bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated systems biology identifies disruptions in mitochondrial function and metabolism as key contributors to heart failure with preserved ejection fraction (HFpEF)
Authors: Gibb Andrew A. , LaPenna Kyle , Gaspar Ryan B. , Latchman Nadina R. , Tan Yinfei , Choya-Foces Carmen , Doiron Jake E. , Li Zhen , Xia Huijing , Lazaropoulos Michael P. , Conwell Mariell , Sharp Thomas E. , Goodchild Traci T. , Lefer David J. , Elrod John W.
Published: October 2024

Background

Heart failure with preserved ejection fraction (HFpEF) accounts for ∼50% of HF cases, with no effective treatments. The ZSF1-obese rat model recapitulates numerous clinical features of HFpEF including hypertension, obesity, metabolic syndrome, exercise intolerance, and LV diastolic dysfunction. Here, we utilized a systems-biology approach to define the early metabolic and transcriptional signatures to gain mechanistic insight into the pathways contributing to HFpEF development.

Methods

Male ZSF1-obese, ZSF1-lean hypertensive controls, and WKY (wild-type) controls were compared at 14w of age for extensive physiological phenotyping and LV tissue harvesting for unbiased metabolomics, RNA-sequencing, and assessment of mitochondrial morphology and function. Utilizing ZSF1-lean and WKY controls enabled a distinction between hypertension-driven molecular changes contributing to HFpEF pathology, versus hypertension + metabolic syndrome.

Results

ZSF1-obese rats displayed numerous clinical features of HFpEF. Comparison of ZSF1-lean vs WKY (i.e., hypertension-exclusive effects) revealed metabolic remodeling suggestive of increased aerobic glycolysis, decreased β-oxidation, and dysregulated purine and pyrimidine metabolism with few transcriptional changes. ZSF1-obese rats displayed worsened metabolic remodeling and robust transcriptional remodeling highlighted by the upregulation of inflammatory genes and downregulation of the mitochondrial structure/function and cellular metabolic processes. Integrated network analysis of metabolomic and RNAseq datasets revealed downregulation of nearly all catabolic pathways contributing to energy production, manifesting in a marked decrease in the energetic state (i.e., reduced ATP/ADP, PCr/ATP). Cardiomyocyte ultrastructure analysis revealed decreased mitochondrial area, size, and cristae density, as well as increased lipid droplet content in HFpEF hearts. Mitochondrial function was also impaired as demonstrated by decreased substrate-mediated respiration and dysregulated calcium handling.

Conclusions

Collectively, the integrated omics approach applied here provides a framework to uncover novel genes, metabolites, and pathways underlying HFpEF, with an emphasis on mitochondrial energy metabolism as a potential target for intervention.
Microglia respond to elevated intraocular pressure and synapse loss in the visual thalamus in a mouse model of glaucoma
Authors: Thompson Jennifer L. , McCool Shaylah , Smith Jennie C. , Schaal Victoria , Pendyala Gurudutt , Yelamanchili Sowmya , Van Hook Matthew J.
Published: October 2024

Microglia are resident immune cells of the central nervous system and mediate a broad array of adaptations and responses during disease, injury, and development. Typically, microglia morphology is understood to provide a window into their functional state. However, it is apparent that they have the capacity to adopt a broad spectrum of functional phenotypes characterized by numerous morphological profiles and associated gene expression profiles. Glaucoma, which leads to blindness from retinal ganglion cell (RGC) degeneration, is commonly associated with elevated intraocular pressure and has been shown to trigger microglia responses within the retinal layers, at the optic nerve head, and in retinal projection targets in the brain. The goal of this study was to determine the relationship of microglia morphology to intraocular pressure and the loss of retinal ganglion cell output synapses in the dorsolateral geniculate nucleus (dLGN), a RGC projection target in the thalamus that conveys information to the primary visual cortex. We accomplished this by analyzing dLGN microglia morphologies in histological sections from DBA/2J mice, which develop a form of inherited glaucoma. Microglia morphology was analyzed using skeletonized Iba1-fluorescence images and fractal analyses of individually reconstructed microglia cells. We found that microglia adopted more simplified morphologies, characterized by fewer endpoints and less total process length per microglia cell. There was an age-dependent shift in microglia morphology in tissue from control mice (DBA/2JGpnmb+) that was accelerated in DBA/2J mice. Microglia morphological measurements correlated with cumulative intraocular pressure, immunofluorescence labeling for the complement protein C1q, and density of vGlut2-labeled RGC axon terminals. Additionally, fractal analysis revealed a clear distinction between control and glaucoma dLGN, with microglia from ocular hypertensive DBA/2J dLGN tissue showing an elongated rod-like morphology. RNA-sequencing of dLGN tissue samples showed an upregulation of immune system-related gene expression and several specific genes associated with microglia activation and potential neuroprotective functions. These results suggest that microglia in the dLGN alter their physiology to respond to RGC degeneration in glaucoma, potentially contributing to CNS adaptations to neurodegenerative vision loss.
From raw footage to behaviour: an automated pipeline for activity monitoring and behaviour identification in the wild
Authors: Silva Liliana R. , Ferreira André C. , Doutrelant Claire , Covas Rita
Published: October 2024

Studies of animal behaviour usually rely on direct observations or manual annotations of video recordings for data collection. However, such methods can be very time-consuming and inefficient, leading to sub-optimal sample sizes. Recent advances in deep-learning have shown great potential to overcome such limitations. Nonetheless, for behavioural recognition, solutions currently available are mostly focused on laboratory and/or standardized settings.

