bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel in-vivo phagocytosis assay to gain cellular insights on sponge-microbe interactions
Authors: Marulanda-Gomez Angela M. , Bayer K Kristina , Pita Lucia , Hentschel Ute
Published: March 2023

Sponges harbor diverse, specific, and stable microbial communities, but at the same time, they efficiently feed on microbes from the surrounding water column. This filter-feeding lifestyle poses the need to distinguish between three categories of bacteria: food to digest, symbionts to incorporate, and pathogens to eliminate. How sponges discriminate between these categories is still largely unknown. Phagocytosis is conceivable as the cellular mechanism taking part in such discrimination, but experimental evidence is missing. We developed a quantitative in-vivo phagocytosis assay using an emerging experimental model, the spongeHalichondria panicea. We incubated whole sponge individuals with different particles, recovered the sponge (host) cells, and tracked the particles into the sponge cells to quantify the sponge’s phagocytic activity. Fluorescence-activated cell sorting (FACS) and fluorescent microscopy were used to quantify and verify phagocytic activity (i.e., the population of sponge cells with internalized particles). Sponges were incubated with a green microalgae to test the effect of particle concentration on the percentage of phagocytic activity, and to determine the timing where the maximum of phagocytic cells are captured in a pulse-chase experiment. Lastly, we investigated the application of our phagocytic assay with other particle types (i.e., bacteria and fluorescent beads). The percentage of phagocytic cells that had incorporated algae, bacteria, and beads ranged between 5 to 24 %. We observed that the population of phagocytic sponge cell exhibited different morphologies and sizes depending on the type of particle presented to the sponge. Phagocytosis was positively related to algal concentration suggesting that sponge cells adjust their phagocytic activity depending on the number of particles they encounter. Our results further revealed that sponge phagocytosis initiates within minutes after exposure to the particles. Fluorescent and TEM microscopy rectified algal internalization and potential digestion in sponge cells, and suggests translocation between choanocyte and archeocyte-like cells over time. To our knowledge, this is the first quantitative in-vivo phagocytosis assay established in sponges that could be used to further explore phagocytosis as a cellular mechanism for sponges to differentiate between different microorganisms.
Agronomic treatments combined with embryo rescue for rapid generation advancement in tomato speed breeding
Authors: Gimeno-Páez Esther , Prohens Jaime , Moreno-Cerveró María , de Luis-Margarit Ana , Díez María José , Gramazio Pietro
Published: March 2023

Unlike other major crops, little research has been performed on tomato for reducing generation time for speed breeding. We evaluated several agronomic treatments for reducing the generation time of tomato in the M82 (determinate) and Moneymaker (indeterminate) varieties and evaluated the best combination in conjunction with embryo rescue. In a first experiment under the autumn cycle, five container sizes, from 0.2 1 (XS) to 6 1 (XL), were evaluated. We found that plants from the XL containers exhibited better development and required less time from sowing to anthesis (DSA) and for anthesis to fruit ripening (DAR). In a second experiment, using XL containers in the autumn-winter cycle, we evaluated cold priming at the cotyledonary stage, water stress, P supplementation, and K supplementation on generation time. We found that, compared to the control, cold priming significantly reduced the number of leaves and plant height to first inflorescence as well as DSA (2.7 d), while K supplementation reduced DAR (8.8 d). No effects of these treatments were observed for other growth of physiological traits. In a third experiment with XL containers in the spring-summer cycle, the combination of cold priming plus K supplementation was tested, confirming the significant effect of the combination on generation time (2.9 d for DSA and 3.9 d for DAR). Embryo rescue during the cell expansion cycle (average of 22.0 d and 23.3 d after anthesis for M82 and Moneymaker, respectively) allowed shortening the generation time by 8.7 d in M82 and 11.6 d in Moneymaker compared to thein plantafruit ripening. The combination of agronomic treatments with embryo rescue can make an effective contribution to increase the number of generations per year for speed breeding in tomato from the current three to four.
In vivo ephaptic coupling allows memory network formation
Authors: Pinotsis Dimitris A. , Miller Earl K.
Published: March 2023

It is increasingly clear that memories are distributed across multiple brain areas. Such “engram complexes” are important features of memory formation and consolidation. Here, we test the hypothesis that engram complexes are formed in part by bioelectric fields that sculpt and guide the neural activity and tie together the areas that participate in engram complexes. Like the conductor of an orchestra, the fields influence each musician or neuron and orchestrate the output, the symphony. Our results use the theory of synergetics, machine learning and data from a spatial delayed saccade task and provide evidence for in vivo ephaptic coupling in memory representations.
MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis
Authors: Zeng Yong , Wenbin Ye , Stutheit-Zhao Eric Y. , Han Ming , Bratman Scott V. , Pugh Trevor J. , He Housheng Hansen
Published: March 2023

cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising non-invasive technology to detect cancers and monitor treatments. Several bioinformatics tools are available for cfMeDIP-seq data analysis. However, an easy to implement and flexible pipeline, particularly, for large-scale cfMeDIP-seq profiling, is still lacking. Here we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification and sample aggregation. The major advantages of MEDIPIPE are: 1) it is easy to implement and reproduce with automatically deployed execution environments; 2) it can handle different experimental settings with a single input configuration file; 3) it is computationally efficient for large-scale cfMeDIP-seq profiling data analysis and aggregation.

