bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genusPseudozyma(Ustilaginales)
Authors: Steins Lena , Guerreiro Marco Alexandre , Duhamel Marine , Liu Fei , Wang Qi-Ming , Boekhout Teun , Begerow Dominik
Published: January 2023

Background

The Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genusPseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilag-inales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi.

Results

In this study, we sequenced genomes of fivePseudozymaspecies together with parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate functional mating and meiosis genes that are conserved throughout the whole group.

Conclusion

Our data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.
Integration of transcriptomics data into agent-based models of solid tumor metastasis
Authors: Retzlaff Jimmy , Lai Xin , Berking Carola , Vera Julio
Published: January 2023

Most of the recent progress in our understanding of cancer relies in the systematic profiling of patient samples with high throughput techniques like transcriptomics. This approach has helped in finding gene signatures and networks underlying cancer aggressiveness and therapy resistance. However, -omics data alone is not sufficient to generate insights into the spatiotemporal aspects of tumor progression. Here, multi-level computational models are promising approaches, which would benefit from the possibility to integrate in their characterization the data and knowledge generated by the high throughput profiling of patient samples.

We present a computational workflow to integrate transcriptomics data from tumor patients into hybrid, multi-scale models of cancer. In the method, we employ transcriptomics analysis to select key differentially regulated pathways in therapy responders and non-responders and link them to agent-based model parameters. We next utilize global and local sensitivity together with systematic model simulations to assess the relevance of variations in the selected parameters in triggering cancer progression and therapy resistance. We illustrate the methodology with ade novogenerated agent-based model accounting for the interplay between tumor and immune cells in melanoma micrometastasis. Application of the workflow identifies three different scenarios of therapy resistance.
Decoding the genetic and chemical basis of sexual attractiveness in parasitic wasps
Authors: Sun Weizhao , Lange Michelle Ina , Gadau Jürgen , Buellesbach Jan
Published: January 2023

Attracting and securing potential mating partners is of fundamental importance for successfully initiating reproduction and thus assuring the passing of genes to the next generation. Therefore, signaling sexual attractiveness is expected to be tightly coordinated in communication systems synchronizing senders and receivers. Chemical signaling has permeated through all taxa of life as the earliest and most wide-spread form of communication and is particularly prevalent in insects. However, it has been notoriously difficult to decipher how exactly information related to sexual signaling is encoded in complex chemical profiles. Similarly, our knowledge of the genetic basis of sexual signaling is very limited and usually restricted to a few case studies with comparably simple pheromonal communication mechanisms. The present study jointly addresses these two knowledge gaps by characterizing a single gene simultaneously impacting sexual attractiveness and complex chemical surface profiles in parasitic wasps. Knocking down a fatty acid synthase gene in female wasps dramatically reduces their sexual attractiveness coinciding with a drastic decrease in male courtship and copulation behavior. Concordantly, we found a striking shift of methyl-branching patterns in the female surface pheromonal compounds, which we subsequently demonstrate to be the main cause for the greatly reduced male response. Intriguingly, this suggests a potential coding mechanism for sexual attractiveness mediated by specific methyl-branching patterns, whose genetic underpinnings are not well understood despite their high potential for encoding information. Our study sheds light on how biologically relevant information can be encoded in complex chemical profiles and on the genetic basis of sexual attractiveness.

Significance Statement

Unraveling the genetic basis of chemical signaling is one of the most prevalent yet challenging topics in functional genetics and animal communication studies. Here we present the characterization of a biosynthetic gene in parasitoid wasps that simultaneously impacts sexual attractiveness as well as majorly shifts complex surface pheromone compositions. The shifted pattern primarily constitutes up- and down-regulated methyl-branched compounds with very distinct branching positions. Therefore, these findings immediately suggest a potential coding mechanism for sexual attractiveness in complex chemical profiles. This advances our understanding of how genetic information can be translated into biologically relevant chemical information and reveals that sexual attractiveness can have a comparably simple genetic basis.
Phylogenomics reveals incomplete lineage sorting and ancient hybrid drove the radiation of macaques
Authors: Tan Xinxin , Qi Jiwei , Liu Zhijin , Fan Pengfei , Liu Gaoming , Zhang Liye , Shen Ying , Li Jing , Roos Christian , Zhou Xuming , Li Ming
Published: January 2023

The genusMacaca, with 23 species assigned into four to seven species groups, exhibits the largest geographic range and represents the most successful adaptive radiation of nonhuman primates. Here, we conducted phylogenomic analyses of 16 newly generated and eight published macaque genomes and found a strong support for the division of this genus into seven species groups. Both ancient hybrid and incomplete lineage sorting (ILS) have contributed to the radiation and evolution of macaques. Particularly, the contradicting phylogenetic positions amongsilenus/nigra, fascicularis/mulattaandarctoides/sinicalineages were likely resulted from high level of ILS and potential hybridization between the ancestors of thearctoides/sinicaandsilenus/nigralineages. Furthermore, an integrated scenario for macaque radiation is reconstructed by the help of the dated phylogenetic tree combined with documented history records. This study provides insights into ancient introgression involved in the radiation of macaques, which may help us to understand the rapid speciation of nonhuman primates.
Unique amino acid substitution in RBD region of SARS-CoV-2 Omicron XAY.2
Authors: Salsekar Lekha , Rahangdale Shefali , Tamboli Ekant , Khairnar Krishna
Published: January 2023

