bluuebunny/crossref_metadata_2025 huggingface dataset:
Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation
Authors: Lin Yuefan , Pan Zixiang , Zeng Yuansong , Yang Yuedong , Dai Zhiming
Published: July 2024

Recent advances in single-cell technologies enable the rapid growth of multi-omics data. Cell type annotation is one common task in analyzing single-cell data. It is a challenge that some cell types in the testing set are not present in the training set (i.e. unknown cell types). Most scATAC-seq cell type annotation methods generally assign each cell in the testing set to one known type in the training set but neglect unknown cell types. Here, we present OVAAnno, an automatic cell types annotation method which utilizes open-set domain adaptation to detect unknown cell types in scATAC-seq data. Comprehensive experiments show that OVAAnno successfully identifies known and unknown cell types. Further experiments demonstrate that OVAAnno also performs well on scRNA-seq data. Our codes are available online at https://github.com/lisaber/OVAAnno/tree/master.
Phylogeography of Père David’s red-backed vole, Eothenomys melanogaster (Rodentia: Cricetidae), in Taiwan
Authors: Oshida Tatsuo , Chang Yu-Cheng , Harada Masashi , Iwasa Masahiro A , Chang Shih-Wei , Ando Akiro , Koyasu Kazuhiro , Lin Liang-Kong
Published: July 2024

Sympatrically distributed mammal species do not always show congruent phylogeographical traits. In Taiwan, montane mammals show two different phylogeographical patterns: some species have no clear genetic diversification, whereas others show clear north–south genetic divergence. The ecological characteristics of each species might be important factors determining each pattern. The former species group is adapted to rich forest habitats, whereas the latter species group requires more complicated habitats consisting of both forested and non-forested areas. If the latter group has experienced similar historical processes, we might find a congruent zoogeographical pattern that separates its northern and southern populations. To test this hypothesis, we examined the phylogeographical characteristics of Eothenomys melanogaster found in the habitat of the latter species group, based on mitochondrial and nuclear DNA sequences and chromosomes. All genetic markers demonstrated clear north–south divergence. The boundary between the two populations was in the mountainous areas, including Mount Houhuan. Our results suggested that the southern population was the first to immigrate from the Asian continent to the south of the boundary, followed by the immigration of the northern population to the north of the boundary. Both populations could have been isolated from each other by a boundary in Taiwan during the Pleistocene.
Remimazolam vs. propofol for general anaesthesia in elderly patients: a meta-analysis with trial sequential analysis
Authors: Pereira Eduardo Maia , Moraes Vitor Ryuiti , Gaya da Costa Mariana , Nascimento Tatiana Souza do , Slawka Eric , Júnior Carlos Galhardo , Struys Michel MRF
Published: July 2024

BACKGROUND

Elderly patients comprise an increasing proportion of patients undergoing surgery, and they require special attention due to age-related physiological changes. Propofol is the traditional agent for anaesthesia, and recently, remimazolam, a novel ultra-short-acting benzodiazepine, has emerged as an alternative to propofol in general anaesthesia.

OBJECTIVES

We aim to compare remimazolamvs. propofol for general anaesthesia in elderly patients regarding hypotension, induction characteristics, haemodynamics and recovery outcomes.

DESIGN

Meta-analysis with sensitivity and trial sequential analyses (TSA) to assess inconsistencies. Risk ratios and mean differences with 95% confidence intervals (95% CIs) were computed using a random effects model. Subgroups and meta-regression according to anaesthesia methods were also performed.

DATA SOURCES

We systematically searched MEDLINE, Embase and Cochrane for randomised controlled trials (RCTs) up to January 1, 2024.

ELIGIBILITY CRITERIA

Patients at least 60 years old, comparing remimazolamvs. propofol for general anaesthesia.

RESULTS

Eleven RCTs (947 patients) were included. Compared with propofol, remimazolam was associated with lower postinduction and intra-operative hypotension (RR 0.41, 95% CI 0.27 to 0.62,P < 0.001) and incidence of bradycardia (risk ratio 0.58, 95% CI 0.34 to 0.98,P = 0.04), with a higher heart rate (P = 0.01). The incidence of injection pain was lower (P < 0.001), but remimazolam was associated with a longer time to loss of consciousness (P < 0.001) and a higher bispectral index at loss of consciousness (P = 0.04). No differences were found for mean arterial pressure, emergence time, extubation time and incidence of emergence agitation. The TSA was consistent and achieved the required information size for hypotension.