Availability and implementation

This pipeline is an open-source software under the MIT license and it is freely available athttps://github.com/yzeng-lol/MEDIPIPE.

Contact

yzeng@uhnresearch.caortrevor.pugh@utoronto.caorhansenhe@uhnresearch.ca

Supplementary information

Supplementary data are appended.
Evaluating Tuning Strategies for Sequence Generation with Protein Language Models
Authors: Nathansen Andrea , Klein Kevin , Renard Bernhard Y. , Nowicka Melania , Bartoszewicz Jakub M.
Published: March 2023

Designing artificial proteins with specialized functions promises new solutions for biological, medical, and environmental use cases. This field benefits from advances in natural language processing, with state-of-the-art text generation models already being successfully applied to protein sequences. Openly available pre-trained protein language models are able to generate artificial protein sequences and can be finetuned on very specific tasks. Considering the high computational cost of finetuning a model exclusively for one downstream task, prompt tuning has been proposed as a more cost-efficient alternative that shares one model across different tasks. However, no openly available implementation of this approach compatible with protein language models has been previously published. Thus, we adapt an open-source codebase designed for NLP models to build a pipeline for prompt tuning on protein sequence data, supporting the protein language models ProtGPT2 and RITA. We benchmark this implementation for generating proteins of a specific family and evaluate the approach using text processing metrics as well as family membership prediction and protein activity prediction of generated sequences. Our results confirm the advantages of prompt tuning in resource usage, especially storage, encouraging further research and expansion of this technique to related use cases. For our evaluated use case, prompt tuning does not reach up to finetuning in terms of the quality of generated protein sequences, indicating the need for more extensive optimization. Lastly, we observe discrepancies between results of similar evaluation tools, highlighting open problems for principled assessment of protein sequence generation quality.
Predicting CRISPR-Cas12a guide efficiency for targeting using Machine Learning
Authors: O’Brien Aidan , Bauer Denis C. , Burgio Gaetan
Published: March 2023

Genome editing through the development of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) – Cas technology has revolutionized many fields in biology. Beyond Cas9 nucleases, Cas12a (formerly Cpf1) has emerged as a promising alternative to Cas9 for editing AT-rich genomes. Despite the promises, guide RNA efficiency prediction through computational tools search still lacks accuracy. Through a computational meta-analysis, here we report that Cas12a target and off-target cleavage behaviour are factor of nucleotide bias combined with nucleotide mismatches relative to the protospacer adjacent motif (PAM) site. These features helped to train a machine learning random forest algorithm to improve the accuracy by at least 15% to existing algorithms to predict guide RNA efficiency for Cas12a enzyme. Despite the progresses, our report underscores the need for more representative datasets and further benchmarking to reliably and accurately predict guide RNA efficiency and off-target effects for Cas12a enzymes.
Importance of genetic architecture in marker selection decisions for genomic prediction
Authors: Coletta Rafael Della , Fernandes Samuel B. , Monnahan Patrick J. , Mikel Mark A. , Bohn Martin O. , Lipka Alexander E. , Hirsch Candice N.
Published: March 2023

Breeders commonly use genetic markers to predict the performance of untested individuals as a way to improve the efficiency of breeding programs. These genomic prediction models have almost exclusively used single nucleotide polymorphisms (SNPs) as their source of genetic information, even though other types of markers exist, such as structural variants (SVs). Given that SVs are associated with environmental adaptation and not all of them are in linkage disequilibrium to SNPs, SVs have the potential to bring additional information to multi-environment prediction models that are not captured by SNPs alone. Here, we evaluated different marker types (SNPs and/or SVs) on prediction accuracy across a range of genetic architectures for simulated traits across multiple environments. Our results show that SVs can improve prediction accuracy by up to 19%, but it is highly dependent on the genetic architecture of the trait. Differences in prediction accuracy across marker types were more pronounced for traits with high heritability, high number of QTLs, and SVs as causative variants. In these scenarios, using SV markers resulted in better prediction accuracies than SNP markers, especially when predicting untested genotypes across environments, likely due to more predictors being in linkage disequilibrium with causative variants. The simulations revealed little impact of different effect sizes between SNPs and SVs as causative variants on prediction accuracy. This study demonstrates the importance of knowing the genetic architecture of a trait in deciding what markers and marker types to use in large scale genomic prediction modeling in a breeding program.

