bluuebunny/crossref_metadata_2025_split huggingface dataset:
The efficacy of spatio‐temporal predictors in forecasting the risk of Cydia nigricana infestation
Authors: Riemer Natalia , Schieler Manuela , Saucke Helmut 
Published: March 2024

AbstractThe ability to estimate the risk of pest infestation can help farmers to reduce pesticide application and provide guidance that would result in better management decisions. This study tested whether different combinations of spatial and temporal risk factors may be used to predict the damage potential of pea moth, Cydia nigricana Fabricius (Lepidoptera: Tortricidae), a major pest in field pea (Pisum sativum L., Fabaceae). Over four consecutive years, the abundance of pea moth was monitored by placing pheromone traps at various field pea‐cultivation sites. We also assessed the phenological development stages and the percentage of damaged seeds per 100 pods collected from each growing pea field in a region of approximately 30 km in diameter. The study found the significant infestation risk indicators to be the time of flowering, the date on which male pea moths are first detected in the monitoring traps and the minimum distance to pea fields that were planted and harvested in the previous growing season. The combination of all three factors using a general additive model approach yielded the best results. The model proposed by this study accurately discriminated between low‐infestation and high‐infestation fields in 95% of cases.
Phenotypic plasticity of a Baetid mayfly larvae (Baetis rhodani) at sites with high levels of deposited fine sediment
Authors: McKenzie Morwenna , Scott Jennifer , Wood Paul J. , Mathers Kate L. 
Published: March 2024

Abstract
Excess fine sediment (particles <2 mm) delivery and deposition in freshwater systems is a significant factor in structuring aquatic communities and populations.
Invertebrate gill surfaces can become covered with fine sediment, potentially compromising osmoregulatory function.
Ionocytes are specialised structures for osmoregulation found on the tracheal gills of mayflies. The number of cells has been shown to change in order to maintain osmoregulatory demands under environmentally variable conditions.
To investigate whether ionocytes vary in response to fine sediment pressure, individuals of Baetis rhodani were collected from two high and low fine sediment cover sites, respectively, in the UK. Tracheal gills were subsequently examined for the number of ionocytes present on the upper and lower gill surfaces, standardised by gill size.
Results indicated that the number of ionocytes was significantly higher for mayflies collected from areas with high fine sediment cover. High fine sediment sites were also characterised by lower altitude and dissolved oxygen concentrations. Mayfly gills collected from high sediment cover sites were also significantly larger than those collected from low sediment sites.
The results illustrate the potential for mayfly larvae to demonstrate phenotypic plasticity to the pressures associated with fine sediment but that these responses are likely dependent on the composition of fine sediment deposits (organic or mineral) and associated oxygen concentrations.
Re‐evaluating patient communication and care in angiographically negative subarachnoid hemorrhage: Balancing realism and optimism
Authors: Khosdelazad Sara , Spikman Jacoba M. , Solvang Sofie , Wermer Marieke J. H. , Pender Niall , Jorna Lieke S. , Rakers Sandra E. , van der Hoorn Anouk , Javadpour Mohsen , Groen Rob J. M. , Buunk Anne M. 
Published: March 2024

AbstractAngiographically negative subarachnoid hemorrhage (anSAH) has traditionally been considered a benign condition, mainly because of favorable outcomes in the acute stage in comparison to the often negative acute outcomes of aneurysmal subarachnoid hemorrhage. However, a growing body of research in recent years shows that anSAH often leads to cognitive impairments, emotional distress, and difficulties in resuming work or other daily life activities. Therefore, in this position paper, we call for a change in neurological care and a shift in patient communication, emphasizing the importance of addressing patient needs and fostering realistic expectations rather than solely focusing on the benign nature of the condition.
Clinical and molecular characterization of patients with YWHAG‐related epilepsy
Authors: Cetica Valentina , Pisano Tiziana , Lesca Gaetan , Marafi Dana , Licchetta Laura , Riccardi Florence , Mei Davide , Chung Hon‐yin B. , Bayat Allan , Balasubramanian Meena , Lowenstein Daniel H. , Endzinienė Milda , Alotaibi Maha , Villeneuve Nathalie , Jacobs Julia , Isidor Bertrand , Solazzi Roberta , den Hollander Nicolette S. , Marjanovic Dragan , Rougeot‐Jung Christelle , Jung Julien , Lesieur‐Sebellin Marion , Accogli Andrea , Salpietro Vincenzo , Saadi Nebal W. , Panagiotakaki Eleni , Foiadelli Thomas , Redon Sylvia , Tsai Meng‐Han , Bisulli Francesca , Hammer Trine B. , Lupski James R. , Parrini Elena , Guerrini Renzo ,   the YWHAG Study Group
Published: March 2024

