bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of cytoneme-like structures and extracellular vesicles inTrichomonas vaginalisparasite: parasite communication
Authors: Salas Nehuén , Pedreros Manuela Blasco , Santos Melo Tuanne dos , Maguire Vanina G. , Sha Jihui , Wohlschlegel James A. , Pereira-Neves Antonio , de Miguel Natalia
Published: January 2023

Trichomonas vaginalis, the etiologic agent of the most common non-viral sexually transmitted infection worldwide, colonizes the human urogenital tract where it remains extracellular and adheres to epithelial cells. With an estimated prevalence of 276 million new cases annually, mixed infections with different parasite strains are expected. Although it is considered as obvious that parasites interact with their host to enhance their own survival and transmission, evidence of mixed infection call into question the extent to which unicellular parasites communicate with each other. Here, we demonstrated that differentT. vaginalisstrains are able to communicate through the formation of cytoneme-like membranous cell connections. We showed thatT. vaginalisadherent strains form abundant membrane protrusions and cytonemes formation of an adherent parasite strain (CDC1132) is affected in the presence of a different strain (G3 or B7RC2). Using a cell culture inserts assays, we demonstrated that the effect in cytoneme formation is contact independent and that extracellular vesicles (EVs) are responsible, at least in part, of the communication among strains. In this sense, we found that EVs isolated from G3, B7RC2 and CDC1132 strains contain a highly distinct repertoire of proteins, some of them involved in signaling and communication, among other functions. Finally, we showed that parasite adherence to host cells is affected by this communication between strains as binding of adherentT. vaginalisCDC1132 strain to prostate cells is significantly higher in the presence of G3 or B7RC2 strains. Demonstrating that interaction of isolates with distinct phenotypic characteristics may have significant clinical repercussions, we also observed that a poorly adherent parasite strain (G3) adheres more strongly to prostate cells in the presence of an adherent strain. The study of signaling, sensing and cell communication in parasitic organisms will surely enhance our understanding of the basic biological characteristics of parasites that might have important consequences in pathogenesis.
Excitation and inhibition delays within a feedforward inhibitory pathway modulate cerebellar Purkinje cell output in mice
Authors: Binda Francesca , Spaeth Ludovic , Kumar Arvind , Isope Philippe
Published: January 2023

The cerebellar cortex computes sensorimotor information from many brain areas through a feedforward inhibitory (FFI) microcircuit between the input stage, the granule cell layer, and the output stage, the Purkinje cells. While in other brain areas FFI underlies a precise excitation vs inhibition temporal correlation, recent findings in the cerebellum highlighted more complex behaviors at the granule cell (GC) – molecular layer interneuron (MLI) – Purkinje cell (PC) FFI pathway. To dissect the temporal organization of the cerebellar FFI pathway, we combined exvivo patch clamp recordings of PCs with a viral-based strategy to express Channelrhodopsin2 in a subset of mossy fibers (MFs), a major excitatory input to GCs. We show that light-mediated MF activation elicits excitatory and inhibitory currents in PCs with a wide range of temporal delays. Furthermore, in many recordings, excitation and inhibition were initiated by different groups of GCs, expanding PCs synaptic temporal integration. Using a computational model of the FFI pathway we demonstrated that this temporal expansion could strongly influence how PCs integrate MF inputs. Our findings suggest that MF inputs are also encoded by specific delays between excitation and inhibition in PCs.
Bioengineering of aLactococcus lactissubsp.lactisstrain enhances nisin production and bioactivity
Authors: Portieles Roxana , Xu Hongli , Chen Feng , Gao Jingyao , Du Lihua , Gao Xiangyou , Nordelo Carlos Borroto , Yue Qiulin , Zhao Lin , Gonzalez Nayanci Portal , Bermudez Ramon Santos , Borrás-Hidalgo Orlando
Published: January 2023

Lactococcus lactissubsp.lactisis a food bacterium that has been utilized for decades in food fermentation and the development of high-value industrial goods. Among these, nisin is produced by several strains ofL. lactissubsp.lactisplays a crucial role as a food bio-preservative. The relative expression of the gene cluster involved in nisin production was evaluated using qPCR analysis. Additionally, a series of re-transformations of the strain introducing multi copies of thenisAandnisRKgenes involved in nisin biosynthesis were developed. The simultaneous expression ofnisAandnisZgenes was used to potentiate the effective inhibition of foodborne pathogens. Further, qPCR analysis revealed a low expression of thenisAandnisRKgenes in wild-typeL. lactissubsp.lactis. After several re-transformations of the strain with thenisAandnisRKgenes, a high expression of these genes was obtained, contributing to improved nisin production. Also, the co-expression ofnisAandnisZgenes results in highly efficient antimicrobial activity. Hence, this study would supply an approach to enhancing nisin production during industrial processes and antimicrobial activity.
Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors
Authors: Pöll Gisela , Griesenbeck Joachim , Tschochner Herbert , Milkereit Philipp
Published: January 2023

RpS0/uS2, rpS2/uS5, and rpS21/eS21 form a cluster of ribosomal proteins (S0-cluster) at the head-body junction near the central pseudoknot of eukaryotic small ribosomal subunits (SSU). Previous work in yeast indicated that S0-cluster assembly is required for the stabilisation and maturation of SSU precursors at specific post-nucleolar stages.

