bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acoustic communication in bark beetles (Scolytinae): 150 years of research
Authors: Arjomandi Elham , Turchen Leonardo M. , Connolly Amanda A. , Léveillée Michelle B. , Yack Jayne E. 
Published: June 2024

AbstractFor over a century, the role of acoustic communication in the sensory ecology of bark beetles (Scolytinae) has been recognized. However, their ‘world of sound’ remains largely unexplored. Here, we review 153 years of bark beetle bioacoustics publications to summarize current knowledge, identify gaps and suggest future research directions. Our survey identified 117 publications covering 170 species. Morphological reports revealed five stridulatory organs across 125 species, with elytro‐tergal, gular‐prosternal and vertex‐pronotum mechanisms being the most prevalent for sound production. However, confirmed sound recordings exist for only 40 species. Acoustic signalling in adults is proposed to function in avoiding enemies, pair formation, sexual selection and spacing, while in juveniles, vibratory communication is proposed for gallery spacing. However, experimental evidence supporting these functions is lacking. Acoustic sensory organs remain unidentified, and comprehension of signal transmission—whether through airborne sounds or solid‐borne vibrations (or both)—is limited. Bioacoustic technologies have emerged as tools for potential management practices and are also discussed. Based on these findings, we recommend three directions for future research: (1) characterize acoustic morphology and behaviours in more species, particularly unrepresented taxa, with recordings in various contexts, preferably under natural conditions; (2) test hypotheses to explain the functions of acoustic communication through experimental and comparative phylogenetic methods and (3) investigate how sounds or vibrations are transmitted and received through behavioural and neurophysiological experiments. Advancements in bark beetle acoustic sensing and communication research will enhance our understanding of their sensory ecology and facilitate potential control measures of these fascinating insects.
Overcoming (vegan) burnout: Mass gatherings can provide respite and rekindle shared identity and social action efforts in moralized minority groups
Authors: Prosser Annayah M. B. , O'Neill Saffron , Whitmarsh Lorraine , Bolderdijk Jan Willem , Kurz Tim , Blackwood Leda 
Published: June 2024

AbstractMoralized minority actors can play important roles in social change processes by rejecting majority social norms and modeling alternative societal pathways. However, being a minority actor can be difficult, often resulting in stigma, derogation, and hostility from the majority group. For actions intrinsically linked with daily life (e.g., eating), such social obstacles might become so great that individuals acting alone experience activist burnout' and social isolation, and may stop pursuing social change altogether. Event‐based interventions are a promising (yet currently understudied) avenue for ameliorating these negative consequences and maintaining minority‐driven social change. Through on‐site field interviews (N = 20), we explore how attending an identity‐centering mass gathering (“The Vegan Campout”) acts to validate and empower a minority group (vegans) seeking social change. We show how the event functioned as a space where vegan identity, food, and action were centered and celebrated, in stark contrast to vegans' experiences of a majority meat‐eating society, where they often experienced negativity. Experiencing a 'temporary social majority' context provided important respite for vegans to gain strength, rekindle their vegan identities, and (re)affirm their commitment to activism. Our findings provide insight into the benefits of identity‐centering events for sustaining social change efforts among moralized minority groups.
Persistence in the benefits of foreign ownership: Evidence from divestment
Authors: Ho Chun‐Yu , Sung Ji Hee , Sung Won 
Published: June 2024

AbstractIn this paper, we examine the persistence of benefits from foreign ownership, which informs the proper FDI policies. We exploit the divestment of foreign affiliates in South Korea from 2007 to 2019 as a quasi‐experiment to estimate such persistence of benefits. Our empirical analysis at firm‐level based on the propensity score reweighted difference‐in‐differences model leads to several conclusions. First, on average, the productivity benefit from foreign ownership does not persist after the divestment. Second, the productivity benefit of foreign ownership is persistent in firms with a higher absorptive capacity, measured by R&D intensity, intangible assets, and skilled workers. Such persistence is strengthened if the former foreign affiliate has a longer duration of ownership before the divestment. It suggests that absorptive capacity and time input are helpful for foreign affiliates to persistently absorb knowledge from their owners. Finally, we find that the productivity benefits of foreign ownership are less persistent at former foreign affiliates relying more on external trade.
Functional characterization of polyphenol oxidase OfPPO2 supports its involvement in parallel biosynthetic pathways of acteoside
Authors: Liu Yating , Han Xiaoyang , Zhao Mengya , Liu Lan , Deng Zixin , Zhao Qiu , Yu Yi 
Published: June 2024