We attempted to explain the rare mutation at the receptor binding domain of the spike protein in the XAY.2 variant of SARS-CoV-2 from the perspective of hydrophobic interactions. We propose that decreasing hydrophobicity at position 446 and 486 of the RBD region of the spike protein might affect the infectivity of SARS-CoV-2. We also estimated the probable mutations at the 446 and 486 position the virus may acquire, leading to a decreased hydrophobicity.
At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring
Authors: Jung Kirsten J. , Rasor Blake J. , Rybnicky Grant A. , Silverman Adam D. , Standeven Janet , Kuhn Robert , Granito Teresa , Ekas Holly M. , Wang Brenda M. , Karim Ashty S. , Lucks Julius B. , Jewett Michael C.
Published: January 2023

As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by just-adding-water and DNA to freeze-dried crude extracts ofEscherichia coli. We introduce activities and supporting curricula to teach the structure and function of thelacoperon, dose-responsive behavior, considerations for biosensor outputs, and a ‘build-your-own’ activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high school students in their classrooms – and at home – without professional laboratory equipment or researcher oversight. This work promises to catalyze access to interactive synthetic biology education opportunities.
Imbalanced gut microbiota predicts and drives the progression of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in a fast-food diet mouse model
Authors: Fei Na , Miyoshi Sawako , Hermanson Jake B. , Miyoshi Jun , Xie Bingqing , DeLeon Orlando , Hawkins Maximilian , Charlton William , D’Souza Mark , Hart John , Sulakhe Dinanath , Martinez-Guryn Kristina B. , Chang Eugene B. , Charlton Michael R. , Leone Vanessa A.
Published: January 2023

Nonalcoholic fatty liver disease (NAFLD) is multifactorial in nature, affecting over a billion people worldwide. The gut microbiome has emerged as an associative factor in NAFLD, yet mechanistic contributions are unclear. Here, we show fast food (FF) diets containing high fat, added cholesterol, and fructose/glucose drinking water differentially impact short- vs. long-term NAFLD severity and progression in conventionally-raised, but not germ-free mice. Correlation and machine learning analyses independently demonstrate FF diets induce early and specific gut microbiota changes that are predictive of NAFLD indicators, with corresponding microbial community instability relative to control-fed mice. Shotgun metagenomics showed FF diets containing high cholesterol elevate fecal pro-inflammatory effectors over time, relating to a reshaping of host hepatic metabolic and inflammatory transcriptomes. FF diet-induced gut dysbiosis precedes onset and is highly predictive of NAFLD outcomes, providing potential insights into microbially-based pathogenesis and therapeutics.

Highlights

Germ-free mice are protected from fast-food diet-induced NAFLD.

Fast-food diets rapidly shift gut microbiota composition and function.

Increasing dietary cholesterol exacerbates hepatic inflammation only in SPF mice.

Fast-food diet-induced gut dysbiosis precedes and predicts late-stage NAFLD severity.
Profiling the bloodstream form and procyclic formTrypanosoma bruceicell cycle using single cell transcriptomics
Authors: Briggs Emma M. , Marques Catarina A. , Oldrieve Guy R. , Hu Jihua , Otto Thomas D. , Matthews Keith R.
Published: January 2023

African trypanosomes proliferate as bloodstream forms and procyclic forms in the mammal and tsetse fly midgut, respectively. This allows them to colonise the host environment upon infection and ensure life cycle progression. Yet, understanding of the mechanisms that regulate and drive the cell replication cycle of these forms is limited. Using single cell transcriptomics on unsynchronised cell populations, we have obtained high resolution cell cycle regulated transcriptomes of both procyclic and slender bloodstream formTrypanosoma bruceiwithout prior cell sorting or synchronisation. Additionally, we describe an efficient freeze-thawing protocol that allows single cell transcriptomic analysis of cryopreservedT. brucei. Computational reconstruction of the cell cycle using periodic pseudotime inference allowed the dynamic expression patterns of cycling genes to be profiled for both life cycle forms. Comparative analyses identify a core cycling transcriptome highly conserved between forms, as well as several genes where transcript levels dynamics are form-specific. Comparing transcript expression patterns with protein abundance revealed that the majority of genes with periodic cycling transcript and protein levels exhibit a relative delay between peak transcript and protein expression. This work reveals novel detail of the cell cycle regulated transcriptomes of both forms, which are available for further interrogation via an interactive webtool.
Is high-frequency activity evidence of an anterior temporal lobe network or micro-saccades?
Authors: O’Neill George C. , Mellor Stephanie , Seymour Robert A. , Alexander Nicholas , Tierney Tim M. , Timms Ryan C. , Maguire Eleanor A. , Barnes Gareth R.
Published: January 2023