Here, we present a pipeline to guide researchers in building their own behavioural recognition system from their video data. Our pipeline is replicable and especially useful for studies in the wild. We take advantage of over 12215hs of manually annotated behaviours of sociable weavers (Philetarius socius). As behaviour classifiers we used long-short term neural networks (LSTMs) known to be suitable to classify temporal sequences of data such as video-based behavioural data.

LSTMs allowed us to: 1) monitor nest activity by detecting the birds’ presence and simultaneously classifying the type of trajectory: i.e., nest-chamber entrance or exit; and 2) identify the respective behaviour performed: provisioning, building or aggression. With our pipeline we reduced the behavioural annotation error by 21%, while increasing by eight times the analyses speed.

This work demonstrates how previously analysed long-term data can be used to develop highly-efficient automated behavioural analyses, whereas this pipeline is easily adaptable to other species and behaviours, requiring only labelled video data.
RNA toehold switch-based reporter assay to assess bacterial uptake of antisense oligomers
Authors: Sarkar Paramita , Popella Linda , Pérez-Jiménez Sandra , Vogel Jörg
Published: October 2024

Antisense oligomers (ASOs) hold promise as antibiotics for selective targeting of bacterial pathogens and as tools for the modulation of gene function in genetically intractable microbes. However, their efficient delivery across the complex bacterial envelope remains a major challenge. There are few methods to assess the efficiency of carrier-mediated ASO uptake by bacteria. Here, we have developed a “switch-on” reporter assay to measure ASO uptake efficiency in a semi-quantitative manner. The assay uses a synthetic RNA toehold switch fused to the mRNA of a fluorescent reporter protein, which is activatedin vivoby a peptide nucleic acid (PNA)-based ASO upon delivery into the bacterial cytosol. We have used this assay to screen different cell penetrating peptides (CPPs) as ASO carriers inEscherichia coliandSalmonella entericaand observed up to 60-fold activation, depending on the CPP and bacterial strain used. Our assay shows high dynamic range and sensitivity, which should enable high-throughput screens for bacterial ASO carriers. We also show that the reporter can be used to study routes of PNA uptake, as demonstrated by reduced reporter activity in the absence of the inner membrane protein SbmA. In summary, we present a portable tool for the discovery of species-specific and efficient ASO carriers that will also be useful for a broader investigation of cellular uptake mechanisms of antibacterial ASOs.

Importance

The rise of antimicrobial resistance presents a major global health challenge. If not addressed, the death toll from resistant infections is expected to rise dramatically in the coming years. As a result, it is essential to explore alternative antimicrobial therapies. One promising approach is to target bacterial mRNAs using antisense oligomers (ASOs) to silence genes involved in essential functions, virulence, or resistance. However, delivering ASOs across bacterial membranes remains a major challenge and effective methods to monitor their uptake are limited. In this study, we develop a reporter assay to facilitate the high-throughput discovery of bacterial ASO carriers. This research paves the way for developing novel precision antisense-based antibacterial therapies.
Barley miRNAs and their targets regulation in response to heat stress at the early stage of development
Authors: Kruszka Katarzyna , Pacak Andrzej , Swida-Barteczka Aleksandra , Kesy Jacek , Jarmolowski Artur , Szweykowska-Kulinska Zofia
Published: October 2024

MiRNAs are key regulators of gene expression controlling plant development and response to environmental stresses. In this work we studied global dynamics of accumulation of conserved and identified novel barley miRNAs at early stage of plant development during heat stress (1h, 3h and 6h of heat stress). The majority of miRNAs responds to heat stress after 3h and 6h of heat stress duration (124 and 155, respectively). The comparison of heat-induced changes in mature miRNA accumulation to their cognate precursor levels allowed to indicate a smaller group of miRNAs that are controlled at transcriptional level and a larger group that is controlled posttranscriptionally in response to heat stress. For miRNAs with the significant accumulation changes during heat treatment, target mRNAs were identified. Moreover, novel targets have been experimentally assigned for selected miRNAs. mRNA of the effector protein of miRNA activity, AGO1B was found to be downregulated by increased miR168 during heat stress. Importantly, miRNA/mRNA target module miR399c/PHO2 responsible for the phosphorus uptake exhibits dynamic changes under heat stress conditions suggesting adaptation of plant development to stress conditions. This study provides new data for developing miRNA and their mRNA target-based strategies in barley breeding in response to heat stress.

Keypoints

- Involvement of small RNAs in response to the heat stress conditions have been studied in young barley plants.

- The largest number of heat responsive miRNAs was found after 3h and 6h of heat duration.

- Heat-induced mature miRNA accumulation and their precursor levels showed complex transcriptional or posttranscriptional regulation.

