bluuebunny/crossref_metadata_2025 huggingface dataset:
Extrusion fountains are hallmarks of chromosome organization emerging upon zygotic genome activation
Authors: Galitsyna Aleksandra , Ulianov Sergey V. , Bykov Nikolai S. , Veil Marina , Gao Meijiang , Perevoschikova Kristina , Gelfand Mikhail , Razin Sergey V. , Mirny Leonid , Onichtchouk Daria
Published: July 2023

The first activation of gene expression during development (zygotic genome activation, ZGA) is accompanied by massive changes in chromosome organization. The connection between these two processes remains unknown. Using Hi-C for zebrafish embryos, we found that chromosome folding starts by establishing “fountains”, novel elements of chromosome organization, emerging selectively at enhancers upon ZGA. Using polymer simulations, we demonstrate that fountains can emerge as sites of targeted cohesin loading and require two-sided, yet desynchronized, loop extrusion. Specific loss of fountains upon loss of pioneer transcription factors that drive ZGA reveals a causal connection between enhancer activity and fountain formation. Finally, we show that fountains emerge in early Medaka andXenopusembryos; moreover, we found cohesin-dependent fountain pattern on enhancers of mouse embryonic stem cells. Taken together, fountains are the first enhancer-specific elements of chromosome organization; they constitute starting points of chromosome folding during early development, likely serving as sites of targeted cohesin loading.
Introducingπ-HelixNovo for practical large-scale de novo peptide sequencing
Authors: Yang Tingpeng , Ling Tianze , Sun Boyan , Liang Zhendong , Xu Fan , Huang Xiansong , Xie Linhai , He Yonghong , Li Leyuan , He Fuchu , Wang Yu , Chang Cheng
Published: July 2023

De novo peptide sequencing is a promising approach for novel peptide discovery. We use a novel concept of complementary spectra to enhance ion information and propose a de novo sequencing modelπ-HelixNovo based on Transformer architecture.π-HelixNovo outperforms other state-of-the-art models and enhances the taxonomic resolution of gut metaproteome, taking a significant step forward in de novo sequencing.
GIS-FA: An approach to integrate thematic maps, factor-analytic and envirotyping for cultivar targeting
Authors: Araújo Maurício S. , Chaves Saulo F. S. , Dias Luiz A. S. , Ferreira Filipe M. , Pereira Guilherme R. , Bezerra André R. G. , Alves Rodrigo S. , Heinemann Alexandre B. , Breseghello Flávio , Carneiro Pedro C. S. , Krause Matheus D. , Costa-Neto Germano , Dias Kaio O. G.
Published: July 2023

Key message: We propose an enviromics prediction model for cultivar recommendation based on thematic maps for decision-makers.

Parsimonious methods that capture genotype-by-environment interaction (GEI) in multi-environment trials (MET) are important in breeding programs. Understanding the causes and factors of GEI allows the utilization of genotype adaptations in the target population of environments through environmental features and Factor-Analytic (FA) models. Here, we present a novel predictive breeding approach called GIS-FA that integrates geographic information systems (GIS) techniques, FA models, Partial Least Squares (PLS) regression, and Enviromics to predict phenotypic performance in untested environments. The GIS-FA approach allows: (i) predict the phenotypic performance of tested genotypes in untested environments; (ii) select the best-ranking genotypes based on their over-all performance and stability using the FA selection tools; (iii) draw thematic maps showing overall or pairwise performance and stability for decision-making. We exemplify the usage of GIS-FA approach using two datasets of rice [Oryza sativa(L.)] and soybean [Glycine max(L.) Merr.] in MET spread over tropical areas. In summary, our novel predictive method allows the identification of new breeding scenarios by pinpointing groups of environments where genotypes have superior predicted performance and facilitates/optimizes the cultivar recommendation by utilizing thematic maps.
Disrupting actin filaments enhances glucose-stimulated insulin secretion independent of the cortical actin cytoskeleton
Authors: Polino Alexander J. , Ng Xue Wen , Rooks Rebecca , Piston David W.
Published: July 2023

Just under the plasma membrane of most animal cells lies a dense meshwork of actin filaments called the cortical cytoskeleton. In insulin-secreting pancreatic β cells, a longstanding model posits that the cortical actin layer primarily acts to restrict access of insulin granules to the plasma membrane. Here we test this model and find that stimulating β cells with pro-secretory stimuli (glucose and/or KCl) has little impact on the cortical actin layer. Chemical perturbations of actin polymerization, by either disrupting or enhancing filamentation, dramatically enhances glucose-stimulated insulin secretion. We find that this enhancement does not correlate with the state of the cortical actin layer, suggesting filament disruptors act on insulin secretion independently of the cortical cytoskeleton.
A bespoke analytical workflow for the confident identification of sulfopeptides and their discrimination from phosphopeptides
Authors: Daly Leonard A. , Byrne Dominic P. , Perkins Simon , Brownridge Philip J , McDonnell Euan , Jones Andrew R. , Eyers Patrick A. , Eyers Claire E.
Published: July 2023