Here, we analysed the role of S0-cluster formation for rRNA folding. Structures of SSU precursors isolated from yeast S0-cluster expression mutants or control strains were analysed by cryogenic electron microscopy. The obtained resolution was sufficient to detect individual 2’-O-methyl RNA modifications using an unbiased scoring approach.

The data show how S0-cluster formation enables the initial recruitment of the pre-rRNA processing factor Nob1 in yeast. Furthermore, they reveal hierarchical effects on the pre-rRNA folding pathway, including the final maturation of the central pseudoknot.

Based on these structural insights we discuss how formation of the S0-cluster determines at this early cytoplasmic assembly checkpoint if SSU precursors further mature or are degraded.
Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature
Authors: Knafou Julien , Haas Quentin , Borissov Nikolay , Counotte Michel , Low Nicola , Imeri Hira , Ipekci Aziz Mert , Buitrago-Garcia Diana , Heron Leonie , Amini Poorya , Teodoro Douglas
Published: January 2023

Background

The COVID-19 pandemic has led to an unprecedented amount of scientific publications, growing at a pace never seen before. Multiple living systematic reviews have been developed to assist professionals with up-to-date and trustworthy health information, but it is increasingly challenging for systematic reviewers to keep up with the evidence in electronic databases. We aimed to investigate deep learning-based machine learning algorithms to classify COVID-19 related publications to help scale-up the epidemiological curation process.

Methods

In this retrospective study, five different pre-trained deep learning-based language models were fine-tuned on a dataset of 6,365 publications manually classified into two classes, three subclasses and 22 sub-subclasses relevant for epidemiological triage purposes. In ak-fold cross-validation setting, each standalone model was assessed on a classification task and compared against an ensemble, which takes the standalone model predictions as input and uses different strategies to infer the optimal article class. A ranking task was also considered, in which the model outputs a ranked list of sub-subclasses associated with the article.

Results

The ensemble model significantly outperformed the standalone classifiers, achieving a F1-score of 89.2 at the class level of the classification task. The difference between the standalone and ensemble models increases at the sub-subclass level, where the ensemble reaches a micro F1-score of 70% against 67% for the best performing standalone model. For the ranking task, the ensemble obtained the highest recall@3, with a performance of 89%. Using an unanimity voting rule, the ensemble can provide predictions with higher confidence on a subset of the data, achieving detection of original papers with a F1-score up to 97% on a subset of 80% of the collection instead of 93% on the whole dataset.

Conclusion

This study shows the potential of using deep learning language models to perform triage of COVID-19 references efficiently and support epidemiological curation and review. The ensemble consistently and significantly outperforms any standalone model. Fine-tuning the voting strategy thresholds is an interesting alternative to annotate a subset with higher predictive confidence.
Medial entorhinal cortex plays a specialized role in learning of flexible, context-dependent interval timing behavior
Authors: Bigus Erin R. , Lee Hyun-Woo , Bowler John C. , Shi Jiani , Heys James G.
Published: January 2023

Episodic memory requires encoding the temporal structure of experience and relies on brain circuits in the medial temporal lobe, including the medial entorhinal cortex (MEC). Recent studies have identified MEC ’time cells’, which fire at specific moments during interval timing tasks, collectively tiling the entire timing period. It has been hypothesized that MEC time cells could provide temporal information necessary for episodic memories, yet it remains unknown whether MEC time cells display learning dynamics required for encoding different temporal contexts. To explore this, we developed a novel behavioral paradigm that requires distinguishing temporal contexts. Combined with methods for cellular resolution calcium imaging, we find that MEC time cells display context-dependent neural activity that emerges with task learning. Through chemogenetic inactivation we find that MEC activity is necessary for learning of context-dependent interval timing behavior. Finally, we find evidence of a common circuit mechanism that could drive sequential activity of both time cells and spatially selective neurons in MEC. Our work suggests that the clock-like firing of MEC time cells can be modulated by learning, allowing the tracking of various temporal structures that emerge through experience.
Structure and DNA bridging activity of the essential Rec114–Mei4 trimer interface
Authors: Liu Kaixian , Grasso Emily M. , Pu Stephen , Liu Shixin , Eliezer David , Keeney Scott
Published: January 2023

The DNA double-strand breaks (DSBs) that initiate meiotic recombination are formed by an evolutionarily conserved suite of factors that includes Rec114 and Mei4 (RM), which regulate DSB formation both spatially and temporally.In vivo, these proteins form large immunostaining foci that are integrated with higher order chromosome structures.In vitro, they form a 2:1 heterotrimeric complex that binds cooperatively to DNA to form large, dynamic condensates. However, understanding of the atomic structures and dynamic DNA binding properties of RM complexes is lacking. Here, we report a structural model of a heterotrimeric complex of the C-terminus of Rec114 with the N-terminus of Mei4, supported by nuclear magnetic resonance experiments. This minimal complex, which lacks the predicted intrinsically disordered region of Rec114, is sufficient to bind DNA and form condensates. Single-molecule experiments reveal that the minimal complex can bridge two or more DNA duplexes and can generate force to condense DNA through long-range interactions. AlphaFold2 predicts similar structural models for RM orthologs across diverse taxa despite their low degree of sequence similarity. These findings provide insight into the conserved networks of protein-protein and protein-DNA interactions that enable condensate formation and promote formation of meiotic DSBs.
Lysine-deficient proteome can be regulated through non-canonical ubiquitination and ubiquitin-independent proteasomal degradation
Authors: Szulc Natalia A. , Piechota Małgorzata , Thapa Pankaj , Pokrzywa Wojciech
Published: January 2023