- MiRNA-target modules responsive to heat stress were identified
High-throughput biodiversity surveying sheds new light on the brightest of insect taxa
Authors: Iwaszkiewicz-Eggebrecht Ela , Goodsell Robert M. , Bengsson Bengt-Åke , Mutanen Marko , Klinth Mårten , van Dijk Laura , Lukasik Piotr , Miraldo Andreia , Andresson Anders F. , Tack Ayco J. M. , Roslin Tomas , Ronquist Fredrik
Published: October 2024

Sampling of species-rich taxa followed by DNA metabarcoding is quickly becoming a popular high-throughput method for biodiversity inventories. Unfortunately, we know little about its accuracy and efficiency, as the results mostly pertain to poorly-known organism groups in underexplored environments or regions of the world. Here we ask what an extensive sampling effort based on Malaise trapping and metabarcoding can tell us about the lepidopteran fauna of Sweden – one of the best-understood insect taxa in one of the most-surveyed countries of the world. Specifically, we deployed 197 Malaise traps for a single year across Sweden in a systematic sampling design, then metabarcoded the resulting 4,749 bulk samples, and compared the results to existing data sources. We detected more than half (1,535) of the 2,990 lepidopteran species ever recorded as occurring in Sweden, and 323 species not reported during the sampling period by other data providers. Full-length barcoding of individual specimens confirmed three new species for the country and extensive range extensions for two species. It also corroborated eight genetically distinct COI variants that may represent new species to science, one of which has since been described. Most of the new records are for small and inconspicuous species and poorly surveyed regions, suggesting that they represent previously overlooked components of the fauna. Our findings, corroborated by independent metagenomic analyses, show that DNA metabarcoding can be a highly efficient and accurate method of biodiversity sampling, to the extent that it can generate significant new discoveries even for the most well-known of insect faunas.
In vivo imaging of ferroptosis through nanodynamic changes in lipid membranes
Authors: Sonay Ali Yasin , Mc Larney Benedict Edward , Apfelbaum Elana , Grimm Jan
Published: October 2024

Ferroptosis emerged as a cell death modality for drug resistant cancer cells, but there are currently no available biomarkers for imaging ferroptosis based therapies. To address this gab, we evaluated the nanodynamic changes in lipid membranes occurring during cell death to explore potential targeting opportunities to image cell death. We nano-sized gaps at late stages of ferroptosis can serve as entry points for dyes that can bind to cellular structures. These changes were accompanied with cellular signaling components similar to platelet activation, with phosphatidyl serine emerging on the surface of the cells and therefore as a potential target for imaging of programed cell death, including ferroptosis. Taking advantage of these changes in cell membrane dynamics, we employed a novel tumor-seeking dye CJ215 that can label apoptotic cells as recently described by us. We show that CJ215 accumulates in ferroptotic cells both in vitro and in vivo by binding to phosphatidyl serine, a process that is prevented by inhibition of ferroptosis. Since phosphatidyl serine exposure also occurs during apoptosis, CJ215 can serve to image both apoptosis and ferroptosis based therapy.
Overt visual attention modulates decision-related signals in ventral and dorsal medial prefrontal cortex
Authors: Shevlin Blair , Gwinn Rachael , Makwana Aidan , Krajbich Ian
Published: October 2024

When indicating a preference between two options, decision makers are thought to compare and accumulate evidence in an attention-guided process. Little is known about this process’s neural substrates or how visual attention affects the representations of accumulated evidence. We conducted a simultaneous eye-tracking and fMRI experiment in which human subjects gradually learned about the value of two food-lotteries. With this design we were able to extend decisions over a prolonged time-course, manipulate the temporal onset of evidence, and therefore dissociate sampled and accumulated evidence. Consistent with past work, we found correlates of sampled evidence in ventromedial prefrontal cortex (vmPFC), and correlates of accumulated evidence in the prefrontal and parietal cortex. We also found that more gaze at an option increased its choice probability and that gaze amplified sampled-value signals in the vmPFC and ventral striatum. Most importantly, we found that gaze modulated accumulated-value signals in the pre-supplementary motor area (pre-SMA), providing novel evidence that visual attention has lasting effects on decision variables and suggesting that activity in the pre-SMA reflects accumulated evidence and not decision conflict. These results shed new light on the neural mechanisms underlying gaze-driven decision processes.
Zymocin-like killer toxin gene clusters in the nuclear genomes of filamentous fungi
Authors: Heneghan Padraic G. , Salzberg Letal I. , Wolfe Kenneth H.
Published: October 2024