CONCLUSIONS

Remimazolam significantly reduced the risk of hypotension, bradycardia and injection pain, despite an increase in the time to loss of consciousness. Remimazolam appears to be an effective and well tolerated alternative to propofol in elderly patients undergoing general anaesthesia.
Diversity of microglial transcriptional responses during opioid exposure and neuropathic pain
Authors: Sypek Elizabeth I. , Tassou Adrien , Collins Hannah Y. , Huang Karen , McCallum William M. , Bourdillon Alexandra T. , Barres Ben A. , Bohlen Christopher J. , Scherrer Grégory
Published: July 2024

Microglia take on an altered morphology during chronic opioid treatment. This morphological change is broadly used to identify the activated microglial state associated with opioid side effects, including tolerance and opioid-induced hyperalgesia (OIH). Microglia display similar morphological responses in the spinal cord after peripheral nerve injury (PNI). Consistent with this observation, functional studies have suggested that microglia activated by opioids or PNI engage common molecular mechanisms to induce hypersensitivity. In this article, we conducted deep RNA sequencing (RNA-seq) and morphological analysis of spinal cord microglia in male mice to comprehensively interrogate transcriptional states and mechanistic commonality between multiple models of OIH and PNI. After PNI, we identify an early proliferative transcriptional event across models that precedes the upregulation of histological markers of microglial activation. However, we found no proliferative transcriptional response associated with opioid-induced microglial activation, consistent with histological data, indicating that the number of microglia remains stable during morphine treatment, whereas their morphological response differs from PNI models. Collectively, these results establish the diversity of pain-associated microglial transcriptomic responses and point towards the targeting of distinct insult-specific microglial responses to treat OIH, PNI, or other central nervous system pathologies.
Noninvasive targeted modulation of pain circuits with focused ultrasonic waves
Authors: Riis Thomas S. , Feldman Daniel A. , Losser Adam J. , Okifuji Akiko , Kubanek Jan
Published: July 2024

Direct interventions into deep brain circuits constitute promising treatment modalities for chronic pain. Cingulotomy and deep brain stimulation targeting the anterior cingulate cortex have shown notable improvements in the unpleasantness of pain, but these interventions require brain surgeries. In this study, we have developed an approach that can modulate this deep brain affective hub entirely noninvasively, using low-intensity transcranial-focused ultrasound. Twenty patients with chronic pain received two 40-minute active or sham stimulation protocols and were monitored for one week in a randomized crossover trial. Sixty percent of subjects experienced a clinically meaningful reduction of pain on day 1 and on day 7 following the active stimulation, while sham stimulation provided such benefits only to 15% and 20% of subjects, respectively. On average, active stimulation reduced pain by 60.0% immediately following the intervention and by 43.0% and 33.0% on days 1 and 7 following the intervention. The corresponding sham levels were 14.4%, 12.3%, and 6.6%. The stimulation was well tolerated, and no adverse events were detected. Side effects were generally mild and resolved within 24 hours. Together, the direct, ultrasonic stimulation of the anterior cingulate cortex offers rapid, clinically meaningful, and durable improvements in pain severity.
Impact of the 2022 Infant Formula Shortage on Self-Reported Rates of Anxiety and Depression
Authors: DuBois Dominique , Sundell Joe , Thomsen Michael R. , Brown Clare C.
Published: July 2024

Purpose:

To evaluate the impact of the 2022 infant formula shortage on self-reported anxiety and depression.

Background:

The US national infant formula shortage of 2022 originated from supply chain disruptions triggered by the COVID-19 pandemic, and the shortage was further compounded by a recall of tainted formula products.

Methods:

We used survey-weighted data from the Household Pulse Survey (HPS) to measure self-reported anxiety and depression among individuals with formula-fed infants less than 1 year of age. We evaluated the association between 2 formula disruption variables (being impacted by the infant formula shortage or having difficulty obtaining formula in the last 7 days) with 2 mental health outcomes (anxiety and depression) using multivariable logistic regressions.

Results:

We found increased odds of self-reported anxiety (aOR: 3.13; P < .001) and depression (aOR: 3.05; P = .005) for respondents affected by the infant formula shortage. There were no adjusted associations between having difficulty obtaining formula in the last 7 days and anxiety and depression.

Conclusions:

Individuals affected by the infant formula shortage had increased odds of both anxiety and depression. Continued efforts to improve food security for low-income infants is critical for ensuring equitable nutritional and health outcomes across infant populations.

Implications for practice and research:

Continued efforts to reduce food insecurity for low-income infants are critically needed, as infant nutrition impacts caregiver mental health and infant health. Efforts to improve lactation support and breastfeeding initiation are needed in addition to improvements in access to formula.
Ex-Vivo 3D Cellular Models of Pancreatic Ductal Adenocarcinoma
Authors: Acimovic Ivana , Gabrielová Viktorie , Martínková Stanislava , Eid Michal , Vlažný Jakub , Moravčík Petr , Hlavsa Jan , Moráň Lukáš , Cakmakci Riza Can , Staňo Peter , Procházka Vladimír , Kala Zdeněk , Trnka Jan , Vaňhara Petr
Published: July 2024

Pancreas is a vital gland of gastrointestinal system with exocrine and endocrine secretory functions, interweaved into essential metabolic circuitries of the human body. Pancreatic ductal adenocarcinoma (PDAC) represents one of the most lethal malignancies, with a 5-year survival rate of 11%. This poor prognosis is primarily attributed to the absence of early symptoms, rapid metastatic dissemination, and the limited efficacy of current therapeutic interventions. Despite recent advancements in understanding the etiopathogenesis and treatment of PDAC, there remains a pressing need for improved individualized models, identification of novel molecular targets, and development of unbiased predictors of disease progression. Here we aim to explore the concept of precision medicine utilizing 3-dimensional, patient-specific cellular models of pancreatic tumors and discuss their potential applications in uncovering novel druggable molecular targets and predicting clinical parameters for individual patients.
Dynamic continualization of mechanical metamaterials with quasi-periodic microstructure
Authors: Del Toro Rosaria , De Bellis Maria Laura , Bacigalupo Andrea
Published: July 2024