SUMMARYActeoside is a bioactive phenylethanoid glycoside widely distributed throughout the plant kingdom. Because of its two catechol moieties, acteoside displays a variety of beneficial activities. The biosynthetic pathway of acteoside has been largely elucidated, but the assembly logic of two catechol moieties in acteoside remains unclear. Here, we identified a novel polyphenol oxidase OfPPO2 from Osmanthus fragrans, which could hydroxylate various monophenolic substrates, including tyrosine, tyrosol, tyramine, 4‐hydroxyphenylacetaldehyde, salidroside, and osmanthuside A, leading to the formation of corresponding catechol‐containing intermediates for acteoside biosynthesis. OfPPO2 could also convert osmanthuside B into acteoside, creating catechol moieties directly via post‐modification of the acteoside skeleton. The reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) analysis and subcellular localization assay further support the involvement of OfPPO2 in acteoside biosynthesis in planta. These findings suggest that the biosynthesis of acteoside in O. fragrans may follow “parallel routes” rather than the conventionally considered linear route. In support of this hypothesis, the glycosyltransferase OfUGT and the acyltransferase OfAT could direct the flux of diphenolic intermediates generated by OfPPO2 into acteoside. Significantly, OfPPO2 and its orthologs constitute a functionally conserved enzyme family that evolved independently from other known biosynthetic enzymes of acteoside, implying that the substrate promiscuity of this PPO family may offer acteoside‐producing plants alternative ways to synthesize acteoside. Overall, this work expands our understanding of parallel pathways plants may employ to efficiently synthesize acteoside, a strategy that may contribute to plants' adaptation to environmental challenges.
In‐depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis
Authors: Tariq Arslan , Meng Minghui , Jiang Xiaohui , Bolger Anthony , Beier Sebastian , Buchmann Jan P. , Fernie Alisdair R. , Wen Weiwei , Usadel Björn 
Published: June 2024

SUMMARYTea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health‐related compounds. In this study, we present the construction and analysis of a tea pangenome comprising a total of 11 genomes, with a focus on three newly sequenced genomes comprising the purple‐leaved assamica cultivar “Zijuan”, the temperature‐sensitive sinensis cultivar “Anjibaicha” and the wild accession “L618” whose assemblies exhibited excellent quality scores as they profited from latest sequencing technologies. Our analysis incorporates a detailed investigation of transposon complement across the tea pangenome, revealing shared patterns of transposon distribution among the studied genomes and improved transposon resolution with long read technologies, as shown by long terminal repeat (LTR) Assembly Index analysis. Furthermore, our study encompasses a gene‐centric exploration of the pangenome, exploring the genomic landscape of the catechin pathway with our study, providing insights on copy number alterations and gene‐centric variants, especially for Anthocyanidin synthases. We constructed a gene‐centric pangenome by structurally and functionally annotating all available genomes using an identical pipeline, which both increased gene completeness and allowed for a high functional annotation rate. This improved and consistently annotated gene set will allow for a better comparison between tea genomes. We used this improved pangenome to capture the core and dispensable gene repertoire, elucidating the functional diversity present within the tea species. This pangenome resource might serve as a valuable resource for understanding the fundamental genetic basis of traits such as flavour, stress tolerance, and disease resistance, with implications for tea breeding programmes.
Cell‐free DNA kinetics in response to muscle‐damaging exercise: A drop jump study
Authors: Juškevičiūtė Ema , Neuberger Elmo , Eimantas Nerijus , Heinkel Kirsten , Simon Perikles , Brazaitis Marius 
Published: June 2024

AbstractA significant increase in circulating cell‐free DNA (cfDNA) occurs with physical exercise, which depends on the type of exertion and the duration. The aims of this study were as follows: (1) to investigate the time course of cfDNA and conventional markers of muscle damage from immediately after to 96 h after muscle‐damaging exercise; and (2) to investigate the relationship between cfDNA and indicators of primary (low‐frequency fatigue and maximal voluntary isometric contraction) and secondary (creatine kinase and delayed‐onset muscle soreness) muscle damage in young healthy males. Fourteen participants (age, 22 ± 2 years; weight, 84.4 ± 11.2 kg; height, 184.0 ± 7.4 cm) performed 50 intermittent drop jumps at 20 s intervals. We measured cfDNA and creatine kinase concentrations, maximal voluntary isometric contraction torque, low‐frequency fatigue and delayed‐onset muscle soreness before and at several time points up to 96 h after exercise. Plasma cfDNA levels increased from immediately postexercise until 72 h postexercise (P < 0.01). Elevation of postexercise cfDNA was correlated with both more pronounced low‐frequency fatigue (r = −0.52, P = 3.4 × 10−11) and delayed‐onset muscle soreness (r = 0.32, P = 0.00019). Levels of cfDNA change in response to severe primary and secondary muscle damage after exercise. Levels of cfDNA exhibit a stronger correlation with variables related to primary muscle damage than to secondary muscle damage, suggesting that cfDNA is a more sensitive marker of acute loss of muscle function than of secondary inflammation or damaged muscle fibres.
Rapid Rail Transit (Metro) System. Implementation and Expansion Technical and Operational Challenges Review - The D.C. Metrorail Case Study
Authors: Barbosa Fábio C. 
Published: June 2024

