bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Adverse Outcome Pathways: towards the implementation of transcriptomics data in risk assessments
Authors: Martens Marvin , Meuleman Anna Baya , Kearns Jeroen , de Windt Chesley , Evelo Chris T. , Willighagen Egon L.
Published: March 2023

Adverse Outcome Pathways (AOPs) are designed to provide mechanistic insights into toxicological processes after exposure to a stressor and facilitate the replacement of animal studies with in vitro testing systems. Starting with a Molecular Initiating Event (MIE) and ending with an Adverse Outcome, the sequence of Key Events (KEs) spans across biological levels, but the majority of KEs in AOP-Wiki describe molecular and cellular processes.

That suggests that established transcriptome-wide studies can be used to validate or measure a multitude of KEs simultaneously and be a goldmine of useful information about cellular responses.

Currently, in toxicology, omics technologies are not widely applied in risk assessments of chemicals because of their complexity and lack of consensus on aspects such as standardization, analysis and interpretation. Given their value in hypothesis generation and ability to provide a vast amount of information about a biological response, the challenge lies in the acceptance of using transcriptomics data in regulatory risk assessments.

We here introduce molecular AOPs to define the connections between KEs of the AOP-Wiki and curated biological pathways in WikiPathways, thereby providing a new method for the analysis and interpretation of transcriptomics data to identify KE activation.

To study this, we performed case studies on liver steatosis and mitochondrial complex I inhibition, for which molecular AOPs were developed and public transcriptomics datasets were selected. Upon extension of the molecular AOP networks in Cytoscape, we mapped and analysed transcriptomics data, and calculated an enrichment score for individual KEs. Further interpretation of the data was done through the visualisation of the data on the specific molecular pathways.

Two molecular AOPs were developed and KEs were linked to the appropriate molecular pathways, allowing a detailed exploration of molecular processes with the selected transcrip-tomics datasets. This has shown us that we can verify the activation of specific MIEs and KEs, and assess progression across the AOP in the steatosis case study through variables in exposure time and dose.

These case studies have shown that transcriptomics data can be used for identifying the potential activation of KEs. However, it is also clear that extensive datasets are required to fully test the capabilities of molecular AOPs, and the process of linking molecular pathways and KEs can be challenging, not always allowing one-to-one mapping. While proven valuable to analyse and understand transcriptomic data, pathways linked to KEs appear to show inconsistent levels of activation and should be looked into and refined. More case studies are required to optimize the approaches used for the development and use of molecular AOPs with transcriptomics datasets.
Genome biology and evolution of mating type loci in four cereal rust fungi
Authors: Luo Zhenyan , McTaggart Alistair , Schwessinger Benjamin
Published: March 2023

Obligate heterozygous loci such as sex- or mating-compatibility regions often display suppression of recombination and signals of genomic degeneration. In Basidiomycota, two distinct gene loci confer mating compatibility. These encode for homeodomain (HD) transcription factors and pheromone receptor (Pra)-ligand pairs. To date genome level mating type (MAT) loci analysis is lacking for obligate biotrophic basidiomycetes in the orderPucciniales, which contains many economically important plant pathogens.

Here, we focus on fourPucciniacereal rust species, includingP. coronataf. sp.avenae,Puccinia graminisf. sp.tritici,P. triticinaandP. striiformisf. sp.tritici, which infect oat and wheat.MATloci are located on two separate chromosomes supporting previous hypotheses of tetrapolar mating types in thePucciniales. TheHDlocus is multiallelic in all four species while thePRlocus appears to be biallelic except forP. graminisf. sp.triticiwhich displays genetic features of more than two alleles.HDloci were largely conserved in their macrosynteny within and between species without strong signals of recombination suppression.PRloci proximate regions, however, displayed extensive signs of recombination suppression and genomic degeneration in the three species with a clear biallelicPRlocus. These observations suggest a correlation between recombination suppression, genomic degeneration and allele status ofMATloci which is consistent with recent mathematical modelling and simulations. Finally, we confirm the evolutionary conservation ofMATgene expression during the asexual infection cycle of the cereal host which we propose is related to correct nuclear pairing during spore formation. Together, our study provides insights into the evolution ofMATloci of key pathogenicPucciniaspecies. This detailed understanding is important to predict possible combinations of nuclear pairs that can arise via sexual reproduction or somatic recombination to enable the evolution of newly virulent isolates of these important plant pathogens.

