bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Adjustment or Adaptation to the Formation of a Temporary Versus a Permanent Ostomy
Authors: Whiteley Ian , Randall Sue , Stanaway Fiona F. 
Published: November 2023

PURPOSE:The aim of this systematic review was to review evidence on adjustment or adaptation to an ostomy in persons with a temporary versus permanent ostomy.METHOD:Systematic review.SEARCH STRATEGY:We comprehensively searched the following bibliographic databases: MEDLINE (Ovid SP), EMBASE (Ovid SP), PsycINFO, CINAHL, Joanna Briggs, Scopus, and EThOS and ProQuest dissertations from inception to July 21, 2021. We located 570 studies. Data were extracted into Covidence, and the risk of bias was assessed using the Newcastle-Ottawa Scale and the Joanna Briggs tool.FINDINGS:Thirty-one studies met inclusion criteria and were included; only 2 assessed adjustment using a validated adjustment tool (Ostomy Adjustment Inventory, OAI-23). One found better adjustment in those with a permanent ostomy at 6 months; the second did not formally test for statistically significant differences between groups. Other included studies assessed aspects of adjustment such as health-related quality of life and psychological symptoms. Findings differed between studies; the majority of studies were deemed at a high risk of bias.CONCLUSIONS:The quality of evidence among studies evaluating adjustment to an ostomy in permanent versus temporary stomas was poor; the majority did not measure adjustment using a validated adjustment instrument. Therefore, differences in the ways those with a temporary ostomy or permanent ostomy adjust or adapt remain largely unknown.IMPLICATIONS:Further high-quality studies are needed that compare adjustment to a temporary or permanent ostomy using a validated instrument. An understanding of differences in adjustment in those with a temporary and permanent ostomy is important for planning how health care services can be better tailored to meet the needs of ostomy patients beyond the initial postoperative period of recovery.
Little Evidence for Homoeologous Gene Conversion and Homoeologous Exchange Events inGossypiumAllopolyploids
Authors: Conover Justin L , Grover Corrinne E , Sharbrough Joel , Sloan Daniel B , Peterson Daniel G , Wendel Jonathan F 
Published: November 2023

ABSTRACTA complicating factor in analyzing allopolyploid genomes is the possibility of physical interactions between homoeologous chromosomes during meiosis, resulting in either crossover (homoeologous exchanges) or non-crossover products (homoeologous gene conversion). This latter process was first described in cotton by comparing SNP patterns in sequences from two diploid progenitors with those from the allopolyploid subgenomes. These analyses, however, did not explicitly account for autapomorphic SNPs that may lead to similar patterns as homoeologous gene conversion, creating uncertainties about the reality of the inferred gene conversion events. Here, we use an expanded phylogenetic sampling of high-quality genome assemblies from seven allopolyploidGossypiumspecies (all derived from the same polyploidy event), four diploid species (two closely related to each subgenome), and a diploid outgroup to derive a robust method for identifying potential genomic regions of gene conversion and homoeologous exchange. Using this new method, we find little evidence for homoeologous gene conversion in allopolyploid cottons and that only two of the forty best-supported events are shared by more than one species. We do, however, reveal a single, shared homoeologous exchange event at one end of chromosome 1, which occurred shortly after allopolyploidization but prior to divergence of the descendant species. Overall, our analyses demonstrate that homoeologous gene conversion and homoeologous exchanges are uncommon inGossypium, affecting between zero and 24 genes per subgenome (0.0 - 0.065%) across the seven species. More generally, we highlight the potential problems of using simple four-taxon tests to investigate patterns of homoeologous gene conversion in established allopolyploids.SIGNIFICANCE STATEMENTAllopolyploidy is a prominent process in plant diversification, involving the union of two divergent genomes in a single nucleus via interspecific hybridization and genome doubling. The merger of genomes sets in motion a variety of inter-genomic and epigenomic interactions that are thought to lead to the origin of new phenotypes. Among these is recombinational exchange between duplicated chromosomes, which can involve sequence lengths ranging from several bases to entire chromosome arms, and which can be either reciprocal or unidirectional in their effects. Here we present a new analytical framework for detecting these inter-genomic recombinational processes in allopolyploids, and demonstrate that they have been rare in a group of allopolyploid species in the cotton genus.
Benchmarking kinship estimation tools for ancient genomes using pedigree simulations
Authors: Aktürk Şevval , Mapelli Igor , Güler Merve Nur , Gürün Kanat , Katırcıoğlu Büşra , Vural Kıvılcım Başak , Sağlıcan Ekin , Çetin Mehmet , Yaka Reyhan , Sürer Elif , Atağ Gözde , Çokoğlu Sevim Seda , Sevkar Arda , Altınışık N. Ezgi , Koptekin Dilek , Somel Mehmet 
Published: November 2023