Zymocin-like killer toxins are anticodon nucleases secreted by some budding yeast species, which kill competitor yeasts by cleaving tRNA molecules. They are encoded by virus-like elements (VLEs), cytosolic linear DNA molecules that are also called killer plasmids. To date, toxins of this type have been found only in budding yeast species (Saccharomycotina). Here, we show that the nuclear genomes of many filamentous fungi (Pezizomycotina) contain small clusters of genes coding for a zymocin-like ribonuclease (γ-toxin), a chitinase (toxin α/β-subunit), and in some cases an immunity protein. The γ-toxins fromFusarium oxysporumandColletotrichum siamenseabolished growth when expressed intracellularly inS. cerevisiae. Phylogenetic analysis of glycoside hydrolase 18 (GH18) domains shows that the chitinase genes in the gene clusters are members of the previously described C-II subgroup of Pezizomycotina chitinases. We propose that the Pezizomycotina gene clusters originated by integration of a yeast-like VLE into the nuclear genome, but this event must have been ancient because (1) phylogenetically, the Pezizomycotina C-II chitinases and the Saccharomycotina VLE-encoded toxin α/β subunit chitinases are sister clades with neither of them nested inside the other, and (2) many of the Pezizomycotina toxin cluster genes contain introns, whereas VLEs do not. One of the toxin gene clusters inFusarium graminearumis a locus that has previously been shown to be under diversifying selection in North American populations of this plant pathogen. We also show that two genera of agaric mushrooms (Basidiomycota) have acquired toxin gene clusters by horizontal transfers from different Pezizomycotina donors.
Improved protein interaction models predict differences in complexes between human cell lines
Authors: Wilkins Gary R. , Lugo-Martinez Jose , Murphy Robert F.
Published: October 2024

The interactions of proteins to form complexes play a crucial role in cell function. Data on protein-protein or pairwise interactions (PPI) typically come from a combination of sample separation and mass spectrometry. Since 2010, several extensive, high-throughput mass spectrometry-based experimental studies have dramatically expanded public repositories for PPI data and, by extension, our knowledge of protein complexes. Unfortunately, challenges of limited overlap between experiments, modality-oriented biases, and prohibitive costs of experimental reproducibility continue to limit coverage of the human protein assembly map, both underscoring the need for and spurring the development of relevant computational approaches.

Here, we present a new method for predicting the strength of protein interactions. It addresses two important issues that have limited past PPI prediction approaches: incomplete feature sets and incomplete proteome coverage. For a given collection of protein pairs, we fused data from heterogeneous sources into a feature matrix and identified the minimal set of feature partitions for which a non-empty set of protein pairs had complete values. For each such feature partition, we trained a classifier to predict PPI probabilities. We then calculated an overall prediction for a given protein pair by weighting the probabilities from all models that applied to that pair. Our approach accurately identified known and highly probable PPI, far exceeding the performance of current approaches and providing more complete proteome coverage. We then used the predicted probabilities to assemble complexes using previously-described graph-based tools and clustering algorithms and again obtained improved results. Lastly, we used features for three human cell lines to predict PPI and complex scores and identified complexes predicted to differ between those cell lines.
Ivory-billed Woodpecker and Blue Jay kent comparisons at spectrogram level reveal differences
Authors: Williams John D
Published: October 2024

A representative audio file for Blue Jay (Cyanocitta cristata), that is thought to be most similar to suspected kent sounds of the Ivory-billed Woodpecker (Campephilus principalis), was examined at the spectrogram level. A total of 136 other Blue Jay files were looked at and compared to kents (n>200) from six Ivory-billed Woodpecker expeditions. At this precision, differences are seen such that these two species cannot be mistaken for each other.
Microglial states determine lesion dynamics in multiple sclerosis
Authors: van den Bosch Aletta M.R. , Khoo Jia Hui , Lu Zhigang , Liang Han , Wever Dennis , Pu Li , Eggen Bart J.L. , Uhlén Mathias , Smolders Joost , Hamann Jörg , Shang Zhouchun , Mulder Jan , Huitinga Inge
Published: October 2024

Summary paragraph

Multiple sclerosis (MS) is a neuroinflammatory disease of the central nervous system, characterized by demyelinating lesions1. Lesion expansion contributes to progression and increased disability, while remyelination can recover neurological deficits. However, mechanisms driving lesion dynamics are largely unclear, hindering the development of effective therapeutics. We propose that distinct states of microglia are involved in lesion expansion and remyelination2,3. Using Stereo-seq, an RNA capture based high-resolution spatial transcriptomics technology with single-cell resolution, on post-mortem human brain tissue, we compared mixed active/inactive lesions with lipid-laden foamy microglia with lesions containing ramified microglia. We identified distinct cellular and molecular mechanisms underlying lesion activity and remyelination, linked to microglia phenotypes and states. Lesions with foamy microglia were characterized by elevated immune activation, increased lymphocyte densities, upregulated immunoglobulin production (IGHG1,IGHG3), increased complement system activity, indication of iron dysregulation (FTL,FTH1), and increased demyelination. In contrast, lesions with ramified microglia exhibited gene expression profiles indicative of myelin stability (ABCA2,QKI) and neuro-axonal protection, fostering an environment conducive to repair and remyelination. Our findings highlight the role of microglial states in lesion expansion and repair in MS and offer promising avenues for the development of therapeutic approaches aimed at preventing MS disability progression.
Human-mouse proteomics reveals the shared pathways in Alzheimer’s disease and delayed protein turnover in the amyloidome
Authors: Yarbro Jay M. , Han Xian , Dasgupta Abhijit , Yang Ka , Liu Danting , Shrestha Him K. , Zaman Masihuz , Wang Zhen , Yu Kaiwen , Lee Dong Geun , Vanderwall David , Niu Mingming , Sun Huan , Xie Boer , Chen Ping-Chung , Jiao Yun , Zhang Xue , Wu Zhiping , Fu Yingxue , Li Yuxin , Yuan Zuo-Fei , Wang Xusheng , Poudel Suresh , Vagnerova Barbora , He Qianying , Tang Andrew , Ronaldson Patrick T. , Chang Rui , Yu Gang , Liu Yansheng , Peng Junmin
Published: October 2024

