From 9796469ec09d26985498cf0efd525c1a87ba4d85 Mon Sep 17 00:00:00 2001 From: nfrerebeau Date: Mon, 30 Sep 2024 23:58:27 +0200 Subject: [PATCH] Add citations --- data/citations.yml | 1437 ++++++++++++++++++++++++++++++++++++++++++++ data/doi.csv | 27 + index.qmd | 31 + utilities.R | 14 + 4 files changed, 1509 insertions(+) create mode 100644 data/citations.yml create mode 100644 data/doi.csv diff --git a/data/citations.yml b/data/citations.yml new file mode 100644 index 0000000..dd7a6e2 --- /dev/null +++ b/data/citations.yml @@ -0,0 +1,1437 @@ +kairos: +- id: https://openalex.org/W4378902656 + title: 'shoredate: An R package for shoreline dating coastal Stone Age sites' + display_name: 'shoredate: An R package for shoreline dating coastal Stone Age sites' + author: + - ~ + ab: As a result of glacio-isostatic rebound, large regions of Fennoscandia have + undergone a process of relative sea-level fall following the retreat of the Fennoscandian + Ice Sheet.Furthermore, coastal Stone Age sites in the region appear to have been + predominantly located on or close to the shoreline when they were in use.Based + on their altitude relative to the present-day sea-level, this can be combined + with a reconstruction of past relative sea-level change to assign an approximate + date to when the sites were in use.This method, called shoreline dating, has been + used in the region since the early 1900s (e.g.Brøgger, 1905) and is still widely + applied today (e.g. + publication_date: '2023-05-31' + so: The Journal of Open Source Software + so_id: https://openalex.org/S4210214273 + host_organization: Open Journals + issn_l: 2475-9066 + url: https://doi.org/10.21105/joss.05337 + pdf_url: https://joss.theoj.org/papers/10.21105/joss.05337.pdf + license: cc-by + version: publishedVersion + first_page: '5337' + last_page: '5337' + volume: '8' + issue: '85' + is_oa: yes + is_oa_anywhere: yes + oa_status: diamond + oa_url: https://joss.theoj.org/papers/10.21105/joss.05337.pdf + any_repository_has_fulltext: yes + language: en + grants: .na + cited_by_count: 3 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4378902656 + ids: + - ~ + doi: https://doi.org/10.21105/joss.05337 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4388670873 + title: A Bayesian alternative for Aoristic analyses in archaeology + display_name: A Bayesian alternative for Aoristic analyses in archaeology + author: + - ~ + ab: Aoristic analysis is often used to handle chronological uncertainties of datasets + where scientific dates (e.g. 14C, OSL, etc.) are not available, and observations + are described by association to archaeological periods or phases. While several + advances have been made over the last two decades, the basic principle of this + approach remains fundamentally the same. Temporal windows of analyses are first + divided into regularly sized time-blocks and probability weight is assigned to + each of these for every observation. Weights are then aggregated by time-block, + and the resulting vector of summed probabilities is interpreted as a curve representing + changes in the intensity over time of a particular phenomenon. This paper reviews + the basic principles and assumptions of aoristic analyses in archaeology, highlighting + several issues with its application and interpretation and advocating for a Bayesian + alternative implemented via baorista, a new package written in R statistical computing + language. The robustness of the proposed solution is evaluated through a series + of experiments based on simulated datasets, which showcase key advantages over + aoristic analysis. Two specific solutions are considered, a parametric approach + where data are fitted to specific growth models and a non-parametric approach + that allows a visualisation of the changing frequencies of events that account + for sampling error and the peculiarities of archaeological periodisation. + publication_date: '2023-11-13' + so: .na.character + so_id: .na.character + host_organization: .na.character + issn_l: .na.character + url: https://doi.org/10.31219/osf.io/98qkx + pdf_url: https://osf.io/98qkx/download + license: .na.character + version: submittedVersion + first_page: .na.character + last_page: .na.character + volume: .na.character + issue: .na.character + is_oa: yes + is_oa_anywhere: yes + oa_status: green + oa_url: https://osf.io/98qkx/download + any_repository_has_fulltext: yes + language: en + grants: .na + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4388670873 + ids: + - ~ + doi: https://doi.org/10.31219/osf.io/98qkx + type: preprint + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +khroma: +- id: https://openalex.org/W4392712976 + title: How Does the Southern Annular Mode Control Surface Melt in East Antarctica? + display_name: How Does the Southern Annular Mode Control Surface Melt in East Antarctica? + author: + - ~ + ab: Abstract Surface melt in East Antarctica is strongly correlated with the Southern + Annular Mode (SAM) index, but the spatiotemporal variability of the relationship, + and the physical processes responsible for it, have not been examined. Here, using + melt flux estimates and climate variables from the RACMO2.3p3 regional climate + model, we show that a decreasing SAM index is associated with increased melt in + Dronning Maud Land primarily owing to reduced precipitation and greater absorption + of solar radiation. Conversely, in Wilkes Land, a decreasing SAM index corresponds + to increased melt because of greater incoming longwave radiation from a warmer + atmosphere. We also demonstrate that SAM‐melt correlations are strongest in December + as the melt season develops, and that the SAM’s influence on peak melt intensities + in January occurs indirectly through the snowmelt‐albedo feedback. Future work + must account for such variability in the physical processes underlying the SAM‐melt + relationship to reduce uncertainty in surface melt projections. + publication_date: '2024-03-11' + so: Geophysical Research Letters + so_id: https://openalex.org/S36624081 + host_organization: American Geophysical Union + issn_l: 0094-8276 + url: https://doi.org/10.1029/2023gl105475 + pdf_url: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1029/2023GL105475 + license: cc-by + version: publishedVersion + first_page: .na.character + last_page: .na.character + volume: '51' + issue: '6' + is_oa: yes + is_oa_anywhere: yes + oa_status: gold + oa_url: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1029/2023GL105475 + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 1 + counts_by_year: + - ~ + publication_year: 2024 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4392712976 + ids: + - ~ + doi: https://doi.org/10.1029/2023gl105475 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4401182215 + title: Genome-wide local ancestry and the functional consequences of admixture in + African and European cattle populations + display_name: Genome-wide local ancestry and the functional consequences of admixture + in African and European cattle populations + author: + - ~ + ab: Abstract Bos taurus (taurine) and Bos + indicus (indicine) cattle diverged at least 150,000 years ago and, since + that time, substantial genomic differences have evolved between the two lineages. + During the last two millennia, genetic exchange in Africa has resulted in a complex + tapestry of taurine-indicine ancestry, with most cattle populations exhibiting + varying levels of admixture. Similarly, there are several Southern European cattle + populations