Abstract
The Rapid Rail Transit (Metro) systems have been set as an important tool for world cities to supply the transit riders (users) the mobility and accessibility requirements in the high demand (highly loaded) urban corridors, which require a combination of large passenger capacity and service quality.
Given their large capacity and the associated high service level and environmental performance, the metro systems provide a high quality accessibility, which ultimately, set them as a structural tool to drive the long term urban spatial and economic development.
Metro systems are set as urban megaprojects, given their required very large outlays of capital intensive investments on long-lived assets, such as guideways, stations, rolling stock, and the associated systems (electrification and signaling). The system’s design features might strongly affect its capacity, operational flexibility, service performance, and cost, with the passenger-carrying capacity in the highest-demand sections of the network being one of the most critical design parameters, given its effect on the system’s investments.
This work presents, based on the state of the art available public technical data, a review of the rail metro technology challenges associated with their implementation and expansion initiatives. To do so, it reports the Washington D.C. (District of Columbia) Metrorail experience, at the United States (U.S.), an iconic metro system, which has been successfully planned in the sixties and implemented in the, which has revolutionized the greater Washington Metropolitan Area mobility and urban planning and that currently is set among the busiest metro systems in the U.S.
Nevertheless, despite its groundbreaking transit performance, it currently faces both refurbishment (rehabilitation) and expansion demands, whose diagnosis and proposed solutions are reported in this paper to illustrate the metro rail challenges to provide the required adequate transit service throughout its service life.
ComI inhibits transformation in
Bacillus subtilis
by selectively killing competent cells
Authors: Smith Dominique R. , Kearns Daniel B. , Burton Briana M. 
Published: June 2024

ABSTRACT

Many bacteria build elaborate molecular machines to import DNA via natural competence, yet this activity is often not identified until strains have been handled and domesticated in laboratory settings. For example, one of the best studied Gram-positive model organisms,
Bacillus subtilis,
has a poorly transformable ancestor. Transformation in the ancestral strain is inhibited by a transmembrane peptide, ComI, which is encoded on an extrachromosomal plasmid. Although ComI was shown to be necessary and sufficient to inhibit transformation when produced at high levels under an inducible promoter, the mechanism by which ComI inhibits transformation is unknown. Here, we examine the native regulation and mechanism of transformation inhibition by ComI. We find that under native regulation, ComI expression is restricted in the absence of the plasmid. In the presence of the plasmid, we find that ComI is expressed at higher levels in cells that are differentiating into a competent state. The subcellular localization of ComI, however, does not depend on any other competence proteins, and permeabilization activity is concentration-dependent. Time-lapse microscopy reveals that competent cells producing ComI are first permeabilized and then die. Based on these observations, we propose a new model for the mechanism of ComI in which response to competence activation leads to selective elimination of the competent subpopulation.

IMPORTANCE

Natural transformation mechanisms have been studied across several bacterial systems, but few examples of inhibition exist. This work investigates the mechanism of action of a plasmid-encoded transmembrane inhibitor of natural transformation. The data reveal that the peptide can cause cell permeabilization. Permeabilization is synergistic with entry of
Bacillus subtilis
into the “competent” state, such that cells with the ability to be transformed are preferentially killed. These findings reveal a self-preservation mechanism coupled to the physiological state of the cells that ensures that the population can maintain an unaltered plasmid and its predicted prophage.
Unraveling the cryptic functions of mitogen-activated protein kinases Cpk2 and Mpk2 in
Cryptococcus neoformans
Authors: ­Jang Yu-Byeong , Kim Jin-Young , Bahn Yong-Sun 
Published: June 2024