Key message

We demonstrate potential for improved multi-environment genomic prediction accuracy using structural variant markers. However, the degree of observed improvement is highly dependent on the genetic architecture of the trait.
Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs
Authors: Pherribo Gordon J. , Taga Michiko E.
Published: March 2023

The majority of microbes are auxotrophs – organisms unable to synthesize one or more metabolites required for their growth. Auxotrophy is thought to confer an evolutionary advantage, yet auxotrophs must rely on other organisms that produce the metabolites they require. The mechanisms of metabolite provisioning by “producers” remain unknown. In particular, it is unclear how metabolites such as amino acids and cofactors, which are found inside the cell, are released by producers to become available to auxotrophs. Here, we explore metabolite secretion and cell lysis as two distinct possible mechanisms that result in release of intracellular metabolites from producer cells. We measured the extent to which secretion or lysis ofEscherichia coliandBacteroides thetaiotaomicronamino acid producers can support the growth of engineeredEscherichia coliamino acid auxotrophs. We found that cell-free supernatants and mechanically lysed cells provide minimal levels of amino acids to auxotrophs. In contrast, bacteriophage lysates of the same producer bacteria can support as many as 47 auxotroph cells per lysed producer cell. Each phage lysate released distinct levels of different amino acids, suggesting that in a microbial community the collective lysis of many different hosts by multiple phages could contribute to the availability of an array of intracellular metabolites for use by auxotrophs. Based on these results, we speculate that viral lysis could be a dominant mechanism of provisioning of intracellular metabolites that shapes microbial community structure.
Inhibition of broomrape germination by 2,4-diacetylphloroglucinol produced by environmentalPseudomonas
Authors: Lurthy Tristan , Perot Ségolène , Gerin-Eveillard Florence , Rey Marjolaine , Wisniewski-Dyé Florence , Vacheron Jordan , Prigent-Combaret Claire
Published: March 2023

Phloroglucinol compounds (PGCs) produced by environmentalPseudomonasare well known for their capacity to limit plant-pathogen infection. Although PGCs and more specifically 2,4-diacetylphloroglucinol (DAPG) are well studied for their antimicrobial properties, they are to some extent toxic for crop plants. Parasitic weeds such as broomrapes (Phelipanche ramosaandOrobanche cumana) cause severe damage to crops and their development must be controlled. Here, we assessed the potential herbicidal effect of the bacterial modelPseudomonas ogaraeF113, a PGCs-producing bacterium, on parasitic weed germination. We show using a mutagenesis approach that PGCs produced in bacterial supernatants are the main determinant inhibiting the germination of broomrapes. The use of individual or cocktails of pure PGCs revealed that the inhibition of the germination depends on the PGCs molecular structure and their concentrations as well as the broomrape species and pathovars. Furthermore, the inhibition caused by the PGCs is irreversible, causing a brown coloration of the broomrape seeds. Then, we evaluated in non-sterile soils the ability of bacterial inoculants or chemical DAPG to limit the infection of broomrapes on oil seed rape. Only the inoculation of PGCs-producing bacteria limited the infection ofP. ramosa. Moreover, elemental profiling analysis of oil seed rape revealed that neither the inoculant nor applied DAPG affected the nutrition capacity of the oil seed rape. Our study expands the knowledge on the role that these multi-talented plant-beneficialPseudomonasplay in the environment and open new avenues for the development of natural bioherbicides to ward off parasitic plant infection.
Humoral and T-cell-mediated responses to a pre-clinical Zika vaccine candidate that utilizes a unique insect-specific flavivirus platform
Authors: Porier Danielle L. , Adam Awadalkareem , Kang Lin , Michalak Pawel , Tupik Juselyn , Santos Matthew A. , Lee Christy , Allen Irving C. , Wang Tian , Auguste Albert J.
Published: March 2023

Vaccination is critical for the control and prevention of viral outbreaks, yet conventional vaccine platforms may involve trade-offs between immunogenicity and safety. Insect-specific viruses have emerged as a novel vaccine platform to overcome this challenge. Detailed studies of humoral and T-cell responses induced by new insect-specific flavivirus (ISFV)-based vaccine platforms are needed to better understand correlates of protection and improve vaccine efficacy. Previously, we used a novel ISFV called Aripo virus (ARPV) to create a Zika virus (ZIKV) vaccine candidate (designated ARPV/ZIKV). ARPV/ZIKV demonstrated exceptional safety and single-dose efficacy, completely protecting mice from a lethal ZIKV challenge. Here, we explore the development of immune responses induced by ARPV/ZIKV immunization and evaluate its correlates of protection. Passive transfer of ARPV/ZIKV-induced immune sera to naïve mice prior to challenge emphasized the importance of neutralizing antibodies as a correlate of protection. Depletion of T-cells in vaccinated mice and adoptive transfer of ARPV/ZIKV-primed T-cells to naïve mice prior to challenge indicated that ARPV/ZIKV-induced CD4+and CD8+T-cell responses contribute to the observed protection but may not be essential for protection during ZIKV challenge. However, vaccination of Rag1 KO, Tcra KO, and muMt−mice demonstrated the critical role for ARPV/ZIKV-induced T-cells in developing protective immune responses following vaccination. Overall, both humoral and T-cell-mediated responses induced by ISFV-based vaccines are important for comprehensive immunity, and ISFV platforms continue to be a promising method for future vaccine development.
Bulk RNA-Sequencing of small airway cell cultures from IPF and post-COVID lung fibrosis patients illustrates disease signatures and differential responses to TGF-β1 treatment
Authors: Uhl Katie , Paithankar Shreya , Leshchiner Dmitry , Jager Tara E , Abdelgied Mohamed , Tripp Kaylie , Peraino Angela M , Kakazu Maximiliano Tamae , Lawson Cameron , Chesla Dave W , Murphy Edward R. , Prokop Jeremy , Chen Bin , Girgis Reda E , Li Xiaopeng
Published: March 2023