Protein tyrosine sulfation (sY) is a post-translational modification (PTM) catalysed by Golgi-resident Tyrosyl Protein SulfoTransferases (TPSTs). Information on protein tyrosine sulfation is currently limited to ∼50 human proteins with only a handful having verified sites of sulfation. The contribution of this chemical moiety for the regulation of biological processes, both inside and outside the cell, remains poorly defined, in large part due to analytical limitations. Mass spectrometry-based proteomics is the method of choice for PTM analysis, but has yet to be applied for the systematic investigation and large-scale analysis of biomolecular sulfation (constituting the ‘sulfome’), primarily due to issues associated with discrimination of sY-from phosphotyrosine (pY)-containing peptides. In this study, we developed a mass spectrometry (MS)-based workflow centred on the characterization of sY-peptides, incorporating optimised Zr4+-IMAC and TiO2enrichment strategies. Extensive characterization of a panel of sY- and pY-peptides using an array of MS fragmentation regimes (CID, HCD, EThcC, ETciD, UVPD) highlights differences in the ability to generate site-determining product ions, which can be exploited to differentiate sulfated peptides from nominally isobaric phosphopeptides based on precursor ion neutral loss at low collision energy. Application of our analytical workflow to a HEK-293 cell extracellular secretome facilitated identification of 21 new sulfotyrosine-containing proteins, several of which we validate enzymatically usingin vitrosulfation assays. This study demonstrates the applicability of our strategy for confident, high-throughput, ‘sulfomics’ studies, and reveals new sY interplay between enzymes relevant to both protein and glycan sulfation.
Loss of Progranulin Results in Increased Pan-Cathepsin Activity and Reduced LAMP1 Lysosomal Protein
Authors: Anderson Abigail , Tansey Malú G.
Published: July 2023

Mutations in the progranulin (PGRN) encoding gene,GRN, cause familial frontotemporal dementia (FTD) and neuronal ceroid lipofuscinosis (NCL) and PGRN is also implicated in Parkinson’s disease (PD). These mutations result in decreased PGRN expression. PGRN is highly expressed in peripheral immune cells and microglia and regulates cell growth, survival, repair, and inflammation. When PGRN is lost, the lysosome becomes dysfunctional, but the exact mechanism by which PGRN plays a role in lysosome function and how this contributes to inflammation and degeneration is not entirely understood. To better understand the role of PGRN in regulating lysosome function, this study examined how loss ofGRNimpacts total LAMP1 protein expression and cathepsin activities. Using mouse embryonic fibroblasts (MEFs), immunocytochemistry and immunoblotting assays were performed to analyze fluorescent signal from LAMP1 (lysosomal marker) and BMV109 (marker for pan-cathepsin activity).GRN-/-MEFs exhibit increased expression of pan-cathepsin activity relative toGRN+/+MEFs, and significantly impacts expression of LAMP1. The significant increase in pan-cathepsin activity in theGRN-/-MEFs confirms that PGRN loss does alter cathepsin expression, which may be a result of compensatory mechanisms happening within the cell. Using NTAP PGRN added toGRN-/-MEFs, specific cathepsin activity is rescued. Further investigations should include assessing LAMP1 and BMV109 expression in microglia fromGRN-/-mice, in the hopes of understanding the role of PGRN in lysosomal function in immune cells of the central nervous system and the diseases in which it is implicated.
A multiplexed time-resolved fluorescence resonance energy transfer ultrahigh-throughput screening assay for targeting SMAD4-SMAD3-DNA complex
Authors: Ouyang Wukun , Niu Qiankun , Qui Min , Fu Haian , Du Yuhong , Mo Xiulei
Published: July 2023

The signaling pathway of transforming growth factor-beta (TGFβ) plays crucial roles in the establishment of an immunosuppressive tumor microenvironment, making anti-TGFβ agents a significant area of interest in cancer immunotherapy. However, the clinical translation of current anti-TGFβ agents that target upstream cytokines and receptors remains challenging. Therefore, the development of small molecule inhibitors specifically targeting SMAD4, the downstream master regulator of TGFβ pathway, would offer an alternative approach with significant therapeutic potential for anti-TGF-β signaling. In this study, we present the development of a cell lysate-based multiplexed time-resolved fluorescence resonance energy transfer (TR-FRET) assay in an ultrahigh-throughput screening (uHTS) 1536-well plate format. This assay enables simultaneous monitoring of the protein-protein interaction (PPI) between SMAD4 and SMAD3, as well as the protein-DNA interaction (PDI) between SMADs and their consensus DNA binding motif. The multiplexed TR-FRET assay exhibits high sensitivity, allowing the dynamic analysis of the SMAD4-SMAD3-DNA complex at single amino acid resolution. Moreover, the multiplexed uHTS assay demonstrates robustness for screening small molecule inhibitors. Through a pilot screening of an FDA-approved and bioactive compound library, we identified gambogic acid and gambogenic acid as potential hit compounds. These proof-of-concept findings underscore the utility of our optimized multiplexed TR-FRET platform for large-scale screening to discover small molecule inhibitors that target the SMAD4-SMAD3-DNA complex as novel anti-TGFβ signaling agents.
Ubiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality ofwtfmeiotic drivers
Authors: Zheng Jin-Xin , Du Tong-Yang , Shao Guang-Can , Ma Zhu-Hui , Jiang Zhao-Di , Hu Wen , Suo Fang , He Wanzhong , Dong Meng-Qiu , Du Li-Lin
Published: July 2023