The ubiquitin-proteasome system (UPS) removes damaged and unwanted proteins by attaching ubiquitin to lysines in a process termed ubiquitination. Little is known how functional components of the UPS, often exposed to erroneous labeling by ubiquitin during functioning, avoid premature proteolysis. An extensive lysine-less region (lysine desert) in the yeast E3 ligase Slx5 was shown to counteract its ubiquitin-dependent turnover. We conducted bioinformatic screens among prokaryotes and eukaryotes to describe the scope and conservation of this phenomenon. We found that lysine deserts are widespread among bacteria using pupylation-dependent proteasomal degradation, an analog of the UPS. In eukaryotes, lysine deserts appear with increasing organismal complexity, and the most evolutionarily conserved are enriched in the UPS members. Using VHL and SOCS1 E3 ligases, which elongate their lysine desert in the course of evolution, we established that they are non-lysine ubiquitinated, which does not influence their stability, and can be subject to proteasome turnover irrespective of ubiquitination. Our data suggest that a combination of non-lysine ubiquitination and ubiquitin-independent degradation may control the function and fate of the lysine-deficient proteome, as the presence of lysine deserts does not correlate with the half-life.
The N-coil and the globular N-terminal domain of plant ARGONAUTE1 are interaction hubs for regulatory factors
Authors: Bressendorff Simon , Kausika Swathi , Sjøgaard Ida Marie Zobbe , Oksbjerg Emilie Duus , Michels Alec , Poulsen Christian , Brodersen Peter
Published: January 2023

The effector complex of RNA interference (RNAi) contains at its core an ARGONAUTE (AGO) protein bound to a small guide RNA. AGO proteins adopt a two-lobed structure in which the N-terminal (N) and Piwi-Argonaute-Zwille (PAZ) domains make up one lobe, while the middle (MID) and Piwi domains make up the other. Specific biochemical functions of PAZ, MID and Piwi domains of eukaryotic AGO proteins have been described, but the functions of the N-terminal domain remain less clear. Here, we use yeast two-hybrid screening with the N-terminal domain of the founding member of the AGO protein family, arabidopsis AGO1, to reveal that it interacts with many factors involved in regulated proteolysis. Interaction with a large group of proteins, including the autophagy cargo receptors ATI1 and ATI2, requires residues in a short, linear region, the N-coil, that joins the MID-Piwi lobe in the three-dimensional structure of AGO. In contrast, the F-box protein AUF1 interacts with AGO1 independently of the N-coil and requires distinct residues in the globular N domain itself. Mutation of AGO1 residues necessary for interaction with protein degradation factors in yeast stabilizes reporters fused to the AGO1 N-terminal domain in plants, supporting theirin vivorelevance. Our results define distinct regions of the N domain implicated in protein-protein interaction, and point to a particular importance of the AGO1 N-coil as a site of interaction with regulatory factors.
Engineering a Scalable and Orthogonal Platform for Synthetic Communication in Mammalian Cells
Authors: Pistikou Anna-Maria Makri , Cremers Glenn A.O. , Nathalia Bryan L. , Bögels Bas W.A. , Eijkens Bruno V. , de Dreu Anne , Bezembinder Maarten T.H. , Stassen Oscar M.J.A. , Bouten Carlijn C.V. , Merkx Maarten , Jerala Roman , de Greef Tom F. A.
Published: January 2023

The rational design and implementation of synthetic, orthogonal mammalian communication systems has the potential to unravel fundamental design principles of mammalian cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics and artificial tissue engineering. We lay here the foundations for the engineering of an orthogonal, and scalable mammalian synthetic intercellular communication platform that exploits the programmability of synthetic receptors and selective affinity and tunability of diffusing coiled-coil (CC) peptide heterodimers. Leveraging the ability of CCs to exclusively bind to a selected cognate receptor, we demonstrate orthogonal receptor activation, as well as Boolean logic computations. Next, we reveal synthetic intercellular communication based on synthetic receptors and secreted multidomain CC ligands and demonstrate a minimal, three-cell population system that can perform distributed AND gate logic. Our work provides a modular and scalable framework for the engineering of complex cell consortia, with the potential to expand the aptitude of cell therapeutics and diagnostics.
Morphological changes and twoNodalparalogs drive left-right asymmetry in the squamate veiled chameleon (C. calyptratus)
Authors: Shylo Natalia A. , Smith Sarah E. , Price Andrew , Guo Fengli , McClain Melainia , Trainor Paul
Published: January 2023

