bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concentration-dependent effect of plant secondary metabolites on bacterial and fungal microbiomes in caterpillar guts
Authors: Šigutová Hana , Pyszko Petr , Šigut Martin , Czajová Kateřina , Kostovčík Martin , Kolařík Miroslav , Hařovská Denisa , Drozd Pavel 
Published: November 2023

ABSTRACT

Plant–herbivore interactions have been modulated by plant secondary metabolites (PSM), which exert a strong pressure on herbivore microbiome. This study examined the effects of different PSM types and concentrations on caterpillar fitness, composition of gut bacterial and fungal assemblages, and microbiome network stability and symbiotic bonds in relation to the caterpillar diet breadth. Polyphagous and monophagous caterpillars sampled from oak were reared on an artificial diet (AD) containing PSM native (tannic acid) and non-native (tannivin and salicylic acid) to oak at varying concentrations, along with control treatments (starving and fed by oak leaves or AD without PSM). Their gut microbiome was profiled using 16S and ITS2 rRNA gene metabarcoding. Contrary to expectations, the diet breadth combined with the PSM type had no effect on weight gain. The bacterial composition was shaped by PSM concentration, while caterpillar species and diet breadth had no effect. Compared with bacteria, concentration had no effect on the fungal composition, which was more influenced by diet breadth than by caterpillar species. Leaf-fed caterpillars harbored the highest microbial richness. In AD-fed caterpillars, bacteria formed more complex networks than fungi, and the complexity was simplified with higher PSM concentrations. We identified taxa significantly associated with caterpillar guts. Notably, the association
Lactobacillus–Lactococcus–Streptococcus
was universally present across all caterpillar species, regardless of diet breadth. Our findings emphasize the importance of considering PSM concentration and composition in understanding caterpillar–gut microbiome interactions. Further research will validate the functional roles of identified microbial taxa and their significance for caterpillar hosts.

IMPORTANCE
The caterpillar gut is an excellent model system for studying host–microbiome interactions, as it represents an extreme environment for microbial life that usually has low diversity and considerable variability in community composition. Our study design combines feeding caterpillars on a natural and artificial diet with controlled levels of plant secondary metabolites and uses metabarcoding and quantitative PCR to simultaneously profile bacterial and fungal assemblages, which has never been performed. Moreover, we focus on multiple caterpillar species and consider diet breadth. Contrary to many previous studies, our study suggested the functional importance of certain microbial taxa, especially bacteria, and confirmed the previously proposed lower importance of fungi for caterpillar holobiont. Our study revealed the lack of differences between monophagous and polyphagous species in the responses of microbial assemblages to plant secondary metabolites, suggesting the limited role of the microbiome in the plasticity of the herbivore diet.
Phosphoproteomic landscape of pseudorabies virus infection reveals multiple potential antiviral targets
Authors: Bo Zongyi , Li Xiaojuan , Zhang Chengcheng , Guo Mengjiao , Cao Yongzhong , Zhang Xiaorong , Wu Yantao 
Published: November 2023

ABSTRACT
Phosphorylation, a significant posttranslational modification, is implicated in nearly two-thirds of all proteins. The involvement of phosphorylation in various cellular responses is known to play a crucial role in the replication of pseudorabies virus (PRV). However, the phosphoproteomic landscape during PRV infection remains unknown. To address this, a tandem mass tag-based liquid chromatography-tandem mass spectrometry was performed. It was found that a total of 7,342 phosphosites were detected; among these, 1,197 phosphosites were significantly upregulated, and 1,120 phosphosites were significantly downregulated when the threshold was set at 1.5. Gene ontology analysis of these significantly changed proteins showed that they mainly participated in mRNA processing, RNA splicing, stress granule assembly, and other pathways. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that these proteins were associated with cell cycle, spliceosome, tight junction, mRNA surveillance, and other pathways. Additionally, an immunoblotting assay confirmed the phosphoproteomic results by detecting the protein level of several upregulated phosphorylated proteins, which included pBRAF, pRPS6KA1, and pSTMN1. Further experiments using siRNA showed that knockdown of BRAF, RPS6KA1, and STMN1 significantly inhibited the replication of PRV. In summary, this study provides insight into the phosphoproteomic landscape during PRV infection and contributes to a better understanding of the mechanisms underlying PRV replication.