IPF is a condition in which an injury to the lung leads to the accumulation of scar tissue. This fibrotic tissue reduces lung compliance and impairs gas exchange. Studies have shown that infection with COVID-19 significantly worsens the clinical outcomes of IPF patients. The exact etiology of IPF is unknown, but recent evidence suggests that the distal small airways, (those having a diameter less than 2 mm in adults), play a role in the early pathogenesis of IPF. TGF-β1 is a main driver of fibrosis in a variety of tissues; the binding of TGF-β1 to its receptor triggers a signaling cascade that results in inflammatory signaling, accumulation of collagen and other components of the extracellular matrix, and immune system activation. This study aimed to investigate possible mechanisms that contribute to worsening lung fibrosis in IPF patients after being diagnosed with COVID-19, with a particular focus on the role of TGF-β1. Small airway cell cultures derived from IPF and post-COVID-19 IPF patient transplant tissues were submitted for RNA-sequencing and differential gene expression analysis. The genetic signatures for each disease state were determined by comparing the differentially expressed genes present in the cells cultured under control conditions to cells cultured with TGF-β1. The genes shared between the culture conditions laid the framework for determining the genetic signatures of each disease. Our data found that genes associated with pulmonary fibrosis appeared to be more highly expressed in the post-COVID fibrosis samples, under both control and TGF-β1-treated conditions. A similar trend was noted for genes involved in the TGF-β1 signaling pathway; the post-COVID fibrosis cell cultures seemed to be more responsive to treatment with TGF-β1. Gene expression analysis, RT-PCR, and immunohistochemistry confirmed increased levels of BMP signaling in the IPF small airway cell cultures. These findings suggest that TGF-β1 signaling in IPF small airway cells could be inhibited by BMP signaling, leading to the differences in genetic signatures between IPF and post-COVID fibrosis.
Small Molecule Screen Identifies Non-Catalytic USP3 Chemical Handle
Authors: Mann Mandeep K. , Wolf Esther , Silva Madhushika , Kwak Haejin , Wilson Brian , Wilson Derek J. , Harding Rachel J. , Schapira Matthieu
Published: March 2023

Zinc-finger ubiquitin binding domains (ZnF-UBDs) are non-catalytic domains mostly found in deubiquitylases (DUBs). They represent an underexplored opportunity for the development of deubiquitylase-targeting chimeras (DUBTACs) to pharmacologically induce the deubiquitination of target proteins. We have previously shown that ZnF-UBDs are ligandable domains. Here, a focused small molecule library screen against a panel of eleven ZnF-UBDs led to the identification of59, a ligand engaging the ZnF-UBD of USP3 with a KDof 14 µM. The compound binds the expected C-terminal ubiquitin binding pocket of USP3 as shown by hydrogen-deuterium exchange mass spectrometry experiments and does not inhibit the cleavage of K48-linked di-ubiquitin by USP3. As such this compound could serve as a chemical starting point to develop bifunctional DUBTACs recruiting USP3 for targeted deubiquitination.

Table of contents graphic
Enhancing building performance of post-fire refurbished apparel manufacturing buildings in Sri Lanka
Authors: Rathnayake Ishara , Sridarran Pournima , Abeynayake Mahesh , Jayakodi Shashini
Published: March 2023

Purpose

The creation of occupant satisfaction can be reached through the involvement of building performance mandates (BPMs) while enhancing the functionality of buildings. BPMs comprise five mandates namely, spatial performance, thermal performance, indoor air quality performance, acoustic performance, and visual performance. BPMs have been recognized as a vital element when refurbishing post-fire apparel buildings. However, the evaluation of post-fire refurbishment projects is mainly focused on mechanical and physical properties while ignoring the BPMs. Further, there is insufficient literature on the BPMs in post-fire building refurbishment. Hence, the purpose of this research is to identify the importance of BPMs, and its challenges and propose strategies to enhance the building performance of post-fire refurbished apparel manufacturing buildings in Sri Lanka.

Design/methodology/approach

The study was conducted by involving a qualitative research approach. An extensive literature review and eighteen semi-structured interviews under three fire-affected apparel cases were involved as data collection methods and collected data were analyzed using content analysis.

Findings

Findings highlighted the procedure of post-fire refurbishment and the importance of BPMs for apparel buildings to enhance building performance in post-fire situations. The research identified 42 challenges encountered in maintaining BPMs of post-fire refurbished apparel buildings and provided 70 strategies to overcome the identified challenges.

Originality/value

This study offers a comprehensive analysis of challenges in maintaining BPMs and strategies to overcome the identified challenges which facilitate enhancing the performance of post-fire refurbished apparel buildings in Sri Lanka.
High-pass negative group delay analysis of single capacitor three-port circuit
Authors: Murad Nour Mohammad , Jaomiary Antonio , Yazdani Samar , Haddad Fayrouz , Guerin Mathieu , Chan George , Rahajandraibe Wenceslas , Baccar Sahbi
Published: March 2023

Purpose

This paper aims to develop high-pass (HP) negative group delay (NGD) investigation based on three-port lumped circuit. The main particularity of the proposed three-port passive topology is the consideration of only a single circuit element represented by a capacitor.