This article focuses on characterizing a class of quasi-periodic metamaterials created through the repeated arrangement of an elementary cell in a fixed direction. The elementary cell consists of two building blocks made of elastic materials and arranged according to the generalized Fibonacci sequence, giving rise to a quasi-periodic finite microstructure, also called Fibonacci generation. By exploiting the transfer matrix method, the frequency band structure of selected periodic approximants associated with the Fibonacci superlattice, i.e. the layered quasi-periodic metamaterial, is determined. The self-similarity of the frequency band structure is analysed by means of the invariants of the symplectic transfer matrix as well as the transmission coefficients of the finite clusters of Fibonacci generations. A high-frequency continualization scheme is then proposed to identify integral-type or gradient-type non-local continua. The frequency band structures obtained from the continualization scheme are compared with those derived from the Floquet–Bloch theory to validate the proposed scheme.

This article is part of the theme issue ‘Current developments in elastic and acoustic metamaterials science (Part 1).’
Salinibacterium soli sp. nov., isolated from lakeside soil
Authors: Wan Yingying , Xiong Miaohuan , Zhu Lingfeng , Ni Haiyan , Chen Xuelan , Liu Bin , He Jian
Published: July 2024

A Gram-stain-positive, rod-shaped, non-spore-forming and non-motile bacterium, designated strain WY-16T. Growth was observed at 20–42 °C (optimum, 30 °C), pH 6–9 (optimum, pH 7) and salinity of 0–3 % (w/v; optimum, 1 %). Phylogenetic analysis based on genome sequences indicated that WY-16T was affiliated to the family Microbacteriaceae and most closely related to Salinibacterium xinjiangense and Salinibacterium amurskyense. The average nucleotide identity values between strain WY-16T and S. xinjiangense and S. amurskyense were 74.7 and 72.5 %, respectively. The digital DNA–DNA hybridization values between strain WY-16T and S. xinjiangense and S. amurskyense were 19.6 and 18.6 %, respectively. The predominant fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C16 : 0 10-methyl. The major menaquinones were MK-12, MK-13, MK-14 and MK-15. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified glycolipid and one unidentified phospholipid. The cell-wall peptidoglycan contained 2,4-diaminobutyric acid as the diamino acid and ribose, rhamnose, glucose and galactose were the major cell-wall sugars. Based on phenotypic, genotypic and phylogenetic evidence, strain WY-16T represents a novel species in the genus Salinibacterium, for which the name Salinibacterium soli sp. nov. is proposed. The type strain is WY-16T (=GDMCC 1.4011T=JCM 36421T).
Myo5B plays a significant role in the hyphal growth and virulence of the human pathogenic fungus Mucor lusitanicus
Authors: Trieu Trung Anh , Duong Lam Minh , Nguyen Phuong Anh , Doan Thuoc Van , Nguyen Hung Phuc
Published: July 2024

Mucormycosis is an emerging and deadly invasive fungal infection caused by fungi belonging to the Mucorales order. We investigated the myosin superfamily, which encompasses diverse actin-based motor proteins with various cellular functions. Specifically, the role of the Myo5B (ID 179665) protein from the myosin class V family in Mucor lusitanicus was explored by generating silencing phenotypes and null mutants corresponding to the myo5B gene. Silencing fungal transformants exhibited a markedly reduced growth rate and a nearly complete absence of sporulation compared to the wild-type strain. The myo5BΔ null mutant strain displayed atypical characteristics, including abnormally short septa and inflated hyphae. Notably, there were a majority of small yeast-like cells instead of filamentous hyphae in the mutant. These yeast-like cells cannot germinate normally, resulting in a loss of polarity. In vivo virulence assays conducted in the Galleria mellonella invertebrate model revealed that the myo5BΔ mutant strain was avirulent. These findings shed light on the crucial contributions of the Myo5B protein to the dimorphism and pathogenicity of M. lusitanicus. Therefore, the myosin V family is a potential target for future therapeutic interventions aimed at treating mucormycosis.
RNA recognition by minimal ProQ fromNeisseria meningitidis
Authors: Basczok Maciej , Olejniczak Mikołaj
Published: July 2024