that also show evidence for historical gene flow from indicine cattle, + the highest levels of which are found in the Central Italian White breeds. Here + we use two different software tools (MOSAIC and ELAI) for local ancestry inference + (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African + and Italian cattle populations and obtained broadly similar results despite critical + differences in the two LAI methodologies used. Our analyses identified genomic + regions with elevated levels of retained or introgressed ancestry from the African + taurine, European taurine, Asian indicine lineages. Functional enrichment of genes + underlying these ancestry peaks highlighted biological processes relating to immunobiology + and olfaction, some of which may relate to differing susceptibilities to infectious + diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. + Notably, for retained African taurine ancestry in admixed trypanotolerant cattle + we observed enrichment of genes associated with haemoglobin and oxygen transport. + This may reflect positive selection of genomic variants that enhance control of + severe anaemia, a debilitating feature of trypanosomiasis disease, which severely + constrains cattle agriculture across much of sub-Saharan Africa. + publication_date: '2024-07-31' + so: Research Square (Research Square) + so_id: https://openalex.org/S4306402450 + host_organization: Research Square (United States) + issn_l: .na.character + url: https://doi.org/10.21203/rs.3.rs-4622059/v1 + pdf_url: https://www.researchsquare.com/article/rs-4622059/latest.pdf + license: cc-by + version: submittedVersion + first_page: .na.character + last_page: .na.character + volume: .na.character + issue: .na.character + is_oa: yes + is_oa_anywhere: yes + oa_status: green + oa_url: https://www.researchsquare.com/article/rs-4622059/latest.pdf + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2024 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4401182215 + ids: + - ~ + doi: https://doi.org/10.21203/rs.3.rs-4622059/v1 + type: preprint + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4308147631 + title: Aerosolized aqueous dust extracts collected near a drying lake trigger acute + neutrophilic pulmonary inflammation reminiscent of microbial innate immune ligands + display_name: Aerosolized aqueous dust extracts collected near a drying lake trigger + acute neutrophilic pulmonary inflammation reminiscent of microbial innate immune + ligands + author: + - ~ + ab: A high incidence of asthma is prevalent among residents near the Salton Sea, + a large inland terminal lake in southern California. This arid region has high + levels of ambient particulate matter (PM); yet while high PM levels are often + associated with asthma in many environments, it is possible that the rapidly retreating + lake, and exposed playa or lakebed, may contribute components with a specific + role in promoting asthma symptoms.Our hypothesis is that asthma may be higher + in residents closest to the Salton Sea due to chronic exposures to playa dust. + Playa emissions may be concentrating dissolved material from the lake, with microbial + components capable of inducing pulmonary innate immune responses. To test this + hypothesis, we used a mouse model of aerosol exposures to assess the effects of + playa dust.From dust collected around the Salton Sea region, aqueous extracts + were used to generate aerosols, which were injected into an environmental chamber + for mouse exposure studies. We compared the effects of exposure to Salton Sea + aerosols, as well as to known immunostimulatory reference materials. Acute 48-h + and chronic 7-day exposures were compared, with lungs analyzed for inflammatory + cell recruitment and gene expression.Dust from sites nearest to the Salton Sea + triggered lung neutrophil inflammation that was stronger at 48-h but reduced at + 7-days. This acute inflammatory profile and kinetics resembled the response to + innate immune ligands LTA and LPS while distinct from the classic allergic response + to Alternaria.Lung inflammatory responses to Salton Sea dusts are similar to acute + innate immune responses, raising the possibility that microbial components are + entrained in the dust, promoting inflammation. This effect highlights the health + risks at drying terminal lakes from inflammatory components in dust emissions + from exposed lakebed. + publication_date: '2022-11-02' + so: The Science of The Total Environment + so_id: https://openalex.org/S86852077 + host_organization: Elsevier BV + issn_l: 0048-9697 + url: https://doi.org/10.1016/j.scitotenv.2022.159882 + pdf_url: .na.character + license: cc-by + version: publishedVersion + first_page: '159882' + last_page: '159882' + volume: '858' + issue: .na.character + is_oa: yes + is_oa_anywhere: yes + oa_status: hybrid + oa_url: https://doi.org/10.1016/j.scitotenv.2022.159882 + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 2 + counts_by_year: + - ~ + publication_year: 2022 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4308147631 + ids: + - ~ + doi: https://doi.org/10.1016/j.scitotenv.2022.159882 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4297851717 + title: 'Aerosolized Desert Dusts Collected Near a Drying Lake and Pulmonary Inflammation + in Mice: Implications for Environmental Exposures and Asthma' + display_name: 'Aerosolized Desert Dusts Collected Near a Drying Lake and Pulmonary + Inflammation in Mice: Implications for Environmental Exposures and Asthma' + author: + - ~ + ab: Abstract Background A high incidence of asthma is prevalent among residents + near the Salton Sea, a large inland terminal lake in southern California. This + arid region has high levels of ambient particulate matter (PM); yet while high + PM levels are often associated with asthma in many environments, it is possible + that the rapidly retreating lake may contribute components with a specific role + in promoting asthma symptoms. Objectives Our hypothesis is that asthma may be + higher in residents closest to the Salton Sea due to chronic exposures to playa + dust. Playa emissions may be concentrating dissolved material from the lake, with + microbial components capable of inducing pulmonary innate immune responses. Such + inflammatory responses may contribute to the development of asthma-like symptoms + in residents. To test this hypothesis, we used a mouse model of aerosol exposures + to assess the effects of playa dust. Methods From dust collected around the Salton + Sea region, aqueous extracts were used to generate aerosols, which were injected + into an environmental chamber for mouse exposure studies. We compared the effects + of exposure to Salton Sea aerosols, as well as to known immunostimulatory reference + materials. Acute 48-hour and chronic 7-day exposures were compared, with lungs + analyzed for inflammatory cell recruitment and gene expression. Results Dust from + sites nearest to the Salton Sea triggered lung neutrophil inflammation that was + stronger at 48-hours but reduced at 7-days. This acute inflammatory profile and + kinetics resembled the response to innate immune ligands LTA and LPS while distinct + from the classic allergic response to Alternaria . Conclusion Lung inflammatory + responses to Salton Sea dusts are similar to acute innate immune responses, raising + the possibility that microbial components are entrained in the dust, promoting + inflammation. This effect highlights the health risks at drying terminal lakes + from inflammatory