bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning
Authors: Karlicki Michał , Bednarska Anna , Hałakuc Paweł , Maciszewski Kacper , Karnkowska Anna 
Published: July 2024

Abstract
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
Modeling dominant height with USGS 3DEP LiDAR to determine site index in even-aged loblolly pine (Pinus taeda L.) plantations in the southeastern US
Authors: Ribas-Costa Vicent A , Gastón Aitor , Cook Rachel L 
Published: July 2024

Abstract
Accurate quantification and mapping of forest productivity are critical to understanding and managing forest ecosystems. Local LiDAR or photogrammetric surveys have been used to obtain reliable estimates of canopy heights, yet these acquisitions can entail substantial expenses. Therefore, we developed models using freely available US Geological survey (USGS) LiDAR data for prediction of dominant height to map site index across loblolly pine (Pinus taeda L.) plantations in the southeastern US. We used 2017–2020 national USGS 3D Elevation Program LiDAR acquisitions and explored how different height percentiles, grid output resolutions, time difference between LiDAR and ground acquisitions, tree height, and dominant height definition affected the proposed model. We built the dominant height models using 1301 ground plots. The final regression model was constructed with the 95th percentile of the height distribution of the first returns above-ground and had values of R2 = 0.89, RMSE = 1.55 m, and RRMSE = 7.66 per cent at a 20-m pixel grid, yet all the examined percentile-resolution combinations were acceptable. No effect evidence was found for time difference when the flight was less than 4 months in advance or after the ground measurement, and it was also found independent of pulse density when this variable was lower than 9.5 pulses m−2. Using the recorded age of the plantations, we assessed the error propagation when translating dominant height to site index in two site index models, obtaining an RRMSE lower than 10 per cent in both. We found that USGS LiDAR acquisitions can be reliably used to map dominant height at a large scale, and consequently used to map forest productivity when age is known. This ability adds more value to a tool proven widely applicable in time and space and offers a great opportunity for stakeholders in different fields of use.
Redesigning the Drosophila histone gene cluster: an improved genetic platform for spatiotemporal manipulation of histone function
Authors: Crain Aaron T , Nevil Markus , Leatham-Jensen Mary P , Reeves Katherine B , Matera A Gregory , McKay Daniel J , Duronio Robert J 
Published: July 2024

Abstract
Mutating replication-dependent (RD) histone genes is an important tool for understanding chromatin-based epigenetic regulation. Deploying this tool in metazoans is particularly challenging because RD histones in these organisms are typically encoded by many genes, often located at multiple loci. Such gene arrangements make the ability to generate homogenous histone mutant genotypes by site-specific gene editing quite difficult. Drosophila melanogaster provides a solution to this problem because the RD histone genes are organized into a single large tandem array that can be deleted and replaced with transgenes containing mutant histone genes. In the last ∼15 years several different RD histone gene replacement platforms were developed using this simple strategy. However, each platform contains weaknesses that preclude full use of the powerful developmental genetic capabilities available to Drosophila researchers. Here we describe the development of a newly engineered platform that rectifies many of these weaknesses. We used CRISPR to precisely delete the RD histone gene array (HisC), replacing it with a multifunctional cassette that permits site-specific insertion of either one or two synthetic gene arrays using selectable markers. We designed this cassette with the ability to selectively delete each of the integrated gene arrays in specific tissues using site-specific recombinases. We also present a method for rapidly synthesizing histone gene arrays of any genotype using Golden Gate cloning technologies. These improvements facilitate the generation of histone mutant cells in various tissues at different stages of Drosophila development and provide an opportunity to apply forward genetic strategies to interrogate chromatin structure and gene regulation.
The inclined conductive column effect: a new simple model for magnetotelluric anomalous phases
Authors: Inoue Tomohiro , Hashimoto Takeshi 
Published: July 2024

SUMMARY
Magnetotelluric data are sometimes accompanied by ‘anomalous’ impedance phases ($\phi $xy and $\phi $yx) in the off-diagonal components deviating from the first (0° &lt; $\phi $xy &lt; 90°) or third (−180° &lt; $\phi $yx &lt; −90°) quadrant, especially in long-period bands. This phenomenon is called the phases out-of-quadrant (POQ). The POQ poses a challenge in magnetotelluric modelling because simple 1-D or 2-D models cannot explain it. Previous studies have reported that strong inhomogeneity, anisotropy, or particular 3-D structures, such as the L-shaped or cross-shaped conductors, could explain the POQ. Aside from these models, we have discovered that a slanted columnar conductor also generates the POQ. Our systematic investigation through the synthetic forward modelling of an inclined conductive column with a varying geometry showed that the inclination angle and the column length may affect the POQ appearance. We investigated herein the behaviour of the electric currents around the inclined conductive column embedded in a resistive half-space. We found that the induced electric field in the region with the POQ tends to point in the opposite direction to the surrounding vectors. This result can reasonably explain the inverted phase in long-period bands. Furthermore, we confirmed that current is sucked into one end of the column, but discharged from the other end, suggesting that the column works as a current channel. The localized reverse vectors are associated with the current channelling along the inclined conductor, which generates the POQ. A volcanic conduit within a resistive host rock is one of the typical field examples of such an inclined channel. Our study suggests that the POQ is a helpful clue in imaging the geometry of a volcanic magma plumbing system through magnetotelluric surveys.
Quantifying the mineral magnetic signature of petroleum systems and their source rocks: a study on the Inner Moray Firth, UK North Sea
Authors: Perkins J R , Muxworthy A R , Fraser A J , Hu P 
Published: July 2024