There is renewed interest in electrical activity that extends beyond the typical electrophysiological 100 Hz bandwidth. This activity, often in the anterior temporal lobe, has been attributed to processes ranging from memory consolidation to epileptiform activity. Here, using an open-access resting state magnetoencephalography (MEG) dataset (n = 89), and a second task-based MEG dataset, we could reliably localise high-frequency power to the temporal lobes across multiple bands up to 300–400 Hz. A functional connectivity analysis of this activity revealed a robust resting state bilateral network between the temporal lobes. However, we also found robust coherence in the 100–200 and 200–300 Hz bands between source reconstructed MEG data and the electrooculography (EOG) localised to within the temporal poles. Additional denoising schemes applied to the data could reduce power localisation to the temporal poles but the topography of the functional network did not drastically alter. Whilst it is clear that this network is biological and robust to established denoising methods, we cannot definitively rule yet on whether this is of neural or myogenic origin.
Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue
Authors: Dhavale Dhruva D. , Barclay Alexander M. , Borcik Collin G. , Basore Katherine , Gordon Isabelle R. , Liu Jialu , Milchberg Moses H. , O’shea Jennifer , Rau Michael J. , Smith Zachary , Sen Soumyo , Summers Brock , Smith John , Warmuth Owen A. , Chen Qian , Fitzpatrick James A. J. , Schwieters Charles D. , Tajkhorshid Emad , Rienstra Chad M. , Kotzbauer Paul T.
Published: January 2023

The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. We developed and validated a novel method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and used solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise two protofilaments with pseudo-21helical screw symmetry, very low twist and an interface formed by antiparallel beta strands of residues 85-93. The fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural landscape of LBD Asyn fibrils and inform further studies of disease mechanisms, imaging agents and therapeutics targeting Asyn.
Force-regulated spontaneous conformational changes of integrins α5β1and αVβ3
Authors: Chen Yunfeng , Kong Fang , Li Zhenhai , Ju Lining Arnold , Zhu Cheng
Published: January 2023

Force can modulate the properties and functions of macromolecules by inducing conformational changes, such as coiling/uncoiling, zipping/unzipping, and folding/unfolding. Here we compared force-modulated bending/unbending of two purified integrin ectodomains, α5β1and αVβ3, using single-molecule approaches. Similar to previously characterized mechano-sensitive macromolecules, the conformation of α5β1is determined by a threshold head-to-tail tension, suggesting a canonical energy landscape with a deep energy well that traps the integrin in the bent state until sufficient force tilts the energy landscape to accelerate transition to the extended state. By comparison, αVβ3exhibits bi-stability even without force and can spontaneously transition between the bent and extended conformations in a wide range of forces without energy supplies. Molecular dynamics simulations revealed consecutive formation and disruption of 7 hydrogen bonds during αVβ3bending and unbending, respectively. Accordingly, we constructed an energy landscape with hexa-stable intermediate states to break down the energy barrier separating the bent and extended states into smaller ones, making it possible for the thermal agitation energy to overcome them sequentially and to be accumulated and converted into mechanical work required for αVβ3to bend against force. Our study elucidates the different inner workings of α5β1and αVβ3at the sub-molecular level, sheds lights on how their respectively functions are facilitated by their distinctive mechano-sensitivities, helps understand their signal initiation processes, and provides critical concepts and useful design principles for engineering of protein-based biomechanical nanomachines.
Single-nucleus transcriptional profiling of GAD2-positive neurons from mouse lateral habenula reveals distinct expression of neurotransmission- and depression-related genes
Authors: Green Matthew V. , Gallegos David A. , Boua Jane-Valeriane , Bartelt Luke C. , Narayanan Arthy , West Anne E.
Published: January 2023

Glutamatergic projection neurons of the lateral habenula (LHb) drive behavioral state modulation by regulating the activity of midbrain monoaminergic neurons. Identifying circuit mechanisms that modulate LHb output is of interest for understanding control of motivated behaviors. A small population of neurons within the medial subnucleus of the mouse LHb express the GABAergic synthesizing enzyme GAD2, and they can inhibit nearby LHb projection neurons; however, these neurons lack markers of classic inhibitory interneurons and they co-express the vesicular glutamate transporter VGLUT2. To determine the molecular phenotype of these neurons, we genetically tagged the nuclei of GAD2-positive cells and used fluorescence-activated nuclear sorting to isolate and enrich these nuclei for single nuclear RNA sequencing (FANS-snRNAseq). Our data confirm that GAD2+/VGLUT2+ neurons intrinsic to the LHb co-express markers of both glutamatergic and GABAergic transmission and that they are transcriptionally distinct from either GABAergic interneurons or habenular glutamatergic neurons. We identify gene expression programs within these cells that show sex-specific differences in expression and that are implicated in major depressive disorder (MDD), which has been linked to LHb hyperactivity. Finally, we identify theNtng2gene encoding the cell adhesion protein Netrin-G2 as a marker of LHb GAD2+/VGLUT+ neurons and a gene product that may contribute to their target projections. These data show the value of using genetic enrichment of rare cell types for transcriptome studies, and they advance understanding of the molecular composition of a functionally important class of GAD2+ neurons in the LHb.
Ribonucleoprotein condensation driven by retrotransposon LINE-1 sustains RNA integrity and translation in mouse spermatocytes
Authors: Luca Chiara De , Gupta Anuj , Bortvin Alex
Published: January 2023