Author summary

Sex of animals and some plants is determined by sex chromosomes. In fungi, mate compatibility is determined by mating type (MAT) loci, which share some features with sex chromosomes including recombination suppression around heterozygous loci. Here, we study theMATloci in fungal pathogens from the orderPuccinialesthat can cause rust diseases on many economically important plants including wheat and oat. We show that one of theMATloci is multiallelic, while the other is biallelic. The biallelic locus shows strong signs of recombination suppression and genetic deterioration with an increase in transposable elements and gene deserts surrounding the locus. Our findings on the genome biology ofMATloci in four economically important pathogens will lead to a better understanding and prediction of evolution of novel virulent isolates that can lead to large scale pandemics in agriculture.
BRD9-SMAD2/3 orchestrates stemness and tumorigenesis in pancreatic ductal adenocarcinoma
Authors: Feng Yuliang , Cai Liuyang , Pook Martin , Liu Feng , Chang Chao-Hui , Mouti Mai Abdel , Nibhani Reshma , Wu Shihong , Deng Siwei , Militi Stefania , Dunford James , Philpott Martin , Fan Yanbo , Fan Guo-Chang , Liu Qi , Qi Jun , Sadayappan Sakthivel , Jegga Anil G. , Oppermann Udo , Wang Yigang , Huang Wei , Jiang Lei , Pauklin Siim
Published: March 2023

The dismal prognosis of pancreatic ductal adenocarcinoma (PDAC) is linked to the presence of pancreatic cancer stem-like cells (CSCs) that respond poorly to current chemotherapy regimens. By small molecule compound screening targeting 142 epigenetic enzymes, we identified that bromodomain-containing protein BRD9, a component of the BAF histone remodelling complex, is a key chromatin regulator to orchestrate the stemness of pancreatic CSCs via cooperating with the TGFβ/Activin-SMAD2/3 signalling pathway. Inhibition and genetic ablation of BDR9 block the self-renewal, cell cycle entry into G0 phase and invasiveness of CSCs, and improve the sensitivity of CSCs to gemcitabine treatment. In addition, pharmacological inhibition of BRD9 significantly reduced the tumorigenesis in patient-derived xenografts mouse models and eliminated CSCs in tumours from pancreatic cancer patients. Mechanistically, inhibition of BRD9 disrupts enhancer-promoter looping and transcription of stemness genes in CSCs. Collectively, the data suggest BRD9 as a novel therapeutic target for PDAC treatment via modulation of CSC stemness.
Hypoxic volatile metabolic markers in the MDA-MB-231 breast cancer cell line
Authors: Issitt Theo , Reilly Matthew , Sweeney Sean T. , Brackenbury William J. , Redeker Kelly
Published: March 2023

Hypoxia in disease describes persistent low oxygen conditions, observed in a range of pathologies, including cancer. In the discovery of biomarkers in biological models, pathophysiological traits present a source of translatable metabolic products for the diagnosis of disease in humans. Part of the metabolome is represented by its volatile, gaseous fraction; the volatilome. Human volatile profiles, such as those found in breath, are able to diagnose disease, however accurate volatile biomarker discovery is required to target reliable biomarkers to develop new diagnostic tools. Using custom chambers to control oxygen levels and facilitate headspace sampling, the MDA-MB-231 breast cancer cell line was exposed to hypoxia (1% oxygen) for 24 hours. The maintenance of hypoxic conditions in the system was successfully validated over this time period. Targeting and non-targeting gas chromatography mass spectrometry approaches revealed four significantly altered volatile organic compounds when compared to control cells. Three compounds were actively consumed by cells: methyl chloride, acetone and n-Hexane. Cells under hypoxia also produced significant amounts of styrene. This work presents a novel methodology for identification of volatile metabolisms under controlled gas conditions with novel observations of volatile metabolisms by breast cancer cells.
Efficient transgene-free genome editing in plants in the T0 generation based on a co-editing strategy
Authors: Huang Xiaoen , Jia Hongge , Xu Jin , Wang Yuanchun , Wen Jiawen , Wang Nian
Published: March 2023

Transgene-free genome editing of plants in the T0 generation is highly desirable but challenging, especially in perennials and vegetatively propagated plants. Here, we investigated the co-editing strategy for generating transgene-free, gene-edited plants viaAgrobacterium-mediated transient expression of cytosine base editor (CBE)/gRNA-Cas12a/crRNA-GFPin planta. Specifically, CBE/gRNA was used to base edit theALSgene to confer resistance to herbicide chlorsulfuron as a selection marker, which has no negative effects on plant phenotypes; Cas12a/crRNA was used for editing genes(s) of interest; GFP was used for selecting transgene-free transformants. Using this approach, transgene-free genome-edited plants were efficiently generated for various genes (either individual or multiplex) in tomato, tobacco, potato, and citrus in the T0 generation. The biallelic/homozygous transgene-free mutation rates for target genes among herbicide-resistant transformants ranged from 8% to 50%. Whole genome sequencing further confirmed transgene-free and absence of off-target mutations in the edited plants. The co-editing strategy is efficient for generating transgene-free, genome-edited plants in the T0 generation, thus being a potent tool for plant genetic improvement.
A native herbaceous community exerts a strong allelopathic effect on the woody range-expanderBetula fruticosa
Authors: Wang Lichao , Oduor Ayub M. O. , Liu Yanjie
Published: March 2023