AbstractThere is growing interest in uncovering genetic kinship patterns in past societies using low-coverage paleogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD-estimation methods and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1K to 50K) of shared SNPs (with minor allele frequency ≥0.01) are available. The performance of all four tools was comparable using ≥20K SNPs. We found that first-degree related pairs can be accurately classified even with 1K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 >90%) with 5K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69% and 79%, respectively). Meanwhile, noise in population allele frequencies and inbreeding (first cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low coverage genomes.
Lipid metabolism drives allele-specific early-stage hypertrophic cardiomyopathy
Authors: Vaniya Arpana , Karlstaedt Anja , Gulkok Damla Ates , Thottakara Tilo , Liu Yamin , Fan Sili , Eades Hannah , Fukunaga Ryuya , Vernon Hilary J. , Fiehn Oliver , Roselle Abraham M. 
Published: November 2023

AbstractHypertrophic cardiomyopathy (HCM) results from pathogenic variants in sarcomeric protein genes, that increase myocyte energy demand and lead to cardiac hypertrophy. But it is unknown whether a common metabolic trait underlies the cardiac phenotype at early disease stage. This study characterized two HCM mouse models (R92W-TnT, R403Q-MyHC) that demonstrate differences in mitochondrial function at early disease stage. Using a combination of cardiac phenotyping, transcriptomics, mass spectrometry-based metabolomics and computational modeling, we discovered allele-specific differences in cardiac structure/function and metabolic changes. TnT-mutant hearts had impaired energy substrate metabolism and increased phospholipid remodeling compared to MyHC-mutants. TnT-mutants showed increased incorporation of saturated fatty acid residues into ceramides, cardiolipin, and increased lipid peroxidation, that could underlie allele-specific differences in mitochondrial function and cardiomyopathy.Graphical Abstract
Biomechanical filtering supports tactile encoding efficiency in the human hand
Authors: Tummala Neeli , Reardon Gregory , Dandu Bharat , Shao Yitian , Saal Hannes P. , Visell Yon 
Published: November 2023

ABSTRACTTouching an object elicits skin oscillations that are biomechanically transmitted throughout the hand, driving responses in thousands of tactile receptors, including numerous exquisitely sensitive Pacinian corpuscles (PCs). Accepted descriptions of PC functionality characterize their response properties as highly stereotyped, based on experimental data gathered when stimuli are applied near the receptor. However, during natural touch, spiking activity in the majority of PCs is evoked by transmitted skin oscillations that are modified by biomechanical filtering. This filtering mechanism, stemming from dispersive wave dynamics in the skin, bears some similarity to the pre-neuronal filtering of auditory signals by the basilar membrane, a mechanical process that is instrumental to perception. Thus, we sought to clarify how skin biomechanics might influence tactile information encoding in the periphery. We used vibrometry imaging and computational neural experiments to examine the influence of biomechanical filtering on neural activity in whole-hand PC populations. We observed complex, location- and frequency-dependent patterns of filtering that were shaped by tissue mechanics and hand morphology. This source of biomechanical modulation diversified PC population spiking activity and enhanced tactile information encoding efficiency. These findings indicate that biomechanics furnishes a pre-neuronal mechanism that facilitates efficient tactile encoding and processing.
Wintering, rather than breeding, oceanic conditions may modulate declining survival in a long-distance migratory seabird
Authors: Snell Katherine R. S. , Santos Inês Alexandre Machado dos , van Bemmelen Rob SA , Moe Børge , Thorup Kasper 
Published: November 2023

ABSTRACTSteep declines in Arctic skua populations in the southern extent of their breeding range have been reported during the last half of the 20thcentury. We used 24 years of ringing and re-encounter data from the Faroe Islands, North Atlantic, to investigate if patterns in survival probabilities can be explained by large scale climatic events. Having first determined the migratory phenology and wintering regions, we estimated the effects on survival of the North Atlantic Oscillation (NAO) index during breeding and Oceanic Niño index (ONI) during the non-breeding period within a capture-mark-recapture framework. Temporal trends, and direct and time-lagged effects of the environment on annual survival were modelled. We found support for a substantial decrease in adult annual survival, from ca. 0.93 in 1985 to ca. 0.77 in 2008, and weak support for a decrease in young (1styear) survival over the duration of the study period. Furthermore, models indicated increased young survival following an El Niño winter. We suggest this time-lagged effect reflects downstream propagation of environmental conditions, particularly food availability, or a potential carry-over effect of El Niño conditions positively impacting the performance of the parents in the subsequent breeding season, leading to improved young survival prospects. While adult mortality cannot be attributed to the oceanic climate oscillations tested here; the negative trend in survival may account for the substantial population declines observed over the last decades.
Spatial Metabolomics co-registered with Multiplex Phenotyping for the Evaluation of Human Kidney Tissue
Authors: Zickuhr Greice M , Um In Hwa , Laird Alexander , Harrison David J , Dickson Alison L 
Published: November 2023