Transposable elements (TE) are mobile DNA sequences whose excessive proliferation endangers the host. Although animals have evolved robust TE-targeting defenses, including Piwi-interacting (pi)RNAs, retrotransposon LINE-1 (L1) still thrives in humans and mice. To gain insights into L1 endurance, we characterized L1 Bodies (LBs) and ORF1p complexes in germ cells of piRNA-deficientMaelstromnull mice. We report that ORF1p interacts with TE RNAs, genic mRNAs, and stress granule proteins, consistent with earlier studies. We also show that ORF1p associates with the CCR4-NOT deadenylation complex and PRKRA, a Protein Kinase R factor. Despite ORF1p interactions with these negative regulators of RNA expression, the stability and translation of LB-localized mRNAs remain unchanged. To scrutinize these findings, we studied the effects of PRKRA on L1 in cultured cells and showed that it elevates ORF1p levels and L1 retrotransposition. These results suggest that ORF1p-driven condensates promote L1 propagation, without affecting the metabolism of endogenous RNAs.
Preneoplastic cells switch to Warburg metabolism from their inception exposing multiple vulnerabilities for targeted elimination
Authors: Myllymäki Henna , Kelly Lisa , Elliot Abigail M. , Carter Roderick N. , Morton Nicholas M. , Feng Yi
Published: January 2023

Otto Warburg first described tumour cells as displaying enhanced aerobic glycolysis whilst maintaining defective oxidative phosphorylation (OXPHOS) for energy production almost 100 years ago1,2. Since then, the ‘Warburg effect’ has been widely accepted as a key feature of rapidly proliferating cancer cells3,4. Targeting cancer metabolism is now being considered as a promising precision oncology therapeutic approach5. What is not clear is how early “Warburg metabolism” initiates during cancer progression and whether changes in energy metabolism might influence tumour progressionab initio. We set out to investigate energy metabolism in HRASG12Vdriven preneoplastic cell (PNC) at inception, in a zebrafish skin PNC model; and to test how the impact of manipulating energy metabolism in the whole animal may impact PNC initiation. We find that, within 24 hours of HRASG12Vinduction, PNCs upregulate “Warburg metabolism”, and that this is required for their expansion. We show that blocking glycolysis reduces PNC proliferation, whilst increasing available glucose both enhances PNC proliferation and also reduces apoptosis. Impaired OXPHOS of PNCs might be exploited therapeutically since a mild complex I inhibitor, metformin, selectively induces apoptosis and suppresses proliferation of PNCs. In addition, we find mitochondrial fragmentation in PNCs occur prior to metabolic alteration and this is important for their survival since exposure to Drp1/Dnml1 inhibitor, mdivi, which blocks mitochondrial fragmentation leads to enhanced PNC apoptosis. Our data indicate that altered energy metabolism is one of the earliest events upon oncogene activation in somatic cells, which provide a targeted and effective tumour prevention therapy.

Key findings

Glycolysis is upregulated in HRASG12Vexpressing preneoplastic cells (PNCs) in zebrafish skin, and is required for PNC proliferation

OXPHOS respiration is impaired in PNCs and metformin complex I inhibition specifically eliminates PNCs

PNC undergo mitochondrial fragmentation and exhibit reduced membrane potential

Mdivi reverses mitochondrial fragmentation in PNCs and triggers apoptosis
Heterologous production of cyanophycin withTatumella morbiroseicyanophycin synthetase
Authors: Swain Kyle , Sharon Itai , Blackson Wyatt , Tekel Stefan , Schmeing T. Martin , Nielsen David R. , Nannenga Brent L.
Published: January 2023

Microbial production of biopolymers represents a promising, sustainable alternative to current approaches for plastic production. Cyanophycin synthetase 1 (CphA1) produces cyanophycin - an attractive biopolymer consisting of a poly-L-aspartic acid backbone decorated with L-arginine side groups. In this work, a series of CphA1 enzymes from different bacteria were screened for heterologous cyanophycin production in engineeredEscherichia coli, from which it was found that CphA1 fromTatumella morbirosei(TmCphA1) was especially productive.TmCphA1 was capable of supporting up to ~2-fold greater yields of insoluble cyanophycin than any other tested CphA1 enzymes, including 10.8-times more than CphA1 fromSynechocystissp. PCC6308. Finally, using a bench-scale bioreactor, cyanophycin production byTmCphA1-expressingE. colireached up to 1.9 g per liter of culture by 48 h.
Oncogene-like addiction to aneuploidy in human cancers
Authors: Girish Vishruth , Lakhani Asad A. , Scaduto Christine M. , Thompson Sarah L. , Brown Leanne M. , Hagenson Ryan A. , Sausville Erin L. , Mendelson Brianna E. , Lukow Devon A. , Yuan Monet Lou , Kandikuppa Pranav K. , Stevens Eric C. , Lee Sophia N. , Salovska Barbora , Li Wenxue , Smith Joan C. , Taylor Alison M. , Martienssen Robert A. , Liu Yansheng , Sun Ruping , Sheltzer Jason M.
Published: January 2023