ABSTRACT

Mitogen-activated protein kinase (MAPK) pathways are fundamental to the regulation of biological processes in eukaryotic organisms. The basidiomycete
Cryptococcus neoformans
, known for causing fungal meningitis worldwide, possesses five MAPKs. Among these, Cpk1, Hog1, and Mpk1 have established roles in sexual reproduction, stress responses, and cell wall integrity. However, the roles of Cpk2 and Mpk2 are less understood. Our study elucidates the functional interplay between the Cpk1/Cpk2 and Mpk1/Mpk2 MAPK pathways in
C. neoformans
. We discovered that
CPK2
overexpression compensates for
cpk1
Δ mating deficiencies via the Mat2 transcription factor, revealing functional redundancy between Cpk1 and Cpk2. We also found that Mpk2 is phosphorylated in response to cell wall stress, a process regulated by the MAPK kinase (MAP2K) Mkk2 and MAP2K kinases (MAP3Ks) Ssk2 and Ste11. Overexpression of
MPK2
partially restores cell wall integrity in
mpk1
Δ by influencing key cell wall components, such as chitin and the polysaccharide capsule. Contrarily,
MPK2
overexpression cannot restore thermotolerance and cell membrane integrity in
mpk1
Δ. These results suggest that Mpk1 and Mpk2 have redundant and opposing roles in the cellular response to cell wall and membrane stresses. Most notably, the dual deletion of
MPK1
and
MPK2
restores wild-type mating efficiency in
cpk1
Δ mutants via upregulation of the mating-regulating transcription factors
MAT2
and
ZNF2
, suggesting that the Mpk1 and Mpk2 cooperate to negatively regulate the pheromone-responsive Cpk1 MAPK pathway. Our research collectively underscores a sophisticated regulatory network of cryptococcal MAPK signaling pathways that intricately govern sexual reproduction and cell wall integrity, thereby controlling fungal development and pathogenicity.

IMPORTANCE

In the realm of fungal biology, our study on
Cryptococcus neoformans
offers pivotal insights into the roles of specific proteins called mitogen-activated protein kinases (MAPKs). Here, we discovered the cryptic functions of Cpk2 and Mpk2, two MAPKs previously overshadowed by their dominant counterparts Cpk1 and Mpk1, respectively. Our findings reveal that these “underdog” proteins are not just backup players; they play crucial roles in vital processes like mating and cell wall maintenance in
C. neoformans
. Their ability to step in and compensate when their dominant counterparts are absent showcases the adaptability of
C. neoformans
. This newfound understanding not only enriches our knowledge of fungal MAPK mechanisms but also underscores the intricate balance and interplay of proteins in ensuring the organism’s survival and adaptability.
JCPyV infection of primary choroid plexus epithelial cells reduces expression of critical junctional proteins and increases expression of barrier disrupting inflammatory cytokines
Authors: Haley Sheila A. , O'Hara Bethany A. , Schorl Christoph , Atwood Walter J. 
Published: June 2024

ABSTRACT

The human polyomavirus, JCPyV, establishes a lifelong persistent infection in the peripheral organs of a majority of the human population worldwide. Patients who are immunocompromised due to underlying infections, cancer, or to immunomodulatory treatments for autoimmune disease are at risk for developing progressive multifocal leukoencephalopathy (PML) when the virus invades the CNS and infects macroglial cells in the brain parenchyma. It is not yet known how the virus enters the CNS to cause disease. The blood-choroid plexus barrier is a potential site of virus invasion as the cells that make up this barrier are known to be infected with virus both
in vivo
and
in vitro
. To understand the effects of virus infection on these cells we challenged primary human choroid plexus epithelial cells with JCPyV and profiled changes in host gene expression. We found that viral infection induced the expression of proinflammatory chemokines and downregulated junctional proteins essential for maintaining blood-CSF and blood-brain barrier function. These data contribute to our understanding of how JCPyV infection of the choroid plexus can modulate the host cell response to neuroinvasive pathogens.

IMPORTANCE

The human polyomavirus, JCPyV, causes a rapidly progressing demyelinating disease in the CNS of patients whose immune systems are compromised. JCPyV infection has been demonstrated in the choroid plexus both
in vivo
and
in vitro
and this highly vascularized organ may be important in viral invasion of brain parenchyma. Our data show that infection of primary choroid plexus epithelial cells results in increased expression of pro-inflammatory chemokines and downregulation of critical junctional proteins that maintain the blood-CSF barrier. These data have direct implications for mechanisms used by JCPyV to invade the CNS and cause neurological disease.
Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets
Authors: Tzfadia Oren , Gijsbers Abril , Vujkovic Alexandra , Snobre Jihad , Vargas Roger , Dewaele Klaas , Meehan Conor J. , Farhat Maha , Hakke Sneha , Peters Peter J. , de Jong Bouke C. , Siroy Axel , Ravelli Raimond B. G. 
Published: June 2024

ABSTRACT

Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all
Mycobacterium tuberculosis
complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein–protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens.

IMPORTANCE

We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins’ structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with
Mycobacterium tuberculosis
complex virulence.