Neisseria meningitidisminimal ProQ is a global RNA binding protein belonging to the family of FinO-domain proteins. TheN. meningitidisProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions. To better understand how this minimal FinO-domain protein recognizes RNAs, we compared its binding to seven different natural RNA ligands of this protein. Next, two of these RNAs,rpmG-3’ and AniS, were subject to further mutational studies. The data showed thatN. meningitidisProQ binds the lower part of the intrinsic transcription terminator hairpin, and that the single-stranded sequences on the 5’ and 3ʹ side of terminator stem are required for tight binding. However, the specific lengths of 5’ and 3ʹ RNA sequences required for optimal binding differed between the two RNAs. Additionally, our data show that the 2ʹ-OH and 3ʹ-OH groups of the 3ʹ terminal ribose contribute to RNA binding byN. meningitidisProQ. In summary, the minimal ProQ protein fromN. meningitidishas generally similar requirements for RNA binding as the isolated FinO domains of other proteins of this family, but differs from them in detailed RNA features that are optimal for specific RNA recognition.
Early life psychosocial stress increases binge-like ethanol consumption and CSF1R inhibition prevents stress-induced alterations in microglia and brain macrophage population density
Authors: Gironda Stephen C. , Centanni Samuel W. , Weiner Jeffrey L.
Published: July 2024

Early life stress (ELS) has lasting consequences on microglia and brain macrophage function. During ELS, microglia and brain macrophages alter their engagement with synapses leading to changes in neuronal excitability. Further, ELS can induce innate immune memory formation in microglia and brain macrophages resulting in altered responsivity to future environmental stimuli. These alterations can result in lasting adaptations in circuit function and may mediate the relationship between ELS and the risk to develop alcohol use disorder (AUD). Whether microglia and brain macrophages truly mediate this relationship remains elusive. Here, we report: 1) an ELS model, psychosocial stress (PSS), increases binge-like ethanol consumption in early adulthood. 2) Repeated binge-like ethanol consumption increases microglia and brain macrophage population densities across the brain. 3) PSS may elicit innate immune memory formation in microglia and brain macrophages leading to altered population densities following repeated binge-like ethanol consumption. 4) Microglia and brain macrophage inhibition trended towards preventing PSS-evoked changes in binge-like ethanol consumption and normalized microglia and brain macrophage population densities. Therefore, our study suggests that acutely inhibiting microglia and brain macrophage function during periods of early life PSS may prevent innate immune memory formation and assist in reducing the risk to develop AUD.

Highlights

An early life psychosocial stress (PSS) exposure increases ethanol consumption

Microglial inhibition during PSS trends towards reducing ethanol consumption

Binge ethanol consumption increases microglial count and alters cell proximity

Early life PSS alters microglial responsivity to binge ethanol consumption

Microglial inhibition may prevent microglial innate immune memory formation
Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models
Authors: Roche Rahmatullah , Tarafder Sumit , Bhattacharya Debswapna
Published: July 2024

Ground-breaking progress has been made in structure prediction of biomolecular assemblies, including the recent breakthrough of AlphaFold 3. However, it remains challenging for AlphaFold 3 and other state-of-the-art deep learning-based methods to accurately predict protein-RNA complex structures, in part due to the limited availability of evolutionary and structural information related to protein-RNA interactions that are used as inputs to the existing approaches. Here, we introduce ProRNA3D-single, a new deep-learning framework for protein-RNA complex structure prediction with only single-sequence input. Using a novel geometric attention-enabled pairing of biological language models of protein and RNA, a previously unexplored avenue, ProRNA3D-single enables the prediction of interatomic protein-RNA interaction maps, which are then transformed into multi-scale geometric restraints for modeling 3D structures of protein-RNA complexes via geometry optimization. Benchmark tests show that ProRNA3D-single convincingly outperforms current state-of-the-art methods including AlphaFold 3, particularly when evolutionary information is limited; and exhibits remarkable robustness and performance resilience by attaining better accuracy with only single-sequence input than what most methods can achieve even with explicit evolutionary information. Freely available athttps://github.com/Bhattacharya-Lab/ProRNA3D-single, ProRNA3D-single should be broadly useful for modeling 3D structures of protein-RNA complexes at scale, regardless of the availability of evolutionary information.
Maintenance of taste receptor cell presynaptic sites requires gustatory nerve fibers
Authors: Landon Shannon M. , Holder Emily , Ng Amber , Wood Ryan , Gutierrez Kuri Eduardo , Pinto Laura , Humayun Saima , Macpherson Lindsey J.
Published: July 2024

The turnover and re-establishment of peripheral taste synapses is vital to maintain connectivity between the primary taste receptor cells and the gustatory neurons which relay taste information from the tongue to the brain. Despite the importance of neuron-taste cell reconnection, mechanisms governing synapse assembly and the specificity of synaptic connections is largely unknown. Here we use the expression of presynaptic proteins, CALHM1 and Bassoon, to probe whether nerve fiber connectivity is an initiating factor for the recruitment of presynaptic machinery in different populations of taste cells. Under homeostatic conditions, the vast majority (>90%) of presynaptic sites are directly adjacent to nerve fibers. In the days immediately following gustatory nerve transection and complete denervation, Bassoon and CALHM1 puncta are markedly reduced. This suggests that nerve fiber innervation is crucial for the recruitment and maintenance of presynaptic sites. In support of this, we find that expression ofBassoonandCalhm1mRNA transcripts are significantly reduced after denervation. During nerve fiber regeneration into the taste bud, presynaptic sites begin to replenish, but are not as frequently connected to nerve fibers as intact controls (∼50% compared to >90%). This suggests that gustatory neuron proximity, rather than direct contact, likely drives taste receptor cells to express and aggregate presynaptic proteins at the cell membrane. Together, these data support the idea that trophic factors secreted by gustatory nerve fibers prompt taste receptor cells to produce presynaptic specializations at the cell membrane, which in turn may guide neurons to form mature synapses. These findings provide new insights into the mechanisms driving synaptogenesis and synaptic plasticity within the rapidly changing taste bud environment.
PerturbAtlas: A Comprehensive Atlas of Public Genetic Perturbation Bulk RNA-seq Datasets
Authors: Zhang Yiming , Zhang Ting , Yang Gaoxia , Pan Zhenzhong , Tang Min , Wen Yue , He Ping , Wang Yuan , Zhou Ran
Published: July 2024