Design/methodology/approach

The methodology of the paper is to consider the S-matrix equivalent model derived from admittance matrix approach. So, an S-matrix equivalent model of a three-port circuit topology is established from admittance matrix approach. The frequency-dependent basic expressions are explored to perform the HP-NGD analysis. Then, the existence condition of HP-NGD function type is analytically demonstrated. The specific characteristics and synthesis equations of HP-NGD circuit with respect to the desired optimal NGD value are established.

Findings

After computing the frequency expressions to perform the HP-NGD analysis, this study demonstrated the existence condition of HP-NGD function type analytically. The validity of the HP-NGD theory is verified by a prototype of three-port circuit. The proof-of-concept (POC) single capacitor three-port circuit presents an NGD response and characteristics from analytical calculation and simulation is in very good correlation.

Originality/value

An innovative theory of HP-NGD three-port circuit is studied. The proposed HP-NGD topology is constituted by only a single capacitor. After the topological description, the S-matrix model is established from the Y-matrix by means of Kirchhoff voltage law and Kirchhoff current law equations. A POC of single capacitor three-port circuit was designed and simulated with a commercial tool. Then, a prototype with a surface-mounted device component was fabricated and tested. As expected, simulation and measurement results in very good agreement with the calculated model show the feasibility of the HP-NGD behavior. This work is compared to other NGD-type function with diverse number of ports and components.
The effect of life cycle stages on capital expenditures: evidence from an emerging market
Authors: Can Gökberk , Demiraj Rezart , Mersni Hounaida
Published: March 2023

Purpose

The purpose of the article is to examine the effect of life cycle stages on capital expenditures, using Borsa Istanbul-listed companies.

Design/methodology/approach

The panel data estimation procedure was used as the primary method to test the hypothesis. The authors used four additional analyses to check the robustness of the results. The model was tested for endogeneity using the generalized method of moments (GMM) estimation. Quantile regression was utilized for the non-parametric test of the model. In the third robustness test, the sample was divided into two using financial constraints with the Size-Age (SA) Index proposed by Hadlock and Pierce (2010). The last analysis removed the global financial crisis (GFC) years from the sample.

Findings

Borsa Istanbul-listed companies tend to invest less as they move forward in their life cycle stages. The results show that market capitalization, operating cash flow levels and leverage positively affect capital expenditure investments. The empirical evidence also revealed that cash holding levels have a negative effect on capital expenditure decisions. Robustness tests support the results.

Practical implications

The findings are potentially useful for investors and managers. Having the information that decreasing capital expenditures signals that the company is in the last stages of its life would be a sign for managers to improve their investment strategies to avoid getting out of business and survive. They need to find options and solutions to propel their companies back on a path of growth. Additionally, the same information could be vital for investors' investment decisions.

Originality/value

This paper contributes to the literature by providing evidence about the effect of life cycle stages on capital expenditures from an emerging market. To the best of the authors’ knowledge, it is the first paper to investigate empirically how moving forward in the life cycle stages affects capital expenditures in an emerging market.
A bibliometric analysis of psychological contract research: current status development and future research directions
Authors: Kozhakhmet Sanat , Rofcanin Yasin , Nurgabdeshov Assylbek , Las Heras Mireia
Published: March 2023

Purpose

The purpose of this paper is to review and analyse the literature on psychological contract (PC) phenomena to date as well as give future research directions in this research area.

Design/methodology/approach

The authors have conducted a bibliometric analysis of 33 years of research on PC. The bibliometric findings have identified various perspectives by drawing the landscape and developmental trajectory of PC research over time. A specific bibliographic analysis and visualization tool VOSviewer was employed to evaluate and process 1999 publications in the Scopus and Web of Science (WoS) database from 1989 to 2022, also author citation analysis, journal co-citation analysis, reference analysis and analysis of 100 milestone articles.

Findings

The authors detected and visualized the landscape of PC area and track how this landscape has developed. Secondly, the authors present the findings emerged from this study’s bibliometric review, with emphasize on future research directions and implications.

Originality/value

This paper presents bibliometric analysis of more than 1,000 research articles from main databases and review of 100 most prominent papers on PC research topic. This article offers academicians and researchers a more sophisticated understanding of the intellectual and conceptual framework of the research body. The authors are providing insights about its structural body of knowledge through an overview of the current state of scholarly development in the field of PC.
Irish transgender voices on mental health and mental health care
Authors: de Vries Jan , Downes Carmel , Sharek Danika , Doyle Louise , Murphy Rebecca , Begley Thelma , McCann Edward , Sheerin Fintan , Smyth Siobhan , Higgins Agnes
Published: March 2023

Purpose

People who identify as transgender face stigma, isolation and harassment while often struggling to come to terms with their gender identity. They also disproportionately experience mental health difficulties. The purpose of this paper is to present the voices of transgender people in the Republic of Ireland (RoI) in regard to the issues they are facing, improvements they would like to see made to schools, workplaces, services and society in general and whether mental health supports fulfil their needs.