IMPORTANCE
Pseudorabies virus (PRV) is a kind of alpha herpesvirus that infects a wide range of animals and even human beings. Therefore, it is important to explore the mechanisms behind PRV replication and pathogenesis. By conducting a tandem mass tag-based phosphoproteome, this study revealed the phosphorylated proteins and cellular response pathways involved in PRV infection. Findings from this study shed light on the relationship between the phosphorylated cellular proteins and PRV infection, as well as guiding the discovery of targets for the development of antiviral compounds against PRV.
Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation
Authors: Gudeta Dereje D. , Foley Steven L. 
Published: November 2023

ABSTRACT

The ability to better understand the function of proteins expressed by bacteria has typically relied upon the development of genetic mutant strains. This approach has been especially challenging for plasmid-encoded genes, as most of the previously described allelic replacement vectors are inefficient for plasmid genome mutation as they either rely on plasmid-derived counterselection toxins or depend on other strategies such
sacB
,
tetA
, and
rpsL
which have been proven to be less efficient for mutant selection. Integrative vectors lack chromophore indicators, thus requiring laborious screening or excision of the vector’s backbone relies on the introduction of a flippase (FLP)-expressing plasmid. The allelic replacement vector, designated here as pDG1, expresses an X-Gal hydrolyzing enzyme (BgaB) that can be used for blue/white screening allowing identification of colonies that integrated and successfully removed the mutagenesis plasmid without a bias for those still carrying it. pDG1 was further improved by including the rhamnose-inducible Tse2 toxin as a potent counterselection system. The efficacy of pDG1 was validated by deleting portions of the plasmid-encoded VirB4/D4 type IV secretion system and aerobactin-synthesizing operons in
Salmonella enterica
. The integrative vectors, which contain an ΦC31
attP
site and genes encoding ΦC31 integrase (
int
), can seamlessly integrate to target ΦC31
attB
on
Salmonella
plasmids or chromosome. These vectors were improved by inserting
bgaB
and FLP-encoding genes so that, following integration, most of the vector’s backbone encompassing
int
,
bgaB
, and FLP genes can be excised by FLP, without the need for another FLP-expressing vector, creating white colonies carrying a stably integrated target gene. As such, we were able to integrate a 9.3-kb DNA fragment to
Salmonella
chromosome and flipped out most of the integrated vector in one step, leaving the target fragment in the chromosome.

IMPORTANCE

In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including
in vivo
studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.
Clinical validation of the ‘C-arm rotational view (CARV)’: study protocol of a prospective randomised controlled trial
Authors: Bleeker Nils Jan , Doornberg Job N , ten Duis Kaj , El Moumni Mostafa , Jaarsma Ruurd L , IJpma Frank F A 
Published: November 2023

IntroductionRotational malalignment occurs in up to 30% of cases after intramedullary nailing of tibial shaft fractures. The aim of this study is to assess the clinical feasibility of a newly introduced standardised intraoperative fluoroscopy protocol coined ‘C-arm rotational view (CARV)’ in order to reduce the risk of rotational malalignment during intramedullary nailing of tibial shaft fractures. The CARV includes predefined fluoroscopy landmark views of the uninjured side to obtain correct alignment of the injured side with use of the rotation of the C-arm.Methods and analysisThis randomised controlled trial will be conducted in a level 1 trauma centre. Adult patients with an open or closed tibial fracture, eligible for intramedullary nailing, will be enrolled in the study. The interventional group will undergo intramedullary nailing guided by the CARV protocol to obtain accurate alignment. The control group is treated according to current clinical practice, in which alignment control of the tibia is based on clinical estimation of the treating surgeon. The primary endpoint is defined as the degree of rotation measured on low-dose postoperative CT scans.Ethics and disseminationThe study protocol will be performed in line with local ethical guidelines and the Declaration of Helsinki. The results of this trial will be disseminated in a peer-reviewed manuscript. Future patients are likely to benefit from this trial as it aims to provide a clinically feasible and easy-to-use standardised fluoroscopy protocol to reduce the risk for rotational malalignment during intramedullary nailing of tibial shaft fractures.Trial registration numberNCT05459038.
Prevalence, correlates and common methods of non-suicidal self-injury in South Asia: a systematic review
Authors: Haregu Tilahun , Chen Quan , Arafat S M Yasir , Cherian Anish , Armstrong Gregory 
Published: November 2023