Killer meiotic drivers (KMDs) skew allele transmission in their favor by killing meiotic progeny not inheriting the driver allele. Despite their widespread presence in eukaryotes, the molecular mechanisms behind their selfish behavior are poorly understood. Here we investigate how the toxin and antidote products of a fission yeastwtf-family KMD gene can act antagonistically. Both the toxin and the antidote are multi-transmembrane proteins, differing only in their N-terminal cytosolic tails. We find that the antidote employs N-terminal PY motifs (Leu/Pro-Pro-X-Tyr) to bind Rsp5/NEDD4 family ubiquitin ligases, which ubiquitinate the antidote. Mutating PY motifs or attaching a deubiquitinating enzyme transforms the antidote into a toxic protein. Ubiquitination promotes the transport of the antidote from the trans-Golgi network to the endosome, thereby preventing it from causing toxicity. A physical interaction between the antidote and the toxin enables the ubiquitinated antidote to translocate the toxin to the endosome and neutralize its toxicity. We propose that post-translational modification-mediated protein localization and/or activity changes may be a common mechanism governing the antagonistic duality of single-gene KMDs.
Cardiomyocyte-specific adenylyl cyclase type-8 overexpression induces activation of RelA together with myocardial and systemic inflammation
Authors: Kumar Vikas , Bermea Kevin Christian , Kumar Dhaneshwar , Singh Amit , Verma Anjali , Kaileh Mary , Sen Ranjan , Lakatta Edward G. , Adamo Luigi
Published: July 2023

Background

Mice with cardiac-specific overexpression of adenylyl cyclase (AC) type 8 (TGAC8) are under a constant state of severe myocardial stress. They have a remarkable ability to adapt to this stress, but they eventually develop accelerated cardiac aging and experience reduced longevity.

Results

Here we demonstrate that activation of ACVIII in cardiomyocytes results in cell-autonomous RelA-mediated NF-κB signaling. This is associated with non-cell-autonomous activation of proinflammatory and age-associated signaling in myocardial endothelial cells and myocardial smooth muscle cells, expansion of myocardial immune cells, increase in serum levels of inflammatory cytokines, and changes in the size or composition of lymphoid organs. These changes precede the appearance of cardiac fibrosis. We provide evidence indicating that ACVIII-driven RelA activation in cardiomyocytes is mediated by calcium-Protein Kinase A (PKA) signaling.

Conclusions

Using a model of chronic cardiomyocyte stress and accelerated aging we highlight a novel, PKA/RelA-dependent connection between cardiomyocyte stress, myocardial para-inflammation and systemic inflammation. These findings point to RelA-mediated signaling in cardiomyocytes and inter-organ communication between the heart and lymphoid organs as novel potential therapeutic targets to reduce age-associated myocardial deterioration.
Rapid Identification of Bacterial isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy
Authors: Chatzimichail Stelios , Turner Piers , Feehily Conor , Farrar Alison , Crook Derrick , Andersson Monique , Oakley Sarah , Barrett Lucinda , Sayyed Hafez El , Kyropoulos Jingwen , Nellåker Christoffer , Stoesser Nicole , Kapanidis Achillefs N.
Published: July 2023

We demonstrate the rapid capture, enrichment, and identification of bacterial pathogens using Adaptive Channel Bacterial Capture (ACBC) devices. Using controlled tuning of device backpressure in polydimethylsiloxane (PDMS) devices, we enable the controlled formation of capture regions capable of trapping bacteria from low cell density samples with near 100% capture efficiency. The technical demands to prepare such devices are much lower compared to conventional methods for bacterial trapping and can be achieved with simple benchtop fabrication methods. We demonstrate the capture and identification of seven species of bacteria with bacterial concentrations lower than 1000 cells/mL, including common Gram-negative and Gram-positive pathogens such asEscherichia coliandStaphylococcus aureus. We further demonstrate that species identification of the trapped bacteria can be undertaken in the order of one-hour using multiplexed 16S rRNA-FISH with identification accuracies of 73-99% with unsupervised classification methods.
An AluYb8 retrotransposon characterises a risk haplotype of TMEM106B associated in neurodegeneration
Authors: Salazar Alex , Tesi Niccolò , Knoop Lydian , Pijnenburg Yolande , van der Lee Sven , Wijesekera Sanduni , Krizova Jana , Hiltunen Mikko , Damme Markus , Petrucelli Leonard , Reinders Marcel , Hulsman Marc , Holstege Henne
Published: July 2023