AbstractObjectiveYWHAG variant alleles have been associated with a rare disease trait whose clinical synopsis includes an early onset epileptic encephalopathy with predominantly myoclonic seizures, developmental delay/intellectual disability, and facial dysmorphisms. Through description of a large cohort, which doubles the number of reported patients, we further delineate the spectrum of YWHAG‐related epilepsy.MethodsWe included in this study 24 patients, 21 new and three previously described, with pathogenic/likely pathogenic variants in YWHAG. We extended the analysis of clinical, electroencephalographic, brain magnetic resonance imaging, and molecular genetic information to 24 previously published patients.ResultsThe phenotypic spectrum of YWHAG‐related disorders ranges from mild developmental delay to developmental and epileptic encephalopathy (DEE). Epilepsy onset is in the first 2 years of life. Seizure freedom can be achieved in half of the patients (13/24, 54%). Intellectual disability (23/24, 96%), behavioral disorders (18/24, 75%), neurological signs (13/24, 54%), and dysmorphisms (6/24, 25%) are common. A genotype–phenotype correlation emerged, as DEE is more represented in patients with missense variants located in the ligand‐binding domain than in those with truncating or missense variants in other domains (90% vs. 19%, p < .001).SignificanceThis study suggests that pathogenic YWHAG variants cause a wide range of clinical presentations with variable severity, ranging from mild developmental delay to DEE. In this allelic series, a genotype–phenotype correlation begins to emerge, potentially providing prognostic information for clinical management and genetic counseling.
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted Atlantic salmon populations
Authors: Lecomte Laurie , Árnyasi Mariann , Ferchaud Anne‐Laure , Kent Matthew , Lien Sigbjørn , Stenløkk Kristina , Sylvestre Florent , Bernatchez Louis , Mérot Claire 
Published: March 2024

AbstractGenomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short‐read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine‐scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (<50 bp) segregating in the Romaine and Puyjalon salmon, two putatively locally adapted populations inhabiting neighboring rivers (Québec, Canada) and showing pronounced variation in life history traits, namely growth, fecundity, and age at maturity and smoltification. We first catalogued polymorphism using a hybrid SV characterization approach pairing both short‐ (16X) and long‐read sequencing (20X) for variant discovery with graph‐based genotyping of SVs across 60 salmon genomes, along with characterization of SNPs and small indels from short reads. We thus identified 115,907 SVs, 8,777,832 SNPs and 1,089,321 short indels, with SVs covering 4.8 times more base pairs than SNPs. All three variant types revealed a highly congruent population structure and similar patterns of FST and density variation along the genome. Finally, we performed outlier detection and redundancy analysis (RDA) to identify variants of interest in the putative local adaptation of Romaine and Puyjalon salmon. Genes located near these variants were enriched for biological processes related to nervous system function, suggesting that observed variation in traits such as age at smoltification could arise from differences in neural development. This study therefore demonstrates the feasibility of large‐scale SV characterization and highlights its relevance for salmonid population genomics.
Adaptation to seasonal reproduction and environment‐associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow
Authors: Fuentes‐Pardo Angela P. , Stanley Ryan , Bourne Christina , Singh Rabindra , Emond Kim , Pinkham Lisa , McDermid Jenni L. , Andersson Leif , Ruzzante Daniel E. 
Published: March 2024

AbstractUnderstanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome–environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so‐called ‘islands of divergence’ related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
Resource level modifies heatwave responses in the freshwater snail Lymnaea stagnalis
Authors: Seppälä Otto , Katsianis Georgios , Stabauer Veronika , Seppälä Katri , Salo Tiina 
Published: March 2024

Abstract

Predicting climate change‐mediated environmental effects on organisms is difficult because their direction and strength may depend on multiple ecological factors that vary in nature. This is because the effects of environmental factors often interact. One potentially important factor modifying organisms' thermal performance is their resource level.

We experimentally examined the dependence of phenotypic responses to heatwaves on resource/food availability in the freshwater snail, Lymnaea stagnalis. We maintained snails at different food levels (unlimited, reduced [50% of expected consumption], no food), and exposed them to either a heatwave temperature (27°C) or a benign temperature (17°C) for 1 week, followed by a post‐heatwave week (17°C). To estimate snail performance, we quantified their metabolic activity (respiration rate), growth rate, fecundity, and immune activity.

All examined traits responded to temperature, and changes in fitness‐related traits (growth rate, fecundity) depended on snail resource level. During the heatwave phase, the benefits of the elevated temperature (enhanced growth rate and fecundity) were higher with unlimited than with limited resources. Additionally, during the post‐heatwave phase, the performance of previously heat‐challenged snails reduced most strongly in resource‐limited snails. The high‐temperature treatment negatively affected snail immune activity even under the high food supply, but immune traits recovered after the heatwave. Interestingly, the phenotypic effects of the high temperature were mainly direct rather than driven by increased metabolic activity.