Manipulating gene expression is crucial for understanding gene function, with high-throughput sequencing techniques such as RNA-seq elucidating the downstream mechanisms involved. However, the lack of a standardized metadata format for small-scale perturbation expression datasets in public repositories hinders their reuse. To address this issue, we developed PerturbAtlas, an add-value resource that re-analyzes publicly archived RNA-seq libraries to provide quantitative data on gene expression, transcript profiles, and alternative splicing events following genetic perturbation. PerturbAtlas assists users in identifying trends at the gene and isoform levels in perturbation assays by re-analyzing a curated set of 122,801 RNA-seq libraries across 13 species. This resource is freely available athttps://perturbatlas.kratoss.siteas both raw data tables and an interactive browser, allowing searches by species, tissue, or genomic features. The results provide detailed information on alterations following perturbations, accessible through both forward and reverse approaches, thereby enabling the exploration of perturbation consequences and the identification of potential causal perturbations.

GRAPHICAL ABSTRACT
Lifespan Oscillatory Dynamics in Lexical Production: A Population-based MEG Resting-State Analysis
Authors: Guichet Clement , Harquel Sylvain , Achard Sophie , Mermillod Martial , Baciu Monica
Published: July 2024

Lexical production remains relatively preserved across the lifespan, but cognitive control demands increase with age to support efficient semantic access. It suggests a domain-general and a language-specific component. Current neurocognitive models suggest the Default Mode Network (DMN) may drive the interplay between these components, impacting the trajectory of production performance with a pivotal shift around midlife. However, the corresponding time-varying architecture still needs clarification. Here, we leveraged MEG resting-state data from healthy adults aged 18-88 from a CamCAN population-based sample. We found that DMN temporal dynamics shift from anterior-ventral to posterior-dorsal states until midlife to mitigate word-finding challenges. Similarly, sensorimotor integration along this posterior path enhances cross-talk with lower-level circuitry as the dynamic information flow with more anterior, higher-order cognitive states gets compromised. It suggests a bottom-up, exploitation-based form of cognitive control in the aging brain, highlighting the interplay between abstraction, control, and perceptive-motor systems in preserving lexical production.
Coordinated regulation of chemotaxis and resistance to copper by CsoR inPseudomonas putida
Authors: He Meina , Tao Yongxin , Mu Kexin , Feng Haoqi , Fan Ying , Liu Tong , Huang Qiaoyun , Xiao Yujie , Chen Wenli
Published: July 2024

Copper is an essential enzyme cofactor in bacteria, but excess copper is highly toxic. Bacteria can cope with copper stress by increasing copper resistance and initiating chemorepellent response. However, it remains unclear how bacteria coordinate chemotaxis and resistance to copper. By screening proteins that interacted with the chemotaxis kinase CheA, we identified a copper-binding repressor CsoR that interacted with CheA inPseudomonas putida. CsoR interacted with the HPT (P1), Dimer (P3), and HATPase_c (P4) domains of CheA and inhibited CheA autophosphorylation, resulting in decreased chemotaxis. The copper-binding of CsoR weakened its interaction with CheA, which relieved the inhibition of chemotaxis by CsoR. In addition, CsoR bound to the promoter of copper-resistance genes to inhibit gene expression, and copper-binding released CsoR from the promoter, leading to increased gene expression and copper resistance.P. putidacells exhibited a chemorepellent response to copper in a CheA-dependent manner, and CsoR inhibited the chemorepellent response to copper. Besides, the CheA-CsoR interaction also existed in proteins from several other bacterial species. Our results revealed a mechanism by which bacteria coordinately regulated chemotaxis and resistance to copper by CsoR.
Degradability tunes ECM stress relaxation and cellular mechanics
Authors: Narasimhan Badri Narayanan , Fraley Stephanie I.
Published: July 2024

In native extracellular matrices (ECM), cells can use matrix metalloproteinases (MMPs) to degrade and remodel their surroundings. Likewise, synthetic matrices have been engineered to facilitate MMP-mediated cleavage that enables cell spreading, migration, and interactions. However, the intersection of matrix degradability and mechanical properties has not been fully considered. We hypothesized that immediate mechanical changes result from the action of MMPs on the ECM and that these changes are sensed by cells. Using atomic force microscopy (AFM) to measure cell-scale mechanical properties, we find that both fibrillar collagen and synthetic degradable matrices exhibit enhanced stress relaxation after MMP exposure. Cells respond to these relaxation differences by altering their spreading and focal adhesions. We demonstrate that stress relaxation can be tuned through the rational design of matrix degradability. These findings establish a fundamental link between matrix degradability and stress relaxation, which may impact a range of biological applications.