Murine models of Alzheimer’s disease (AD) are crucial for elucidating disease mechanisms but have limitations in fully representing AD molecular complexities. We comprehensively profiled age-dependent brain proteome and phosphoproteome (n> 10,000 for both) across multiple mouse models of amyloidosis. We identified shared pathways by integrating with human metadata, and prioritized novel components by multi-omics analysis. Collectively, two commonly used models (5xFAD and APP-KI) replicate 30% of the human protein alterations; additional genetic incorporation of tau and splicing pathologies increases this similarity to 42%. We dissected the proteome-transcriptome inconsistency in AD and 5xFAD mouse brains, revealing that inconsistent proteins are enriched within amyloid plaque microenvironment (amyloidome). Determining the 5xFAD proteome turnover demonstrates that amyloid formation delays the degradation of amyloidome components, including Aβ-binding proteins and autophagy/lysosomal proteins. Our proteomic strategy defines shared AD pathways, identify potential new targets, and underscores that protein turnover contributes to proteome-transcriptome discrepancies during AD progression.
Pre-processing annotated homologous regions in protein sequences concerning machine-learning applications
Authors: Malhis Nawar
Published: October 2024

While annotated protein sequences are widely used in machine learning applications, pre-processing these sequences regarding homology is mainly limited to clustering complete sequences based on global alignment without considering their annotations. Here, I am introducing new tools that identify all possible local homologies between annotated sequences within the same or across two datasets and then resolve these homologies.

Availability

orca.msl.ubc.ca/nmshare/ham.tar.gz
NewtCap: an efficient target capture approach to boost genomic studies in Salamandridae (True Salamanders and Newts)
Authors: de Visser Manon Chantal , France James , McCartney-Melstad Evan , Bucciarelli Gary M. , Theodoropoulos Anagnostis , Shaffer Howard Bradley , Wielstra Ben
Published: October 2024

Salamanders have large and complex genomes, hampering whole genome sequencing, but reduced representation sequencing provides a feasible alternative. We present NewtCap: a sequence capture bait set that targets c.7k coding regions across the genomes of all True Salamanders and Newts (the family Salamandridae, also known as ‘salamandrids’). We test the efficacy of NewtCap, originally designed for the EurasianTriturusnewts, in 30 species, belonging to 17 different genera, that cover all main Salamandridae lineages. We also test NewtCap in two other salamander families. We discover that NewtCap performs well across all Salamandridae lineages (but not in the salamander families Ambystomatidae and Hynobiidae). As expected, the amount of genetic divergence from the genusTrituruscorrelates negatively to capture efficacy and mapping success. However, this does not impede our downstream analyses. We showcase the potential of NewtCap in the contexts of; 1) phylogenomics, by reconstructing the phylogeny of Salamandridae, 2) phylogeography, by sequencing the four closely related species comprising the genusTaricha, 3) hybrid zone analysis, by genotyping twoLissotritonspecies and different classes of interspecific hybrids, and 4) conservation genetics, by comparingTriturus ivanbureschisamples from several wild populations and one captive-bred population. Overall, NewtCap has the potential to boost straightforward, reproducible, and affordable genomic studies, tackling both fundamental and applied research questions across salamandrids.
Early perturbations to fluid homeostasis alter development of hypothalamic feeding circuits with context-specific changes in ingestive behavior
Authors: Sweet Serena R. , Biddinger Jessica E. , Zimmermann Jessie B. , Yu Gina L. , Simerly Richard B.
Published: October 2024

Drinking and feeding are tightly coordinated homeostatic events and the paraventricular nucleus of the hypothalamus (PVH) represents a possible node of neural integration for signals related to energy and fluid homeostasis. We usedTRAP2;Ai14and Fos labeling to visualize neurons in the PVH and median preoptic nucleus (MEPO) responding to both water deprivation and hunger. Moreover, we determined that structural and functional development of dehydration-sensitive inputs to the PVH from the MEPO precedes those of agouti-related peptide (AgRP) neurons, which convey hunger signals and are known to be developmentally programmed by nutrition. We also determined that osmotic hyperstimulation of neonatal mice led to enhanced AgRP inputs to the PVH in adulthood, as well as disruptions to ingestive behaviors during high-fat diet feeding and dehydration-anorexia. Thus, development of feeding circuits is impacted not only by nutritional signals, but also by early perturbations to fluid homeostasis with context-specific consequences for coordination of ingestive behavior.
Planarians Develop Radiotolerance to Recurrent Ionizing Radiation Exposure
Authors: Barghouth Paul G. , Ziman Benjamin , Maciel Eli Isael , Karabinis Peter , Rojas Salvador , Flores Natasha M. , Pfister Edelweiss , Oviedo Néstor J.
Published: October 2024