Design/methodology/approach

Ten open questions were embedded within a quantitative online survey (LGBTIreland study) on factors impacting social inclusion, mental health and care. These open questions were re-analysed with exclusive focus on the transgender participants (n = 279) using content/thematic analysis.

Findings

The participants in this study reported significant signs of mental distress. The following themes emerged: impact of stigma, deficiencies in mental health services, need for education on transgender identity, importance of peer support, achieving self-acceptance and societal inclusion questioned.

Research limitations/implications

Efforts to recruit young participants have led to a possible over-representation in this study.

Practical implications

The findings suggest the need for improvement in mental health support services, including further education in how to meet the needs of transgender individuals.

Social implications

Transgender people in Ireland experience social exclusion. The need for more inclusivity was emphasised most in secondary schools. Education on transgender identities in all contexts of society is recommended by the participants.

Originality/value

This study reports on the largest group of transgender participants to date in RoI. Their voices will affect perceptions on social inclusion and mental health care.
Integrating AI into business processes and corporate strategies to enhance customer value
Authors: Leavy Brian
Published: March 2023

Purpose

This is a thought-leadership interview with digital-era experts Thomas Davenport and Nitin Mittal on the strategic desirability and implications for legacy companies on being fully committed to becoming AI-driven businesses.

Design/methodology/approach

An interview with thought-leaders in the area of digital strategy.

Findings

The interview explains what it means to be an AI-driven company and how to manage the kind of transformation that legacy will need to go through to become AI-fueled leaders in their sector.

Originality/value

The main value is the direct dialog with digital-era experts on their latest research insights.
Fostering inclusion for refugees and migrants and building trust in the digital public space
Authors: Kuneva Leda , Hough Karen Latricia
Published: March 2023

Purpose

The purpose of this paper is to explore the benefits of co-creation methods when designing information and communications technology (ICT) solutions to aid migrant integration by outlining the process of co-creating an innovative platform with migrants, including asylum seekers and refugees, and non-governmental organisation representatives and public service providers.

Design/methodology/approach

The study used mixed methods and was divided into three stages. Researchers carried out an extensive literature review and case studies, whilst data were collected via surveys, focus groups and in-depth interviews.

Findings

The paper demonstrates that co-creation methods are essential in the development of ICT solutions for vulnerable groups like migrants, asylum seekers and refugees enabling researchers to counter the adverse effects of eurocentric bias by improving inclusiveness and trust in the platform vis-à-vis migrant users.

Originality/value

The research reflects on the development of an innovative platform, created and validated in situ with migrants and other end-users. It provides an often-unexplored analysis of the link between methodological approaches in ICT tools development (co-creation), and real-life impacts for migrants in terms of mitigating digital exclusion and white ethnocentric bias. The article complements two whitepapers and other policy briefs written on the results of this research that have informed EC policy-making in the area of migration, including the EU action plan on integration and inclusion 2021–2027.
Species mixtures increase fine root length to support greater stand productivity in a natural boreal forest
Authors: Huang Chenyan , Chen Han Y. H. , Chang Scott X. , Cahill James F. , Ma Zilong
Published: March 2023

Species mixtures have been widely reported to increase aboveground productivity; however, how tree species mixtures affect root systems in natural forests remains unclear. We hypothesize that mixtures have a greater fine root length compared to single species‐dominated stands to support their greater productivity.

Here, we collected monthly root images from the minirhizotrons installed in 18 stands either dominated by Populus tremuloides, Pinus banksiana, and their mixtures for three years (2015–2017) in post‐fire boreal forests of two stand ages (8 and 34 years old) to test our hypotheses.

We found that the fine root length was higher in mixtures than in single species‐dominated stands, and the magnitude of mixture effects was greater in the 34‐ than in the 8‐year‐old stands in the third year. The mixture effects on fine root length revealed a positive relationship with forest net primary productivity. Root length production, which is the growth of new roots within a year, was not affected by tree species mixtures except for the 8‐year‐old stand in 2015. Tree species mixtures did not affect root length turnover. Root length and root biomass were not significantly correlated at stand level.

Synthesis. Our results show that tree species mixtures positively affect fine root length, with that positive effect increasing with stand development in the studied natural forests. Our results suggest that the greater root length in species mixtures supported the greater forest productivity in species mixtures as the greater root length benefits plant uptake of nutrients and water. Therefore, conserving tree species diversity has implications for improving forest productivity and carbon sequestration in forest ecosystems.
Applying core lexicon analysis in patients with anomic aphasia: Based on Mandarin AphasiaBank
Authors: Jiang Yu‐Er , Liao Xiao‐Yu , Liu Na
Published: March 2023

Background

Patients with anomic aphasia experience difficulties in narrative processing. General discourse measures are time consuming and require necessary skills. Core lexicon analysis has been proposed as an effort‐saving approach but has not been developed in Mandarin discourse.