Genome-wide association studies identified a role forTMEM106Bin various neurodegenerative diseases. Based on long-read whole-genome sequencing data of 256 individuals, we identified an AluYb8 retrotransposon in the 3’ UTR of the risk haplotype ofTMEM106B. When transcriptionally active, Alu-elements can propogate throughout the genome, and mediate (post-)transcriptional dysregulation of nearby genes. We found thatTMEM106Bhaplotypes carrying the AluYb8 element are more methylated than those without, likely reflecting an evolutionary selection to suppress propagation. AluYb8 activation can be further suppressed by TDP-43, in its role in post-transcriptional RNA-processing. However, age-related loss of TDP-43, by reduced methylation in the 3’ UTR ofTARDBP,may release AluYb8 suppression. Together, our findings suggest that in the aging brain, the AluYb8 insertion may mediate dysregulation ofTMEM106B, impacting the endolysosomal system via a negative-feedback loop, ultimately leading to neurodegenerative disease. Notably,TMEM106Bhaplotype sequences are different between African and European genomes, which likely explains the different effects on disease-risk between both populations. Overall, our research advances the understanding of the roles of TDP-43 and TMEM106B in neurodegenerative diseases, and provides a novel connection between genetic variation and age-related changes in genomic and cellular regulation.
The impact of accounting comparability on CEO incentive plans in an emerging economy: the moderating role of board independence
Authors: Arianpoor Arash , Efazati Somaye
Published: July 2023

Purpose

The present study investigates the impact of accounting comparability on chief executive officer (CEO) incentive plans and the moderating role of board independence for companies listed in Tehran Stock Exchange (TSE).

Design/methodology/approach

The information about 177 companies in 2014–2021 was examined. In this study, equity-based compensation and cash-based compensation were used as the CEO incentive plans. The equity-based compensation was calculated through the ownership of the CEO shares.

Findings

The results suggest that the higher accounting comparability increases not only CEO equity-based compensation, but also cash-based compensation. Board independence also strengthens the relationship between accounting comparability and CEO compensation. Hypothesis testing based on robustness checks confirmed these results.

Originality/value

The paper is pioneering, to the authors' knowledge, in identifying how board independence moderates the impact of accounting comparability on CEO compensation. The findings provide insights into economic consequences to the firm related to accounting comparability and board monitoring. The results have important practical implications for international investors to evaluate accounting comparability, corporate governance mechanisms and CEO incentives.
Change order effects on labor productivity and mitigation the effects by developing policies using system dynamic modeling: a case study in a construction project
Authors: Nila Nadira Islam , Akter Jhumana , Hossain Md. Mehrab
Published: July 2023

Purpose

Change orders are a typical occurrence in building projects. Change orders indirectly affect labor productivity, resulting in a significant delay in the completion of a building project. Change orders cause labor productivity losses that are difficult to describe, establish and account for contractors and subcontractors. This study aimed to look at the influence of change orders on labor productivity and develop methods to mitigate their adverse effects.

Design/methodology/approach

To assess the change orders' impact on productivity levels a system dynamic model was developed and devise ways were developed to counteract these negative impacts in this research. The impact of change orders on labor productivity and project time was then controlled using techniques established. Finally, a case study of KUET's hall extension was chosen, and the model and principles developed were implemented.

Findings

This study established that if the project delivery date is set and change orders are occurring often, labor productivity will be impacted. With adequate monitoring and supplemental management techniques, it can be reduced by prolonging the project.

Originality/value

The developed policies aid to mitigate the effect of change orders on labor productivity.
Painting art and sustainability: relationship from composite indices and a neural network
Authors: El Kadiri Boutchich Driss
Published: July 2023

Purpose

This work aims to establish the relationship between painting art and sustainability, which allows for highlighting implications likely to improve sustainability for humanity's welfare.

Design/methodology/approach

To achieve this objective, painting art is measured by a composite index aggregating the quantity and quality represented by the market value. As for sustainable development, it is represented by a composite index comprising three variables: the climate change performance index (ecological dimension), the wage index reflecting distributive justice (social dimension) and the gross domestic product (economic dimension). The composite indices were determined through adjusted data envelopment analysis. In addition, two other methods are used in this work: correlation analysis and a neural network method. These methods are applied to data from 2007 to 2021 across the world.

Findings

The correlation method highlighted a perfect positive correlation between painting art and sustainability. As for the neural network method, it revealed that the quality of painting has the greatest impact on sustainability. The neural network method also showed that the most positively impacted variable of sustainability by painting art is the social variable, with a pseudo-probability of 0.90.

Originality/value

The relationship between painting art and sustainability is underexplored, in particular in terms of statistical analysis. Therefore, this research intends to fill this gap. Moreover, analysis of the relationship between both using composite indices computed via an original method (adjusted data envelopment analysis) and a neural network method is nonexistent, which constitutes the novelty of this work.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-01-2023-0006
Macroeconomic cyclical indicators and bank non-performing loans: does country governance matter in African countries?
Authors: Ahiase Godwin , Andriana Denny , Agbemava Edinam , Adonai Bright
Published: July 2023

Purpose

The purpose of this paper is to investigate the influence of macroeconomic cyclical indicators and country governance on bank non-performing loans in African countries.