Exposure to ionizing radiation can induce DNA fragmentation, leading to double-strand breaks, the most toxic form of DNA damage. Some organisms have developed mechanisms to overcome the adverse effects of ionizing radiation by enhancing DNA protection and repair. However, the underlying mechanisms driving radiation resistance to maintain genomic integrity and function remain poorly understood. Here, we provide evidence for the development of radiotolerance in the flatworm planarianSchmidtea mediterranea. We implemented a strategy to select animals capable of overcoming repeated rounds of ionizing radiation exposure. We demonstrate that planarians initially exposed to higher amounts of sub-lethal radiation can adapt, gaining the ability to recover reproductive capabilities faster than animals initially exposed to lower amounts of sub-lethal radiation. Our findings show that DNA integrity is reestablished in about one week after five cycles of sub-lethal ionizing radiation exposure. Planarian stem cells, known as neoblasts, can repair repeated DNA double-strand breaks by activating Rad51-mediated homologous recombination. The expression of the neoblast markersmedpiwi-1and the mitotic activity reach levels similar to unirradiated animals between two and three weeks post-radiation. We describe that planarians develop radiotolerance through recurrent ionizing radiation exposure over several years and survive without apparent functional or morphological defects for an undetermined time.
The potential use of immersive virtual environments for collecting and archiving heritage gameplay activities in digital libraries
Authors: Lau Kung Wong
Published: October 2024

Purpose

This paper aims to discuss and propose the potential use of immersive virtual environments (IVEs) for archiving and collecting heritage gameplay activities in digital libraries, which is expected to triangulate further discussions on the said knowledge scopes.

Design/methodology/approach

The key question of this paper is, how we can preserve and revitalize fading heritage game activities in digital libraries? To answer this, the paper is going to understand the applications of IVEs in heritage studies; the use of telepresence experiences in IVEs for activity-based collection; the creation of virtual and telepresence experiences in digital libraries; and a proposed use of IVEs for archiving heritage gameplay activities.

Findings

The applications of IVEs and/or other virtual technologies have certainly been gaining positive feedback about their ability to provide vivid images of artefacts and art pieces; perform a high level of interactivity between the exhibits and visitors; enhance visitors’ sense of immersion that evoke their memories of heritage issues; facilitate visitors’ learning process in libraries; increase enjoyment in digital libraries. As mentioned in the previous section, the activity-based historical collection, for instance, the heritage gameplay activities, can be preserved and archived vividly using IVEs.

Research limitations/implications

This paper is explorative, there is no empirical result for generalization.

Originality/value

This paper aims to provide librarians with valuable insight to apply IVEs for archiving and collecting heritage gameplay activities. Setting up a new type of digital library is affected greatly by the openness of librarians, visitors’ expectations and a whole lot of things that are happening around the technological world and digital culture. This paper addresses the applications of IVEs in heritage studies, the importance of creating virtual and telepresence experiences for library visits as well as proposing the use of IVEs for archiving heritage gameplay activities.
A neural network approach for unstructured mesh quality evaluation
Authors: Chen Xinhai , Wang Zhichao , Liu Yang , Pang Yufei , Chen Bo , Chen Jianqiang , Gong Chunye , Liu Jie
Published: October 2024

Purpose

The quality of the unstructured mesh has a considerable impact on the stability and accuracy of aerodynamic simulation in computational fluid dynamics (CFD). Typically, engineers spend a significant portion of their time on mesh quality evaluation to ensure a valid, high-quality mesh. The extensive manual interaction and a priori knowledge required to undertake an accurate and timely evaluation process have become a bottleneck in the idealized efficient CFD workflow. This paper aims to introduce a neural network-based quality evaluation approach for unstructured meshes to enable higher efficiency and the level of automation.

Design/methodology/approach

The paper investigates the capability of deep neural networks for the quality evaluation of unstructured meshes. For training the network, we build a training dataset for mesh quality learning algorithms. The dataset contains a rich variety of unstructured aircraft meshes with different mesh sizes, densities, cell distribution, growth ratios and cell numbers to ensure its diversity and availability. We also design a neural network, AircraftNet, to learn the effect of mesh quality on the convergent properties of the numerical solutions. The proposed network directly manipulates raw point data in mesh source files rather than passing it to an intermediate data representation. During training, AircraftNet extracts non-linear quality features from high-dimensional data spaces and then automatically predicts the overall quality of the input unstructured mesh.

Findings

The paper provides a series of experimental results on GPUs. It shows that AircraftNet is able to effectively analyze the quality-related features like mesh density and distribution from the extracted features and achieve high prediction accuracy on the proposed dataset with even a small number of training runs.

Research limitations/implications

Because of the limited training dataset, the research results may lack generalizability. Therefore, researchers are encouraged to test the proposed propositions further.