Our results indicate that heatwave responses of L. stagnalis snails are sensitive to their resource level. Such condition dependence may have important ecological and evolutionary implications by: (1) making natural populations in low‐quality habitats the most susceptible to heatwaves; and (2) altering climate change‐mediated evolution by modifying the expression of phenotypic variation in thermal performance. By demonstrating condition‐dependent heatwave responses, our study highlights the importance of examining the interactive effects of climate change‐mediated environmental alterations and ecological factors that vary in nature.
Depth‐dependent responses of soil organic carbon under nitrogen deposition
Authors: Hu Yuanliu , Deng Qi , Kätterer Thomas , Olesen Jørgen Eivind , Ying Samantha C. , Ochoa‐Hueso Raúl , Mueller Carsten W. , Weintraub Michael N. , Chen Ji 
Published: March 2024

AbstractEmerging evidence points out that the responses of soil organic carbon (SOC) to nitrogen (N) addition differ along the soil profile, highlighting the importance of synthesizing results from different soil layers. Here, using a global meta‐analysis, we found that N addition significantly enhanced topsoil (0–30 cm) SOC by 3.7% (±1.4%) in forests and grasslands. In contrast, SOC in the subsoil (30–100 cm) initially increased with N addition but decreased over time. The model selection analysis revealed that experimental duration and vegetation type are among the most important predictors across a wide range of climatic, environmental, and edaphic variables. The contrasting responses of SOC to N addition indicate the importance of considering deep soil layers, particularly for long‐term continuous N deposition. Finally, the lack of depth‐dependent SOC responses to N addition in experimental and modeling frameworks has likely resulted in the overestimation of changes in SOC storage under enhanced N deposition.
Rethinking ‘causality’ in quantitative human geography
Authors: Zhang Jing , Wolf Levi John 
Published: March 2024

AbstractCausality is at the core of much contemporary discussion in social sciences, philosophy, and computer science—from the establishment of basic definitions of causality to developing methods for causal inference, this discussion is increasingly finding voice within geographical literature. However, geographers have long discussed (and differed) about the role “causality” plays in our work. We present a history of contemporary definitions of causality arising from philosophy and examine how these intellectual currents interact with past and present geographical thinking about causal relations. In particular, we focus on how new thinking about counterfactual causality can help re‐route inquiry around a well‐known impasse: law‐based causality in geography. In other words, while different perspectives around “laws” of geography exist, we argue that it is more productive to put aside these differences and find common ground in counterfactual causal thinking. To demonstrate, we outline new kinds of scholarship enabled by counterfactual causality and contemporary challenges that counterfactual causality faces in spatial analysis. Throughout, we refer interested readers to contemporary work on spatial causal inference and methods useful for scholars interested in analysing causal relationships in geographical systems.
Integrated crop‐livestock versus conventional systems: Effects on the chemical and physical characteristics of an Oxisol
Authors: Augusto Jeferson Garcia , de Paz Claudia Cristina Paro , Mendonça Gabriela Geraldi , Moitinho Mara Regina , Menegatto Leonardo Sartori , Bolonhezi Denizart , Salles Márcia Saladini Vieira , Simili Flávia Fernanda 
Published: March 2024

AbstractStudies have reported improvements in soil quality in integrated crop‐livestock systems (ICLS) when compared to conventional systems. The hypothesis of this study was that ICLS improve Oxisol quality due to the use of intercropping, adding pasture and cattle to the systems. The aim of the study was to evaluate the chemical and physical characteristics of an Oxisol and pasture production in the integrated system versus conventional system. We compared two conventional systems: crop system (maize grain production) and livestock system (beef cattle on single pasture) and, four ICLS: maize plus Marandu palisade grass sown simultaneously without herbicide (ICLS‐1); maize plus Marandu palisade grass sown simultaneously with herbicide (ICLS‐2); maize plus Marandu palisade grass in lagged sowing (ICLS‐3); and maize plus Marandu palisade grass sown simultaneously in maize rows and inter‐rows with herbicide (ICLS‐4). A randomized block design with six treatments and three replicates was used. The results suggest improvements in soil quality, including soil organic carbon (ICLS‐4), total nitrogen, and nitrogen stocks (ICLS‐1, ICLS‐2, and ICLS‐4). The intercropping technique influenced pasture production and soil quality during the implementation of integrated systems. The lowest soil strength was obtained for the crop system compared to systems with grazing animals but there were no changes in the soil physical characteristics that could compromise the production system.
Engaging patients in designing a transmural allied health pathway: A qualitative exploration of hospital‐to‐home transitions
Authors: van Grootel Juul W. M. , Collet Romain J. , Major Mel E. , Wiertsema Suzanne , van Dongen Hanneke , van der Leeden Marike , Geleijn Edwin , Ostelo Raymond , van der Schaaf Marike 
Published: March 2024