Biological invasions by range-expanding native and alien plant species often reduce native plant community diversity and productivity. Superior performance of some invasive plants over native plants is due to production of allelochemicals by invaders that suppress growth of native plants. Nevertheless, native plants can also produce allelopathic compounds, which may provide biotic resistance against invasive plant species, in accordance with the homeland security hypothesis. In support of the hypothesis, several previous studies found evidence for allelopathic effects of native plant species on alien plant species. However, as most of these studies tested allelopathic effects of single native plant species on invasive plant species, the contribution of allelopathy to the resistance of native plant communities to invasion has received considerably less attention. Here, we performed two competition experiments in a greenhouse to test for potential pairwise allelopathic effects on each other of a woody range-expanderBetula fruticosaand a community of four native herbaceous species in China. We tested whetherB. fruticosaand the herbaceous community differed in their competitive effects and responses, and whether these were changed by the presence of activated carbon – an allelopathy neutralizer in the soil. Results show that presence of activated carbon ameliorated suppressive effects of the resident herbaceous community on above-ground biomass ofB. fruticosa. By contrast, presence of activated carbon tended to aggravate suppressive effects ofB. fruticosaon the resident herbaceous community. Overall, these results provide support to the homeland security hypothesis and suggest that strong biotic resistance of the resident herbaceous community may limit invasion success of the woody range-expanderB. fruticosa.
Agricultural drivers of field margin plant communities are scale dependent
Authors: Poinas Isis , Fried Guillaume , Henckel Laura , Meynard Christine N
Published: March 2023

In recent decades, agricultural intensification has led to a strong decline in biodiversity. Field margins act as shelters and dispersal corridors for biodiversity in highly disturbed landscapes, and are critical to the maintenance of ecosystem services. However, they are also impacted by agricultural practices in neighbouring fields. Agricultural impacts are often studied at field to landscape scales, and rarely across biogeographic regions. One of the challenges in large-scale studies is the lack of standardized monitoring schemes including both biodiversity and accurate estimation of agricultural practices. Here, we take advantage of a national monitoring scheme in 462 sites in France, to assess the effects of agricultural practices on field margin flora at different extents and resolutions. We used spatial simultaneous autoregressive and generalized dissimilarity models to assess the response of plant richness and composition to climatic, soil and landscape conditions, and to agricultural (fertilization, herbicides) and margin management drivers. Analyses were repeated at the site-level, 40 and 75 km resolutions, and at regional and national extents. We found that the impact of agricultural practices on species richness was most important at the site-level, whereas climate and crop diversity became more important at the 75 km resolution. Compositional variations responded differently, with climate being more important at the site-level, and fertilization and crop diversity at the coarsest resolution. There was a strong variation in the variance explained by models among regions, but climate effects were weaker within biogeographic units compared to the national level, and different agricultural practices stood out as influential in different regions, suggesting that the regional context is fundamental in determining plant community structure. To efficiently conserve biodiversity, we therefore recommend the implementation of agricultural measures adapted to each region.
Physiological stress drives the emergence of aSalmonellasubpopulation through ribosomal RNA regulation
Authors: Mattioli Camilla Ciolli , Eisner Kfir , Rosenbaum Aviel , Wang Mengyu , Amir Ariel , Golding Ido , Avraham Roi
Published: March 2023

Bacteria undergo cycles of growth and starvation, to which they must adapt swiftly. One important strategy for adjusting growth rates relies on ribosomal levels. While high ribosomal levels are required for fast growth, their dynamics during starvation remain unclear. Here, we analyzed ribosomal RNA (rRNA) content of individualSalmonellacells using Fluorescence In-Situ Hybridization (rRNA-FISH). During the transition from exponential to stationary phase we measured a dramatic decrease in rRNA numbers only in a subpopulation, resulting in a bimodal distribution of cells with high and low rRNA content. We showed that the two subpopulations are phenotypically distinct when subjected to nutritional upshifts. Using a transposon screen coupled with rRNA-FISH, we identified two mutants acting on rRNA transcription shutdown and degradation, that abolished the formation of the subpopulation with low rRNA content. Our work suggests thatSalmonellaemploys a bet-hedging strategy in regulating ribosomal levels that may be beneficial for survival.
Small volume blood-brain barrier opening in macaques with a 1 MHz ultrasound phased array
Authors: Manuel Thomas J. , Sigona Michelle K. , Phipps M. Anthony , Kusunose Jiro , Luo Huiwen , Yang Pai-Feng , Newton Allen T. , Gore John C. , Grissom William , Chen Li Min , Caskey Charles F.
Published: March 2023