The ancestral mode of left-right (L-R) patterning involves cilia in the L-R organizer. However, the mechanisms regulating L-R patterning in non-avian reptiles remains an enigma, since most squamate embryos are undergoing organogenesis at oviposition. In contrast, veiled chameleon (Chamaeleo calyptratus) embryos are pre-gastrula at oviposition, making them an excellent organism for studying L-R patterning evolution. Here we show that veiled chameleon embryos lack motile cilia in their L-R organizer, consistent with the loss of motile cilia being a synapomorphy of all reptiles. Furthermore, in contrast to avians, geckos and turtles, which have oneNodalgene, veiled chameleon exhibits expression of two paralogs ofNodalin the left lateral plate mesoderm, albeit in non-identical patterns. Using live imaging, we observed asymmetric morphological changes that precede, and likely trigger, asymmetric expression of the Nodal cascade. Thus, veiled chameleons are a new and unique model for studying the evolution of L-R patterning.
Natural Killer cell contractility and cytotoxicity is driven by TLR3 agonist-mediated TAZ cytoplasmic sequestration
Authors: Pei Wong Darren Chen , Xia Zekun , Shao Nandi , Yeo Jin Ye , Yow Ivan , Thivakar T. , Salazar Andres M. , Liou Yih-Cherng , Low Boon Chuan , Ding Jeak Ling
Published: January 2023

The evolutionarily conserved YAP/TAZ mechano-responsive transcription cofactors regulate development and tumorigenesis. Here, we show for the first time that human natural killer (NK) cells specifically express TAZ but not YAP, and TAZ serves to limit NK cytotoxicity. The TLR3 agonist, hiltonol, was able to trigger cytoplasmic sequestration of TAZ, which increased NK cytotoxicity. Mechanistically, a low dose of hiltonol enhanced the intracellular contractility of NK cells accompanied by an increase in active RhoA and myosin light chain phosphorylation, conceivably through an increase in ERK1/2 activation-dependent ROS production. Importantly, we showed that the dissociation of LATS1 from actin upon activation of contractility, is required to sequester TAZ in the cytoplasm. Functionally, hiltonol also reduced the NK cell surface inhibitory receptors, KIR3DL1 through c-Myc inhibition and PD-1 through enhanced contractility. Direct inhibition of c-Myc promoted NK cytotoxicity against K562 lymphoblast. We corroborated our findings by coculturing hiltonol-pretreated NK cells with breast and lung cancer cells, and demonstrated increased NK-mediated cancer killing, which conceivably occurred via sequestration of TAZ to the cytoplasm which facilitated NK cytotoxicity. Our findings pave the way forex vivorejuvenation of NK cells forin vivoimmunotherapies, which could involve a cocktail of hiltonol and c-Myc inhibitor.
Crystal structure of the insecticide ethiprole (C13H9Cl2F3N4OS): a case study of whole-molecule configurational disorder
Authors: Vinaya  , Basavaraju Yeriyur B. , Srinivasa Gejjelegere R. , Shreenivas Mellekatte T. , Yathirajan Hemmige S. , Parkin Sean
Published: January 2023

The crystal structure of ethiprole {systematic name: 5-amino-1-[2,6-dichloro-4-(trifluoromethyl)phenyl]-4-ethanesulfinyl-1H-imidazole-3-carbonitrile}, C13H9Cl2F3N4OS, a phenylpyrazole-based insecticide, is presented. The pyrazole ring carries four substituents: an N-bound 2,6-dichloro-4-trifluoromethylphenyl ring and C-bound amine, ethanesulfinyl, and cyano groups. The sulfur atom of the ethanesulfinyl group is trigonal–pyramidal and stereogenic. The structure exhibits whole-molecule configurational disorder due to superposition of enantiomers. The crystal packing is dominated by strong N—H...O and N—H...N hydrogen bonds, which form R
4
4(18) and R
2
2(12) ring motifs. Since the ethiprole molecule is quite small, and structure solution and refinement were straightforward, the structure presents a convenient instructional example for modelling whole-body disorder of a non-rigid molecule. To this end, a step-by-step overview of the model-building and refinement process is also given. The structure could form the basis of a useful classroom, practical, or workshop-style example.
Students' adoption of AI-based teacher-bots (T-bots) for learning in higher education
Authors: Pillai Rajasshrie , Sivathanu Brijesh , Metri Bhimaraya , Kaushik Neeraj
Published: January 2023

Purpose

The purpose of this paper is to investigate students' adoption intention (ADI) and actual usage (ATU) of artificial intelligence (AI)-based teacher bots (T-bots) for learning using technology adoption model (TAM) and context-specific variables.

Design/methodology/approach

A mixed-method design is used wherein the quantitative and qualitative approaches were used to explore the adoption of T-bots for learning. Overall, 45 principals/directors/deans/professors were interviewed and NVivo 8.0 was used for interview data analysis. Overall, 1,380 students of higher education institutes were surveyed, and the collected data was analyzed using the Partial Least Squares Structural Equation Modeling (PLS-SEM) technique.

Findings

The T-bot's ADI’s antecedents found were perceived ease of use, perceived usefulness, personalization, interactivity, perceived trust, anthropomorphism and perceived intelligence. The ADI influences the ATU of T-bots, and its relationship is negatively moderated by stickiness to learn from human teachers in the classroom. It comprehends the insights of senior authorities of the higher education institutions in India toward the adoption of T-bots.