SUMMARY
This study aims to expand on existing connections between magnetic minerals and hydrocarbons within petroleum systems. Previous studies have focussed on single-source petroleum systems whereas this study, for the first time, analyses a multi-source petroleum system to investigate potential correlations between different kerogen type source rocks and magnetic minerals. To do this, the study investigates the magnetic mineral characteristics of the Inner Moray Firth (IMF), UK North Sea, through room-, low- and high-temperature techniques, and correlates this to published basin and petroleum systems modelling results that show a three-source hydrocarbon mix. Magnetic mineral analysis identifies extensive evidence for magnetite, goethite and siderite, alongside more minor lepidocrocite and iron sulphides. Although we find that magnetite is ubiquitous within the IMF, its abundance is relatively low, and, in contrast, the relatively magnetically weak goethite is more likely the most abundant magnetic mineral throughout the IMF. In agreement with previous studies, we find magnetic enhancement at oil-water contacts (OWCs); however, here, we identify two different magnetic enhancement processes at OWCs in wells, which are dependent on the amount of sulphur available in the local environment. Wells with low levels of sulphur have increasing levels of magnetite towards the OWC, with the magnetic enhancement occurring at the top of the water-saturated section. Sulphur-rich environments display an increase in iron sulphides near the OWC at the bottom of the oil-saturated sediments. Additionally, we confirm the presence of siderite as indicator of upward vertical migration. Combining with petroleum system model predictions, we find direct links between iron hydroxide presence and Type I and II–III kerogen source rocks, and iron sulphide presence with Type II kerogen source rocks. This study shows the potential for further utilization of magnetic mineral analysis within hydrocarbon exploration and petroleum system definition.
Accumulation of Heavy Metals in Conyza canadensis
Authors: Wright Patrick B , Steven Janet C 
Published: July 2024

Synopsis
Many plant species are known to take up metals from the soil and accumulate them to potentially toxic levels. This may provide tolerance to soils with high metal content or a defensive mechanism against herbivores and pathogens. Accumulators, plants that uptake and store elevated concentrations of metals, can be used in phytoremediation as a means to remove metals from contaminated soils. In this study, the native weed Conyza canadensis was grown in soils contaminated with elevated levels of lead (Pb), barium (Ba), zinc (Zn), copper (Cu), or chromium (Cr). All metals, except for Cr, were accumulated by the plants. Zinc and Cu, both essential elements, accumulated to the highest levels, while Pb and Ba were present at lower levels. All treatments except Cr showed accelerating rates of accumulation over the eight-week experiment. Barium, Cu, and Cr reduced aboveground biomass of the plants, indicating toxicity or a cost to metal accumulation. Lead and Zn promoted early flowering, while plants accumulating Ba, Cr, and Cu flowered in lower numbers. Overall, C. canadensis has promise in the phytoremediation of Pb, Cu, and Zn.
Predicted ecological consequences of wave energy extraction and climate-related changes in wave exposure on rocky shore communities
Authors: Want Andrew , Waldman Simon , Burrows Michael T , Side Jonathan C , Venugopal Vengatesan , Bell Michael C 
Published: July 2024

Abstract
Wave energy has the potential to contribute in the transition to decarbonized electricity generation. Extracting wave energy might be expected to have ecological impacts on rocky shore intertidal communities where exposure is one of the most important factors determining species structure and composition. With global climatic change, coastal exposure is predicted to increase with greater significant wave height. The wave-exposed west coast of Orkney, Scotland, UK, is the site of pre-commercial wave device testing. Surveys of 39 rocky shore sites along this coast identified key species and abundances, and quantified exposure-modifying topographic variables. A spectral wave model was constructed to compare baseline, wave extraction, climate change, and combined scenarios. Generalized additive modelling was used to describe the relationship between species, topography, and exposure. Results show that individual species differentially respond to exposure changes with ‘winners’ and ‘losers’ at site level. Overall, community responses are expected to be far greater following predicted climatic change than to industrial-scale wave energy extraction, depending on spatial scale. In combination, energy extraction may reduce the effects of climate-change-related increases in wave exposure of rocky shores. Predicting how location-specific biotic assemblages respond to changes in wave energy as a result of long-term forcing agents provides a valuable marine resource management tool.
Robust discontinuous Galerkin-based scheme for the fully-coupled nonlinear thermo-hydro-mechanical problem
Authors: Bonetti Stefano , Botti Michele , Antonietti Paola F 
Published: July 2024