Focused ultrasound blood-brain barrier (BBB) opening is a promising tool for targeted delivery of therapeutic agents into the brain. The volume of opening determines the extent of therapeutic administration and sets a lower bound on the size of targets which can be selectively treated. We tested a custom 1 MHz array transducer optimized for cortical regions in the macaque brain with the goal of achieving small volume openings. We integrated this device into a magnetic resonance image guided focused ultrasound system and demonstrated twelve instances of small volume BBB opening with average opening volumes of 59 ± 37 mm3and 184 ± 2 mm3in cortical and subcortical targets, respectively. We developed real-time cavitation monitoring using a passive cavitation detector embedded in the array and characterized its performance on a bench-top flow phantom mimicking transcranial BBB opening procedures. We monitored cavitation duringin-vivoprocedures and compared cavitation metrics against opening volumes and safety outcomes measured with FLAIR and susceptibility weighted MR imaging. Our findings show small BBB opening at cortical targets in macaques and characterize the safe pressure range for 1 MHz BBB opening. Additionally, we used subject-specific simulations to investigate variance in measured opening volumes and found high correlation (R2= 0.8577) between simulation predictions and observed measurements. Simulations suggest the threshold for 1 MHz BBB opening was 0.53 MPa. This system enables BBB opening for drug delivery and gene therapy to be targeted to more specific brain regions.
Is STEM a better adaptor than non-STEM groups with online education: an Indian peri-urban experience
Authors: Das Aakash Ranjan , Bhattacharyya Asmita
Published: March 2023

Purpose

The existing literature contains few references on the better adaptors of online distance education amongst STEM (read as science, technology, engineering and mathematics) and non-STEM (composed of humanities, social science and commerce) study groups in an Indian peri-urban context. The study's objective is to determine the better adaptor amongst these two study groups in online distance learning in higher education systems in an Indian peri-urban context.

Design/methodology/approach

The investigation was carried out prior to COVID-19 and during the pandemic. The inquiry is triangulated in nature with a disproportionate stratified random sampling approach used to pick 312 post-graduate students (STEM = 135 and non-STEM = 177) from a peri-urban higher education institute in West Bengal, India, using the “Raosoft” scale. Given the prevailing social distance norms, 235 samples of respondents from 312 students were evaluated via telephonic/online interviews during the COVID-19 period. The data were analysed using SPSS 22.

Findings

This study's investigations reveal that the STEM respondents have better digital profiles, better basic computing and Internet knowledge and greater digital usage for academic purposes before the pandemic times than the non-STEM group. This prior digital exposure has enabled the STEM group to cope with regular online distance education during the pandemic more quickly than the non-STEM group, as evidenced by their regular attendance in online classes and their greater awareness of its utilitarian role than the other group.

Originality/value

The study offers a way forward direction to evolve with more inclusive online distance learning in peri-urban Indian regions.
Perceptions of food business operators in relation to importance of official food control in food safety: a case of Kirklees Council
Authors: Babatola Samuel Soledayo
Published: March 2023

Purpose

The purpose of this paper is to critically examine the perceptions of food business operators (FBOs) in Kirklees Council in relation to the importance of official food inspection of food premises, performed by the local authority.

Design/methodology/approach

A semi-structured questionnaire was developed to survey the opinions of FBOs in Kirklees Council in relation to the significance and consistency of official food control. The business types included were retailers, commercial restaurants, schools, care homes, pub, bars and cafes.

Findings

Based on the total of 236 respondents, the results show that 45.8% of the respondents opined that official food control has considerably improved their food hygiene practices and that official inspection is their only source of information about the latest food safety legislation. Moreover, another 168(71.2%) believed that the instructions given by the inspectors are clear and easily understandable. However, some respondents, especially the small and medium-sized businesses believed that remedying noncompliance caused them financial burden. In addition, significant positive correlations exist between the bigger FBOs and high frequencies of negotiating noncompliance with the inspectors due to the high cost of capital that will be needed to remedy the spotted noncompliance by an officer during control (Kruskal–Wallis r = 0.034, p < 0.003).

Research limitations/implications

As with most studies, it is important to borne in mind that the design of the current study is subject to limitations and these limitations could be addressed in future research. The self-reported data collection employed in this study is limited by the fact that it rarely can be independently verified. In other words, the self-reported data used in this study might be subject to (1) selective memory: respondents might remember or not able to remember all the details of the inspections that occurred at some point in the past, however, inspections are often documented, and businesses usually have a copy of every inspection reports. (2) exaggeration: respondents might over or underrepresent outcomes of inspections and (3) attribution: respondents might attribute positive events and outcomes to their own agency but attribute negative events and outcomes to external forces. Nonetheless, the strength of this study lies in its large sample size and high response rate which makes it easier to assess the representativeness of the sample and to generalise the results.

Originality/value

The behaviour of the FBOs towards food control and the opinion of the FBOs about food safety may have an important effect on the organisation of official food control in Kirklees Council, but there is no scientific data to back it up. Furthermore, the perceptions of FBOs and the role of food control in food safety in Kirklees Council have not been investigated, which makes this research a novelty.
Spillovers of underground gas storage facilities and their role in the sustainable energy markets: assessment and policy recommendations
Authors: Chrysochoou Anastasios , Zissis Dimitris , Chalvatzis Konstantinos , Andriosopoulos Kostas
Published: March 2023

Purpose

The purpose of this study is to investigate the impact of the construction and operation of underground gas storage (UGS) facilities, under the prism of the recent rise in energy prices. The focus is on developing energy markets interconnected with gas producers through pipelines and has access to liquefied natural gas (LNG) facilities in parallel.

