Find research datasets worth reusing

opencc-zeroMay 2023View details →

~550-year climate periodicity in the Yunnan-Guizhou plateau during the late mid-Holocene: Insights and implications

This is the Supporting Information for Li et al. "550-Year Climate Periodicity in the Yunnan-Guizhou Plateau during the late Mid-Holocene: Insights and Implications" published in Geophysical Research Letters. The data comes from a stalagmite in southwestern China (27° 4' N, 105° 5' E). The dataset includes the speleothem 230Th dating data (Table S1 in Supporting Information S1), the speleothem 230Th dating, 13C, lamina thickness, 18O, Sr/Ca and Mg/Ca data (Table S2), the updated 14C database from archaeological sites in southwestern China (Table S3), the calculated minimal occupation events as the unit of analysis by combining more than one 14C date (Table S4) and the summed 14C probability (SCP) records (Table S5). The Supporting Information S1 includes a pdf file (available through Zenodo) provided also contains details on the methods of all the lab work, the results of the trace elements, the demonstration of annual lamina and application of least-squares fit, the practices of calculating summed 14C probability (SCP) distributions in southwestern China and a discussion on how ENSO and local precipitation can influence the proxies. Additionally, there are supporting figures (Figure S1-S8) for the main text in Supporting Information S1. The speleothem 230Th dating, 13C, lamina thickness, 18O, Sr/Ca and Mg/Ca data in this study are also available in the public paleoclimate database of the National Oceanic and Atmospheric Administration (NOAA) (https://www.ncei.noaa.gov/access/paleo-search/study/38059).

opencc-zeroMay 2023View details →

Unexpected colour pattern variation in mimetic frogs: implication for the diversification of warning signals in the genus Ranitomeya

Predation is expected to promote uniformity in the warning colouration of defended prey, but also mimicry convergence between aposematic species. Despite selection constraining both colour-pattern and population divergence, many aposematic animals display numerous geographically structured populations with distinct warning signals. Here, we explore the extent of phenotypic variation of sympatric species of Ranitomeya poison frogs and test for theoretical expectations on variation and convergence in mimetic signals. We demonstrate that both warning signal and mimetic convergence are highly variable and are negatively correlated: some localities display high variability and no mimicry while in others the phenotype is fixed and mimicry is perfect. Moreover, variation in warning signals is always present within localities, and in many cases, this variation overlaps between populations, such that variation is continuous. Finally, we show that coloration is consistently the least variable element and is likely of greater importance for predator avoidance compared to patterning. We discuss the implications of our results in the context of warning signal diversification and suggest that, like many other locally adapted traits, a combination of standing genetic variation and founding effect might be sufficient to enable divergence in colour pattern.

opencc-zeroMay 2023View details →

Supporting data for: Physical controls and ecological implications of the timing of the spring phytoplankton bloom on the Newfoundland and Labrador shelf

The Newfoundland and Labrador (NL) shelf and the Grand Banks of Newfoundland have been known as iconic fishing areas for centuries. In such areas with seasonal sea ice coverage, the timing of the spring bloom has been linked to sea ice melting, which stratifies the water column and promotes favorable conditions for phytoplankton to grow and accumulate. With sea ice gradually disappearing, we revisited the physical drivers controlling the initiation of the spring bloom in the region. We found that the timing of the phytoplankton bloom on the Grand Banks corresponds to the timing of ocean re-stratification following winter mixing. We also found that large-scale climate indicators are good proxies for the timing of the bloom and the abundance of Calanus finmarchicus, a key zooplankton species for the ecosystem. By revealing links between physical and biological processes, this work paves the way for an improved ecosystem approach to fisheries management.

opencc-zeroDec 2022View details →

Going, going, gone: evidence for loss of an endemic species pair of threespine sticklebacks (Gasterosteus aculeatus) with implications for protection under species-at-risk legislation