Design/methodology/approach

Data was collected from the 53 African countries covering 2005–2021. The paper develops an empirical model to examine the impact of country governance in reducing macroeconomic cycle-induced adverse effects on bank credit risk. This research estimates Random Effects models and the General Method of Moment to examine the link between microeconomic and governance factors on bank non-performing loans. Stata version 15.1 was used to conduct panel regression analysis.

Findings

The findings of the study revealed that the generalized method of moments findings contributes valuable insights into the persistence of NPLs over time and the specific effects of variables on NPL levels. The study findings highlight that the debt-to-GDP ratio, unemployment, regulatory quality, government effectiveness and inflation have significant relationships with NPLs, shedding light on their specific contributions to credit risk dynamics.

Research limitations/implications

The focus on a specific set of determinants for NPLs, which may not capture all the factors that influence NPL levels. Thus, the study did not consider the impact of macroeconomic shocks, such as natural disasters or global economic crises, which can have a significant impact on NPLs.

Practical implications

Policymakers should prioritize maintaining sustainable debt levels, promoting employment growth and controlling inflation rates to mitigate credit risk and reduce nonperforming loans. Also, enhancing regulatory quality and government effectiveness is crucial in ensuring financial stability and minimizing non-performing loans in Africa.

Originality/value

This paper provides a new possible solution to minimise bank non-performing loans risk by examining interactions of country governance regarding the macroeconomic cycle behaviour.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-11-2022-0729
The link between advanced servitization, global distribution channels and the longitudinal performance of sales in international markets
Authors: Shleha Waleed , Vaillant Yancy , Calleja-Blanco Jonathan
Published: July 2023

Purpose

The research presented in this paper has been conducted to understand the impact of advanced-servitized-products on the longitudinal sales performance of manufacturing companies across international markets. The research strives to understand how the onsite presence leverages this impact.

Design/methodology/approach

To reach this objective, an empirical sample of more than 4,000 sales transactions covering the period 2010–2019 in 74 foreign markets was collected from a single high-tech manufacturer producing and selling servitized solutions. The authors use a time fixed-effects model to test the authors' theoretically deduced hypotheses.

Findings

The authors' find the proportion of advanced-servitized products to positively impact sales performance over time and that this relation is moderated by the choice of international distribution channel. As compared to direct exports, onsite presence and intermediaries present a positive and negative moderating effect, respectively.

Originality/value

The paper offers a rare look into the international sales performance of advance-servitized-products. This paper does so using a service-dominant logic, which is still scarcely used within the servitization literature, despite the logic's adequacy for the study of the market behavior of service-augmented products.
A comparative study of the performance of Iran and G7 countries in the management of COVID-19
Authors: Pourshahabi Vahid
Published: July 2023

Purpose

The purpose of this paper is to compare the performance of Iran and G7 countries in the management of the COVID-19 crisis.

Design/methodology/approach

The indicators and statistics provided by the Oxford Government Response Tracker are used in this research. Sixteen indicators and their related items have been analyzed for eight countries including Iran, Canada, Germany, France, Great Britain, Italy, Japan, and the United States. For data analysis, Multivariate analysis of variance (MANOVA) and Tukey’s post hoc test were applied, and structural equation modeling performed with the help of SPSS and Smart-PLS software.

Findings

The results show that 8 indicators of closing schools, cancellation of public events, restriction of gatherings, restriction of domestic travel, restriction of international travel, reduction of household debt, testing policy, and contact tracing, have an effect on the number of deaths in the countries under review. The results also showed that the countries exhibit behaviors outside their normal culture during the crisis.

Originality/value

This paper will be helpful for scholars, as well as policymakers when making policies on the appropriate responses to COVID-19 and similar pandemics.
Creating spaces of well-being in academia to mitigate academic burnout: a collaborative auto-ethnography
Authors: de Villiers Scheepers Margarietha , Williams Paul , Schaffer Vikki , Grace Anthony , Walling Carl , Campton Jenna , Hands Karen , Fisher Deborah , Banks Hannah , Loth Jo , Scheelings Aurora
Published: July 2023

Purpose

In contrast to prior studies examining burnout in academic employees, this paper explores how academic employee agency mitigates burnout risks in the context of the coronavirus pandemic (COVID-19) and how this agency facilitates research productivity and influences well-being in the face of changes in learning and teaching practices.

Design/methodology/approach

The authors use collaborative auto-ethnography (CAE) in the higher education (HE) sector to probe how an employee productivity group supported the group's members during the pandemic.

Findings

Thematic analysis revealed four emerging themes: burnout, beneficial habits for research productivity, blocking-out-time and belonging. The authors' findings suggest that by acknowledging and legitimising employee-initiated groups, feelings of neglect can be combatted. Purposeful employee groups have the potential to create a therapeutic, safe space and, in addition to the groups' productivity intent, diminish the negative effects of a crisis on organisational effectiveness.