AbstractIntroductionThe transition from hospital to home is often suboptimal, resulting in patients not receiving the necessary allied healthcare after discharge. This may, in turn, lead to delayed recovery, a higher number of readmissions, more emergency department visits and an increase in mortality and healthcare costs. This study aimed to gain insight into patients' experiences, perceptions, and needs regarding hospital‐to‐home transition, focusing on allied healthcare as a first step towards the development of a transitional integrated allied healthcare pathway for patients with complex care needs after hospital discharge.MethodsWe conducted semistructured interviews with patients. Participants were recruited from universities and general hospitals in the Amsterdam region between May and July 2023. They were eligible if they (1) were discharged from the hospital minimally 3 and maximally 12 months after admission to an oncologic surgery department, internal medicine department, intensive care unit, or trauma centre, (2) received hospital‐based care from at least one allied healthcare provider, who visited the patient at least twice during hospital admission, (3) spoke Dutch or English and (4) were 18 years or older. Interviews were audio‐recorded and transcribed verbatim. We performed a thematic analysis of the interview data.ResultsNineteen patients were interviewed. Three themes emerged from the analysis. ‘Allied healthcare support during transition’ depicts patients' positive experiences when they felt supported by allied health professionals during the hospital‐to‐home transition. ‘Patient and family involvement’ illustrates how much patients value the involvement of their family members during discharge planning. ‘Information recall and processing’ portrays the challenges of understanding and remembering overwhelming amounts of information, sometimes unclear and provided at the wrong moment. Overall, patients' experiences of transitional care were positive when they were involved in the discharge process. Negative experiences occurred when their preferences for postdischarge communication were ignored.ConclusionsThis study suggests that allied health professionals need to continuously collaborate and communicate with each other to provide patients and their families with the personalized support they need. To provide high‐quality and person‐centred care, it is essential to consider how, when, and what information to provide to patients and their families to allow them to contribute to their recovery actively.Patient or Public ContributionThe interview guide for this manuscript was developed with the assistance of patients, who reviewed it and provided us with feedback. Furthermore, patients provided us with their valuable lived experiences by participating in the interviews conducted for this study.
Dandruff lesional scalp skin exhibits epidermal T cell infiltration and a weakened hair follicle immune privilege
Authors: Limbu Susan L. , Purba Talveen S. , Harries Matthew , Kundu Rhia , Bhogal Ranjit K. , Paus Ralf 
Published: March 2024

AbstractObjectiveDandruff is characterised by the presence of perivascular leukocytes and mild inflammation; however, the immune microenvironment of dandruff‐affected scalp skin and the potential changes to the hair follicle's (HF) physiological immune privilege (HF IP) remain unknown. Here, we characterised the HF immune microenvironment and immune privilege status in dandruff‐affected scalp skin.MethodsWe assessed relevant key parameters in healthy versus dandruff‐affected human scalp biopsies using quantitative immunohistomorphometry, laser capture microdissection, and RNA sequencing.ResultsThe number of epidermal CD4+ and CD8+ T cells was increased in lesional dandruff scalp skin, while the number of MHC class II+/CD1a+ Langerhans cells was decreased in the infundibulum. The number of intrafollicular and perifollicular CD4+ T cells and CD8+ T cells, perifollicular CD68+ macrophages, and tryptase+ mast cells remained unchanged. Interestingly, MHC class Ia and ß2‐microglobulin protein expression were significantly increased specifically in the suprabulbar outer root sheath (ORS) compartment of dandruff‐associated HFs. RNAseq analysis of laser capture micro‐dissected suprabulbar ORS compartment revealed antigen presentation pathway as the top regulated canonical pathway, along with the upregulation of HF‐IP genes such as HLA‐C, HLA‐DP, and TAP1, which are normally down‐regulated in healthy HFs. Intrafollicular protein expression of known HF IP guardians (CD200 and α‐MSH) and ‘danger signals’ (MICA and CXCL10) remained unaltered at the IP sites of dandruff lesional HFs compared to non‐lesional and healthy HFs. Instead, the expression of macrophage migration inhibiting factor (MIF), another HF IP guardian, was reduced.ConclusionTogether, this work shows that dandruff is associated with epidermal T‐cell infiltration and a weakened HF IP in the suprabulbar ORS of HFs in dandruff lesional scalp.