components in dust emissions from exposed lakebed. + publication_date: '2022-09-09' + so: bioRxiv (Cold Spring Harbor Laboratory) + so_id: https://openalex.org/S4306402567 + host_organization: Cold Spring Harbor Laboratory + issn_l: .na.character + url: https://doi.org/10.1101/2022.09.07.506987 + pdf_url: https://www.biorxiv.org/content/biorxiv/early/2022/09/09/2022.09.07.506987.full.pdf + license: .na.character + version: submittedVersion + first_page: .na.character + last_page: .na.character + volume: .na.character + issue: .na.character + is_oa: yes + is_oa_anywhere: yes + oa_status: green + oa_url: https://www.biorxiv.org/content/biorxiv/early/2022/09/09/2022.09.07.506987.full.pdf + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2022 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4297851717 + ids: + - ~ + doi: https://doi.org/10.1101/2022.09.07.506987 + type: preprint + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +tabula: +- id: https://openalex.org/W4323320164 + title: Divergent vertebral formulae shape the evolution of axial complexity in mammals + display_name: Divergent vertebral formulae shape the evolution of axial complexity + in mammals + author: + - ~ + ab: Complexity, defined as the number of parts and their degree of differentiation, + is a poorly explored aspect of macroevolutionary dynamics. The maximum anatomical + complexity of organisms has undoubtedly increased through evolutionary time. However, + it is unclear whether this increase is a purely diffusive process or whether it + is at least partly driven, occurring in parallel in most or many lineages and + with increases in the minima as well as the means. Highly differentiated and serially + repeated structures, such as vertebrae, are useful systems with which to investigate + these patterns. We focus on the serial differentiation of the vertebral column + in 1,136 extant mammal species, using two indices that quantify complexity as + the numerical richness and proportional distribution of vertebrae across presacral + regions and a third expressing the ratio between thoracic and lumbar vertebrae. + We address three questions. First, we ask whether the distribution of complexity + values in major mammal groups is similar or whether clades have specific signatures + associated with their ecology. Second, we ask whether changes in complexity throughout + the phylogeny are biased towards increases and whether there is evidence of driven + trends. Third, we ask whether evolutionary shifts in complexity depart from a + uniform Brownian motion model. Vertebral counts, but not complexity indices, differ + significantly between major groups and exhibit greater within-group variation + than recognized hitherto. We find strong evidence of a trend towards increasing + complexity, where higher values propagate further increases in descendant lineages. + Several increases are inferred to have coincided with major ecological or environmental + shifts. We find support for multiple-rate models of evolution for all complexity + metrics, suggesting that increases in complexity occurred in stepwise shifts, + with evidence for widespread episodes of recent rapid divergence. Different subclades + evolve more complex vertebral columns in different configurations and probably + under different selective pressures and constraints, with widespread convergence + on the same formulae. Further work should therefore focus on the ecological relevance + of differences in complexity and a more detailed understanding of historical patterns. + publication_date: '2023-03-06' + so: Nature Ecology & Evolution + so_id: https://openalex.org/S2764884935 + host_organization: Nature Portfolio + issn_l: 2397-334X + url: https://doi.org/10.1038/s41559-023-01982-5 + pdf_url: https://www.nature.com/articles/s41559-023-01982-5.pdf + license: cc-by + version: publishedVersion + first_page: '367' + last_page: '381' + volume: '7' + issue: '3' + is_oa: yes + is_oa_anywhere: yes + oa_status: hybrid + oa_url: https://www.nature.com/articles/s41559-023-01982-5.pdf + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 9 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4323320164 + ids: + - ~ + doi: https://doi.org/10.1038/s41559-023-01982-5 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4385603962 + title: 'Diversity of diversity indices: Which diversity measure is better?' + display_name: 'Diversity of diversity indices: Which diversity measure is better?' + author: + - ~ + ab: 'The article evaluates the dependence of the most common indices of species + diversity on sample size and determines their ability to differentiate between + different types of ecosystems, with a special emphasis on discriminating between + natural and anthropogenic ecosystems. An approach to adjusting the indices to + reduce their dependence on sample size was also proposed. The study was conducted + in seven types of ecosystems: four were natural and three were anthropogenically + transformed. Samples of soil animals were selected in 2011–2013 and 2021 using + the same methods. A total of 20,518 soil animal specimens belonging to 202 species + were collected in all study locations. The null alternative was generated by randomly + selecting samples containing 2, 3, ..., 110 soil animals from the combined soil + animal sample. For each gradation of sample size, 200 sample variants were formed. + The density of soil macrofauna in natural ecosystems ranged from 3.6 ± 1.5 to + 15.2 ± 6.9 specimens per sample, and in artificial ecosystems – from 13.2 ± 7.6 + to 21.0 ± 11.9 specimens per sample. The number of species ranged from 22–80 species, + and in artificial ecosystems it was 38–99 species. Indicators of species diversity + correlated with each other. A high level of correlation was observed between indicators + within groups of indices: indices of species richness and indices of heterogeneity + and evenness. Fisher’s log-series alpha and the fundamental parameter of biodiversity + were highly correlated with each other, as well as with the Margalef, species + richness, and Chao’s species abundance indices. The log-normal distribution best + describes the dominance patterns in terms of abundance in the natural ecosystems, + and the Zipf-Mandelbrot distribution best describes the dominance patterns in + terms of abundance in the artificial ecosystems. Diversity indices were ordered + in the space of two dimensions, one explaining the variation between ecosystems + and the other depending on sample size. The ordering of the traditional indices + showed that there is a vacancy for the best index in the sense that such an index + should best explain differences between ecosystems and differences between natural + and artificial ecosystems. It should also be independent of sample size. The Simpson + heterogeneity index and the Simpson evenness index were the best of the traditional + indices, but they did not explain differences between ecosystems very well, especially + when it came to distinguishing between natural and artificial ecosystems. The + Margalef index, which is supposed to be independent of sample size, on the other + hand, showed a very high level of dependence. Such a dependence was also found + for the Menhinick index, though to a lesser extent. Obviously, size dependence + negatively affects the differential ability of the indices. The corrected indices + of species richness and the Shannon index are practically independent of sample + size and have a greater ability