Originality/value

This paper contributes to the literature by utilising a CAE approach to provide greater insight into how academics enact agency by creating digital research workspaces, attending to the spatial dimensions of well-being especially during turbulent times.
Accounting for behaviour in fine‐scale habitat selection: A case study highlighting methodological intricacies
Authors: Beumer Larissa T. , Schmidt Niels M. , Pohle Jennifer , Signer Johannes , Chimienti Marianna , Desforges Jean‐Pierre , Hansen Lars H. , Højlund Pedersen Stine , Rudd Daniel A. , Stelvig Mikkel , van Beest Floris M.
Published: July 2023

Animal habitat selection—central in both theoretical and applied ecology—may depend on behavioural motivations such as foraging, predator avoidance, and thermoregulation. Step‐selection functions (SSFs) enable assessment of fine‐scale habitat selection as a function of an animal's movement capacities and spatiotemporal variation in extrinsic conditions.

If animal location data can be associated with behaviour, SSFs are an intuitive approach to quantify behaviour‐specific habitat selection. Fitting SSFs separately for distinct behavioural states helped to uncover state‐specific selection patterns. However, while the definition of the availability domain has been highlighted as the most critical aspect of SSFs, the influence of accounting for behaviour in the use‐availability design has not been quantified yet.

Using a predator‐free population of high‐arctic muskoxen Ovibos moschatus as a case study, we aimed to evaluate how (1) defining behaviour‐specific availability domains, and/or (2) fitting separate behaviour‐specific models impacts (a) model structure, (b) estimated selection coefficients and (c) model predictive performance as opposed to behaviour‐unspecific approaches. To do so, we first applied hidden Markov models to infer different behavioural modes (resting, foraging, relocating) from hourly GPS positions (19 individuals, 153–1062 observation days/animal). Using SSFs, we then compared behaviour‐specific versus behaviour‐unspecific habitat selection in relation to terrain features, vegetation and snow conditions.

Our results show that incorporating behaviour into the definition of the availability domain primarily impacts model structure (i.e. variable selection), whereas fitting separate behaviour‐specific models mainly influences selection strength. Behaviour‐specific availability domains improved predictive performance for foraging and relocating models (i.e. behaviours with medium to large spatial displacement), but decreased performance for resting models. Thus, even for a predator‐free population subject to only negligible interspecific competition and human disturbance we found that accounting for behaviour in SSFs impacted model structure, selection coefficients and predictive performance.

Our results indicate that for robust inference, both a behaviour‐specific availability domain and behaviour‐specific model fitting should be explored, especially for populations where strong spatiotemporal selection trade‐offs are expected. This is particularly critical if wildlife habitat preferences are estimated to inform management and conservation initiatives.
Species‐level drivers of avian centrality within seed‐dispersal networks across different levels of organisation
Authors: Moulatlet Gabriel M. , Dáttilo Wesley , Villalobos Fabricio
Published: July 2023

Bird–plant seed‐dispersal networks are structural components of ecosystems. The role of bird species in seed‐dispersal networks (from less [peripheral] to more connected [central]), determines the interaction patterns and their ecosystem services. These roles may be driven by morphological and functional traits as well as evolutionary, geographical and environmental properties acting at different spatial extents.

It is still unknown if such drivers are equally important in determining species centrality at different network levels, from individual local networks to the global meta‐network representing interactions across all local networks.

Using 308 networks covering five continents and 11 biogeographical regions, we show that at the global meta‐network level species' range size was the most important driver of species centrality, with more central species having larger range sizes, which would facilitate the interaction with a higher number of plants and thus the maintenance of seed‐dispersal interactions.

At the local network level, body mass was the only driver with a significant effect, implying that local factors related to resource availability are more important at this level of network organisation than those related to broad spatial factors such as range sizes. This could also be related to the mismatch between species‐level traits, which do not consider intraspecific variation, and the local networks that can depend on such variation.

Taken together, our results show that the drivers determining species centrality are relative to the levels of network organisation, suggesting that prediction of species functional roles in seed‐dispersal interactions requires combined local and global approaches.
Warming stabilizes alpine ecosystem facing extreme rainfall events by changing plant species composition
Authors: Yan Yingjie , Ma Fangfang , Wang Jinsong , Zhang Ruiyang , Peng Jinlong , Liao Jiaqiang , Zhou Qingping , Niu Shuli
Published: July 2023

Climate warming and extreme climatic events are threatening ecosystem processes and functions. However, it remains unclear how climate warming changes ecosystem stability in facing extreme rainfall events.

Here, we investigated the temporal stability of above‐ground net primary productivity (ANPP) in an alpine meadow via a 5‐year warming experiment, during which two flooding events occurred, in an alpine meadow.

We first found that warming significantly increased the temporal stability of ANPP in facing flooding events by increasing resistance to and decreasing recovery from flooding events. Second, we found that warming shifted the plant community structure by increasing the dominance of grasses and reducing species richness and asynchrony. Last, we detected the higher temporal stability of ANPP under warming, which was mainly ascribed to the warming‐induced increase in dominant species stability (Deschampsia caespitosa).