Practical implications

The research provides distinctive insights for principals, directors and professors in higher education institutes to understand the factors affecting the students' behavioral intention and use of T-bots. The developers and designers of T-bots need to ensure that T-bots are more interactive, provide personalized information to students and ensure the anthropomorphic characteristics of T-bots. The education policymakers can also comprehend the factors of T-bot adoption for developing the policies related to T-bots and their implications in education.

Originality/value

T-bot is a new disruptive technology in the education sector, and this is the first step in exploring the adoption factors. The TAM model is extended with context-specific factors related to T-bot technology to offer a comprehensive explanatory power to the proposed model. The research outcome provides the unique antecedents of the adoption of T-bots.
Remote integration of advanced manufacturing technologies into production systems: integration processes, key challenges and mitigation actions
Authors: Fattouh Anas , Chirumalla Koteshwar , Ahlskog Mats , Behnam Moris , Hatvani Leo , Bruch Jessica
Published: January 2023

Purpose

The study examines the remote integration process of advanced manufacturing technology (AMT) into the production system and identifies key challenges and mitigating actions for a smoother introduction and integration process.

Design/methodology/approach

The study adopts a case study approach to a cyber-physical production system at an industrial technology center using a mobile robot as an AMT.

Findings

By applying the plug-and-produce concept, the study exemplifies an AMT's remote integration process into a cyber-physical production system in nine steps. Eleven key challenges and twelve mitigation actions for remote integration are described based on technology–organization–environment theory. Finally, a remote integration framework is proposed to facilitate AMT integration into production systems.

Practical implications

The study presents results purely from a practical perspective, which could reduce dilemmas in early decision-making related to smart production. The proposed framework can improve flexibility and decrease the time needed to configure new AMTs in existing production systems.

Originality/value

The area of remote integration for AMT has not been addressed in depth before. The consequences of lacking in-depth studies for remote integration imply that current implementation processes do not match the needs and the existing situation in the industry and often underestimate the complexity of considering both technological and organizational issues. The new integrated framework can already be deployed by industry professionals in their efforts to integrate new technologies with shorter time to volume and increased quality but also as a means for training employees in critical competencies required for remote integration.
Effect of business intelligence on operational performance: the mediating role of supply chain ambidexterity
Authors: Mbima Daniel , Tetteh Francis Kamewor
Published: January 2023

Purpose

This study aims to examined the impact of business intelligence (BI) and supply chain ambidexterity (SCA) on operational performance (OP), contributing to dwarf knowledge in small- and medium-sized enterprises (SMEs) in the context of emerging economies. The mediating role of SCA was considered in the proposed model.

Design/methodology/approach

The study used the quantitative method to investigate the interdependencies between variables. As a result, 216 senior and middle managers/owners of SMEs in Ghana were surveyed using a purposive and convenient sampling method. SPSS version 23 and Smart PLS version 3 were used to conduct the research.

Findings

While the direct link among BI, SCA and OP was confirmed. The outcome also showed that SCA plays a significant mediating role between BI and OP among SMEs.

Practical implications

The outcome of the study indicates that SCA encourages the use of BI to generate superior OP among SMEs. This knowledge will improve the performance of SMEs and their ability to withstand the competition in the global market.

Originality/value

With the discovery of this study, the theory of a resource-based view now has some empirical evidence behind it. As a result, SMEs prioritize aspects that could improve their operations and implement tactics that would nurture better performance and competitive advantages.
Time and frequency uncertainty spillover among macro uncertainty, financial stress and asset markets
Authors: Sawarn Ujjawal , Dash Pradyumna
Published: January 2023

Purpose

This study aims to examine the uncertainty spillover among eight important asset classes (cryptocurrencies, US stocks, US bonds, US dollar, agriculture, metal, oil and gold) using weekly data from 2014 to 2020. This study also examines the US macro uncertainty and US financial stress spillover on these assets.

Design/methodology/approach

The authors use time–frequency connectedness method to study the uncertainty spillover among the asset classes.

Findings

This study’s findings revealed that the uncertainty spillover is time-varying and peaked during the 2016 oil supply glut and COVID-19 pandemic. US stocks are the highest transmitter of uncertainty to all other assets, followed by the US dollar and oil. US stocks (US dollar and oil) transmit uncertainty in long (short) term. Furthermore, US macro uncertainty is the net transmitter of uncertainty to the US stocks, industrial metals and oil markets. In contrast, US financial stress is the net transmitter of uncertainty to the US bonds, cryptocurrencies, the US dollar and gold markets. US financial stress (US macro uncertainty) has long (short)-term effects on asset price volatility.

Originality/value

This study complements the studies on volatility spillover among the important asset classes. This study also includes recently financialized asset classes such as cryptocurrencies, agricultural and industrial commodities. This study examines the macro uncertainty and financial stress spillover on these assets.
Linking rhizosphere soil microbial activity and plant resource acquisition strategy
Authors: Han Mengguang , Chen Ying , Sun Lijuan , Yu Miao , Li Rui , Li Shuaifeng , Su Jianrong , Zhu Biao
Published: January 2023

Plants live in association with a diversity of soil microorganisms, which are extremely important in affecting plant growth and soil biogeochemical cycling.