Genomic extinction occurs when the unique combination of genetic traits that characterize distinct phenotypes is eliminated by introgressive hybridization even if population size is greater than zero. Benthic and limnetic threespine sticklebacks (Gasterosteus aculeatus) constitute reproductively isolated undescribed biological species that have evolved independently in several lakes in southwestern British Columbia, Canada (known as "species pairs" in each lake). Here we investigated whether the two species that comprise the pair from Enos Lake, southeastern Vancouver Island, remain as two distinct gene pools. Multi-season samples (>1200 fish) obtained over two years from throughout the lake and assayed for variation in morphological traits characteristic of the two species (i.e., body depth, dorsal spine count, gill raker counts) and at 12 microsatellite DNA loci consistently indicated the existence of only a single group of sticklebacks. There was no consistent evidence of two groups in any morphological trait, and mean gill raker counts were consistently intermediate (20–21) to those of known benthics (~18) and limnetics (~24) which together comprised strikingly bimodal distributions in historical samples. Genetic analyses employing model-based clustering also consistently indicated the presence of only a single genetic group of sticklebacks. Compared to historical samples and to benthics and limnetics from other lakes, no Enos Lake fish could be identified confidently as a pure benthic or limnetic. Our results provide the strongest evidence yet that the Enos Lake sticklebacks now consist of a single morphological and genetic population of sticklebacks, that the unique combination of genetic and morphological traits that characterized benthic and limnetic sticklebacks no longer exist, and that their current status under Canada's Species-at Risk Act as Endangered should be re-evaluated.

opencc-by-4.0May 2023View details →

First identification of the Ediacaran Yukengou Formation in western Kuruktag, northeastern Tarim and its implications for the Neoproterozoic rift basin evolution

This supporting information provides three supplemental tables containing the sandstone composition counting and zircon U-Pb dating results.

Spiny tails and clades: A fully sampled phylogeny of hoplocercine lizards (Iguanidae/Hoplocercinae) and its taxonomic and nomenclatural implications

Hoplocercine lizards (Enyalioides, Morunasaurus, and Hoplocercus) form a clade of ca. 20 currently recognized species. The phylogenetic relationships among hoplocercine lizards, whose members exhibit striking differences in morphology (e.g., spiny vs. non-spiny tails), have not been clearly resolved by previous molecular phylogenetic studies. We generated a considerably larger dataset including 130 new DNA sequences from one mitochondrial and four nuclear loci for all named and two unnamed species of Hoplocercinae. We analyzed the data under concatenated maximum likelihood (RAxML) and Bayesian (MrBayes) as well as summary coalescent (ASTRAL) approaches. While our phylogenetic hypotheses strongly supported the monophyly of Hoplocercinae, neither Enyalioides nor Morunasaurus was supported as monophyletic. Instead, M. groi was inferred with strong support to form a clade with E. heterolepis and E. laticeps. This clade was in turn the sister taxon to other species of Morunasaurus (M. annularis, M. peruvianus). The remaining species of Enyalioides formed a separate clade with a basal split between western (3 species) and eastern (13 species) subclades. Tree topology tests rejected the monophyly of Enyalioides but failed to reject monophyly of Morunasaurus, suggesting that further study is needed to resolve its taxonomic status. Based on our results, we establish the converted clade names Hoplocercinae, Hoplocercus, Enyalioides, and Morunasaurus, as well as the new clade name Zimiamviasaurus.

Data from: Effects of temperature and obsidian content on the friction and stability of simulated basalt gouges: Implications for shallow moonquakes

Basalt is a major component of crust on both the Earth and Moon. Mineral composition and temperature influence frictional instability and thus the potential for seismicity on basaltic faults. We performed velocity-stepping shear experiments on basalt gouges at a confining pressure of 100 MPa, temperatures in the range 100-400°C and with varied obsidian contents of 0-100 wt.% under wet/dry conditions to investigate the frictional strength and stability of basaltic faults. We observe a transition from velocity-neutral to velocity-weakening behaviors with increasing obsidian content. The frictional stability response of the mixed obsidian/basalt gouges is characterized by a transition from velocity-strengthening to velocity-weakening at 200°C and another transition to velocity-strengthening at >300°C. Conversely, frictional strengths of the obsidian-bearing gouges are insensitive to temperature and wet/dry conditions. These results suggest that obsidian content dominates the potential seismic response of basaltic faults with the effect of temperature controlling the range of seismogenic depths. These observations contribute to a better understanding of the nucleation mechanism of shallow moonquakes and also seismicity on terrestrial faults in basalt.

opencc-by-4.0Jun 2023View details →

Viscoelasticity modeling of clay minerals by dynamic viscoelasticity measurement and its implications for earthquake faulting