Most cancers exhibit aneuploidy, but its functional significance in tumor development is controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using CRISPR Targeting), a set of chromosome engineering tools that allow us to eliminate specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies, and we demonstrate that trisomy of chromosome 1q is required for malignant growth in cancers harboring this alteration. Mechanistically, gaining chromosome 1q increases the expression of MDM4 and suppresses TP53 signaling, and we show that TP53 mutations are mutually-exclusive with 1q aneuploidy in human cancers. Thus, specific aneuploidies play essential roles in tumorigenesis, raising the possibility that targeting these “aneuploidy addictions” could represent a novel approach for cancer treatment.
Activation of basal forebrain astrocytes induces wakefulness without compensatory changes in sleep drive
Authors: Ingiosi Ashley M. , Hayworth Christopher R. , Frank Marcos G.
Published: January 2023

Mammalian sleep is regulated by a homeostatic process that increases sleep drive and intensity as a function of prior wake time. Sleep homeostasis has traditionally been thought to be a product of neurons, but recent findings demonstrate that this process is also modulated by glial astrocytes. The precise role of astrocytes in the accumulation and discharge of sleep drive is unknown. We investigated this question by selectively activating basal forebrain (BF) astrocytes using designer receptors exclusively activated by designer drugs (DREADDs). Activation of the Gq-protein-coupled pathway in BF astrocytes produced long and continuous periods of wakefulness that paradoxically did not cause the expected homeostatic response to sleep loss (e.g., increases in sleep time or intensity). Further investigations showed that this was not due to indirect effects of the ligand that activated DREADDs. These findings suggest that the need for sleep is not driven by wakefulness per se, but specific neuronal-glial circuits that are differentially activated in wakefulness.
Weak impact of underground water on corrosion inhibition of resistance-reducing agent
Authors: Su Hui , Liu Lanlan , Yang Yang , Zhong Zhen , Xu Song , Xie Yi , Wu Tangqing
Published: January 2023

Purpose

The purpose of this paper is to study the corrosion behavior of Q235 steel in the bentonite-based resistance-reducing agent (RRA) with different infiltration rates of underground water.

Design/methodology/approach

The corrosion behavior of the steel in underground water was assessed by weight loss experiment, electrochemical impedance spectroscopy and polarization curve.

Findings

The results showed that the corrosion rate of the steel in the RRA pastes was much lower than that in the original acidic soil. The underground water infiltration slightly accelerated the corrosion rate of the steel in the RRA pastes, but the acceleration role is weak. The bentonite-based RRA can be compatibly applied in the acidic soil.

Originality/value

The bentonite-based RRA can significantly reduce the corrosion rate of the steel and is suitable to compatibly apply in the acidic soil.
How was the coronavirus vaccine accepted on Twitter? A computational analysis using big data in Japan
Authors: Tanihara Tsukasa , Yamaguchi Shinichi
Published: January 2023

Purpose

This study aims to reveal how the COVID-19 vaccine was accepted in the Japanese Twitter-sphere. This study explores how the topics related to the vaccine promotion project changed on Twitter and how the topics that were likely to spread changed during the vaccine promotion project.

Design/methodology/approach

The computational social science methodology was adopted. This study collected all tweets containing the word “vaccine” using the Twitter API from March to October 2021 and conducted the following analysis: analyzing frequent words and identifying topics likely to spread through the cosine similarity and Tobit model.

Findings

First, vaccine hesitancy–related words were frequently mentioned during the vaccine introduction and dissemination periods and had diffusing power only during the former period. Second, vaccine administration–related words were frequently mentioned and diffused through April to May and had diffusing power throughout the period. The background to these findings is that the sentiment of longing for vaccines outweighed that of hesitancy toward vaccines during this period.

Originality/value

This study finds that the timing of the rise in vaccine hesitation sentiment and the timing of the start of vaccine supply were misaligned. This is one of the reasons that Japan, which originally exhibited strong vaccine hesitancy, did not face vaccine hesitancy in the COVID-19 vaccine promotion project.
Digitalization and third-party logistics performance: exploring the roles of customer collaboration and government support
Authors: Zhou Haidi , Wang Qiang , Wang Liang , Zhao Xiande , Feng Gengzhong
Published: January 2023

Purpose

The authors investigate how logistics digitalization affects two types of third-party logistics (3PL) performance: financial performance and service performance. In particular, the authors explore the mediating role of customer collaboration between logistics digitalization and firm performance based on organizational information processing theory and examine the moderating role of government support.

Design/methodology/approach

The authors use an SPSS macro program (PROCESS regression analysis) to analyze survey data from 235 3PL firms in China. The mediation model, moderation model and moderated mediation model are tested.

Findings

The empirical results show that in the new age of digitalization transformation, logistics digitalization positively affects 3PL's financial performance and service performance by strengthening customer collaboration. Additionally, government support amplifies the positive effect of customer collaboration on service performance but not financial performance. The moderated mediation test further indicates that government support strengthens the positive indirect effect of digitalization on service performance through customer collaboration.