to differentiate ecosystems by the level of diversity, + with natural ecosystems characterized by consistently higher values of the corrected + indices than artificial ecosystems. The dependence on the sample size makes indices + from different ecosystems practically incomparable, which makes their use meaningless. + Even minor differences in sample size can lead to significant deviations in the + values of diversity indices. The application of the Michaelis-Menten model allowed + us to suggest a method of correction of species richness indices and the Shannon + index. After the correction, the indices are practically independent of the sample + size, and their differential ability to characterize individual ecosystems and + the level of anthropogenic transformation increases significantly.' + publication_date: '2023-05-02' + so: Biosystems Diversity + so_id: https://openalex.org/S4306504439 + host_organization: Oles Honchar Dnipro National University + issn_l: 2519-8513 + url: https://doi.org/10.15421/012314 + pdf_url: https://ecology.dp.ua/index.php/ECO/article/download/1193/1143 + license: cc-by + version: publishedVersion + first_page: '131' + last_page: '146' + volume: '31' + issue: '2' + is_oa: yes + is_oa_anywhere: yes + oa_status: gold + oa_url: https://ecology.dp.ua/index.php/ECO/article/download/1193/1143 + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 4 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4385603962 + ids: + - ~ + doi: https://doi.org/10.15421/012314 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4288748945 + title: 'Archeofrag: an R package for Refitting and Spatial Analysis in Archaeology' + display_name: 'Archeofrag: an R package for Refitting and Spatial Analysis in Archaeology' + author: + - ~ + ab: 'Distinguishing between spatial entities is fundamental in archaeology since + archaeologists deal with spatial phenomena at multiple scales of analysis.During + an excavation, objects are discovered within various types of spatial units e.g., + stratigraphic layers, pits, hearths and houses.Spatial units are far from being + raw data, and the identification and determination of their boundaries is the + result of conjoint lines and methods of investigation, to name only a few: field + observations, geoarchaeology, sedimentology, and the study of archaeological "refits".Refitting + fragments belonged to the same object at some moment in the past.More precisely, + archaeologists deduce former connection relationships from the symmetry and the + possibility of contact of significantly large surface areas from two fragments, + which can be physically adjusted (the fragments "refit").Here, "connection" is + used as a shorthand to refer to the connection relationship that existed in the + past between two areas of an object before they were broken into fragments.Archaeological + refitting analysis has several aims:' + publication_date: '2022-07-30' + so: The Journal of Open Source Software + so_id: https://openalex.org/S4210214273 + host_organization: Open Journals + issn_l: 2475-9066 + url: https://doi.org/10.21105/joss.04335 + pdf_url: https://joss.theoj.org/papers/10.21105/joss.04335.pdf + license: cc-by + version: publishedVersion + first_page: '4335' + last_page: '4335' + volume: '7' + issue: '75' + is_oa: yes + is_oa_anywhere: yes + oa_status: diamond + oa_url: https://joss.theoj.org/papers/10.21105/joss.04335.pdf + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 7 + counts_by_year: + - ~ + publication_year: 2022 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4288748945 + ids: + - ~ + doi: https://doi.org/10.21105/joss.04335 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W2944104845 + title: Characterizing the second wave of fish and invertebrate colonization of an + offshore petroleum platform + display_name: Characterizing the second wave of fish and invertebrate colonization + of an offshore petroleum platform + author: + - ~ + ab: Abstract Offshore Oil and Gas (O&G) infrastructure affords structurally + complex hard substrata in otherwise featurless areas of the seafloor. Opportunistically + collected industrial ROV imagery was used to investigate the colonization of a + petroleum platform in the North Sea 1–2 years following installation. Compared + to pre-construction communities and pioneering colonizers, we documented 48 additional + taxa, including a rare sighting of a pompano (Trachinotus ovatus). The second + wave of motile colonizers presented greater diversity than the pioneering community. + Occurrence of species became more even over the 2 years following installation, + with species occurring in more comparable abundances. No on-jacket sessile taxa + were recorded during first-wave investigations; however, 17 sessile species were + detected after 1 year (decreasing to 16 after 2). Motile species were found to + favour structurally complex sections of the jacket (e.g. mudmat), while sessile + organisms favoured exposed elements. Evidence of on-jacket reproduction was found + for two commercially important invertebrate species - common whelk (Buccinum undatum) + and European squid (Loligo vulgaris). Moreover, abundance of larvae-producing + species experience an 8.5-fold increase over a 2-year period compared to baseline + communities. These findings may have implications for decommissioning and resource-management + strategies, suggesting that a case-by-case reviewing approach should be favoured + over the most common “one size fits all”. + publication_date: '2020-12-13' + so: ICES Journal of Marine Science + so_id: https://openalex.org/S200038611 + host_organization: Oxford University Press + issn_l: 1054-3139 + url: https://doi.org/10.1093/icesjms/fsaa245 + pdf_url: .na.character + license: .na.character + version: .na.character + first_page: '1131' + last_page: '1145' + volume: '78' + issue: '3' + is_oa: no + is_oa_anywhere: no + oa_status: closed + oa_url: .na.character + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 12 + counts_by_year: + - ~ + publication_year: 2020 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W2944104845 + ids: + - ~ + doi: https://doi.org/10.1093/icesjms/fsaa245 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4400609907 + title: Differential amino acid usage leads to ubiquitous edge effect in proteomes + across domains of life that can be explained by amino acid secondary structure + propensities + display_name: Differential amino acid usage leads to ubiquitous edge effect in proteomes + across domains of life that can be explained by amino acid secondary structure + propensities + author: + - ~ + ab: Abstract Background Amino acids are the building blocks of proteins and enzymes, + which are pivotal for life on Earth. Amino acid usage provides critical insights + into the functional constraints acting on proteins and illuminates molecular mechanisms + underpinning traits. Despite this, we have limited knowledge of the genome-wide + signatures of amino acid usage across domains of life, precluding new genome and + proteome patterns to being discovered. Results Here, we analysed the proteomes + of 5,590 species across four domains of life and found that only a small subset + of amino acids is most and least frequently used across proteomes. This creates + a ubiquitous ‘edge effect’ on amino acid usage diversity by rank that arises from + protein secondary structural constrains. This edge effect was not driven by the + evolutionary chronology of amino acids, showing that functional rather than