We conducted dynamic viscoelastic measurements on three clay minerals, kaolinite, illite and smectite with water. These concentrated (dense) suspension systems of clay minerals were investigated using a high-temperature and high-fluid-pressure rheometer to determine their viscoelastic properties, which help further the understanding of tectonic and non-tectonic phenomena in the shallow unconsolidated portion of the lithosphere. Our results suggested that the rheological properties resulting from the network structure of the clay mineral were temperature, pressure and peak shear strain rate dependent. In addition, it was observed during this study that the amount of change in the phase angle varied systematically with the type of clay mineral. This suggests that the viscoelastic behaviour of unconsolidated systems saturated with fluid varies with the type of clay minerals that compose it. (Abstract)

opencc-by-4.0Dec 2022View details →

Lipids of different phytoplankton groups differ in sensitivity to degradation: implications for carbon export

Data were collected on seven cruises on a monthly basis from February to August in 2010 in the northern Adriatic Sea (RV001 (N 45°04.8', E 013°36.6'), SJ107 (N 45°02.9', E 013°19.0'), SJ105 (N 45°02.0', E 0.13°09.3'), SJ103 (N 45°01.0', E 012°59.6'), SJ101 (N 44°59.9', E 012°50.3'), and SJ108 (N 44°48.7', E 012°45.0')).  A CTD probe (Seabird SBE25, Sea–Bird Electronics Inc., Bellevue, Washington, USA) was used to measure temperature and salinity. Total phosphorus, dissolved inorganic orthophosphates (PO43-), total inorganic nitrogen (TIN), including nitrates (NO3¯), nitrites (NO2¯), and ammonium (NH4+)), were determined by spectrophotometric methods (Parsons et al., 1984) on board and immediately after sampling using Shimadzu UV-Mini 1240 spectrophotometer with 10 cm quartz cuvettes. Organic phosphorus concentration was calculated as the difference between total and inorganic phosphorus concentrations. Subsamples for the determination of chlorophyll a (Chl a) were filtered on Whatman GF/C filters and stored frozen at -20°C until further processing. Chl a concentrations were determined following 3 h extraction in 90% acetone (in the dark, with grinding), on a Turner TD–700 fluorimeter (Parsons et al., 1984). We preserved 200 mL of seawater with 2% neutralized formaldehyde (final concentration) and performed nano- and microphytoplankton determination and enumeration within one month of sampling. The stored sample was homogenized by gentle shaking, and a subsample was added to the Utermöhl sedimentation chamber (volume: 50 mL; Hydro-Bios Apparatebau, Altenholz, Germany), where it settled for ~30 h. We performed the analysis on a Zeiss Axiovert 200 (Zeiss, Jena, Germany) following the inverted microscope method (Utermöhl, 1958, Hasle 1978). Total phytoplankton included all species counted in the microphytoplankton (20–200 µm) and nanophytoplankton (2-20 µm) groups (Sieburth et al., 1978). Taxa were identified to species level and subsequently grouped to diatoms, dinoflagellates, and nanophytoplankton coccolithophores and phytoflagellates (which included chlorophytes, chrysophytes, cryptophytes and prasinophytes) according to Tomas (1997). For POC determination, 1 L of seawater was filtered on board through 0.7 mm Whatman GF/F filters precombusted at 450 °C/5h. After filtration, the filters were rinsed with Milli-Q water to remove salts and stored in liquid nitrogen on board and at -80 oC in the laboratory until analysis. POC was analyzed using an SSM–5000A solid sample module connected to a Shimadzu TOC–VCPH carbon analyzer calibrated with glucose (Sugimura and Suzuki, 1988). POC concentrations were corrected based on filter blank measurements. The average filter blank value including the instrument blank value corresponded to 5 mg C L-1. The reproducibility obtained for the glucose standard was 3%. For particulate lipid analysis, we collected 3 L of seawater prefiltered through a 200 μm stainless steel screen to remove larger particles including microzooplankton. Lipids were collected on through precombusted (450 °C/5h) 47 mm GF/F filters and stored in liquid nitrogen until lipid extraction. It was performed using a modified one-phase solvent mixture of dichloromethane-methanol-water procedure (Bligh and Dyer, 1959; Vrana et al., 2023). In short, in order to assess recoveries in later stages of sample analysis we added 5 µg of standard methyl stearate to the sliced filters together with 10 mL of a one-phase solvent mixture (dichloromethane/methanol/deionized water (1:2:0.8 v/v/v)). This was then subjected to an ultrasonic treatment for three minutes and stored overnight in the refrigerator, afterwards we filtered the extracts through a sinter funnel into a separatory funnel, washed once with a the one-phase solvent mixture (10 mL), once with dichloromethane (5 mL) and 0.73% NaCl (5 mL) (1:1 v/v), and once with 10 mL dichloromethane. The dichloromethane extracts were concentrated by rotary evaporation under a nitrogen atmosphere and kept at -20 °C until measurements were made. To prepare the lipid extracts for analysis, the dichloromethane extracts were evaporated to dryness under nitrogen flow and then dissolved in 20 µL dichloromethane prior to analysis. Lipid classes were separated on Chromarods SIII and quantified with external calibration using a mixture of standard lipids by a thin-layer chromatograph-flame ionization detector (TLC-FID) Iatroscan Mark-VI (Iatron), using a hydrogen flow of 160 mL min-1 and an air flow of 2000 mL min-1. This method identify eighteen lipid classes: hydrocarbons (HC), steryl esters (SE), fatty acid methyl esters (ME), fatty ketone (KET), triacylglycerols (TG), free fatty acids (FFA), fatty alcohols (ALC), 1,3-diacylglycerols (1,3DG), sterols (ST), 1,2-diacylglycerols (1,2DG), pigments (PIG), monoacylglycerols (MG), three glycolipids (GL) including monogalactosyl-, digalactosyl-, and sulfoquinovosyl- diacylglycerol (MGDG, DGDG, and SQDG, respectively), and three phospholipids (PL) (phosphatidylglycerols (PG), phosphatidylethanolamines (PE), and phosphatidylcholines (PC)). Total lipid concentration is calculated by summing all detected classes. Full details can be found in Ga&scaron;parović et al. (2015; 2017). In this article we focused on lipid degradation indices trough the lipolysis index (Goutx et al., 2003), which characterize the degree of lipid degradation in seawater. Lipolysis index is calculated as the ratio of the sum of lipid degradation indices (ALC+FFA+MG+DG) to the sum of cell lipids TG, WE, and glyco- and phospho-lipids (Goutx et al., 2003).