By adopting plant trait‐based approaches, we explored the linkages between rhizosphere soil microbial activity and plant resource acquisition strategy of above‐ and below‐ground across a range of tree species in a subtropical evergreen mixed forest. The microbial activities were represented by diverse extracellular enzymes relevant to carbon, nitrogen and phosphorus cycling and soil organic carbon (SOC) mineralization.

At the species level, leaf and root traits were mainly represented by two leading dimensions, that is, the ‘fast‐slow’ economics spectrum on which leaf and root traits were well aligned and the orthogonal collaboration gradient in the root.

Both extracellular enzymes and SOC mineralization in the rhizosphere varied greatly across plant species. We found that diverse rhizosphere soil microbial activities positively correlated with the classical ‘fast‐slow’ conservation gradient of plant resource acquisition (especially above‐ground), that is, the rhizosphere soil microbes associated with fast‐growing plant species feature higher metabolism than that of slow‐growing plant species. In comparison, rhizosphere soil microbial activities were independent of the plant collaboration gradient in the root, and it might be an alternative exploitative strategy in foraging soil nutrients for plants.

Synthesis. Our study strengthens the multivariate nature of plant resource acquisition in adapting to above‐ and below‐ground stresses. The findings on the linkages between rhizosphere soil microbial activity and plant resource acquisition strategy have the potential to improve our understanding and prediction of plant species turnover impacts on soil biogeochemical cycles.
RISK AND RETURNS: Large‐scale Funding for Urban Research
Authors: Keith Michael , Parnell Susan
Published: January 2023

The nature of research funding shapes knowledge outcomes, especially for urban research that is conducted in multiple sites and over multiple years. Recent unplanned cuts in the Global Challenges Research Fund (GCRF) grants, alongside the rupture caused by Covid‐19, created ethical and procedural issues for completing the PEAK Urban programme. Building on durable partnerships, setting principles for the reduced fund distribution and adjusting modes of working enabled PEAK Urban to navigate the fiscal disruption—but the difficult episode highlights lessons for the ethical organization of global urban research under conditions of uncertainty.
THE PARADOX: Economic Growth that Endangers the Future of Research in Colombia
Authors: Duque Juan C.
Published: January 2023

In this paper I analyse how the gradual reduction of research funds in Colombia can interrupt a key process in the generation of solutions to global urban problems. I draw on a bibliometric analysis to show that research funding flowing from North to South has created collaborations between researchers from North and South that have led to a better and more comprehensive understanding of the challenges facing cities around the world. To conclude, I propose four options to counteract these trends towards lower research funding.
THE BENEFITS OF LARGE‐SCALE, MULTI‐SITE INTERNATIONALLY FUNDED RESEARCH PROJECTS: An Example of New Academic Insights and New Funding Possibilities
Authors: Tucker Andrew
Published: January 2023

There are a number of benefits to large‐scale, multi‐site, internationally funded urban research projects if they are operationalized in ways that acknowledge forms of knowledge incommensurability and allow for space to explore the commensurability of different forms of knowledge across different geographies. Such projects are especially important in the context of the precarity of research funding, as such projects can provide the space to explore new urban research avenues that may not have formed core components of the existing urban studies canon and may also bring with them significant and new funding possibilities. In this intervention I use the example of the GCRF‐funded PEAK Urban programme to consider how new urban research questions related to sexuality and health were brought to the fore during the life of the programme, which offer not only new research avenues, but also potential access to significant new funding sources. Programmes such as PEAK Urban therefore have the potential to build the long‐term resilience of urban research. Cutting funding to such programmes may therefore limit the efficacy of the programmes themselves and the long‐term sustainability of urban scholarship.
Mental illness during pregnancy and the importance of well‐developed antenatal care
Authors: Rejnö Gustaf
Published: January 2023

Linked article: This is a mini commentary on Hulsbosch et al., pp.495–505 in this issue. To view this article visit https://doi.org/10.1111/1471‐0528.17273
BarKeeper—a versatile web framework to assemble, analyse and manage DNA barcoding data and metadata
Authors: Wiechers Sarah , Kösters Lara Marie , Quandt Dietmar , Borsch Thomas , Wicke Susann , Müller Kai Frank
Published: January 2023

DNA barcoding aids in rapidly identifying specimens in various contexts by comparing short stretches of DNA to a reference database. Barcoding initiatives generate large reference databases of carefully curated high‐quality sequences to maximize identification success.

BarKeeper provides a flexible tool for barcoding initiatives and in the context of phylogenetic studies to foster shared work on large datasets of raw sequence and associated metadata. It is free, open‐source and available as a set of Docker containers for easy setup. After setting it up once, all project members can use it independently of their operating system or location.

BarKeeper offers features to collect and manage data and metadata about specimens, taxa and DNA sequences from Sanger sequencing and high‐throughput sequencing (HTS) technologies. It provides excellent flexibility by not being restricted to specific markers or taxon groups. Users can view and edit records and associated metadata while the app assists them by trimming and assembling reads. It automatically checks the quality of generated barcodes with a taxonomy‐based tool and offers a wide range of options for data analysis. Extensive search features allow querying the database for specific groups of records and saving the search results in the user's profile or downloading them in various file formats.