evolutionary + constrains shape amino acid usage in the proteome. We also tested contemporary + hypotheses about similarities in amino acid usage profiles and the relationship + between amino acid usage and growth temperature, and found that, contrary to previous + beliefs, amino acid usage varies across domains of life and temperature only weakly + contributes to variance in amino acid usage. Conclusion We have described a novel + and ubiquitous pattern of amino acid usage signature across genomes, which reveals + how structural constrains shape amino acid usage at the proteome level. This can + ultimately influence the way in which we probe deep evolutionary relationships + of protein families across the tree of life and engineer biology in synthetic + biology. + publication_date: '2024-07-12' + so: .na.character + so_id: .na.character + host_organization: .na.character + issn_l: .na.character + url: https://doi.org/10.1101/2024.07.12.599492 + pdf_url: .na.character + license: .na.character + version: submittedVersion + first_page: .na.character + last_page: .na.character + volume: .na.character + issue: .na.character + is_oa: no + is_oa_anywhere: no + oa_status: closed + oa_url: .na.character + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2024 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4400609907 + ids: + - ~ + doi: https://doi.org/10.1101/2024.07.12.599492 + type: preprint + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W3217092927 + title: 'Distribution of chigger mites (Acari: Trombiculidae) over hosts, parasitopes, + collection localities, and seasons in northern Iran' + display_name: 'Distribution of chigger mites (Acari: Trombiculidae) over hosts, + parasitopes, collection localities, and seasons in northern Iran' + author: + - ~ + ab: We studied the distribution of chigger mite species over mammal hosts, attachment + sites on the host body, habitats, and seasons in Iran. The study was based on + 2155 specimens of 36 chigger species collected from 10 species of Muridae, Cricetidae, + and Soricidae across six provinces of northern Iran. A high level of mixed infestation + by chiggers was recorded-76% of hosts parasitized by chiggers were infested by + more than one (2-8) species. Statistically significant differences in the preference + for anterior and posterior parts of the host body were found. Three species-Neotrombicula + lubrica, N. delijani, and Cheladonta firdousii-preferred the posterior part of + the host body; 12 species were characterized by the occurrence in the anterior + part and differed from one another by the frequency of presence in the posterior + part. One species, Hirsutiella alpina, was found only in the anterior part of + the host body (inside the ears of rodents). The most diverse chigger fauna was + on the fringe of Golestan National Park (species richness = 21, Shannon-Wiener + index = 2.823). The chigger fauna of the high-mountain localities on the Alborz + Range was the least diverse (species richness = 16, Shannon-Wiener index = 2.439). + The seasonal aspect of activity was evident for Neotrombicula elegans, which exposed + the autumn-winter period of the occurrence on hosts, and N. vernalis, with the + winter-spring peak of abundance. + publication_date: '2021-11-24' + so: Experimental and Applied Acarology + so_id: https://openalex.org/S150156781 + host_organization: Springer Science+Business Media + issn_l: 0168-8162 + url: https://doi.org/10.1007/s10493-021-00680-w + pdf_url: .na.character + license: .na.character + version: .na.character + first_page: '21' + last_page: '47' + volume: '86' + issue: '1' + is_oa: no + is_oa_anywhere: no + oa_status: closed + oa_url: .na.character + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 7 + counts_by_year: + - ~ + publication_year: 2021 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W3217092927 + ids: + - ~ + doi: https://doi.org/10.1007/s10493-021-00680-w + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4396939306 + title: Ecosystem functional types of the circumpolar Arctic tundra based on the + seasonal dynamics of vegetation productivity + display_name: Ecosystem functional types of the circumpolar Arctic tundra based + on the seasonal dynamics of vegetation productivity + author: + - ~ + ab: Abstract Biodiversity, when viewed through the combined lenses of compositional, + structural, and functional attributes, provides for a holistic understanding of + the complexities found within community assemblages and ecosystems. However, advancement + in our understanding of how ecosystem functional diversity interacts with structural + and compositional diversity metrics is lacking, in part because universally applied + methodologies to derive ecosystem functional classifications are still under development + and vary widely across scales, extents and biomes. This study presents a methodology + to construct ecosystem functional types (EFTs), or areas of the land surface that + function similarly, using the MODIS NDVI record, for the terrestrial circumpolar + Arctic. EFTs were derived from the seasonal dynamics of NDVI, over the Arctic + tundra at 250 m resolution and compared to bioclimate subzones and to structurally + and compositionally defined vegetation units of the Circumpolar Arctic Vegetation + Map (CAVM). Correspondence analyses of CAVM EFTs to previously delineated CAVM + bioclimatic subzones, physiognomic (vegetation) units and floristic provinces + revealed a general congruence, indicating convergence across composition, structure, + and function; yet also demonstrated substantial functional variability even within + bioclimate subzones and vegetation units. Strong latitudinal gradients in ecosystem + function are present, with EFT richness ranging from low (34) in northernmost + regions to high (45) in southernmost regions. Locally, the mountainous regions + of northern Alaska, and eastern and western Siberia had high spatial variability + in ecosystem functioning. Aside from these generalities, we found that EFTs varied + widely within individual mapped vegetation units, successfully capturing the functional + dimension of biodiversity across the circumpolar Arctic tundra. + publication_date: '2024-05-15' + so: Environmental Research Ecology + so_id: https://openalex.org/S4387280329 + host_organization: IOP Publishing + issn_l: 2752-664X + url: https://doi.org/10.1088/2752-664x/ad4beb + pdf_url: https://iopscience.iop.org/article/10.1088/2752-664X/ad4beb/pdf + license: cc-by + version: publishedVersion + first_page: '025003' + last_page: '025003' + volume: '3' + issue: '2' + is_oa: yes + is_oa_anywhere: yes + oa_status: diamond + oa_url: https://iopscience.iop.org/article/10.1088/2752-664X/ad4beb/pdf + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2024 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4396939306 + ids: + - ~ + doi: https://doi.org/10.1088/2752-664x/ad4beb + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4401818357 + title: Object Recognition from Scientific Document Based on Compartment and Text + Blocks Refinement Framework + display_name: Object Recognition from Scientific Document Based on Compartment and + Text Blocks Refinement Framework + author: + - ~ + ab: .na.character + publication_date: '2024-08-23' + so: SN Computer Science + so_id: https://openalex.org/S4210174798 + host_organization: Springer Nature + issn_l: 2661-8907 + url: https://doi.org/10.1007/s42979-024-03130-7 + pdf_url: .na.character + license: .na.character + version: .na.character + first_page: .na.character + last_page: .na.character + volume: '5' + issue: '7' + is_oa: no + is_oa_anywhere: no + oa_status: closed + oa_url: .na.character + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2024 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4401818357 + ids: + - ~ + doi: https://doi.org/10.1007/s42979-024-03130-7 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4388916291 + title: A Text Block Refinement Framework For Text Classification and Object Recognition + From Academic Articles + display_name: A Text Block Refinement Framework For Text Classification and Object + Recognition From Academic Articles + author: + - ~ + ab: With the widespread use of the internet, it has become increasingly crucial + to extract specific information from vast amounts of academic articles efficiently. + Data mining techniques are generally employed to solve this issue. However, data + mining for academic articles is challenging since it requires automatically extracting + specific patterns in complex and unstructured layout documents. Current data mining + methods for academic articles employ rule-based (RB) or machine learning (ML) + approaches. However, using rule-based methods incurs a high coding cost for complex + typesetting articles. On the other hand, simply using machine learning methods + requires annotation work for complex content types within the paper, which can + be costly. Furthermore, only using machine learning can lead to cases where patterns + easily recognized by rule-based methods are mistakenly extracted. To overcome + these issues, from the perspective of analyzing the standard layout and typesetting + used in the specified publication, we emphasize implementing specific methods + for specific characteristics in academic articles. We have developed a novel Text + Block Refinement Framework (TBRF), a machine learning and rule-based scheme hybrid. + We used the well-known ACL proceeding articles as experimental data for the validation + experiment. The experiment shows that our approach achieved over 95% classification + accuracy and 90% detection accuracy for tables and figures. + publication_date: '2023-09-20' + so: .na.character + so_id: .na.character + host_organization: .na.character + issn_l: .na.character + url: https://doi.org/10.1109/inista59065.2023.10310320 + pdf_url: .na.character + license: .na.character + version: .na.character + first_page: .na.character + last_page: .na.character + volume: .na.character + issue: .na.character + is_oa: no + is_oa_anywhere: yes + oa_status: green + oa_url: https://arxiv.org/pdf/2305.17401 + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 1 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4388916291 + ids: + - ~ + doi: https://doi.org/10.1109/inista59065.2023.10310320 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4362560483 + title: Seasonal Variability of Marine Fish Diversity in Relation to Water Quality + of East Midnapore Coast of West Bengal, India + display_name: Seasonal Variability of Marine Fish Diversity in Relation to Water + Quality of East Midnapore Coast of West Bengal, India + author: + - ~ + ab: Marine fishes are one of the important factors in stabilizing the local aquatic + ecosystem and regulating the nutritional socio-economy of local fisher folks. + The recent increases in anthropogenic activity, pollution and overfishing have + led to the decline of marine fish species richness and their local aquatic habitats. + In this study we sought to determine the inter-relationship between water quality, + anthropogenic activity, and fish landing stations through a 31 km stretch of the + East Midnapore coast in West Bengal, India which is known for its tourist destinations. + The study was conducted monthly on different trawler fish landing sites from Dec + 2018 to Dec 2021. During this period, we took fish samples and identified them. + We obtained water quality data regarding Sea Surface Temperature (SST), Concentration + of Chlorophyll-a (Chl-a), Turbidity, and Dissolved Oxygen (DO) in order to identify + further correlation between the water quality analysis and species diversity. + 154 numbers of commercially important marine fish species were documented. As + per the IUCN database, 13% of the total fish species fall under the red list category + and 16% of the species reveal a decreasing population trend. The availability + of those red-listed fish throughout the season has been shown in the matrix plot + to detect their gradual decrease in sighting. After analyzing the water quality + data, we found out that DO, SST, Turbidity, and Chl-a correlate with the species + richness on some sites and the water parameters are also differs during the seasons. + Both fish species richness and water quality have been affected on those fish + landing sites which have been subject to heavy anthropogenic loads. + publication_date: '2023-03-31' + so: Ocean Science Journal + so_id: https://openalex.org/S70934194 + host_organization: Springer Science+Business Media + issn_l: 1738-5261 + url: https://doi.org/10.1007/s12601-023-00107-0 + pdf_url: .na.character + license: .na.character + version: .na.character + first_page: .na.character + last_page: .na.character + volume: '58' + issue: '2' + is_oa: no + is_oa_anywhere: yes + oa_status: green + oa_url: https://www.biorxiv.org/content/biorxiv/early/2022/06/13/2022.06.11.495752.full.pdf + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 1 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4362560483 + ids: + - ~ + doi: https://doi.org/10.1007/s12601-023-00107-0 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W3165485472 + title: datplot + display_name: datplot + author: + - ~ + ab: This article introduces datplot, an R package designed to prepare chronological + data for visualization, focusing on the treatment of objects dated to overlapping + periods of time. Datplot is suitable for all disciplines in which scientists long + for a synoptic method that enables the visualization of the chronology of a collection + of heterogeneously dated objects. It is especially helpful for visualizing trends + in object assemblages over long periods of time—for example, the development of + pottery styles—and it can also assist in the dating of stratigraphy. As both authors + come from the field of classical archaeology, the examples and case study demonstrating + the functionality of the package analyze classical materials. In particular, we + focus on presenting an assemblage of epigraphic evidence from Bithynia (northwestern + Turkey), with a microregional focal point in the territory of Nicaea (modern Iznik). + In the article, we present the internal methodology of datplot and the process + of preparing a dataset of categorically and numerically dated objects. We demonstrate + visualizing the data prepared by datplot using kernel density estimation and compare + the outcome with more established methods such as histograms and line graphs. + publication_date: '2021-05-25' + so: Advances in Archaeological Practice + so_id: https://openalex.org/S2764497410 + host_organization: Cambridge University Press + issn_l: 2326-3768 + url: https://doi.org/10.1017/aap.2021.8 + pdf_url: https://www.cambridge.org/core/services/aop-cambridge-core/content/view/C1A71689C87D911C201EAE658D4AA90A/S2326376821000085a.pdf/div-class-title-datplot-div.pdf + license: cc-by-nc-sa + version: publishedVersion + first_page: '288' + last_page: '298' + volume: '9' + issue: '4' + is_oa: yes + is_oa_anywhere: yes + oa_status: hybrid + oa_url: https://www.cambridge.org/core/services/aop-cambridge-core/content/view/C1A71689C87D911C201EAE658D4AA90A/S2326376821000085a.pdf/div-class-title-datplot-div.pdf + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 2 + counts_by_year: + - ~ + publication_year: 2021 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W3165485472 + ids: + - ~ + doi: https://doi.org/10.1017/aap.2021.8 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4295991218 + title: 'The oases of Baja California Peninsula: overlooked hotspots for wild bees' + display_name: 'The oases of Baja California Peninsula: overlooked hotspots for wild + bees' + author: + - ~ + ab: .na.character + publication_date: '2022-09-14' + so: Journal of Insect Conservation + so_id: https://openalex.org/S92632373 + host_organization: Springer Science+Business Media + issn_l: 1366-638X + url: https://doi.org/10.1007/s10841-022-00432-0 + pdf_url: .na.character + license: .na.character + version: .na.character + first_page: '117' + last_page: '128' + volume: '27' + issue: '1' + is_oa: no + is_oa_anywhere: no + oa_status: closed + oa_url: .na.character + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 1 + counts_by_year: + - ~ + publication_year: 2022 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4295991218 + ids: + - ~ + doi: https://doi.org/10.1007/s10841-022-00432-0 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4317772458 + title: Changes in the Freshwater Mussels of the Missouri Portion of the Ozark Highlands + Eleven Point River, 1982–1985 and 2012–2019 + display_name: Changes in the Freshwater Mussels of the Missouri Portion of the Ozark + Highlands Eleven Point River, 1982–1985 and 2012–2019 + author: + - ~ + ab: Freshwater mussels are important components of aquatic systems, where they cycle + nutrients, stabilize streambeds, increase niche habitats, and are sources of food + for mammals, birds, fish, and aquatic invertebrates. The biogeographically distinct + Ozark Highlands is one of the oldest terrestrial regions on the planet and is + home to over 200 endemic species including freshwater mussels. Key to the conservation + and management of this mussel fauna is documenting their distribution and determining + if any changes have occurred. In this study, our objectives were to document the + diversity and distribution of the mussel fauna of the Missouri portion of the + Eleven Point River, a National Wild and Scenic River, and determine if any changes + had occurred over a 25+ yr period. During 1982–1985 and 2012–2019 we surveyed + 29 locations, including 12 surveyed during both periods, in summer to early fall, + during low flow conditions with timed visual and tactile searches. We calculated + metrics to measure the status, composition, and abundance of the mussel community, + and examined the rate populations were experiencing extirpation or colonization. + Historically, 21 freshwater mussel species were known from Eleven Point River; + 20 were observed live or as shell material in the present surveys. During both + surveys, the Eleven Point River basin was dominated by members of the Lampsilini, + which exhibit periodic life history strategies. We detected significant declines + in the number of live individuals, CPUE, and richness at the 12 resurveyed locations. + Freshwater mussel species in the Eleven Point River are being extirpated at a + significantly higher rate than colonizing areas of the Eleven Point River. Causes + for this decline remain unknown. + publication_date: '2023-01-17' + so: American Malacological Bulletin + so_id: https://openalex.org/S32133967 + host_organization: .na.character + issn_l: 0740-2783 + url: https://doi.org/10.4003/006.039.0110 + pdf_url: .na.character + license: .na.character + version: .na.character + first_page: .na.character + last_page: .na.character + volume: '39' + issue: '1' + is_oa: no + is_oa_anywhere: no + oa_status: closed + oa_url: .na.character + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4317772458 + ids: + - ~ + doi: https://doi.org/10.4003/006.039.0110 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4323543598 + title: 'The metazoan parasite communities of flounders as indicators of chemical + pollution in the southern Gulf of Mexico: taxonomic and trait-based approaches' + display_name: 'The metazoan parasite communities of flounders as indicators of chemical + pollution in the southern Gulf of Mexico: taxonomic and trait-based approaches' + author: + - ~ + ab: 'Abstract Metazoan parasite species composition changes with an increase in + geographical distance, but not their functional traits. We compared the performance + of the taxonomy and functional traits of metazoan parasites as bioindicators of + chemical pollution along the continental shelf of the South Gulf of Mexico (sGOM). + Parasites were obtained from Syacium gunteri and Syacium papillosum , together + with hydrocarbons, heavy metals and physicochemical variables from water and sediments + during 12 oceanographic cruises. We compared regions without oil extraction: Veracruz-Tamaulipas + (VT) and Yucatan shelf (YS) and one with it, north-western end of YS to Coatzacoalcos, + Veracruz (NYV). In addition to taxonomy, the trait-based approach community-weighted + means (CWM) was performed. Species richness was compared between regions using + rarefaction curves, and the taxonomic and trait composition between regions were + compared using multivariate analyses. The relationships between taxonomy, traits + and environmental variables were tested using BIOENV. We identified 57 species + and body tegument, transmission, feeding mode, life stage and attachment organs + as informative traits. By rarefaction, VT and YS had higher species richness than + NYV for both hosts, but there were questionable values due to the small fish sample + size. Except for YS, significant parasite community variability was detected by + PERMANOVA using taxonomy and CWM for all regions, hosts and interactions. The + same group of larval species was detected by SIMPER for regions and hosts, suggesting + low functional turnover. BIOENV showed that polyaromatic hydrocarbons explained + most of the variability. Taxonomy and functional traits produced similar explained + variance, but the latter saved time analysis and financial resources.' + publication_date: '2023-03-08' + so: Research Square (Research Square) + so_id: https://openalex.org/S4306402450 + host_organization: Research Square (United States) + issn_l: .na.character + url: https://doi.org/10.21203/rs.3.rs-2610304/v1 + pdf_url: https://www.researchsquare.com/article/rs-2610304/latest.pdf + license: cc-by + version: submittedVersion + first_page: .na.character + last_page: .na.character + volume: .na.character + issue: .na.character + is_oa: yes + is_oa_anywhere: yes + oa_status: green + oa_url: https://www.researchsquare.com/article/rs-2610304/latest.pdf + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4323543598 + ids: + - ~ + doi: https://doi.org/10.21203/rs.3.rs-2610304/v1 + type: preprint + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4360616814 + title: Changes in the Mussel Fauna of the Jacks Fork, Missouri over 35 Years and + Relationships with Species Traits + display_name: Changes in the Mussel Fauna of the Jacks Fork, Missouri over 35 Years + and Relationships with Species Traits + author: + - ~ + ab: We conducted a mussel survey of the Jacks Fork, Missouri, an Outstanding National + Resource