Abstract
We present and analyze a discontinuous Galerkin method for the numerical modeling of the nonlinear fully-coupled thermo-hydro-mechanic problem. We propose an arbitrary-order weighted symmetric interior penalty scheme that supports general polytopal grids and is robust with respect to strong heterogeneities in the model coefficients. We focus on the treatment of the nonlinear convective transport term in the energy conservation equation and we propose suitable stabilization techniques that make the scheme robust for advection-dominated regimes. The stability analysis of the problem and the convergence of the fixed-point linearization strategy are addressed theoretically under mild requirements on the problem data. A complete set of numerical simulations is presented in order to assess the convergence and robustness properties of the proposed method.
Patterns of community antibiotic use with reference to the AWaRe classification of the World Health Organization
Authors: Gagliotti Carlo , Cangini Agnese , Da Cas Roberto , Ippoliti Ilaria , Trotta Francesco , Fortinguerra Filomena 
Published: July 2024

Abstract

Background
Monitoring consumption through quality indicators and providing feedback is an important activity within programmes for improving antibiotic prescription. This study aims to describe the use of antibiotics for systemic use in community setting in Italy and to compare prescription patterns among regions based on quality prescription indicators to identify any inter-regional variability.

Methods
The 2021 consumption (calculated as DDDs per 1000 inhabitants per day) of antibiotics for systemic use (reimbursed or purchased privately) in community setting were considered. The WHO AWaRe system was used to classify antibiotics into Access, Watch and Reserve groups, using the 60% of prescribed antibiotics belonging to the Access group out of the total DDDs as AWaRe target. The correlation between regional consumption and percentages of DDDs in the Access group was assessed through linear regression. A further indicator ‘ratio of broad to narrow-spectrum antibacterials’ was also calculated to compare the spectrum of prescribed antibiotics.

Findings
Overall community antibiotic consumption in Italy in 2021 was 15.6 DDDs per 1000 inhabitants per day, with an increasing trend from north (13.0 DDDs) to south (19.5 DDDs) and the percentages of non-reimbursed consumption decreasing from north (33.1%) to south (21.5%). Only three regions out of 21 reached the AWaRe target (regional range 47.4%–62.9%), with a negative correlation between regional consumption and percentages of antibiotics belonging to the Access group (correlation coefficient −0.8; R2 = 0.64; P value &lt; 0.001). The ‘ratio of broad to narrow-spectrum antibacterials’ was 8.5 at national level, with the highest value in the centre (11.0) compared to the south (9.1) and north (7.0).

Conclusion
The percentage of consumption of Access group antibiotics correlates very well with regional consumption in Italy, indicating that regions with higher antibiotics consumption also have worse prescribing patterns with a greater impact on bacterial resistance. Additional data are needed to better describe prescription patterns from an antimicrobial stewardship perspective.
Romosozumab followed by denosumab versus denosumab only: a post hoc analysis of FRAME and FRAME extension
Authors: Cosman Felicia , Oates Mary , Betah Donald , Timoshanko Jen , Wang Zhenxun , Ferrari Serge , McClung Michael R 
Published: July 2024

