. Although most medicines were not graded as providing clinical benefit, medicines originating in the academic setting were more likely to be graded as conferring clinical benefit than those originating in the commercial setting.
Topics: Humans; Cross-Sectional Studies; Drug Industry; Commerce; Pharmaceutical Preparations
PubMed: 37983026
DOI: 10.1001/jamainternmed.2023.6249