Originality/value

The paper publishes a benchmarking dataset for mesh quality learning algorithms and designs a novel neural network approach for unstructured mesh quality evaluation.
Simulations of nerve signal propagation in axons
Authors: Pınar İzgi Zehra
Published: October 2024

Purpose

In the literature, soliton solutions of the Heimburg–Jackson model have been proposed by Drab et al. (2022), but for the considered models, i.e. Eq.(1) and Eq.(2), the existence of solitons, the dispersion analysis and the pseudospectral method have been studied (Engelbrecht et al., 2006, 2018, 2020; Tamm et al., 2017, 2022; Peets et al., 2013). Therefore, the gap should be filled by this work.

Design/methodology/approach

When nonlinear terms, dissipative terms and forcing terms are ignored, the system (Eq.(2)) reduces to a single, sixth-order partial differential equation (Tamm et al., 2022). In this work, our aim is to propose analytical solutions in the explicit form via ansatz-based method. Therefore, the parameter effects in wave profile will be proposed clearly in figures.

Findings

While progress has been made in signal propagation in nerves, thanks to many experimental studies and theoretical predictions over the last two centuries, the results obtained in this study may answer new questions that arise.

Originality/value

In the literature, the existence of solitons, dispersion analysis and pseudospectral method have been investigated for the Heimburg-Jackson model (Engelbrecht et al., 2006, 2018, 2020; Tamm et al., 2017, 2022; Peets et al., 2013), and this study fills the gap in soliton solutions. Additionally, when nonlinear terms, dissipative term and forcing terms are ignored, the system (Eq.(2)) reduced to a single equation that is sixth-order partial differential equation (Tamm et al., 2022). In this work, our aim is to propose analytical solutions in the explicit form via ansatz-based method. Therefore, the parameter effects in wave profile will be proposed clearly in figures.
Exploring the key drivers of inter-organizational knowledge transfer in projects: evidence from international construction projects
Authors: Zhou Qianwen , Deng Xiaopeng , Wang Ge , Mahmoudi Amin , Zhang Na
Published: October 2024

Purpose

Despite the knowledge transfer in project contexts which has been extensively studied by scholars, the study on inter-organizational knowledge transfer in international construction projects is still scattered and unsystematic. This research aims to explore the key factors influencing inter-organizational knowledge transfer of international construction projects and analyze how these factors interact to create a synthetic framework that enhances the effectiveness of knowledge transfer (EKT).

Design/methodology/approach

At first, eight factors influencing inter-organizational knowledge transfer within international construction projects were identified, which were from the four dimensions of subject, relationship, channel and context, namely cultural distance, connection strength, organizational climate, intercultural competence, information technology capability, transmit willingness, receive willingness and richness of transfer channels. Then, a conceptual model was developed and 13 hypotheses were formulated, which were derived from a literature review and in-depth survey. After that, data from 353 respondents were collected and analyzed, and the hypotheses were tested by structural equation modeling analysis and bootstrapping test.

Findings

The results suggest that cultural distance hinders transfer willingness, which further affects EKT. Connection strength affects EKT by positively influencing transfer willingness and channel. Besides, organizational climate and intercultural competence positively influence transfer willingness and further affect EKT, while information technology capability affects the richness of transfer channels.

Originality/value

This research gives a thorough examination of the determinants influencing inter-organizational knowledge transfer of international construction projects, thus formulating available approaches that project managers and personnel can employ to effectively facilitate EKT.
Research trends of collaborative governance in climate change: a bibliometric analysis
Authors: Harmawan Bagus Nuari , Ilman Ghulam Maulana , Pertiwi Vidya Imanuari , Bataha Katerina
Published: October 2024

Purpose

Climate change, a complex global issue, has prompted a wide range of actors – from nations to tiny communities – to seek solutions to mitigate its consequences. The growing emphasis on collaborative governance has resulted in substantial research on the topic. This paper aims to address the existing research void by using a bibliometric approach to investigate the evolution of studies on collaborative governance in the context of climate change.

Design/methodology/approach

This study conducted a bibliometric mapping of research on collaborative governance on climate change issues from the first study presented in 2007 to the research conducted in 2023, using 222 articles derived from the Scopus database and Web of Science. Steps for comprehensive bibliometric literature mapping via the VOSviewer software.

Findings

The study includes a complete overview of significant themes, including the most cited research, contributions from authors, countries, and institutions, as well as network analysis including co-citation, bibliographic coupling, and co-occurrence. Notably, the study looks at which countries have made the most substantial contributions, with the United States dominating with 40 studies over the last decade. The analysis reveals that collaborative governance in climate change, emphasizing its importance as a tool for governments and communities to mitigate climate risks. This is consistent with research emphasizing the need for coordination across multiple players to accomplish effective climate adaptation. The paper focuses on nine diverse research clusters, including community engagement, urban governance, disaster response and economic implications.

Research limitations/implications

This study is restricted to bibliometric analysis, which is conducted using sources from the Scopus and Web of Science databases. Future research is required to investigate the use of additional databases that offer a wider range of sources. In the interim, this investigation provides an overview of the concept of Collaborative Governance, which has the potential to serve as a strategy for the adaptation and resilience to climate change in global regions, cities and urban areas.