Synthesis. These findings indicate that climate warming may mitigate the shock of flooding events on the temporal stability of community productivity via altering plant community structure in alpine grasslands. Our study highlights that to buffer ecosystems from climatic extremes, we should focus on promoting the maintenance or selection of dominant species rather than only focusing on increasing species richness.
Criminal record stigma, race, and neighborhood inequality
Authors: DeMarco Laura M.
Published: July 2023

Justice‐involved people experience high levels of housing instability and residential mobility, making the housing search a recurrent part of life. Little is known, however, regarding how criminal record stigma functions in the rental housing market. This article examines how housing providers use criminal records to screen tenants in the rental housing market and whether it varies by type of neighborhood. I conduct an online correspondence audit to test discriminatory behaviors and find an adverse criminal record effect on housing opportunities. Many housing providers disqualify all tenants with a criminal record, even without information about the severity or timing of offenses. The criminal record effect is significantly stronger in gentrifying neighborhoods and in neighborhoods where the proportion of Black residents is dwindling. Tenant screening emerges as a central obstacle faced by the justice‐involved population, vital to understanding the web of disadvantages that traps so many in the wake of the carceral state.
The imaging appearances of non‐calcified ductal carcinoma in situ: A pictorial essay
Authors: Sideris Stephanie Nicole , Falkner Nathalie , Porter Gareth
Published: July 2023

Non‐calcified ductal carcinoma in situ (NCDCIS) presents as a heterogeneous entity on various imaging modalities, most frequently presenting symptomatically as a palpable lump. The combination of multiple modalities and knowledge of its potential radiological appearances are important in minimising misdiagnosis. Compared to conventional 2D mammography, both sonography and digital breast tomosynthesis show higher diagnostic accuracy in the detection of NCDCIS. Newer modalities of contrast‐enhanced digital mammography and MRI have limited data at present, but early results indicate greater sensitivity for the detection of lesions that may be occult on ultrasound or mammography. Here, we present an illustrative study highlighting the varied appearances of NCDCIS on several imaging modalities including a brief review of the literature.
Case report on the radiographic features of epipericardial fat necrosis in a patient presenting with acute chest pain
Authors: Kenyon Sarrinder K , Wijesekera Vishva A , Wesley Allan J
Published: July 2023

Epipericardial fat necrosis (EFN) is a rare and benign condition. The three cardinal features of EFN are acute pleuritic chest pain, radiological features of an encapsulated fatty lesion within the epipericardial fat and the presence of inflammation within the surrounding pericardium. The exact aetiology is still unknown, and there are no known risk factors. The condition appears to be a transient process with no associated long‐term complications. In this case study, we demonstrate the multitude of radiological features associated with this condition. A 29‐year‐old Caucasian female presented with acute pleuritic chest pain. There were no acute changes on her blood work, electrocardiogram (ECG) or echocardiogram. The chest radiograph showed an opacity projected within the anterior mediastinum. Further imaging, with computed tomography (CT) chest with contrast, was performed to define the characteristics of the opacity. This confirmed an encapsulated, mixed fat, soft tissue density in the left pericardiac region deemed to represent EFN. Follow‐up magnetic resonance (MR) cardiac imaging at 1, 4 and 12 months demonstrated the self‐resolving characteristics of this condition. EFN is a rare differential diagnosis to consider in patients presenting with acute pleuritic chest pain when laboratory tests are normal and there are no acute ECG findings. EFN should be excluded by imaging with CT or MRI of the heart. We have demonstrated through follow‐up MR imaging the progression and resolution of EFN over 12 months.
Evaluating the geometric and dosimetric impact of applying anisotropic CTV to PTV margins in image‐guided post‐prostatectomy radiation therapy
Authors: Grierson Emma , Wilkinson Dean , Causer Lauren , de Leon Jeremiah
Published: July 2023

Introduction

Guidelines for clinical target volume (CTV) to planning target volume (PTV) margins in post‐prostatectomy radiation therapy (PPRT) are varied and often not clearly defined. Assessment of appropriateness of margins is commonly measured on prevalence of geographic miss.

Methods

Cone‐beam CT (CBCT) images (n = 92) for 10 PPRT patients were incorporated to provide on‐treatment information on the appropriateness of six different CTV expansion margins in terms of geographic miss and change in dose‐volume statistics for CTV, rectum and bladder. Uniform margins included 10 mm, 5 mm, 10 mm + 5 mm posteriorly and 5 mm + 3 mm posteriorly. In addition, two anisotropic margins were evaluated by separating the superior and inferior portions of the CTV before expansion. Treatment plans were created for each PTV retrospectively.

Results

The frequency of geographic miss was the smallest for the large uniform expansions but resulted in the highest organ‐at‐risk (OAR) doses. Geographic miss in the smaller uniform and anisotropic PTVs was more prevalent but commonly to a small volume < 1% of CTV. When averaged over all CBCT fractions, V95% dose for all CTV margins remained > 99%. The anisotropic expansions generated smaller irradiated target volumes and consequently saw up to 7.3% reduction in bladder dose when compared with similar uniform expansion margins.