Fine-scale intraspecific niche partitioning in a highly mobile, marine megafauna species: implications for ecology and conservation

A species may partition its realized ecological niche along bionomic and/or scenopoetic axes due to intraspecific competition for limited resources. How partitioning manifests depends on resource needs and availability by and for the partitioning groups. Here we demonstrate the utility of analyzing short- and long-term stable carbon and nitrogen isotope ratios from imperiled marine megafauna to elucidate realized niche partitioning in these species. We captured 113 loggerhead (Caretta caretta) sea turtles at a high-use area near Crystal River, Florida, between 2016–2022, comprising 53 subadults, 10 adult males, and 50 adult females. Isotopic analyses indicated that loggerheads partition their realized ecological niche by life stage, along a scenopoetic axis. Most adults likely forage and reside in shallow areas of the study site, with most subadults displaying habitat switching between deeper locations to forage and shallower locations to rest. Some subadults, like adults, also forage and reside in shallow areas, and may display behaviors to avoid intraspecific competition. Analysis of stable isotopes with different turnover rates was critical for this characterization of intraspecific niche partitioning in loggerhead turtles, which has direct implications for ongoing research and conservation efforts for this and other imperiled species.

opencc-zeroDec 2022View details →

Low- and high-intensity fire in the riparian savanna: demographic impacts in an avian model species and implications for ecological fire management