Table of contents

This work reveals that matrix degradability, through its effects on stress relaxation, is an important cellular mechanotransduction cue. Cell-scale mechanical characterization shows that collagen gels and degradable synthetic gels display enhanced stress relaxation post-degradation. Stress relaxation is then tuned by systematically varying degradability, resulting in the regulation of cell spreading. This identifies degradability as a key chemomechanical design feature.
Biregional division angles generate sharp apex and concave joints in leaves
Authors: Wang Zining , Inoue Yasuhiro , Mochizuki Atsushi , Tsukaya Hirokazu
Published: July 2024

Leaf apex, the distal end of the leaf blade, exhibits enormous shape variations across plant species. Among these variations, the sharp apex, characterized by its pointed tip, is important in species identification and environmental adaptation. Despite its taxonomic and ecological importance, the developmental mechanisms underlying the formation of a sharp apex remain unknown. The present study aims to investigate the curvature patterns and morphogenesis of the sharp apex to uncover these mechanisms usingTriadica sebiferaleaves. Our research revealed that the sharp apex marks the maximum positive curvature, and is flanked by concave joints with negative curvatures, suggestive of differential tissue growth and spatially regulated cellular behavior. Through a combination of wet experiments and numerical simulations, we demonstrated that biregional cell division angles, rather than locally differing cell expansion or division frequency, play a determining role in shaping distinct leaf morphology. Our study highlights the importance of spatiotemporal regulation of cell division angles during leaf development, suggesting that a biregional growth pattern and cellular behavior contribute to diversity in leaf apex morphology.
Designing a simple and efficient phage biocontainment system using the amber suppressor initiator tRNA
Authors: Tsoumbris Pamela R. , Vincent Russel M. , Jaschke Paul R.
Published: July 2024

Multidrug-resistant infections are becoming increasingly prevalent worldwide. One of the fastest emerging alternative and adjuvant therapies being proposed is phage therapy. Naturally-isolated phages are used in the vast majority of phage therapy treatments today. Engineered phages are being developed to enhance the effectiveness of phage therapy, but concerns over their potential escape remains a salient issue. To address this problem, we designed a biocontained phage system based on conditional replication using amber stop codon suppression. This system can be easily installed on any natural phage with a known genome sequence. To test the system, we mutated the start codons of three essential capsid genes in the phage ϕX174 to the amber stop codon (TAG). These phages were able to efficiently infect host cells expressing the amber initiator tRNA, which suppresses the amber stop codon and initiates translation at TAG stop codons. The amber phage mutants were also able to successfully infect host cells and reduce their population on solid agar and liquid culture but could not produce infectious particles in the absence of the amber initiator tRNA or complementing capsid gene. We did not detect any growth-inhibiting effects onE. colistrains known to lack a receptor for ϕX174, and we show that engineered phages have a limited propensity for reversion. The approach outlined here may be useful to control engineered phage replication in both the lab and clinic.
Resource-efficiency of cyanobacterium production on Mars: Assessment and paths forward
Authors: Ramalho Tiago P. , Baumgartner Vincent , Kunst Nils , Rodrigues David , Bohuon Emma , Leroy Basile , Pillot Guillaume , Heinicke Christiane , Kerzenmacher Sven , Avila Marc , Verseux Cyprien
Published: July 2024

Space agencies and private companies strive for a permanent human presence on the Moon and ultimately on Mars. Bioprocesses have been advocated as key enablers due to their ability to transform locally available resources into added-value materials. However, the resource-efficiency and scaling of space biosystems remain poorly understood, hindering quantitative estimates of their potential performance. We leveraged extensive cultivation experiments, where a cyanobacterium (Anabaenasp. PCC 7938) was subject to conditions attainable on Mars, to develop a model that can estimate bioprocess productivity and resource-efficiency as a function of water, light, temperature, regolith minerals and perchlorates, and atmospheric carbon and nitrogen. We show that a breakeven can be reached within a few years. We discuss research lines to improve both resource efficiency and the accuracy of the model, thereby reducing the need for costly tests in space and eventually leading to a biotechnology-supported, sustained human presence on Mars.

TEASER

Bioprocess modeling shows that cyanobacterium-based biotechnologies can be a sustainable basis for resource production on Mars.
High-fat and high-sucrose diet-induced hypothalamic inflammation shows sex specific features in mice
Authors: De Paula Gabriela C. , Simões Rui F. , Garcia-Serrano Alba M. , Duarte João M. N.
Published: July 2024