Originality/value

This study offers empirical insights into the growing body of 3PL literature, and the findings contribute to the theoretical and practical understanding of the emerging research topic of digital transformation (DT) and sustainability issues in 3PL firms.
Species composition, abundance and habitat association of non‐volant small mammals in Gibe Sheleko National Park, southwestern Ethiopia
Authors: Kiros Seyoum , Bekele Afework
Published: January 2023

The objective of this study was to assess the species composition, abundance and habitat association of non‐volant small mammals from grassland, Acacia woodland, farmland, riverine forest, bushland and wooded grassland habitats in Gibe Sheleko National Park, southwestern Ethiopia. Data were collected using 49 Sherman live traps in 70 × 70 m sized girds and visual observations from December 2018 to August 2020. A total of 937 small mammals belonging to 10 species were captured and directly identified. The identified small mammal species and their relative abundance include Arvicanthis niloticus (7.04%), Crocidura olivieri (1.92%), Grammomys dolichurus (3.84%), Lemniscomys striatus (10.25%), Mastomys awashensis (24.55%), Mastomys natalensis (33.83%), Mus tenellus (0.85%), Myomys fumatus (6.30%), Rattus rattus (4.70%) and Stenocephalemys albipes (6.72%). Hystrix cristata, Xerus rutilus and Tachyoryctes splendens were documented through observation. The highest number of species (6) was registered at farmland and wooded grassland followed by bushland and riverine forest (5) and Acacia woodland and grassland (4). Lemniscomys striatus, M. awashensis and M. natalensis were common in all habitats. More, 216 (23.05%) individuals were recorded in farmland, while the least, 111 (11.85%) were recorded in Acacia woodland. The study area has various topographical land settings additional study is needed using different traps.
A review of the ecological knowledge on the species Batrachoides liberiensis in estuarine and lagoon environments of West Africa
Authors: Simier Monique , Sadio Oumar , Tito de Morais Luis , Ecoutin Jean‐Marc
Published: January 2023

Scientific fishing programmes were carried out between 1979 and 2013 in several West African estuarine, coastal and lagoon ecosystems. Batrachoides liberiensis represented only 5.2% of the occurrences, of which the majority were recorded in the Sine Saloum estuary. This originality makes it possible to use this population to characterise certain features of the biology and ecology of this little described species. B. liberiensis was recorded in waters with a salinity of 25–46, transparency of 1–3.5 m, at depths of 2–10 m. It was particularly abundant in areas at a distance of 15–35 km from the mouth. The water temperature did not appear to be a determining factor for this species. The sex ratio of the population, whose total length ranged from 10 to 371 mm, was in favour of females (87%) with an estimated size at first maturity of 189 mm (total length). The parameters of the length‐weight relationship were estimated at K = 1.0009*10−5 and b = 3.097. The diet of B. liberiensis consisted mainly of molluscs and crabs, present in respectively, 53.6% and 50.7% of the stomach contents analysed.
Intermitochondrial cement (IMC) harbors piRNA biogenesis machinery and exonuclease domain‐containing proteins EXD1 and EXD2 in mouse spermatocytes
Authors: Olotu Opeyemi , Dowling Mark , Homolka David , Wojtas Magdalena N. , Tran Panyi , Lehtiniemi Tiina , Da Ros Matteo , Pillai Ramesh S. , Kotaja Noora
Published: January 2023

Background

Germ granules are large cytoplasmic ribonucleoprotein complexes that emerge in the germline to participate in RNA regulation. The two most prominent germ granules are the intermitochondrial cement (IMC) in meiotic spermatocytes and the chromatoid body (CB) in haploid round spermatids, both functionally linked to the PIWI‐interacting RNA (piRNA) pathway.

Aims

In this study, we clarified the IMC function by identifying proteins that form complexes with a well‐known IMC protein PIWIL2/MILI in the mouse testis.

Results

The PIWIL2 interactome included several proteins with known functions in piRNA biogenesis. We further characterized the expression and localization of two of the identified proteins, Exonuclease 3′–5′ domain‐containing proteins EXD1 and EXD2, and confirmed their localization to the IMC. We showed that EXD2 interacts with PIWIL2, and that the mutation of Exd2 exonuclease domain in mice induces misregulation of piRNA levels originating from specific pachytene piRNA clusters, but does not disrupt male fertility.