<ol> <li>Climate change is driving changes in fire frequency and intensity, making it more urgent for conservation managers to understand how species and ecosystems respond. In tropical monsoonal savannas – Earth's most fire-prone landscapes – ecological fire management aims to prevent intense wildfires late in the dry season through prescribed low-intensity burns early in the dry season. Riparian habitats embedded within tropical savannas represent critical refuges for biodiversity, yet are particularly fire-sensitive. Better understanding of the impact of fire – including prescribed burns – on riparian habitats is therefore key but requires long-term detailed post-fire monitoring of species' demographic rates, as effects may persist and/or be delayed.</li> <li>We analyse impacts of (prescribed) low-intensity and (prescribed but escaped) high-intensity fire in northern Australian riparian and adjacent savanna habitat. We quantify multi-year impacts on density, survival, reproduction and dispersal of an Endangered riparian bird, the western purple-crowned fairy-wren (Malurus coronatus coronatus), in a well-studied individually-marked population.</li> <li>Following low-intensity fire, bird density was reduced by >20% in burnt compared to adjacent unburnt riparian habitat for ≥2.5 years. This was a result of reduced breeding success and recruitment for two years immediately following fire, rather than mortality or dispersal of adults.</li> <li>In contrast, high-intensity fire (in a dry year) resulted in a sharp decline in population density by 50% 2–8 months after fire, with no signs of recovery after 2.5 years. The decline in density was due to post-fire adult mortality, rather than dispersal. Breeding success of the (few) remaining individuals was low but not detectably lower than in unburnt areas, likely because breeding success was poor overall due to prevailing dry conditions.</li> <li> Synthesis and applications. Even if there is no or very low mortality during fire, and no movement of birds away from burnt areas, both low- and high-intensity fire in the riparian zone reduce population density. However, the mechanism by which this occurs, and recovery time, differs with fire intensity. To minimise impacts of fire on riparian zones in tropical savannas, we suggest employing low-intensity prescribed burns under optimal conditions shortly after the breeding season. </li> </ol>

Data from: First report of silicified wood from a late Pennsylvanian intramontane wetland of the Pyrenees: systematic affinities and paleoecological implications

The first anatomically preserved wood specimens of an upland Carboniferous flora from the Iberian Peninsula are reported from the Erillcastell Basin (Eastern Pyrenees, Catalonia, Spain). Two taxa are described, a calamitacean Equisetale (Arthropitys sp.) and a Cordaitale (Dadoxylon sp.). The Arthropitys specimen shows fusiform multiseriate rays composed of square parenchyma cells with conspicuous uniseriate or multiseriate simple pits. These pits are located near the transverse walls and occasionally in the tangential walls. The tracheids vary in lumen size, with scalariform-bordered pits on their radial walls and multiseriate pits in their cross-field areas. The Dadoxylon specimen commonly has uniseriate fusiform rays. The tracheids are long, with a square shape in transverse section. Their radial walls bear araucarian pitting with a uni- to triseriate arrangement. The pits are circular with a spindle-shaped aperture. Comparison of the Erillcastell specimens with coeval species from Europe indicates that they could belong to new species. The good preservation of the new fossil wood yields significant palaeoenvironmental information. The lack of marked growth rings in both specimens and the presence of tyloses in Dadoxylon suggest that the climate in the intramontane basins of the Pyrenees was slightly seasonal towards the end of the Carboniferous. This contrasts with the marked seasonality of coeval lowland basins. Such upland habitats may have enhanced the survival of plants adapted to humid conditions in a global context of increasing aridity.

Organismal effects of heat in a fixed ecological niche: Implications on the role of behavioral buffering in our changing world

Increasingly frequent and intense heatwaves generate new challenges for many organisms. Our understanding of the ecological predictors of thermal vulnerability is improving, yet, at least in endotherms, we are still only beginning to understand one critical component of predicting resilience: exactly how do wild animals cope with sub-lethal heat? In wild endotherms, most prior work focuses on one or a few traits, leaving uncertainty about organismal consequences of heatwaves. Here, we experimentally generated a 2.8 °C heatwave for free-living nestling tree swallows (Tachycineta bicolor). Over a week-long period coinciding with the peak of post-natal growth, we quantified a suite of traits to test the hypotheses that (a) behavioral or (b) physiological responses may be sufficient for coping with inescapable heat. Heat-exposed nestlings increased panting and decreased huddling, but treatment effects on panting dissipated over time, even though heat-induced temperatures remained elevated. Physiologically, we found no effects of heat on: gene expression of three heat shock proteins in blood, muscle, and three brain regions; secretion of circulating corticosterone at baseline or in response to handling; and telomere length. Moreover, heat had a positive effect on growth and a marginal, but not significant, positive effect on subsequent recruitment. These results suggest that nestlings were generally buffered from deleterious effects of heat, with one exception: heat-exposed nestlings exhibited lower gene expression for superoxide dismutase, a key antioxidant defense. Despite this one apparent cost, our thorough organismal investigation indicates general resilience to a heatwave that may, in part, stem from behavioral buffering and acclimation. Our approach provides a mechanistic framework that we hope will improve understanding of species persistence in the face of climate change.