Hypothalamic inflammation underlies diet-induced obesity and diabetes in rodent models. While diet normalization largely allows for recovery from metabolic impairment, it remains unknown whether long-term hypothalamic inflammation induced by obesogenic diets is a reversible process. In this study, we aimed at determining sex specificity of hypothalamic neuroinflammation and gliosis in mice fed a fat- and sugar-rich diet, and their reversibility upon diet normalization. Mice were fed a 60%-fat diet complemented by a 20% sucrose drink (HFHSD) for 3 days or 24 weeks, followed by a third group that had their diet normalized for the last 8 weeks of the study (reverse diet group, RevD). We determined the expression of pro- and anti-inflammatory cytokines, and of the inflammatory cell markers IBA1, CD68, GFAP and EMR1 in the hypothalamus, and analyzed morphology of microglia (IBA-1+cells) and astrocytes (GFAP+cells) in the arcuate nucleus. After 3 days of HFHSD feeding, male mice showed over-expression of IL-13, IL-18, IFN-γ, CD68 and EMR1 and reduced expression of IL-10, while females showed increased IL-6 and IBA1 and reduced IL-13, compared to controls. After 24 weeks of HFHSD exposure, male mice showed a general depression in the expression of cytokines, with prominent reduction of TNF-α, IL-6 and IL-13, but increased TGF-β, while female mice showed over-expression of IFN-γ and IL-18. Furthermore, both female and male mice showed some degree of gliosis after HFHSD feeding for 24 weeks. In mice of both sexes, diet normalization after prolonged HFHSD feeding resulted in partial neuroinflammation recovery in the hypothalamus, but gliosis was only recovered in females. In sum, HFHSD-fed mice display sex-specific inflammatory processes in the hypothalamus that are not fully reversible after diet normalization.
How do algorithms influence platform workers’ behavior? Relationship between algorithmic autonomy support and platform workers’ stress and incivility
Authors: Deng Ting , Tang Chunyong , Zhou Ang , Lai Yanzhao
Published: July 2024

Purpose

Drawing upon the needs–supplies fit theory, this study aims to examine how the expected and perceived algorithmic autonomy support (AAS) influences platform workers’ work stress and incivility, with a focus on the moderating role of self-direction.

Design/methodology/approach

Using data collected from 422 platform workers in China through multiple waves, the model is tested through polynomial regression and response surface analysis.

Findings

The results indicate that a mismatch between expected and perceived AAS is associated with higher levels of incivility among platform workers, and this relationship is mediated by work stress. These findings are particularly salient when self-direction is emphasized.

Practical implications

This study suggests that a universally high level of AAS may not necessarily reduce workers’ stress and incivility. Instead, it is important for platforms to ensure that their workers’ expectations of autonomy support are met and for workers to be given the space to exercise self-direction.

Originality/value

Previous studies have highlighted the need to pay attention to workers in mobile and ambiguous environments, and this study adds to this literature by focusing specifically on platform organizations and workplaces. This study provides valuable insights into the relationship between AAS, work stress and platform workers’ incivility.
Multiaxial low-cycle fatigue life model for notched specimens considering small sample characteristics
Authors: Wu Shenglei , Liu Jianhui , Wang Yazhou , Lu Jumei , Zhang Ziyang
Published: July 2024

Purpose

Sufficient sample data are the necessary condition to ensure high reliability; however, there are relatively poor fatigue test data in the engineering, which affects fatigue life's prediction accuracy. Based on this, this research intends to analyze the fatigue data with small sample characteristics, and then realize the life assessment under different stress levels.

Design/methodology/approach

Firstly, the Bootstrap method and the principle of fatigue life percentile consistency are used to realize sample aggregation and information fusion. Secondly, the classical outlier detection algorithm (DBSCAN) is used to check the sample data. Then, based on the stress field intensity method, the influence of the non-uniform stress field near the notch root on the fatigue life is analyzed, and the calculation methods of the fatigue damage zone radius and the weighting function are revised. Finally, combined with Weibull distribution, a framework for assessing multiaxial low-cycle fatigue life has been developed.

Findings

The experimental data of Q355(D) material verified the model and compared it with the Yao’s stress field intensity method. The results show that the predictions of the model put forward in this research are all located within the double dispersion zone, with better prediction accuracies than the Yao’s stress field intensity method.

Originality/value

Aiming at the fatigue test data with small sample characteristics, this research has presented a new method of notch fatigue analysis based on the stress field intensity method, which is combined with the Weibull distribution to construct a low-cycle fatigue life analysis framework, to promote the development of multiaxial fatigue from experimental studies to practical engineering applications.
Social media platforms use in startups’ international marketing strategies: a multiple case study
Authors: Olivieri Mirko , Testa Ginevra
Published: July 2024

Purpose

This paper aims to investigate how social media support startups in accessing international markets and interacting with foreign customers and stakeholders, focusing primarily on the social network LinkedIn.

Design/methodology/approach

Given the explorative research aim, the paper adopts a multiple case study approach, analyzing seven Italian food tech startups. 15 semi-structured interviews were conducted, also involving startup accelerators and a business angel to deepen the knowledge on the investigated phenomenon. In addition, a content analysis of the LinkedIn pages of the seven selected startups was conducted using NVivo 14 software.

Findings

The results of this study show that social media support startups to (1) diffuse brand awareness in international markets, (2) position their offering abroad and (3) develop relationships with international stakeholders to penetrate the local business. Furthermore, the main challenges and difficulties related to the use of social media by startups for these purposes were identified.