BarKeeper combines multiple tools to aid barcoding projects in every step, from a reference taxa list to finished barcode sequences, thereby minimizing the number of laborious, potentially error‐prone manual steps and enabling efficient collaborative workflows.
Dissemination and implementation of age‐friendly care and geriatric emergency department accreditation at Veterans Affairs hospitals
Authors: Hwang Ula , Runels Tessa , Han Ling , Gruber Erica , McQuown Colleen M. , Ragsdale Luna , Jetter Ethan , Rossomano Nicole , Javier Denise
Published: January 2023

Objectives

In 2018, the U.S. Department of Veterans Affairs (VA) National Office of Geriatrics and Extended Care (GEC) and the National Emergency Medicine (EM) Program partnered to improve emergency care for older Veterans. A core team disseminated age‐friendly models of care via education and standardization of practice with the goal of multisite geriatric emergency department (GED) accreditation. We compare rates of GED screening at VAs with GED implementation to those without.

Methods

Observational evaluation of GED screening of older Veterans (≥65 years) at VA Emergency Departments (ED) from January 2018 to March 2022, during peak pandemic years. Data were extracted from the VA Corporate Data Warehouse of Veteran ED visit encounters to track documented GED screens and Veteran demographic data. Generalized estimating equation models were used to compare screening completion across different levels of GED accreditation, adjusting for potential confounding.

Results

During this period, over 1.07 million Veterans ≥ 65 years of age made 4.07 million VA ED visits. Mean (±SD) age was 73.4 (±7.2) years, 96.5% were male, 68% were White, and 89.9% made their index ED visit at a non‐GED VA ED. As of early 2022, a total of 50 of 111 VA EDs have achieved or applied for GED accreditation. During early 2022, 8.3% of all visits by older Veterans had at least one GED screen documented; 15% were screened at Levels 1–3 GED versus 2.2% at non‐GED facilities. Screens identifying older adults at risk for poor outcomes, for delirium, and for falls had the highest usage rates within VA GEDs. Veterans seen at Level 1 GEDs had a 76‐fold greater odds of having a GED screen than at Level 3 GEDs (odds ratio 75.8, 95% confidence interval 72.8–79.0).

Conclusions

Through VA National Office of GEC and EM Program partnership, the VA has created, standardized, and disseminated a GED Model of Care, despite the pandemic. GED accreditation was associated with GED screen implementation, with Level 1 having the highest screening prevalence.
Has the degree of outcome reporting bias in surgical randomized trials changed? A meta‐regression analysis
Authors: Wang Andy , Menon Rahul , Li Tom , Harris Laura , Harris Ian A. , Naylor Justine , Adie Sam
Published: January 2023

Background

Outcome reporting bias in individual trials can compromise the validity of pooled estimates within systematic reviews. Recent strategies have attempted to address outcome reporting bias, which favours the full reporting of statistically significant outcomes over non‐significant outcomes. We examined whether the association between full outcome reporting and statistical significance in surgical trials has changed from 2009 to 2019.

Methods

We systematically searched for 350 surgical randomized controlled trials (RCTs) from 2009 and 350 surgical RCTs from 2019. Outcomes were classified as fully reported, partially reported, qualitatively reported or unreported. For each outcome, a contingency table was populated with full outcome reporting (yes/no) and statistical significance (yes/no). We combined odds ratios in random effects meta‐analysis to estimate the association between full outcome reporting and statistical significance in 2009 compared with 2019.

Results

Twenty‐eight percent of outcomes in 2009 were incompletely reported, compared with 30% in 2019. In 2009, significant outcomes were more likely to be fully reported than non‐significant outcomes (OR = 2.4, 95% CI 1.7–3.4, I2 = 35%), but the opposite association was seen in 2019 (OR = 0.51, 95% CI 0.34–0.77, I2 = 43%). RCTs from 2019 were less likely to demonstrate outcome reporting bias favouring significant outcomes (OR = 0.21, 95% CI 0.12–0.35, P < 0.001).

Conclusion

Outcome reporting bias favouring the full reporting of significant over non‐significant outcomes was demonstrated in 2009, but the opposite association was seen in 2019. There remains a high prevalence of incomplete outcome reporting. We recommend ongoing adherence to trial protocol guidelines to improve outcome reporting transparency and completeness.
Estimation of genetic parameters for production, reproduction, and growth curve of Fars indigenous chicken
Authors: Neysi Saeid , Ghaderi‐Zefrehei Mostafa , Rafeie Farjad , Dolatabady Mustafa Muhaghegh , Elahi Torshizi Mahdi , Zakizadeh Sonia , Smith Jacqueline
Published: January 2023