opencc-zeroJul 2023View details →

Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease (CHD) with a likely oligogenic etiology, but our understanding of the genetic complexities and pathogenic mechanisms leading to HLHS is limited. We therefore performed whole genome sequencing (WGS) on a large cohort of HLHS patients and their families to identify candidate genes that were then tested in Drosophila heart model for functional and structural requirements. Bioinformatic analysis of WGS data from an index family comprised of a HLHS proband born to consanguineous parents and postulated to have a homozygous recessive disease etiology, prioritized 9 candidate genes with rare, predicted damaging homozygous variants. Of the candidate HLHS gene homologs tested, cardiac-specific knockdown (KD) of mitochondrial MICOS complex subunit dCHCHD3/6 resulted in drastically compromised heart contractility, diminished levels of sarcomeric actin and myosin, reduced cardiac ATP levels, and mitochondrial fission-fusion defects. Interestingly, these heart defects were similar to those inflicted by cardiac KD of ATP synthase subunits of the electron transport chain (ETC), consistent with the MICOS complex's role in maintaining cristae morphology and ETC complex assembly. Analysis of 183 genomes of HLHS patient-parent trios revealed five additional HLHS probands with rare, predicted damaging variants in CHCHD3 or CHCHD6. Hypothesizing an oligogenic basis for HLHS, we tested 60 additional prioritized candidate genes in these cases for genetic interactions with CHCHD3/6 in sensitized fly hearts. Moderate KD of CHCHD3/6 in combination with Cdk12 (activator of RNA polymerase II), RNF149 (E3 ubiquitin ligase), or SPTBN1 (scaffolding protein) caused synergistic heart defects, suggesting the potential involvement of a diverse set of pathways in HLHS. Further elucidation of novel candidate genes and genetic interactions of potentially-disease-contributing pathways is expected to lead to a better understanding of HLHS and other CHDs.

opencc-zeroJul 2023View details →

Data from: Observational approaches to chimpanzee behavior in an African sanctuary: implications for research, welfare, and capacity-building

Research in African ape sanctuaries has emerged as an important context for our understanding of comparative cognition and behavior. While much of this work has focused on experimental studies of cognition, these animals semi-free-range in forest habitats and therefore can also provide important information about the behavior of primates in socioecologically-relevant naturalistic contexts. In this 'New Approaches' article, we describe a project where we implemented a synthetic program of observational data collection at Ngamba Island Chimpanzee Sanctuary in Uganda, directly modeled after long-term data collection protocols at the Kibale Chimpanzee Project in Uganda, a wild chimpanzee field site. The foundation for this project was a strong partnership between sanctuary staff, field site staff, and external researchers. We describe how we developed a data-collection protocol through discussion and collaboration among these groups, and trained sanctuary caregivers to collect novel observational data using these protocols. We use these data as a case study to examine: (1) how behavioral observations in sanctuaries can inform primate welfare and care practices, such as by understanding aggression within the group; (2) how matched observational protocols across sites can inform our understanding of primate behavior across different contexts, including sex differences in social relationships; and (3) how more robust collaborations between foreign researchers and local partners can support capacity-building in primate range countries, along with mentoring and training students more broadly.

opencc-by-4.0Jul 2023View details →

An over-dominant effect associated with an SNP in a TP63 regulatory region is implicated in susceptibility to non-syndromic orofacial clefts.