Practical implications

This study provides useful managerial implications to enable startups to strategically use social media to access international markets and connect with key foreign networks. Also from a policy perspective, incentives to support the expansion and consolidation of startups into international markets are crucial.

Originality/value

Although a vast literature has dealt with internationalization strategies, this study clarifies the role of social media in changing these dynamics speeding up startups’ access to foreign markets and identifying key local stakeholders.
Intellectual capital through decarbonization for achieving Sustainable Development Goal 8: a systematic literature review and future research directions
Authors: Di Vaio Assunta , Zaffar Anum , Chhabra Meghna
Published: July 2024

Purpose

The aim of this study is to review the literature on how intellectual capital (IC) contributes to the decarbonization efforts of firms. It explores how carbon accounting can measure the components of IC in decarbonization efforts to balance profitability with environmental and social goals, particularly in promoting decent work and economic growth (Sustainable Development Goal [SDG] 8 and its targets [2, 5, 6, 8]). Moreover, it emphasises the importance of multi-stakeholder partnerships for sharing knowledge, expertise, technology, and financial resources (SDG17-Target 17.G) to meet SDG8.

Design/methodology/approach

As a consolidated methodological approach, a systematic literature review (SLR) was used in this study to fill the existing research gaps in sustainability accounting. To consolidate and clarify scholarly research on IC towards decarbonization, 149 English articles published in the Scopus database and Google Scholar between 1990 and 2024 were reviewed.

Findings

The results highlight that the current research does not sufficiently cover the intersection of carbon accounting and IC in the analysis of decarbonization practices. Stakeholders and regulatory bodies are increasingly pressuring firms to implement development-focused policies in line with SDG8 and its targets, requiring the integration of IC and its measures in decarbonization processes, supported by SDG17-Target 17.G. This integration is useful for creating business models that balance profitability and social and environmental responsibilities.

Originality/value

The integration of social dimension to design sustainable business models for emission reduction and provide a decent work environment by focusing on SDG17-Target 17.G has rarely been investigated in terms of theory and practice. Through carbon accounting, IC can be a key source of SDG8-Targets 8.[2, 5, 6, 8] and SDG17-Target 17.G. Historically, these major issues are not easily aligned with accounting research or decarbonization processes.
Navigating egalitarian culture and accountability pressures: shared instructional leadership practices of Danish school leaders
Authors: Laursen Ronni , Gümüş Sedat , Walker Allan David
Published: July 2024

Purpose

Our study presents insights from an exploratory qualitative case study conducted in three primary and lower secondary schools in Denmark, a country renowned for its collaborative and egalitarian culture, to unravel the complexities of shared instructional leadership.

Design/methodology/approach

Interviews with principals, middle leaders, and teachers and document analysis were used to identify themes according to shared and instructional leadership perspectives.

Findings

The study yielded three major findings. First, Danish principals structure schools to prioritize student learning outcomes and distribute responsibility to middle leaders and teachers. Second, reflection among teachers and leaders better prepares them for future demands and obligations. Third, collaboration underpins principals’ vision of reflection and professional development.

Practical implications

The research team’s reflection on the data collected can be used to build future strategies to address unpredictable student learning progression and poor-performing teachers.

Originality/value

Together, these findings contribute to the broader understanding of shared instructional leadership and demonstrate how principals face external pressure for accountability and how egalitarian culture influences principals’ practices.
Integrated model between Three Pillars of Institutions and Mair Noboa model to determine social entrepreneurial intention
Authors: Iqbal Mehree , Geneste Louis , Weber Paull
Published: July 2024

Purpose

This study aims to expand antecedent roles on social entrepreneurial behavioural intention by integrating both the Three Pillars of Institutions and the Mair Noboa model. The literature lacks in investigating both institutional- and individual-level antecedents to determine social entrepreneurial behavioural intention. This proposed integrated model was developed in which the Mair Noboa's model antecedents mediates the positive relationship between the antecedents of Three Pillars of Institutions and social entrepreneurial intention.

Design/methodology/approach

This study uses quantitative research methodologies to answer the research question of the extent that institutional-level antecedents in turn influence individual antecedents and thus determine social entrepreneurial intention. To explore this, a Web-based survey distributed across Bangladesh (n = 412). The confirmation of hypotheses involved using covariance-based structural equation modelling (SEM) for data analysis. The resulting measurement and structural models successfully met all criteria for reliability, model fit, convergent validity and discriminant validity. The hypotheses were subsequently assessed by examining both direct relationships and mediating effects.

Findings

The findings demonstrated a significant relationship between the antecedents of the Three Pillars of Institutions and the Mair Noboa model. The results suggest that the Mair Noboa model antecedents can mediate the relationship between the Three Pillars of Institutions and social entrepreneurial intention.

Originality/value

This paper advances the existing knowledge of social entrepreneurial intention, through the novel lens of combined institutional and individual antecedents. This paper fills an important knowledge gap by exploring both institutional- and individual-level antecedents to determine social entrepreneurial intention. This study findings yield fresh theoretical and practical insights into how institutional and individual antecedents jointly influence social entrepreneurial intention.