ABSTRACTA workflow has been evaluated that utilises a single tissue section to obtain spatially co-registered, molecular, and phenotypical information suitable for AI-enabled analysis. The impact of varying DESI-MSI conditions (e.g., temperature, scan rate, acquisition time) on the detection of small molecules and on tissue quality for integration into typical clinical pathology workflows assessed in human kidney.
A multiscale approach to investigate fluorescence and NDVI imaging as proxy of photosynthetic traits in wheat
Authors: Virlet Nicolas , Pennacchi João Paulo , Sadeghi-Tehran Pouria , Ashfield Tom , Orr Douglas J. , Carmo-Silva Elizabete , Hawkesford Malcolm J. 
Published: November 2023

ABSTRACTWith the development of the digital phenotyping, repeated measurements of agronomic traits over time are easily accessible, notably for morphological and phenological traits. However high throughput methods for estimating physiological traits such as photosynthesis are lacking. This study demonstrates the links of fluorescence and reflectance imaging with photosynthetic traits. Two wheat cultivars were grown in pots in a controlled environment. Photosynthesis was characterised by gas-exchange and biochemical analysis at five time points, from booting to 21 days post anthesis. On the same days imaging was performed on the same pots, at leaf and plant scale, using indoor and outdoor phenotyping platforms, respectively. Five image variables (Fv/Fmand NDVI at the whole plant level and Fv/Fm, Φ(II)532and Φ(NPQ)1077at the leaf scale) were compared to variables from A-Ci and A-Par curves, biochemical analysis, and fluorescence instruments. The results suggested that the image variables are robust estimators of photosynthetic traits, as long as senescence is driving the variability. Despite contrasting cultivar behaviour, linear regression models which account for the cultivar and the interaction effects, further improved the modelling of photosynthesis indicators. Finally, the results highlight the challenge of discriminating functional to cosmetic stay green genotypes using digital imaging.HighlightA temporal and multi-scale study of fluorescence and NDVI imaging used as a proxy for photosynthetic parameters
Levetiracetam Modulates Brain Metabolic Networks and Transcriptomic Signatures in the 5XFAD Mouse Model of Alzheimer’s disease
Authors: Burton Charles P. , Chumin Evgeny J. , Collins Alyssa Y. , Persohn Scott A. , Onos Kristen D. , Pandey Ravi S. , Quinney Sara K. , Territo Paul R. 
Published: November 2023

ABSTRACTINTRODUCTIONSubcritical epileptiform activity is associated with impaired cognitive function and is commonly seen in patients with Alzheimer’s disease (AD). The anti-convulsant, levetiracetam (LEV), is currently being evaluated in clinical trials for its ability to reduce epileptiform activity and improve cognitive function in AD. The purpose of the current study was to apply pharmacokinetics (PK), network analysis of medical imaging, gene transcriptomics, and PK/PD modeling to a cohort of amyloidogenic mice to establish how LEV restores or drives alterations in the brain networks of mice in a dose-dependent basis using the rigorous preclinical pipeline of the MODEL-AD Preclinical Testing Core.METHODSChronic LEV was administered to 5XFAD mice of both sexes for 3 months based on allometrically scaled clinical dose levels from PK models. Data collection and analysis consisted of a multi-modal approach utilizing18F-FDG PET/MRI imaging and analysis, transcriptomic analyses, and PK/PD modeling.RESULTSPharmacokinetics of LEV showed a sex and dose dependence in Cmax, CL/F, and AUC0-∞, with simulations used to estimate dose regimens. Chronic dosing at 10, 30, and 56 mg/kg, showed18F-FDG specific regional differences in brain uptake, and in whole brain covariance measures such as clustering coefficient, degree, network density, and connection strength (i.e. positive and negative). In addition, transcriptomic analysis via nanoString showed dose-dependent changes in gene expression in pathways consistent18F-FDG uptake and network changes, and PK/PD modeling showed a concentration dependence for key genes, but not for network covariance modeling.DISCUSSIONThis study represents the first report detailing the relationships of metabolic covariance and transcriptomic network changes resulting from LEV administration in 5XFAD mice. Overall, our results highlight non-linear kinetics based on dose and sex, where gene expression analysis demonstrated LEV dose- and concentration-dependent changes, along with cerebral metabolism, and/or cerebral homeostatic mechanisms relevant to human AD, which aligned closely with network covariance analysis of18F-FDG images. Collectively, this study show cases the value of a multimodal connectomic, transcriptomic, and pharmacokinetic approach to further investigate dose dependent relationships in preclinical studies, with translational value towards informing clinical study design.
Communicating information about the psychology of a wild carnivore, the red fox, influences perceived attitudinal changes but not overall tolerance in people
Authors: Morton F. Blake , Henri Dom , Adaway Kristy A. , Soulsbury Carl D. , Hopkins Charlotte R. 
Published: November 2023