Conclusion

Altogether, this study highlights the central role of the IMC as a platform for piRNA biogenesis, and suggests that EXD1 and EXD2 function in the IMC‐mediated RNA regulation in postnatal male germ cells.
Carbohydrate‐rich diet increases critical thermal maximum in ants
Authors: Freires Allana Sabrina Alves , Ferreira Carlos André Souza , Nascimento Geraldo , Arnan Xavier
Published: January 2023

To understand species’ responses to climate change, we must better comprehend the factors shaping physiological critical thermal limits. One factor of potential importance is nutrient availability. Carbohydrates are an energy source that can directly affect an organism's physiological state. Ants are among the most omnipresent and ecologically relevant animal groups on Earth, and many ant species consume carbohydrate‐based diets. Additionally, as ectotherms, ants are highly vulnerable to the effects of climate change. Here, we examined the relationship between foraging temperature, carbohydrate availability, and critical thermal maximum (CTmax) in ants (Hymenoptera: Formicidae). First, we conducted a laboratory experiment using 3–4 colonies of two species that forage at high temperatures (Camponotus blandus Smith and Dorymyrmex thoracicus Gallardo) and two species that forage at lower temperatures (Nylanderia fulva Mayr and Dolichoderus quadridenticulatus Roger). Each colony was divided into two experimental subcolonies, which were given diets containing different carbohydrate concentrations (5 vs. 20% sucrose solutions). We then measured CTmax. We also collected ants belonging to these species in the field and measured their CTmax. We found that CTmax was highest for the two species that forage at higher temperatures. For C. blandus and D. thoracicus, workers given 20% sucrose had higher CTmax than workers given 5% sucrose. No diet‐mediated differences in CTmax were seen for N. fulva and D. quadridenticulatus workers. Additionally, the experimental ants in both treatment groups had higher CTmax than their field‐collected conspecifics, except in the case of C. blandus. If carbohydrate‐rich diets can boost heat tolerance in some species, it is possible that changes in resource availability could determine how climate change affects ants, especially species with carbohydrate‐based diets. Furthermore, these impacts could ripple across the entire trophic network.
A cross‐sectional investigation of cognition and epileptiform discharges in juvenile absence epilepsy
Authors: Dharan Anita L. , Bowden Stephen C. , Peterson Andre , Lai Alan , Seneviratne Udaya , Dabscheck Gabriel , Nurse Ewan , Loughman Amy , Parsons Nicholas , D'Souza Wendyl J.
Published: January 2023

Objectives

Despite the prevalence of cognitive symptoms in the idiopathic generalized epilepsies (IGEs), cognitive dysfunction in juvenile absence epilepsy (JAE), a common yet understudied IGE subtype, remains poorly understood. This descriptive study provides a novel, comprehensive characterization of cognitive functioning in a JAE sample and examines the relationship between cognition and 24‐h epileptiform discharge load.

Method

Forty‐four individuals diagnosed with JAE underwent cognitive assessment using Woodcock Johnson III Test of Cognitive Abilities with concurrent 24‐h ambulatory EEG monitoring. Generalized epileptiform discharges of any length, and prolonged generalized discharges ≥3 s were quantified across wakefulness and sleep. The relationship between standardized cognitive scores and epileptiform discharges was assessed through regression models.

Results

Cognitive performances in overall intellectual ability, acquired comprehension‐knowledge, processing speed, long‐term memory storage and retrieval, and executive processes were 0.63–1.07 standard deviation (SD) units lower in the JAE group compared to the population reference mean, adjusted for educational attainment. Prolonged discharges (≥3 s) were recorded in 20 patients (47.6%) from 42 available electroencephalography (EEG) studies and were largely unreported. Duration and number of prolonged discharges were associated with reduced processing speed and long‐term memory storage and retrieval.

Significance

Cognitive dysfunction is seen in patients with JAE across various cognitive abilities, including those representing more stable processes like general intellect. During 24‐h EEG, prolonged epileptiform discharges are common yet underreported in JAE despite treatment, and they show moderate effects on cognitive abilities. If epileptiform burden is a modifiable predictor of cognitive dysfunction, therapeutic interventions should consider quantitative 24‐h EEG with routine neuropsychological screening. The growing recognition of the spectrum of neuropsychological comorbidities of IGE highlights the value of multidisciplinary approaches to explore the causes and consequences of cognitive deficits in epilepsy.
Chemical vapor deposition derived ultralong SiC nanofibers: structural characterization and growth mechanism
Authors: Liu Debao , Zhang Chao , Xue Yahui
Published: January 2023

In this study, the ultralong SiC nanofibers (SiC NFs) were synthesized through the sol–gel method assisted the chemical vapor deposition technique. The scanning electron microscope, transmission electron microscopy, X‐ray diffraction, Raman, Fourier transform infrared, and X‐ray photoelectron spectroscopy techniques were systematically employed to investigate the microstructure, morphology, and phase composition of the as‐prepared products. The results demonstrated that the as‐obtained products were β‐SiC nanofibers with face‐centered cubic crystal structure. Meanwhile, the ultralong SiC NFs present an average diameter of about 18 nm and a length up to several hundreds of micrometers and grew along the [1 1 1] direction with a planar stacking faults. In addition, we also investigated the formation mechanism and growth process of the ultralong SiC NFs. The successful preparation of such ultralong SiC NFs provides new idea for fabricating of other silicon‐based ultralong nanofibers.
Flexible vehicle scheduling with precedence constraints for tourists
Authors: Liu Zhujun , Moon Ilkyeong , Zhang Ruiyou
Published: January 2023