Iranian native chicken, including Fars indigenous chicken, is an important genetic resource due to its adaptation to stressful environmental conditions, good endurance and resistance to disease. The aim of this research was to determine the genetic infrastructure of Fars indigenous chicken using several nonlinear functions. The dataset included body weight at hatch (BW1), body weight at the 8th week (BW8), body weight at the 12th week (BW12), weight at sexual maturity (WSM), age at sexual maturity (ASM), number of eggs in the first 12 weeks of laying period (EN), egg weight at the first day of laying (EW1), average egg weight at the 28thday of laying (EW28), and average egg weight at weeks 28, 30, and 32 of the laying period (AEW). Growth models were fitted using the NLIN procedure and WOMBAT software was used to predict variance components for the best fit model parameters. Results suggested three‐parameter models, for example, Gompertz, fitted better to the data than others. The maturity weight (A), initial weight (B), and maturity rate (K) parameters in the Gompertz model were 1996.8 ± 6.63, 4.11 ± 0.03, and 0.021 ± 0.0001, respectively. The heritability of A, B, and K parameters were 0.03, 0.05, and 0.12, respectively.
Estimating Population Size: The Importance of Model and Estimator Choice
Authors: Schofield Matthew R. , Barker Richard J. , Link William A. , Pavanato Heloise
Published: January 2023

We consider estimator and model choice when estimating abundance from capture–recapture data. Our work is motivated by a mark–recapture distance sampling example, where model and estimator choice led to unexpectedly large disparities in the estimates. To understand these differences, we look at three estimation strategies (maximum likelihood estimation, conditional maximum likelihood estimation, and Bayesian estimation) for both binomial and Poisson models. We show that assuming the data have a binomial or multinomial distribution introduces implicit and unnoticed assumptions that are not addressed when fitting with maximum likelihood estimation. This can have an important effect in finite samples, particularly if our data arise from multiple populations. We relate these results to those of restricted maximum likelihood in linear mixed effects models.
False alarms and information transmission in grouping animals
Authors: Gray Leah , Webster Mike M.
Published: January 2023

A key benefit of grouping in prey species is access to social information, including information about the presence of predators. Larger groups of prey animals respond both sooner and at greater distances from predators, increasing the likelihood that group members will successfully avoid capture. However, identifying predators in complex environments is a difficult task, and false alarms (alarm behaviours without genuine threat) appear surprisingly frequent across a range of taxa including insects, amphibians, fish, mammals, and birds. In some bird flocks, false alarms have been recorded to substantially outnumber true alarms. False alarms can be costly in terms of both the energetic costs of producing alarm behaviours as well as lost opportunity costs (e.g. abandoning a feeding patch which was in fact safe, losing sleep if an animal is resting/roosting, or losing mating opportunities). Models have shown that false alarms may be a substantial but underappreciated cost of group living, introducing an inherent risk to using social information and a vulnerability to the propagation of false information. This review will focus on false alarms, introducing a two‐stage framework to categorise the different factors hypothesised to influence the propensity of animal groups to produce false alarms. A number of factors may affect false alarm rate, and this new framework splits these factors into two core processing stages: (i) individual perception and response; and (ii) group processing of predator information. In the first stage, individuals in the group monitor the environment for predator cues and respond. The factors highlighted in this stage influence the likelihood that an individual will misclassify stimuli and produce a false alarm (e.g. lower light levels can make predator identification more difficult and false alarms more common). In the second stage, alarm information from individuals is processed by the group. The factors highlighted in this stage influence the likelihood of alarm information being copied by group members and propagated through the group (e.g. some animals implement group processing mechanisms that regulate the spread of behavioural responses such as consensus decision making through the quorum response). This review follows the structure of this new framework, focussing on the causes of false alarms, factors that influence false alarm rate, the transmission of alarm information through animal groups, mechanisms to mitigate the spread of false alarms, and the consequences of false alarms.
Not When But Whether: Modality and Future Time Reference in English and Dutch
Authors: Robertson Cole , Roberts Seán G.
Published: January 2023

Previous research on linguistic relativity and economic decisions hypothesized that speakers of languages with obligatory tense marking of future time reference (FTR) should value future rewards less than speakers of languages which permit present tense FTR. This was hypothesized on the basis of obligatory linguistic marking (e.g., will) causing speakers to construe future events as more temporally distal and thereby to exhibit increased “temporal discounting”: the subjective devaluation of outcomes as the delay until they will occur increases. However, several aspects of this hypothesis are incomplete. First, it overlooks the role of “modal” FTR structures which encode notions about the likelihood of future outcomes (e.g., might). This may influence “probability discounting”: the subjective devaluation of outcomes as the probability of their occurrence decreases. Second, the extent to which linguistic structures are subjectively related to temporal or probability discounting differences is currently unknown. To address these, we elicited FTR language and subjective ratings of temporal distance and probability from speakers of English, which exhibits strongly grammaticized FTR, and Dutch, which does not. Several findings went against the predictions of the previous hypothesis: Framing an FTR statement in the present (“Ellie arrives later on”) versus the future tense (“…will arrive…”) did not affect ratings of temporal distance; English speakers rated future statements as relatively more temporally proximal than Dutch speakers; and English and Dutch speakers rated future tenses as encoding high certainty, which suggests that obligatory future tense marking might result in less discounting. Additionally, compared with Dutch speakers, English speakers used more low‐certainty terms in general (e.g., may) and as a function of various experimental factors. We conclude that the prior cross‐linguistic observations of the link between FTR and psychological discounting may be caused by the connection between low‐certainty modal structures and probability discounting, rather than future tense and temporality.