Design/methodology/approach

Through a focal market in Europe, the authors estimate the economic value for both stakeholders and consumers by introducing a methodology, appropriately adjusted to the specificities of the domestic energy market. The Transmission System Operator, the Energy Market Regulator, the Energy Exchange and Eurostat are the main data sources for our calculations and conclusions.

Findings

The authors investigate the perspectives of UGS facilities, identifying financial challenges considering specific energy market conditions which are barriers to new storage facilities. Nevertheless, the energy price rocketing coupled with the security of gas supply issues, which arose in autumn 2021 and were continuing in 2022 due to the Russia–Ukraine crisis, highlight that gas storage remains, at least for the midterm, at the core of European priorities.

Originality/value

The paper emphasizes on developing markets toward green transition, proposing tangible policy recommendations regarding gas storage. A new methodological approach is proposed, appropriate to quantify the economic value of UGSs in such markets. Last, a mix of energy policy options is suggested which include regulatory reforms, support schemes and new energy infrastructures that could make the gas storage investments economically viable.
Identifying determinants in the first turnover of new graduate employees in Korea: applying a discrete-time survival analysis
Authors: Lee Yunsoo , Yang Junyeong , Lee Jae Young
Published: March 2023

Purpose

The high turnover of new graduate employees has become a concern for many organizations in Korea. This study explores when new graduate employees leave first jobs and what makes these employees decide to leave employees' organizations.

Design/methodology/approach

Using national panel data from South Korea, the authors employed a survival analysis and examined the factors that explain the turnover of new graduate employees.

Findings

The findings of this study reveal that many new graduate employees leave the employees' organizations within two years. Moreover, work conditions, work satisfaction and job-skill match were associated with new graduate employee turnover.

Originality/value

Based on the results of survival analysis derived from actual turnover data, not turnover intentions, the authors emphasize appropriate human resources (HR) intervention, a working environment and organizational culture, and employee development opportunities.
Fear of Covid-19 and perceived academic safety: the buffering role of personal resources
Authors: Azila-Gbettor Edem Maxwell , Mensah Christopher , Agbodza Mavis
Published: March 2023

Purpose

The study investigates the moderating effect of personal resources, including optimism and resilience, on the link between fear of Covid-19 and perceptions of academic safety among university students in Ghana.

Design/methodology/approach

A total of 618 students took part in the research by completing an online self-reported questionnaire. The respondents were chosen using a simple random sample method. The data was processed and analysed using IBM SPSS version 24 and SEM-PLS, respectively.

Findings

Results reveal fear of Covid-19 positively influence students' perception of academic safety. Furthermore, both resilience and optimism mitigate the impact of fear of Covid-19 on students' perceptions of academic safety.

Originality/value

This is the first study to examine personal resources as a moderator between fear of Covid-19 and students' perceptions of academic safety. Practical and theoretical implications are added to the text.
Financial inclusion matter for poverty, income inequality and financial stability in developing countries: new evidence from public good theory
Authors: Khan Ismail , Khan Iftikhar
Published: March 2023

Purpose

This paper aims to examine the influence of financial inclusion (FI) on poverty, income inequality and financial stability from the perspective of public good (PG) theory in developing countries.

Design/methodology/approach

This study applies the fixed effects model (FEM), pooled ordinary least square (OLS) regression and generalized method of moment (GMM) across panal data of 69 developing countries from 2002 to 2020 inclusive.

Findings

Multiple regression analyses show that FI reduces poverty and income inequality while improving financial stability. Secondary enrolment ratio, GDP per capita, and trade openness reduce poverty and income inequality. However, a higher inflation rate increases poverty and income inequality while reducing financial stability. Finally, age dependency ratio and population do not affect poverty, income inequality or financial stability.

Research limitations/implications

The regulators and policymakers in developing countries should raise the level of formal FI by expanding the size of the formal financial sector and improving the access of the large unbanked population to financial products/services. Improving FI enables the unbanked population to take over productive activities and ease consumption, which in turn complementing economic growth.

Social implications

The increase in FI enables the developing countries to include the financially excluded population through formal financial products and services, which improve financial stability and eradicate poverty and income inequality in society. Thus, the FI enhances the social welfare of society.

Originality/value

This is the first study that examines the impact of FI poverty, income inequality and financial stability in the context of developing countries. This study contributes to the theoretical implications of the PG theory by examining the influence of FI on poverty, income inequality and financial stability in the context of developing countries.
An international examination of market orientation and performance in residential property management
Authors: Wilson Grant Alexander , Millard Gabriel , Hills Cameron
Published: March 2023

Purpose

The paper offers clarity to the market orientation (MO) and performance relationship in real estate by examining the limited relevant literature, presenting international results and discussing the implications for market orientation researchers and real estate practitioners.