Water, to document mussel diversity and distribution in the watershed, + to determine if changes had occurred since a previous survey in 1982, and to relate + observed changes to species traits. We surveyed mussels with timed tactile or + visual searches at 28 sites during summer from 2017 to 2019 and compared our results + with the 1982 survey. Catch per unit effort, number of live individuals, species + richness, and diversity were significantly lower in 2017–19 than in 1982. The + proportion of extirpation at the 11 resurveyed sites averaged 0.85 (range 0.50–1.00) + among species, and the proportion of colonization was 0.0 for all species. There + were no differences in the relative abundance of tribes, life-history strategies, + or species of conservation concern between the two surveys, suggesting that the + decline has occurred evenly across species, tribes, and life-history strategies. + Ten species are possibly extirpated from the basin. Causes of the mussel decline + in the Jacks Fork basin are unknown. + publication_date: '2023-03-23' + so: Freshwater Mollusk Biology and Conservation + so_id: https://openalex.org/S4210177210 + host_organization: .na.character + issn_l: 2472-2944 + url: https://doi.org/10.31931/fmbc-d-21-00012 + pdf_url: https://bioone.org/journals/freshwater-mollusk-biology-and-conservation/volume-26/issue-1/fmbc-d-21-00012/Changes-in-the-Mussel-Fauna-of-the-Jacks-Fork-Missouri/10.31931/fmbc-d-21-00012.pdf + license: .na.character + version: publishedVersion + first_page: .na.character + last_page: .na.character + volume: '26' + issue: '1' + is_oa: yes + is_oa_anywhere: yes + oa_status: gold + oa_url: https://bioone.org/journals/freshwater-mollusk-biology-and-conservation/volume-26/issue-1/fmbc-d-21-00012/Changes-in-the-Mussel-Fauna-of-the-Jacks-Fork-Missouri/10.31931/fmbc-d-21-00012.pdf + any_repository_has_fulltext: no + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4360616814 + ids: + - ~ + doi: https://doi.org/10.31931/fmbc-d-21-00012 + type: article + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ +- id: https://openalex.org/W4378770596 + title: A Framework For Refining Text Classification and Object Recognition from + Academic Articles + display_name: A Framework For Refining Text Classification and Object Recognition + from Academic Articles + author: + - ~ + ab: With the widespread use of the internet, it has become increasingly crucial + to extract specific information from vast amounts of academic articles efficiently. + Data mining techniques are generally employed to solve this issue. However, data + mining for academic articles is challenging since it requires automatically extracting + specific patterns in complex and unstructured layout documents. Current data mining + methods for academic articles employ rule-based(RB) or machine learning(ML) approaches. + However, using rule-based methods incurs a high coding cost for complex typesetting + articles. On the other hand, simply using machine learning methods requires annotation + work for complex content types within the paper, which can be costly. Furthermore, + only using machine learning can lead to cases where patterns easily recognized + by rule-based methods are mistakenly extracted. To overcome these issues, from + the perspective of analyzing the standard layout and typesetting used in the specified + publication, we emphasize implementing specific methods for specific characteristics + in academic articles. We have developed a novel Text Block Refinement Framework + (TBRF), a machine learning and rule-based scheme hybrid. We used the well-known + ACL proceeding articles as experimental data for the validation experiment. The + experiment shows that our approach achieved over 95% classification accuracy and + 90% detection accuracy for tables and figures. + publication_date: '2023-01-01' + so: arXiv (Cornell University) + so_id: https://openalex.org/S4306400194 + host_organization: Cornell University + issn_l: .na.character + url: https://arxiv.org/abs/2305.17401 + pdf_url: .na.character + license: other-oa + version: submittedVersion + first_page: .na.character + last_page: .na.character + volume: .na.character + issue: .na.character + is_oa: yes + is_oa_anywhere: yes + oa_status: green + oa_url: https://arxiv.org/abs/2305.17401 + any_repository_has_fulltext: yes + language: en + grants: + - ~ + cited_by_count: 0 + counts_by_year: + - ~ + publication_year: 2023 + cited_by_api_url: https://api.openalex.org/works?filter=cites:W4378770596 + ids: + - ~ + doi: https://doi.org/10.48550/arxiv.2305.17401 + type: preprint + referenced_works: + - ~ + related_works: + - ~ + is_paratext: no + is_retracted: no + concepts: + - ~ + topics: + - ~ + diff --git a/data/doi.csv b/data/doi.csv new file mode 100644 index 0000000..681f30a --- /dev/null +++ b/data/doi.csv @@ -0,0 +1,27 @@ +package,doi,target +aion,10.5281/zenodo.8032278,concept +aion,10.32614/cran.package.aion,CRAN +aion,10.21105/joss.06210,JOSS +alkahest,10.5281/zenodo.7081524,concept +alkahest,10.32614/cran.package.alkahest,CRAN +ananke,10.5281/zenodo.13236285,concept +arkhe,10.5281/zenodo.3526659,concept +arkhe,10.32614/cran.package.arkhe,CRAN +dimensio,10.5281/zenodo.4478530,concept +dimensio,10.32614/cran.package.dimensio,CRAN +folio,10.5281/zenodo.4476182,concept +folio,10.32614/cran.package.folio,CRAN +isopleuros,10.5281/zenodo.7940389,concept +isopleuros,10.32614/cran.package.isopleuros,CRAN +kairos,10.5281/zenodo.5653896,concept +kairos,10.32614/cran.package.kairos,CRAN +khroma,10.5281/zenodo.1472077,concept +khroma,10.32614/cran.package.khroma,CRAN +nexus,10.5281/zenodo.10225630,concept +nexus,10.32614/cran.package.nexus,CRAN +tabula,10.5281/zenodo.1489944,concept +tabula,10.32614/cran.package.tabula,CRAN +tabula,10.32614/cran.package.tabula,CRAN +tabula,10.21105/joss.01821,JOSS +tesselle,10.5281/zenodo.6500491,concept +tesselle,10.32614/cran.package.tesselle,CRAN diff --git a/index.qmd b/index.qmd index 9b12b59..8992b38 100644 --- a/index.qmd +++ b/index.qmd @@ -21,6 +21,9 @@ downloads <- read.csv(file.path("data", "downloads_monthly.csv")) downloads$package <- as.factor(downloads$package) downloads$month <- as.Date(downloads$month) +citations <- yaml::read_yaml(file.path("data", "citations.yml")) +citations <- oa_summary(citations) + ## Summarize results <- data.frame( package = levels(downloads$package), @@ -207,3 +210,31 @@ for (i in seq_along(downloads)) { if (i %% 3 == 0) cat("## Row\n") } ``` + +# Citations {scrolling="true"} + +```{r} +#| label: citations +#| results: asis +for (i in seq_along(citations)) { + tbl <- citations[[i]] |> + gt::gt() |> + gt::cols_hide(columns = "url") |> + gt::fmt_markdown(columns = c("title")) |> + gt::sub_missing( + missing_text = "---" + ) |> + gt::cols_label( + title = "Title", + so = "Source", + publication_year = "Date", + ) |> + gt::tab_options( + table.width = "100%" + ) + + cat(sprintf(":::{.card title='%s' fill=false expandable=false}\n", names(citations)[i])) + print(tbl) + cat("\n:::\n") +} +``` diff --git a/utilities.R b/utilities.R index d01ed36..dd38595 100644 --- a/utilities.R +++ b/utilities.R @@ -103,3 +103,17 @@ gh_summary <- function(x, what = c("number", "title", x <- x[x$state == "open", , drop = FALSE] x } + +# OpenAlex ===== +oa_summary <- function(x, what = c("title", "so", "url", "publication_year")) { + lapply( + X = x, + FUN = function(x) { + x <- lapply(x, `[`, what) + x <- lapply(x, as.data.frame) + x <- do.call(rbind, x) + x$title <- sprintf("%s", x$url, x$title) + x + } + ) +}