Originality/value

This study conducts a rigorous bibliometric review that improves our theoretical knowledge and practical use of collaborative governance in addressing climate change. It reveals innovative trends, research gaps and important recommendations for future studies, strengthening the strategic approach to collaborative climate action.
Investigation of effect of recycled polyester ratio and draw frame passages on flame retardancy of chenille fabric properties
Authors: Çelik Halil İbrahim , Tekin İbrahim Halil , Tekin Perihan , Çağlayan Ali , Saycan Serdar
Published: October 2024

Purpose

In this study, both flame retardancy and sustainability properties were combined in the chenille yarn so that functional and sustainable upholstery fabrics can be produced with optimum energy consumption. The chenille yarn samples were produced from recycled polyester (rPET)-blended binder yarns and fully drawn yarn (FDY) polyester pile yarn. While the pile component of the chenille samples was kept constant, the lock yarns were manufactured as 50% r-PET-50% virgin polyester (PES), 100% r-PET and 100% PES. The binder yarns were also produced in two groups. In the first group, a 2-passage draw frame was used, while a 3-passage draw frame was used in the second group. The chenille yarn samples were applied flame-retardant (FR) finishing.

Design/methodology/approach

The knitted upholstery fabric samples were produced from chenille yarn samples via flat knitting machines. The knitted fabrics were applied flame retardancy, bursting strength and abrasion resistance tests according to related standards.

Findings

The test results were analysed, and so the effect of r-PET ratio and draw frame passage number on upholstery fabric flame retardancy, bursting strength and abrasion resistance performance properties were revealed. It was concluded that the number of draw frame passages and the recycled fibre content have no important effect on the flame retardancy. On the other hand, it has been observed that the bursting strength decreases as the recycled fibre content increases and bursting distention results are close to each other. It was seen that the draw frame passage number has no significant effect on both bursting strength and distention. It was revealed that both r-PET fibre content and draw frame passage number have significant effect on abrasion resistance. The samples with 2 draw frame passages provide higher abrasion resistance compared to those with 3 draw frame passage. The lowest abrasion resistance was obtained with 100% r-PET fibre content and the highest abrasion resistance was obtained with 50% r-PET-50% PES.

Originality/value

The results will provide enough knowledge for sustainable chenille yarn design. The recycled fibre content and draw frame passage number can be optimised, and so sustainable chenille yarns can be produced with less energy consumption. Future studies will involve producing chenille yarns with different linear densities and varying draw frame combinations, such as 1, 2 and 3 passages.
Critical analysis of the emerging flood disaster resilience assessment indicators
Authors: Osei-Kyei Robert , Ampratwum Godslove , Komac Ursa , Narbaev Timur
Published: October 2024

Purpose

The world is reeling from the effects of climate change with increased extreme precipitation. Flooding is amongst the most recurring and devastating natural hazards, impacting human lives and causing severe economic damage. This paper aims to conduct a systematic review to critically analyse the most reported and emerging flood disaster resilience indicators.

Design/methodology/approach

A total of 35 papers were selected through a systematic process using both Web of Science and Scopus databases. The selected literature was subjected to a thorough thematic content analysis.

Findings

From the review, 77 emerging flood disaster resilience assessment indicators were identified. Furthermore, based on the individual meanings and relationships of the derived indicators, they were further categorized into six groups, namely, physical, institutional, social, psychological, ecology and economic. More also, it was identified that most of the selected publications have used objective resilience measurement approaches as opposed to subjective resilience measurement approaches.

Originality/value

The generated list of flood disaster resilience indicators will provide insights into the capacities which can be improved to enhance the overall resilience to flood disasters in communities.
Beyond bars: the confining nature of hegemonic masculinity in venture accelerators
Authors: Schoonmaker Mary G. , MacNeil HeatherJean , McAdam Maura
Published: October 2024

Purpose

This paper investigates the intersectionality of entrepreneurial masculinity within the context of venture accelerators. As such, it aims to shed light on how intersecting factors influence the construction and expression of masculinity among male entrepreneurs in venture accelerators.

Design/methodology/approach

This research is based on an in-depth analysis of four distinct accelerator cohort groups, employing a semi-structured interview approach. Interviewees were conducted with four accelerator managers and 52 male accelerator participants across four distinct accelerator cohort groups. Such a methodological choice is deemed instrumental in unravelling the nuanced dynamics within accelerator environments and their implications on hegemonic masculinity.

Findings

This study elucidates the nuanced ways in which men navigate the venture accelerator landscape. The findings revealed that the accelerator environment facilitated the reinforcement of traditional masculine behaviours. Whilst diversity was ostensibly valued, its acceptance decreased if it posed a challenge to male dominance or stereotypical masculine traits. Indeed, there was marginalisation of nontraditional expressions of masculinity, leading to a sense of “othering”.

Originality/value

By integrating intersectionality theory into the examination of masculine dynamics within venture accelerator contexts, this study expands current understanding of venture accelerator environments and their effects on both traditional and nontraditional forms of hegemonic masculinity. In particular, we highlight the impact of non-intersectional institutional norms on male entrepreneurs who deviate from traditional stereotypes. As such, we advance the understanding of venture accelerators by examining how they perpetuate and reinforce traditional masculine norms, even in environments that strive for diversity.