Design/methodology/approach

Based on a survey of 1,251 individual renters in the USA, the United Kingdom (UK) and Canada, this study examines the relationship between residential property managers’ MO and performance. It extends MO research in real estate by focusing on property management as opposed to property development.

Findings

The results show that MO and performance are correlated in all three countries. Commitments to understanding and serving customers and differentiating from competitors are shown to enhance performance measures including residential tenants’ loyalty toward the property manager, trust in the property manager, pride in rental accommodation and commitment to paying rent on time.

Originality/value

This study is one of the largest MO studies in real estate in terms of sample size and offers a unique international perspective. The research is novel as MO is evaluated by tenants as opposed to self-assessed by firms. The paper offers a new measure of property manager performance and provides strategic directives for real estate professionals seeking to enhance competitiveness.
Application of Guba and Lincoln's parallel criteria to assess trustworthiness of qualitative research on indigenous social protection systems
Authors: Enworo Oko Chima
Published: March 2023

Purpose

This paper illustrates how Guba and Lincoln's parallel criteria for establishing trustworthiness, can be adapted and applied to qualitative research on indigenous social protection systems. It provides insights for social protection researchers, exploring plausible qualitative research rigor evaluation criteria, on plausible alternatives.

Design/methodology/approach

The paper draws on qualitative evidence from a larger ethnographic study on the dynamics of indigenous social protection systems in Nigeria. It illustrates the systematic application of Guba and Lincoln's parallel criteria.

Findings

Available evidence from the study shows that Guba and Lincoln's parallel criteria is viable for establishing trustworthiness of qualitative research on indigenous social protection systems. The criteria can facilitate credible and reliable research outcomes in research on improving social protection policy and practice.

Research limitations/implications

Qualitative inquiries that draw on Guba and Lincoln's parallel criteria as evaluation criteria for trustworthiness can complement quantitative research on social protection. This makes it imperative to incorporate both, in social protection research for a holistic system. How this can be done is beyond the scope of this paper but needs to be explored by future research.

Originality/value

Contrary to the use of Guba and Lincoln's parallel criteria in qualitative research in other contexts, the use of the criteria has not been carefully examined in qualitative research on indigenous social protection systems. This paper is an attempt to fill this gap.
Local governance and financial distress in local governments: the mediating role of delivery system
Authors: Wakwabubi Michael Jackson , Nkundabanyanga Stephen Korutaro , Orobia Laura , Kaawaase Twaha Kigongo
Published: March 2023

Purpose

The purpose of this paper is to establish the mediating role of local government delivery system (here after delivery system) in the relationship between local governance (hereafter, governance) and financial distress of local governments in Uganda.

Design/methodology/approach

This study is correlational and cross-sectional. It uses a questionnaire survey on a sample of 109 local governments (districts) of Uganda. The data are analysed using SPSS, partial least squares structural equation modelling and Jose’s MedGraph.

Findings

Results indicate that government delivery system mediates the relationship between governance and financial distress. Delivery system in terms of capacity development and community participation causes positive variances in local government’s financial distress. Also, governance in terms of political clientelism significantly contributes to financial distress more than oversight mechanisms and audit quality. The study finds that delivery system causes more variance in financial distress than governance.

Originality/value

This study applies the new public management and network governance theory and tests the efficacy of delivery system and governance on financial distress in one-go and succeeded in explaining financial distress of local government using Uganda as the setting; the authors join previous scholars that root for multi-theoretical approaches. Also, this study’s design has allowed for the consideration of more than simply the main effects of governance and delivery systems by exploring the mediating role of delivery systems in the link between governance and financial distress. As such, the authors may now have a more accurate and detailed description of the relationships between governance, delivery system and local government financial distress.
Foraging under extreme events: Contrasting adaptations by benthic macrofauna to drastic biogeochemical disturbance
Authors: Wang Yiming V. , Larsen Thomas , Lebrato Mario , Tseng Li‐Chun , Lee Pei‐Wen , Sánchez Nicolás , Molinero Juan‐Carlos , Hwang Jiang‐Shiou , Chan Tin‐Yam , Garbe‐Schönberg Dieter
Published: March 2023

Hydrothermal vent systems are important biodiversity hotspots that host a vast array of unique species and provide information on life's evolutionary adaptations to extreme environments. However, these habitats are threatened by both human exploitation and extreme natural events, both of which can rapidly disrupt the delicate balance of the food webs found in these systems. This is particularly true for shallow vent endemic animals due to their limited dietary niche and specialized adaptations to specific biogeochemical conditions.

In this study, we used the shallow hydrothermal vents of Kueishantao off the coast of Taiwan as a natural laboratory to examine the response of a benthic food web to a M5.8 earthquake and a C5 typhoon that led to a two‐year “near shutdown” of the vents. These perturbations drastically altered the local biogeochemical cycle and the dietary availability of chemosynthetic versus photosynthetic food resources.