Background: Non-syndromic orofacial clefts (NSOC) are complex phenotypes, involving multiple low penetrance genetic and environmental factors. Using a candidate gene approach, we aimed to analyze the role of four single nucleotide polymorphisms (SNPs) in the susceptibility to NSOC. Methods: A total of 254 individuals, 120 patients with NSOC, and 134 controls, all of Portuguese origin and non-consanguineous, were recruited. About 92% of patients had cleft lip with or without cleft palate (NSCL/P) and 8% had cleft palate (NSCP).  Four SNPs in the MTHFR, IRF6, PAX7, and TP63 genes were studied, using a real-time approach with TaqMan probes. Statistical analysis was performed with IBM SPSS Statistics and included chi-squared, Cochran test for trend and binomial logistic regression. Bonferroni correction was applied. Statistical significance was set to 0.05. Results: All SNPs were in Hardy-Weinberg equilibrium. A significant statistical association was found for TP63 rs9332461 in an over-dominant model (p = 0.016; OR 1.897 (1.144 - 3.147)). Discussion and conclusion: Few SNPs have been so far identified in TP63 in population association studies. In our sample, a significant association was only highlighted for rs9332461, localized in upstream regulatory region. Mechanisms involved in heterozygous advantage may underlie the association.

opencc-by-4.0Jul 2023View details →

An Assessment of Medication Errors among Pediatric Patients in Three Hospitals in Freetown Sierra Leone: Findings and Implications for a Low-Income Country

BackgroundPediatric patients are prone to medicine-related problems like medication errors (MEs), which can potentially cause harm. Yet, this has not been studied in this population in Sierra Leone. Therefore, this study investigated the prevalence and nature of MEs, including potential drug-drug interactions (pDDIs) in pediatric patients in three hospitals in Freetown, Sierra Leone.Methods: The study was conducted in three Hospitals among pediatric patients in Freetown and consisted of two phases. Phase one was a cross-sectional retrospective review of prescriptions for completeness and accuracy against standard prescription writing guidelines. Phase two was a point prevalence inpatient chart review of MEs that were categorized into prescription, administration, and dispensing errors and pDDIs. Data was analyzed using frequency, percentages, median, and interquartile range. Kruskal-Wallis H and Mann-Whitney U tests were used to compare the prescription accuracy between the hospitals, with p<0.05 considered statistically significant.Results: In phase one, while no prescription attained the global accuracy score (GAS) gold standard of 100%, 106 (29.0%) achieved the 80-100% mark. The patient 63 (17.2%), treatment 228 (62.3%), and prescriber 33 (9.0%) identifiers achieved an overall GAS range of 80-100%. Although the total GAS was not statistically significant (p=0.065), the date (p=0.041), patient (p=<0.001), treatment (p=0.022), and prescriber (p=<0.001) identifiers were statistically significant across the different hospitals. For phase two, the prevalence of MEs was 74 (56.1%), while that for pDDIs was 54 (40.9%). There was a statistically positive correlation between the occurrence of pDDI and the number of medicines prescribed (r=0.211, P=0.015).Conclusion: Low GAS depicts poor compliance with prescription writing guidelines and high prescribing errors. Medication errors were observed at each phase of the medication use cycle, while clinically significant pDDIs were also reported. Thus, there is a need for training on prescription writing guidelines and medication errors. Keywords:  Pediatrics, Prescription, Medication errors, Drug-drug interactions, Sierra Leone