Aims

This exploratory study was aimed (1) to apply core lexicon analysis in Mandarin patients with anomic aphasia at the discourse level and (2) to verify the problems with core words among people with anomic aphasia.

Methods & Procedure

The core nouns and verbs were extracted from narrative language samples from 88 healthy participants. The production of core words for 12 anomic aphasia and 12 age‐ and education‐matched controls were then calculated and compared. The correlation between the percentages and the Aphasia Quotients of the revised Western Aphasia Battery was analyzed as well.

Outcomes & Results

The core nouns and verbs were successfully extracted. Patients with anomic aphasia produced fewer core words than healthy people, and the percentages differed significantly in different tasks as well as word classes. There was no correlation between the core lexicon use and the severity of aphasia in patients with anomic aphasia.

Conclusions & Implications

Core lexicon analysis may potentially serve as a clinician‐friendly manner of quantifying core words produced at the discourse level in Mandarin patients with anomic aphasia.

WHAT THIS PAPER ADDS

What is already known on the subject

Discourse analyses in aphasia assessment and treatment have increasingly garnered attention. Core lexicon analysis based on English AphasiaBank has been reported in recent years. It is correlated with microlinguistic and macrolinguistic measures in aphasia narratives. Nevertheless, the application based on Mandarin AphasiaBank is still under development in healthy individuals and patients with anomic aphasia.

What this paper adds to existing knowledge

A Mandarin core lexicon set was developed for different tasks. The feasibility of core lexicon analysis to evaluate the corpus of patients with anomic aphasia was preliminarily discussed and the speech performance of patients and healthy people was then compared to provide a reference for the evaluation and treatment of clinical aphasia corpus.

What are the potential or actual clinical implications of this work?

The purpose of this exploratory study was to consider the potential use of core lexicon analysis to evaluate core word production in narrative discourse. Moreover, normative and aphasia data were provided for comparison to develop clinical use for Mandarin patients with anomic aphasia.
Multiple myeloma cell‐derived exosomes promote favorable tumor functional performance by polarizing macrophages toward M2‐like cells
Authors: Razi Bahman , Soleimani Masoud , Soufi‐Zomorrod Mina , Adeli Ahmad , Davoudi Noushin
Published: March 2023

It has long been hypothesized that leukemic cells are able to modulate the fate of resident cells in the tumor microenvironment (TME) toward either supporting or immunosuppressive cells for the development of tumors. Exosomes can be a potential culprit in imposing tumor desire. There is evidence about the impact of tumor‐derived exosomes on different immune cells in different malignancies. However, findings about macrophages are contradictory. Here, we evaluated the potential influence of multiple myeloma (MM)‐cell‐derived exosomes on the polarization of macrophages by examining hallmarks of M1 and M2 macrophages. After treatment of M0 macrophages with isolated exosomes (from U266B1), gene expression (Arg‐1, IL‐10, TNF‐α and IL‐6), immunophenotyping markers (CD206), cytokine secretion (IL‐10 and IL‐6), nitric oxide (NO) production, and redox potentiality of target cells were assessed. Our results revealed significantly increased expression of the genes involved in the development of M2‐like cells but not M1 cells. The CD 206 marker and IL‐10 protein levels were significantly increased at different time points. The expression of IL‐6 mRNA and IL‐6 protein secretion did not change significantly. MM‐cell‐derived exosomes induced significant changes in NO production and intracellular ROS levels in M0 cells.
Outcomes of human immunodeficiency virus‐associated Burkitt lymphoma and diffuse large B‐cell lymphoma treated in Australia: A report from the Australasian Lymphoma Alliance
Authors: Lim Kenneth J. C. , Di Ciaccio Pietro , Polizzotto Mark N. , Milliken Sam , Cochrane Tara , Goh Zhong , Shaw Briony , Perry Evelyn , Gilbertson Michael , Kermode William , Cheah Chan Y. , Latimer Maya , Hamad Nada , Ku Matthew
Published: March 2023

Antiretroviral therapy (ART) has improved outcomes for human immunodeficiency virus‐associated non‐Hodgkin lymphoma (HIV‐NHL). This is an analysis of 44 patients with HIV with Burkitt lymphoma (HIV‐BL) and diffuse large B‐cell lymphoma (HIV‐DLBCL) treated in Australia over a 10‐year period (2009–2019) during the ART and rituximab era. At HIV‐NHL diagnosis, the majority of presenting patients had adequate CD4 counts and undetectable HIV viral load <50 copies/mL. More than 80% of patients received chemotherapy with curative intent, rituximab, and concurrent ART with chemotherapy (immunotherapy). R‐CODOX‐M/IVAC or R‐Hyper‐CVAD (55%) were most commonly used in HIV‐BL. CHOP (58%) was the most commonly used chemotherapy backbone for HIV‐DLBCL, although 45% of patients received more intense chemotherapy regimens. Overall, 93% of patients who received curative therapy completed their intended course. The 2‐year progression‐free survival (PFS) and overall survival (OS) for the HIV‐BL cohort was 67% and 67% respectively. The 2‐year PFS and OS for the HIV‐DLBCL cohort was 77% and 81% respectively. Treatment related mortality was 5%. In all, 83% of patients achieved a CD4 count of >0.2 ×109/L 6 months after the end of treatment. Current Australian practice favours the treatment of HIV‐BL and HIV‐DLBCL similarly to the HIV‐negative population with the use of concurrent ART, achieving outcomes comparable to the HIV‐negative population.
Debate: Academics should collaborate with the technology industry, but not in lieu of noncollaborative research
Authors: Xiao Leon Y.
Published: March 2023