Our analysis of multiple stable isotopes, including those of sulphur, carbon, and nitrogen (δ34S, δ13C, and δ15N), from different benthic macrofauna reveals that endemic and non‐endemic consumers exhibited different responses to sudden disruption in habitat and biogeochemical cycling.

The endemic vent crab, Xenograpsus testudinatus, continued to partially rely on chemosynthetic sulphur bacteria despite photosynthetic sources being the most dominant food source after the disruption. We posit that X. testudinatus has an obligate nutritional dependence on chemoautotrophic sources because the decrease in chemoautotrophic production was accompanied by a dramatic decrease in the abundance of X. testudinatus. The population decline rate was ~19 individuals per m2 per year before the perturbation, but the decline rate increased to 40 individuals per m2 per year after the perturbation. In contrast, the non‐endemic gastropods exhibited much greater dietary plasticity that tracked the overall abundance of photo‐ and chemo‐synthetic dietary sources.

The catastrophic events in shallow hydrothermal vent ecosystem presented a novel opportunity to examine dietary adaptations among endemic and non‐endemic benthic macrofauna in response to altered biogeochemical cycling. Our findings highlight the vulnerability of benthic specialists to the growing environmental pressures exerted by human activities worldwide.

Read the free Plain Language Summary for this article on the Journal blog.
Pathways of glyphosate effects on litter decomposition in grasslands
Authors: Vivanco Lucía , Sánchez María Victoria , Druille Magdalena , Omacini Marina
Published: March 2023

Grasslands store a third of global terrestrial carbon but are vulnerable to carbon loss due to inappropriate livestock grazing. Grasslands management can be improved with a mechanistic understanding of biogeochemical processes that determine carbon storage, such as plant litter decomposition.

Herbicides, such as glyphosate, are used to improve the quantity and quality of the forage. In the Flooding Pampa, the most extensive cattle grazed natural grassland and one of the few remnants' temperate grasslands in South America—glyphosate is applied to promote Lolium multiflorum, a forage grass associated with a fungal endophyte nontoxic for cattle.

We studied five mechanistic pathways in which the application of glyphosate can alter litter decomposition. We grouped them into single application pathways, through effects on living plants (1), leaf litter (2) and bare soil (3), and repeated annual application pathways, through legacies on ecosystem properties (4) and through the growth of an annual forage grass with a fungal endophyte (5). Single application pathways were tested in a greenhouse experiment using leaf litter of L. multiflorum and of a native dominant grass. Repeated annual application pathways were tested through a field experiment with 3‐year annual glyphosate application using leaf and root litter of L. multiflorum with and without endophyte association.

Glyphosate application on living plants produced leaf litter with 70% higher nitrogen content and 140% higher decomposition constant than naturally senesced litter. In contrast, glyphosate application on naturally senesced leaf litter reduced decomposition constant by 20%. Glyphosate application on the soil did not affect the decomposition of naturally senesced leaf litter but accelerated the decomposition of the glyphosate‐killed plants even more.

Legacies of repeated annual application of glyphosate resulted in a notable reduction in plant cover (45%) and potential soil respiration (57%), with a consistent acceleration of leaf (53%) and root (18%) litter decomposition. Furthermore, endophytes in L. multiflorum plants reduced leaf litter decomposition by 22%. On the contrary, endophytes did not alter root litter decomposition.

Glyphosate application on living plants and legacies of repeated application on the ecosystem stimulate litter decomposition, which can result in a net carbon loss from grasslands. In other ecosystems, the net result on decomposition would depend on the relative cover of vegetation, above‐ground litter and bare soil. This study highlights that glyphosate application should be considered when evaluating sustainable management to preserve and enhance soil carbon storage in grasslands.

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Nutrient‐based species selection is a prevalent driver of community assembly and functional trait space in tropical forests
Authors: Peguero Guille , Coello Fernando , Sardans Jordi , Asensio Dolores , Grau Oriol , Llusià Joan , Ogaya Romà , Urbina Ifigenia , Van Langenhove Leandro , Verryckt Lore T. , Stahl Clément , Bréchet Laëtitia , Courtois Elodie A. , Chave Jérôme , Hérault Bruno , Janssens Ivan A. , Peñuelas Josep
Published: March 2023

Soil nutrient availability and functional traits interact in complex ways during the assembly of tree communities hindering our understanding of the implications that this may have for their phylogenetic and functional diversity.

We combined abundance, taxonomic, phylogenetic and functional trait data of 222 tree species distributed along nutrient concentration gradients at 24 plots in two tropical forest study sites. We analysed micro and macronutrient concentration in organic and topsoil horizons and tested for the following: (1) nutrient‐based species sorting due to contrasting trait–environment relationships, (2) whether nutrient filtering has consequences for phylogenetic and functional diversity, and functional space size and occupancy and (3) we mapped trait distributions across the phylogeny of tree species to track the evolutionary signature of nutrient availability.