AbstractStudies on wild animal psychology are growing in popularity due to the important role they play in understanding how wildlife is responding to human-driven environmental changes. However, communicating psychological information to the general public could undermine specific conservation objectives by encouraging greater persecution of a species (e.g., “bold” predators). Through a national-level survey (n = 1,364 participants), we tested whether communicating information about the boldness and problem-solving abilities of a wild carnivore, the red fox (Vulpes vulpes), influences people’s tolerance of them. Half of participants were given information on fox psychology (either a video or a press release about fox boldness and problem-solving), the other half were given content related to animal ecology (either a video or a press release about fox habitat use). Afterwards, all participants completed the same 24-item questionnaire evaluating their tolerance of foxes. Although the participants given information about fox psychology were more likely to report aperceivedattitude change due to the content they were given, their attitudes relating to fox tolerance remained unaffected regardless of content or format. We encourage further research to understand how communicating different types of information might influence, either positively or negatively, people’s tolerance of a species as more studies on wild animal psychology are published, and the public’s awareness of how animal psychology relates to human-wildlife interactions becomes more widespread.HighlightsStudies on wild animal psychology are growing in popularityThe impact of animal psychology research on public attitudes is unclearWe tested if fox psychology research influences public tolerancePeople given fox psychology information reported greater attitude changeThis perceived change did not impact people’s overall tolerance of foxes
Hierarchizing multi-scale environmental effects on agricultural pest population dynamics: a case study on the annual onset ofBactrocera dorsalispopulation growth in Senegalese orchards
Authors: Caumette Cécile , Diatta Paterne , Piry Sylvain , Chapuis Marie-Pierre , Faye Emile , Sigrist Fabio , Martin Olivier , Papaïx Julien , Brévault Thierry , Berthier Karine 
Published: November 2023

ABSTRACTImplementing integrated pest management programs to limit agricultural pest damage requires an understanding of the interactions between the environmental variability and population demographic processes. However, identifying key environmental drivers of spatio-temporal pest population dynamics remains challenging as numerous candidate factors can operate at a range of scales, from the field (e.g. agricultural practices) to the regional scale (e.g. weather variability). In such a context, data-driven approaches applied to pre-existing data may allow identifying patterns, correlations, and trends that may not be apparent through more restricted hypothesis-driven studies. The resulting insights can lead to the generation of novel hypotheses and inform future experimental work focusing on a limited and relevant set of environmental predictors. In this study, we developed an ecoinformatics approach to unravel the multi-scale environmental conditions that lead to the early re-infestation of mango orchards by a major pest in Senegal, the oriental fruit flyBactrocera dorsalis(BD). We gathered abundance data from a three-year monitoring conducted in 69 mango orchards as well as environmental data (i.e. orchard management, landscape structure and weather variability) across a range of spatial scales. We then developed a flexible analysis pipeline centred on a recent machine learning algorithm, which allows the combination of gradient boosting and grouped random effects models or Gaussian processes, to hierarchize the effects of multi-scale environmental variables on the onset of annual BD population growth in orchards. We found that physical factors (humidity, temperature), and to some extent landscape variables, were the main drivers of the spatio-temporal variability of the onset of population growth in orchards. These results suggest that favourable microclimate conditions could provide refuges for small BD populations that could survive, with little or no reproduction, during the mango off-season and, then, recolonize neighbouring orchards at the beginning of the next mango season. Confirmation of such a hypothesis could help to prioritize surveillance and preventive control actions in refuge areas.
Time is Confidence: Monetary Incentives Metacognitive Profile on Duration Judgment
Authors: Sarabi Mitra Taghizadeh , Zimmermann Eckart 
Published: November 2023

AbstractThe question we addressed in the current study is whether the mere prospect of monetary reward affects subjective time perception. To test this question, we collected trail-based confidence reports in a task in which subjects made categorical decisions about probe durations relative to the reference duration. When there was a potential to gain monetary reward, the duration was perceived to be longer than in the neutral condition, and confidence, which reflects the perceived probability of being correct, was higher in the reward condition than in the neutral condition. We found that confidence influences the sense of time in different individuals: subjects with high-confidence reported that they perceived the duration signaled by the monetary gain condition as longer than subjects with low-confidence. Our results showed that only high-confidence individuals overestimated the monetary gain context. Finally, we found a negative relationship between confidence and time perception, and that confidence bias at the maximum uncertainty duration of 450 ms is predictive of time perception. Taken together, the current study demonstrates that subjective measure of the confidence profile caused overestimation of time rather than by the outcome valence of reward expectancy.