opencc-by-4.0Aug 2023View details →

Air Quality-Related Equity Implications of U.S. Decarbonization Policy

This repo includes supporting material for the publication: Paul Picciano, Minghao Qiu, Sebastian Eastham, Mei Yuan, John Reilly, Noelle E. Selin. Air Quality-Related Equity Implications of U.S. Decarbonization Policy. Nature Communications (2023). Please download and unzip the file "climate_policy_pollution_equity.zip". Please see README below for a full description of the scripts and data included in this repo.  For correspondence on the publication, please contact Noelle Selin selin@mit.edu. If you have questions about this data repo, please contact Minghao Qiu mhqiu@stanford.edu or Paul Picciano pauldpicciano@gmail.com   README The materials in this repository allow users to reproduce the main results and figures of the paper. The analysis is performed using R (version 4.3.0).  -- Scripts: <ul> <li>initial_setup.R:  Used to load R packages, set up file paths, variable names, and the functions used in other scripts. Please load this script first before running other scripts.</li> <li>Figure1 - 5.R:  Used to generate figures 1 - 5 in the main paper. </li> <li>optimization_scenarios.R: Used to generate the optimization scenarios and 5000 possible emission reduction scenarios that achieve the same level of CO2 reductions. The results generated by this script are then used to generate Figure 5.</li> </ul>   -- Data: <ul> <li>emission_aggregate_scenarios.csv:  Nationally-aggregated emissions of CO2 and non-CO2 species by different sectors under the three main emission scenarios (scenarios number 1 - 3 as labeled in the paper). The unit of CO2 emissions is billion metric tons. Units of non-CO2 emissions are million metric tons. Used to plot Figure 1.</li> <li>InMAP_pm25_conc_scenarios.rds:  PM2.5 concentration for each InMAP grid cell due to emissions from each sector (and combined sectors) under different emission scenarios. InMAP simulates annual mean PM2.5 concentration (unit: μg/m3). Used to plot Figure 2.</li> <li>US_shapefiles.RData: Shape files of US states. Used to plot Figure 2.</li> <li>exposure_main_scenarios.csv: Population-weighted PM2.5 for each population group xxx under different scenarios (i.e. AvgExposure_xxx, units of exposure: μg/m3); disparities in population-weighted PM2.5 between each population group xxx and the total population (i.e. AvgDisparity_xxx, units of disparity: %). Used to plot Figures 3 and 4. Rows 2-4 correspond to the main scenarios (scenario numbers 1 - 3). Rows 5 - 16 correspond to the sensitivity scenarios (scenario number 4 as labeled in the paper).</li> <li>source_emission_baseline_2030.rds: Emissions from each individual source as projected by the baseline 2030 scenario (scenario number 2). Used as input data for the optimization analysis.</li> <li>source_emission_cap50_2030.rds: Emissions from each individual source as projected by the cap50% scenario (scenario number 3). Used as input data for the optimization analysis.</li> <li>minority_exposure_by_sector.rds: Changes in population-weighted PM2.5 exposure and disparities for the racial/ethnic minority group between the cap50% scenario and baseline 2030 scenario. Used to plot Figure 5.</li> <li>optimization_scenarios.rds: Population-weighted PM2.5 exposure and disparities for the racial/ethnic minority group under different optimization scenarios (scenarios number 5 -10). This file is generated by optimization_scenarios.R and further used to plot Figure 5.</li> <li>cap50_nation_total_5000draws.rds: Population-weighted PM2.5 exposure and disparities for the racial/ethnic minority group under 5000 possible scenarios that achieve the same level of CO2 reductions without any constraints (i.e. the same as the "nation-total" scenario). This file is generated by optimization_scenarios.R and further used to plot Figure 5.</li> </ul> <ul> </ul>

opencc-zeroAug 2023View details →

Investigating the effects of whole genome duplication on phenotypic plasticity: Implications for the invasion success of Giant Goldenrod (Solidago gigantea)

Polyploidy commonly occurs in invasive species and phenotypic plasticity (PP, the ability to alter one's phenotype in different environments), is predicted to be enhanced in polyploids and contribute to their invasive success. However, empirical support that increased PP is frequent in polyploids and/or confers invasive success is limited. Here, we investigated if polyploids are more pre-adapted to become invasive than diploids via the scaling of trait values and PP with ploidy-level, and if post-introduction selection has led to a divergence in trait values and PP responses between native- and non-native cytotypes. We grew diploid, tetraploid (from both native North American and non-native European ranges), and hexaploid Solidago gigantea in pots outside with low, medium, and high soil nitrogen and phosphorus (NP) amendments, and measured traits related to growth, asexual reproduction, physiology, and insects/pathogen resistance. We found little evidence to suggest that polyploidy and post-selection shaped mean trait and PP responses. To examine invasion dynamics, we compared diploids to tetraploids (as their introduction into Europe was more likely), and found that tetraploids had greater pathogen resistance, photosynthetic capacities, and water-use efficiencies and generally performed better under NP enrichments. Furthermore, tetraploids invested more into roots than shoots in low NP and into shoots than roots in high NP and this resource strategy is beneficial under variable NP conditions. Lastly, native-tetraploids exhibited greater plasticity in biomass accumulation, clonal-ramet production and water-use efficiency. Cumulatively, tetraploid S. gigantea possesses traits that might have pre-disposed and enabled them to become successful invaders. Our findings highlight that trait expression and invasive species dynamics are nuance while also providing insight into the invasion success and cyto-geographic patterning of S. gigantea that can be broadly applied to other invasive species with polyploid complexes.