Conclusion

Supplementing the incidence of geographic miss with dosimetric information on target coverage and OAR doses provides more informed assessment of the appropriateness of different CTV expansion margins. Our study extends the evaluation of anisotropic margins for PPRT.
Characteristics of chief investigators and principal investigators in Australian and New Zealand radiation oncology clinical trials
Authors: Nguyen Hanh , Montgomery Rebecca , Sundaresan Puma
Published: July 2023

Introduction

Globally, the research community is coming to realise the need for diversity, equity and inclusion (DEI) amongst research teams and leadership. Diverse teams reduce homogeneous ‘group think’, propagate innovation, propound support for broader more representative research and facilitate the recruitment of patients from diverse backgrounds. Given the above, this study aims to retrospectively examine the characteristics of chief investigators (CI) and principal investigators (PI) in past and present Australian and New Zealand radiation oncology clinical trials.

Methods

Data on CI and PI characteristics were attained from the Trans Tasman Radiation Oncology Group (TROG) website as well as archived master database files provided by the TROG Scientific Committee. Data included CI and PI discipline, clinical trial activation date, institution type (private vs. public) and geographical location if in Australia. Australian and New Zealand health practitioner registration agency websites were used to determine the registered sex of the CIs and PIs and their years of experience.

Results

One hundred and twenty TROG clinical trials have been initiated by 134 CIs from 1989 to 2022 and 463 TROG clinical trials have been opened by 465 PIs at their respective institutions from 2000 to 2022. Most TROG trial investigators have been radiation oncologists and those with over 10 years of experience. Only one in five trials and one in three trials have been led by female PIs and CIs, respectively. Investigators have largely been affiliated with public institutions, with only one in 100 CIs and one in eight PIs being affiliated with the private sector. TROG members from regional and rural areas in Australia have not been engaged as investigators, with all CIs and most PIs affiliated with metropolitan institutions.

Conclusion

This study highlights the gaps in diversity amongst CIs and PIs in TROG clinical trials. Further unpacking and understanding of issues related to CI and PI diversity are important to inform initiatives to improve researcher, leadership and patient diversity in future TROG clinical trials.
Ethnic Visibility
Authors: Robinson Amanda Lea
Published: July 2023

The political utility of ethnicity is typically attributed to the ease with which it can be observed. However, ethnic visibility is not universal, and I argue that its variation has political implications; namely that more visible group members support ethnic parties at higher rates because they have the most to gain (or lose) from ethnopolitical competition. Using original data from Malawi, I find that individual‐level ethnic visibility is indeed strongly associated with ethnic party support. I provide further evidence that visibility induces party support instrumentally by shaping expectations about others’ ability to correctly infer ethnic belonging. I also show that the theory generalizes to the group level, with more visible ethnic groups across Africa being more likely to vote ethnically. These results qualify a central assumption in instrumental theories of ethnic politics—that ethnic identities are always visible—and help explain variation in the success of ethnic political mobilization.
Is Affective Polarization Driven by Identity, Loyalty, or Substance?
Authors: Orr Lilla V. , Fowler Anthony , Huber Gregory A.
Published: July 2023

Partisan Americans like members of their own party more than members of the opposing party. Scholars often interpret this as evidence that party identity or loyalty influence interpersonal affect. First, we reassess previous studies and demonstrate that prior results are also consistent with what we would predict if people cared only about policy agreement. Next, we demonstrate the difficulty of manipulating perceptions of party identity without also manipulating beliefs about policy agreement and vice versa. Finally, we show that partisans care much more about policy agreement than they do about party loyalty when the two come into conflict. Our analyses suggest that partisan Americans care about policy agreement; we have little convincing evidence that they care about partisan identity or loyalty per se, and scholars will have to find new research designs if they want to convincingly estimate the effects of identity or loyalty independent of policy substance.
Do Politicians in Power Receive Special Treatment in Courts? Evidence from India
Authors: Poblete‐Cazenave Rubén
Published: July 2023

Do politicians in power receive special treatment in courts? I study judicial discrimination in the world's largest democracy, India, by analyzing whether pending criminal cases against politicians who marginally win their election are more likely to be closed without a conviction than cases against politicians who marginally lose their election. I find that winning office increases the chances of a favorable outcome only for politicians from the ruling party. Evidence suggests two main explanations for this result: (1) members of the legislative assemblies aligned with the ruling party misuse executive powers to manipulate prosecutors and police officers, and (2) witnesses turn hostile in high‐profile criminal cases.
The Aptness of Envy
Authors: Walters Jordan David Thomas
Published: July 2023

Are demands for equality motivated by envy? Nietzsche, Freud, Hayek, and Nozick all thought so. Call this the Envy Objection. For egalitarians, the Envy Objection is meant to sting. Many egalitarians have tried to evade the Envy Objection. But should egalitarians be worried about envy? In this article, I argue that egalitarians should stop worrying and learn to love envy. I argue that the persistent unwillingness to embrace the Envy Objection is rooted in a common misunderstanding of the nature of the charge, what it reveals, and what can be said in response to it. I develop what Bernard Williams might call a vindicatory genealogy of envy, thereby allowing us to see that envy, rather than undermining egalitarian intuitions, can in fact play a distinct justificatory role (when it is fitting), which undermines the Envy Objection.