This research addresses a flexible vehicle scheduling problem considering precedence constraints (FVS‐P problem), which is prevalent in many scenic areas worldwide. Each group of tourists in the FVS‐P problem comprises a set of visit requests that must be served by shuttle vehicles in a predefined order. A three‐indexed integer linear programming model is introduced. Furthermore, an index‐reduction strategy is proposed to strengthen the model. A math‐heuristic route‐segment generation algorithm embedded in a mathematical model is designed to solve the FVS‐P problem, particularly in the case of large‐sized instances. Experiments on different sizes of near‐practical instances validate the mathematical models and the algorithm. The proposed math‐heuristic can provide better solutions for large‐sized instances in a much shorter time than the models. The trade‐off between tourists’ feelings and the cost of the area is investigated to provide further insights for managers.
DNA barcoding of fresh seafood in Australian markets reveals misleading labelling and sale of endangered species
Authors: Khalil Andrew M. , Gainsford Ashton , van Herwerden Lynne
Published: January 2023

Flake and shark samples were purchased from outlets in several coastal Australian regions and genetically barcoded using the cytochrome oxidase subunit 1 (CO1) gene to investigate labelling reliability and species‐specific sources of ambiguously labelled fillets. Of the 41 shark fillet samples obtained, 23 yielded high‐quality CO1 sequences, out of which 57% (n = 13) were labelled ambiguously (misleading) and 35% (n = 8) incorrectly. In contrast, barramundi fillets, which are widely available and sought after in Australian markets, were shown to be accurately labelled. Species identified from shark samples, including the shortfin mako (n = 3) and the scalloped hammerhead (n = 1), are assessed by the IUCN as endangered and critically endangered, respectively, with several others classified as vulnerable and near threatened.
Visual–spatial and visuomotor functioning in adults with neurofibromatosis type 1
Authors: Castricum J. , Tulen J. H. M. , Taal W. , Pel J. J. M. , Elgersma Y.
Published: January 2023

Background

Neurofibromatosis type 1 (NF1) is a neurodevelopmental genetic disorder associated with visual–spatial and visuomotor deficits, which have not been studied well in adults with NF1.

Methods

In 22 adults with NF1 and 31 controls, visuomotor functioning was assessed by measuring eye latency, hand latency and hand accuracy during visuomotor tasks. Visual–spatial functioning was assessed by measuring eye movement responses during the Visual Threshold Task.

Results

The NF1 group had a significantly shorter eye latency than the control group and was less accurate in their hand movements during specific visuomotor tasks. The groups showed no differences in eye movement responses during the Visual Threshold Task and in hand latency during the visuomotor tasks.

Conclusions

In contrast to studies in children with NF1, we found no alterations in visual–spatial information processing in adults. Impairments in eye latency and hand accuracy during specific visuomotor tasks may indicate deficits in visuomotor functioning in adults with NF1.
Diagnosis and management of hepatic encephalopathy: The French recommendations
Authors: Thabut Dominique , Bouzbib Charlotte , Meunier Lucy , Haas Manon , Weiss Nicolas , Louvet Alexandre , Imbert‐Bismut Francois , Mochel Fanny , Nadjar Yann , Santiago Antoine , Thevenot Thierry , Duhalde Véronique , Oberti Frédéric , Francoz Claire , Coilly Audrey , Hilleret Marie‐Noelle , Lebray Pascal , Liou‐Schischmanoff Amélie , Barbier Louise , Duvoux Christophe , Pageaux Georges‐Philippe , Bismuth Michael , Galanaud Damien , Broucker Thomas De , Cadranel Jean‐François , Leroy Vincent , Di Martino Vincent , Larrey Dominique , Camus Christophe , Scatton Olivier , De Ledinghen Victor , Mallat Ariane , Rudler Marika , Bureau Christophe ,   for the Association Française pour l'Etude du Foie (AFEF) group of experts of HE recommendations
Published: January 2023

Hepatic encephalopathy (HE) is a frequent and severe complication of liver disease with poor patient outcomes. However, it is a poorly understood complication, with no consensus for diagnosis. Therefore, HE is often underdiagnosed. Differential diagnosis may be cumbersome because of non‐specific symptoms, such as confusion, cognitive disorders, the aetiological factors of cirrhosis and comorbidities, which are often observed in cirrhotic patients. Therefore, an overt or covert form of HE should be systematically investigated. Advice is provided to drive patient work‐up. Effective treatments are available to prevent or treat HE bouts, but the issue of single or combination therapy has not been resolved. Transjugular intrahepatic portosystemic shunt (TIPS) placement largely improved the prognosis of cirrhotic patients, but HE occurrence of HE is often a fear, even when post‐TIPS HE can be avoided by a careful selection of patients and preventive treatment. HE is an indication of liver transplantation. However, its reversibility post‐transplantation and the consequences of transplantation in patients with other causes of neurological disorders remain controversial, which supports the performance of an extensive work‐up in expert centres for this subset of patients. The present guidelines assist clinicians in the diagnosis of the overt or covert form of HE to implement curative and preventive treatments and clarify which patients require referral to expert centres for consideration for liver transplantation. These guidelines are very clinically oriented and address different frequent clinical issues to help physicians make bedside decisions.