We found that total nitrogen (N), available phosphorus and total potassium in soil accounted for 68% of the variation in tropical tree species community composition, with strong associations with nutrient concentration for 89% of the tree species included in the analysis. This nutrient‐based species selection was mediated by interactions between the three soil nutrient concentrations with leaf nitrogen, leaf thickness and wood density. Soil N concentration was positively associated with the functional space at site level. At plot level, soil N concentration positively correlated with functional evenness and it was negatively associated with the functional space not occupied by any species in the tree community. Despite the phylogenetic conservatism of leaf N across tree lineages even when not considering legumes, many sister‐species pairs show contrasting values which match with their habitat preferences thus indicating the evolutionary lability of this trait, particularly within recently diversified clades.

Synthesis. Our results demonstrate that soil nutrient‐based species selection is a prevalent driver of community assembly in tropical forests, a process mediated by key functional traits within the leaf and wood economics spectrum. Functional space size and its filling increase with soil nutrient concentration, whereas niche vacancy decreases. This selection process has likely influenced tropical tree species diversification patterns via habitat specialization.
Epigenetic and genetic inactivation of tumor suppressor miR‐135a in non‐small‐cell lung cancer
Authors: Choi Jin Eun , Jeon Hyo Sung , Wee Hyun Jung , Lee Ji Yun , Lee Won Kee , Lee Shin Yup , Yoo Seung Soo , Choi Sun Ha , Kim Dong Sun , Park Jae Yong
Published: March 2023

Background

Despite therapeutic advances, lung cancer prognosis remains poor. Loss of heterozygosity (LOH) in the 3p21 region is well documented in lung cancer, but the specific causative genes have not been identified.

Materials and Methods

Here, we aimed to examine the clinical impact of miR‐135a, located in the 3p21 region, in lung cancer. miR‐135a expression was assessed using quantitative real‐time polymerase chain reaction. LOH was analyzed at microsatellite loci D3S1076 and D3S1478, and promoter methylation status was determined by pyrosequencing of resected samples of primary non‐small‐cell lung cancer (NSCLC). The regulation of telomerase reverse transcriptase (TERT) was evaluated in lung cancer cells H1299 by luciferase report assays after treatment with miR‐135a mimics.

Results

miR‐135a was significantly downregulated in squamous cell cancer (SCC) tumor tissues compared to normal tissues (p = 0.001). Low miR‐135a expression was more frequent in patients with SCC (p = 2.9 × 10−4) and smokers (p = 0.01). LOH and hypermethylation were detected in 27.8% (37/133) and 17.3% (23/133) of the tumors, respectively. Overall, 36.8% (49/133) of the NSCLC cases harbored either miR‐135a LOH or promoter hypermethylation. The frequencies of LOH and hypermethylation were significantly associated with SCCs (p = 2 × 10−4) and late‐stage (p = 0.04), respectively. MiR‐135a inhibited the relative luciferase activity of psiCHECK2‐TERT‐3'UTR.

Conclusion

These results suggest that miR‐135a may act as a tumor suppressor to play an important role in lung cancer carcinogenesis, which will provide a new insight into the translational value of miR‐135a. Further large‐scale studies are required to confirm these findings.
Safety evaluation of immune checkpoint inhibitors combined with chemotherapy for the treatment of small cell lung cancer: A meta‐analysis of randomized controlled trials
Authors: Longo Vito , Rizzo Alessandro , Catino Annamaria , Montrone Michele , Galetta Domenico
Published: March 2023

Background

The addition of immune checkpoint inhibitors (ICIs) to chemotherapy is the new standard of care in the first‐line treatment of small cell lung cancer (SCLC). However, although the concomitant use of immunotherapy and chemotherapy can increase the antitumor efficacy, it can also increase toxicity. The present study evaluated the tolerability of immune‐based combinations in the first‐line treatment of SCLC.

Methods

Relevant trials were identified by searching electronic databases and conference meetings. Seven phase II and III randomized controlled trials and 3766 SCLC patients were included in the meta‐analysis (immune‐based combinations = 2133; chemotherapy = 1633). Outcomes of interest included treatment‐related adverse events (TRAEs) and the rate of discontinuation due to TRAEs.

Results

Immune‐based combination treatment was associated with a higher risk of grade 3–5 TRAEs (odds ratio [OR], 1.16; 95% confidence interval [CI]: 1.01–1.35). Immune‐based combinations were associated with a higher risk of TRAEs leading to discontinuation (OR, 2.30; 95% CI: 1.17–4.54). No differences were observed in grade 5 TRAEs (OR, 1.56; 95% CI: 0.93–2.63).

Conclusion

This meta‐analysis indicates that the addition of immunotherapy to chemotherapy in SCLC patients is associated with a higher risk of toxicity and probably of treatment discontinuation. Tools for identifying SCLC patients that would not benefit from immune‐based therapy are urgently needed.