Abstract
Osteoanabolic-first treatment sequences are superior to oral bisphosphonates for fracture reduction and bone mineral density (BMD) gain. However, data comparing osteoanabolic medications, with the more potent antiresorptive, denosumab (DMAb), are limited. We analyzed FRAME and FRAME Extension data to assess BMD and fracture incidence in patients treated with romosozumab (Romo) followed by DMAb (Romo/DMAb) versus DMAb (DMAb/DMAb) for 24 months. In FRAME, women aged ≥55 years (total hip [TH] or femoral neck [FN] T-score: –2.5 to –3.5) were randomized to Romo or placebo for 12 months followed by DMAb for 12 months. In FRAME Extension, both cohorts received DMAb for another 12 months. This post hoc analysis compared BMD change and fracture incidence in patients on Romo/DMAb (months 0–24) versus DMAb/DMAb (months 12–36). Patient characteristics were balanced by propensity score weighting (PSW) and sensitivity analyses were conducted using PSW with multiple imputation (PSW-MI) and propensity score matching (PSM). Unmeasured confounding was addressed using E-values. After PSW, over 24 months, compared with DMAb/DMAb, treatment with Romo/DMAb produced significantly greater BMD increases at the lumbar spine [LS], TH, and FN (mean differences: 9.3%, 4.4%, and 4.1%, respectively; all p&lt;0.001). At month 24, in women with a baseline T-score of –3.0, the probability of achieving a T-score &gt; –2.5 was higher with Romo/DMAb versus DMAb/DMAb (LS: 92% versus 47%; TH: 50% versus 5%). In the Romo/DMAb versus DMAb/DMAb cohorts, new vertebral fractures were significantly reduced (0.62% versus 1.26% [odds ratio = 0.45; p=0.003]) and rates of clinical, nonvertebral, and hip fractures were lower (differences not significant). Similar BMD and fracture outcomes were observed with PSW-MI and PSM sensitivity analyses. The sequence of Romo/DMAb resulted in greater BMD gains and higher probability of achieving T-scores &gt; –2.5, significantly reduced new vertebral fracture incidence, and numerically lowered the incidence (not significant) of clinical, nonvertebral, and hip fractures versus DMAb only through 24 months.
Longitudinal trials illustrate interactive effects between declining Bt efficacy against Helicoverpa zea (Lepidoptera: Noctuidae) and planting dates of corn
Authors: Reay-Jones Francis P F , Buntin G David , Reisig Dominic D , Bridges William C 
Published: July 2024

Abstract
Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) has evolved resistance to insecticidal toxins from Bacillus thuringiensis (Bt) Berliner (Bacillales: Bacillaceae) expressed in genetically engineered corn, Zea mays L. This study provides an overview of field trials from Georgia, North Carolina, and South Carolina evaluating Bt and non-Bt corn hybrids from 2009 to 2022 to show changes in susceptibility in H. zea to Bt corn. The reduction in kernel injury relative to a non-Bt hybrid averaged across planting dates generally declined over time for Cry1A.105 + Cry2Ab2 corn. In addition, there was a significant interaction with planting date used as a covariate. The reduction in kernel injury remained above 80% and did not vary with planting date from 2009 to 2014, whereas a significant decline with planting date was found in this reduction from 2015 to 2022. For Cry1Ab + Cry1F corn, the reduction in kernel injury relative to a non-Bt hybrid averaged across planting dates did not vary among years. The reduction in kernel injury significantly declined with planting date from 2012 to 2022. Kernel injury as a proxy for H. zea pressure was greater in late-planted trials in non-Bt corn hybrids. Our study showed that Bt hybrids expressing Cry1A.105 + Cry2Ab2 are now less effective in later planted trials in reducing H. zea injury; however, this was not the case during the earlier years of adoption of corn expressing these 2 toxins when resistance alleles were likely less frequent in H. zea populations. The implications for management of H. zea and for insect resistance management are discussed.
Relational hyperevent models for the coevolution of coauthoring and citation networks
Authors: Lerner Jürgen , Hâncean Marian-Gabriel , Lomi Alessandro 
Published: July 2024

Abstract
The development of appropriate statistical models has lagged behind the ambitions of empirical studies analysing large scientific networks—systems of publications connected by citations and authorship. Extant research typically focuses on either paper citation networks or author collaboration networks. However, these networks involve both direct relationships, as well as broader dependencies between references linked by multiple citation paths. In this work, we extend recently developed relational hyperevent models to analyse networks characterized by complex dependencies across multiple network modes. We introduce new covariates to represent theoretically relevant and empirically plausible mixed-mode network configurations. This model specification allows testing hypotheses that recognize the polyadic nature of publication data, while accounting for multiple dependencies linking authors and references of current and prior papers. We implement the model using open-source software to analyse publicly available data on a large scientific network. Our findings reveal a tendency for subsets of papers to be cocited, indicating that the impact of these papers may be partly due to endogenous network processes. More broadly, the analysis shows that models accounting for both the hyperedge structure of publication events and the interconnections between authors and references significantly enhance our understanding of the mechanisms driving scientific production and impact.
Perforated giant peptic ulcer of the stomach in a female patient with multiple sclerosis
Authors: Nikolovski Andrej , Mickovska Kristina , Argirov Ivan , Maznevska Lidija 
Published: July 2024

Abstract
Giant peptic ulcer of the stomach is defined with a diameter of more than 3 cm. About 2/3 of them are benign peptic ulcers and perforate in 1%–2% of all peptic ulcer stomach perforations. High rates of postoperative morbidity and mortality are reported. The treatment options include omental patch repair, jejunal serosal patch repair, duodenal exclusion, and gastric resection. Postoperative omental patch repair failure is reported and is strongly associated with the ulcer diameter. This case reports a giant peptic stomach ulcer perforation in a female patient treated successfully with omental patch repair, according to Cellan–Jones.