Academic research collaborations with the technology industry should be complementary to and, importantly, must not replace noncollaborative research that is independent from the industry (and, in particular, ‘adversarial research’ whose negative findings will likely operate against industry interests). Reflecting on the author's own research projects concerning companies' compliance with video game loot box regulation, he agrees with Livingstone et al.'s proposition (Child and Adolescent Mental Health, 2022, 28, 150) that research seeking to identify problems (and thereby work against the industry's interests) should be conducted independently (p. 151), at least initially. He also echoes the sentiment expressed by Zendle and Wardle (Child and Adolescent Mental Health, 2022, 28, 155) that ‘a moratorium’ (p. 156) or a ban on industry collaborations is not a proportional response to legitimate concerns about conflict of interest stemming from the video game industry's discretionary provision of data access. A combined approach that conducts both noncollaborative and collaborative research, but with the latter being conducted only after the former's unbiased results are known, might prove fruitful. Academics must bear in mind that industry involvement at any particular stage of the research, or at all, is not always appropriate. Some research questions should not and cannot be answered objectively with industry involvement. Funding bodies and other stakeholders should also recognise this and not render industry collaboration compulsory.
Effect of male–female relatedness on aggression and inbreeding in an egg parasitoid wasp
Authors: Yin Si‐Yu , Tao Yu‐Mei , Liu Peng‐Cheng
Published: March 2023

Aggressive behavior is important for acquiring crucial resources in many animals. As such behavior is costly, selection favors contestants that can accurately gather information regarding the likely costs and benefits of conflict to enable appropriate tactical decisions. Mate choice based on relatedness is widespread among animals and has severe consequences. Theoretically, due to the potential costs of inbreeding, contestants may benefit from discriminating between relative and nonrelative mates and adjusting their behavior accordingly. If inbreeding results in fitness costs, related mates might be perceived as less valuable and individuals might be expected to invest less in costly aggression, and vice versa. However, the role of male–female relatedness in aggression has been less addressed. The egg parasitoid wasp Anastatus disparis, which exhibits extreme male–male aggressive behavior for mating opportunities, was used as an experimental model to explore the role of male–female relatedness in aggression. Inconsistent with our prediction, male–female relatedness had no significant effect on male–male fighting frequency or intensity in A. disparis. The ability of males to discriminate relative from nonrelative females is a prerequisite for male–female relatedness to affect males’ aggression. However, A. disparis males did not exhibit any mating preferences for relative or nonrelative females. Besides, inbreeding did not result in depression in terms of longevity, fecundity or sex ratio in A. disparis. Our finding of no effect of male–female relatedness on male–male fights in A. disparis may be caused by a lack of kin discrimination ability or/and a lack of benefits from discriminating relatives from nonrelatives.
Subnetwork ensembling and data augmentation: Effects on calibration
Authors: Demir A. Çağrı , Caton Simon , Dondio Pierpaolo
Published: March 2023

Deep Learning models based on convolutional neural networks are known to be uncalibrated, that is, they are either overconfident or underconfident in their predictions. Safety‐critical applications of neural networks, however, require models to be well‐calibrated, and there are various methods in the literature to increase model performance and calibration. Subnetwork ensembling is based on the over‐parametrization of modern neural networks by fitting several subnetworks into a single network to take advantage of ensembling them without additional computational costs. Data augmentation methods have also been shown to enhance model performance in terms of accuracy and calibration. However, ensembling and data augmentation seem orthogonal to each other, and the total effect of combining these two methods is not well‐known; the literature in fact is inconsistent. Through an extensive set of empirical experiments, we show that combining subnetwork ensemble methods with data augmentation methods does not degrade model calibration.
A survey of mothers' experiences of shared parenting and domestic violence
Authors: Archer‐Kuhn Beth , Saini Michael , Hughes Judith , Tam Dora , Trudgill Diane I. N.
Published: March 2023

This cross‐sectional survey reports on the experiences and impact of mothers in shared parenting arrangements and their young children ages 0–4 years across three provinces in Canada (Alberta, Manitoba, Ontario). The purpose of the study was to explore shared parenting arrangements in the context of domestic violence, and we sought to recruit mothers from a range of experiences regarding reported violence in their relationships with their ex‐partners. The online survey consisted of standardized tools to measure child development, depression, substance use, and anxiety, extent and severity of domestic violence, and coparenting. Recruiting during the pandemic was challenging, which required various recruitment strategies. The total sample included 84 mothers who completed questionnaires. Findings show that while mothers experienced various forms of domestic violence in shared parenting arrangements, experiences of coercive control were most evident. Implications are identified and discussed in relation to parenting plans, shared parenting and all forms of domestic violence including coercive control.