IntroductionThe dynamics of self-harm vary substantially around the world, yet it is severely under-researched outside of a small number of high-income ‘Western’ countries. South Asia is disproportionately impacted by suicide, yet we know less about non-suicidal self-injury (NSSI) in the region.ObjectiveTo review and summarise evidence on the prevalence, correlates and common methods of NSSI in South Asia.MethodsWe searched Medline, Embase and PsycINFO for the period 1 January 2000 to 31 August 2023, for peer-reviewed observational studies. A total of 11 studies from eight South Asian countries that reported prevalence and/or correlates of NSSI were included in this review. We assessed the quality of the studies using the Study Quality Assessment Tools for Observational Cohort and Cross-Sectional Studies. We used meta-regression to describe the sources of heterogeneity. Abstracted data were summarised using thematic synthesis.ResultsFor non-clinical populations, the 12-month prevalence of NSSI ranged from 3.2% to 44.8%, and the lifetime prevalence ranged from 21% to 33%. For clinical populations, the 12-month prevalence of NSSI ranged from 5% to 16.4%, while the lifetime prevalence ranged from 2% to 27%. Male sex, unemployment, financial stress, history of suicidal behaviour and depression were associated with a higher risk of NSSI. Better access to counselling services, higher self-esteem and self-knowledge were associated with a lower risk of NSSI.ConclusionThe burden of NSSI in South Asia appears to be high in both clinical and non-clinical populations. Further research, especially with general population samples, is needed to build evidence on the epidemiology, context and meaning of NSSI in South Asia to inform the design of context-specific interventions.PROSPERO registration numberCRD42022342536.
Lifestyle factors as mediators of area-level socioeconomic differentials in mental health and cognitive function: the Tromsø Study
Authors: Tiwari Sweta , Cerin Ester , Wilsgaard Tom , Løvsletten Ola , Grimsgaard Sameline , Hopstock Laila Arnesdatter , Schirmer Henrik , Rosengren Annika , Kristoffersen Kathrine , Løchen Maja-Lisa 
Published: November 2023

IntroductionLow socioeconomic status (SES) is associated with poor mental health and cognitive function. Individual-level SES and area-level SES (ASES) may affect mental health and cognitive function through lifestyle. We aimed to quantify the associations of ASES with mental health and cognitive function and examine the mediating role of lifestyle behaviours independent of individual-level SES in a Norwegian population.MethodsIn this cross-sectional study, we included 7211 participants (54% women) from the seventh survey of the Tromsø Study (2015–2016) (Tromsø7). The exposure variable ASES was created by aggregating individual-level SES variables (education, income, housing ownership) from Statistics Norway at the geographical subdivision level. Tromsø7 data were used as mediators (smoking, snuff, alcohol, physical activity, diet) and outcomes (cognitive function, anxiety, depression, insomnia). Mediation and mediated moderation analysis were performed with age as a moderator, stratified by sex.ResultsHigher ASES was associated with better cognitive function and fewer depression and insomnia symptoms, independent of individual-level SES. These associations were mediated by smoking and physical activity. Alcohol was a mediator for depression and cognitive function in women. Age was a significant moderator of the association between ASES and global cognitive function in women. The largest total indirect effect of ASES was found for depression, with the joint effect of the mediators accounting for 36% of the total effect.ConclusionsPeople living in areas with lower ASES are at higher risk of poor mental health, such as depression and insomnia, and have lower cognitive function possibly due to unhealthy lifestyle (smoking, alcohol and physical inactivity).
A Permian rhenium–osmium radiometric age for bornite at the Rock Creek deposit, Spar Lake copper–silver district (Montana, USA)—a link to the Sonoma Orogeny and the copper–silver–vanadium Midcontinent Belt?
Authors: Saintilan Nicolas J. , Creaser Robert A. 
Published: November 2023

We report rhenium–osmium (Re–Os) isotope data and age information for bornite, chalcocite, and chalcopyrite from the Spar Lake and Rock Creek copper–silver (Cu–Ag) sediment-hosted deposits in the Spar Lake district, Mesoproterozoic Belt–Purcell Basin, Montana, USA. The Re–Os geochronometers in chalcocite and chalcopyrite do not record plausible mineralization ages at the Spar Lake deposit, which is currently interpreted to have formed at ca. 1410 million years ago (Ma) from prior work. However, a Re–Os isochron date of bornite (253.2 ± 26.9 Ma, n = 6) at Rock Creek with an extremely high initial 187Os/188Os ratio of 19.1 ± 0.2 can be interpreted as resetting of Re–Os in bornite that originally recorded a Mesoproterozoic timing of Cu–Ag mineralization in the Spar Lake district. The new Re–Os age of bornite at Permian–Triassic boundary time is compatible with a resetting at the time of building of the Sonoma Foreland Basin that resulted from the loading of an accretionary prism (i.e., Golconda Allochthon) onto the North American Plate. Our ca. 253 Ma bornite age does not constrain whether Cu was introduced to Spar Lake at this time or simply redistributed, but our findings open the possibility that Cu–Ag mineralization in the Spar Lake district might have taken place not only in the Mesoproterozoic, but also in addition, at Permian–Triassic boundary time. Indeed, numerous Cu–Ag, vanadium–uranium (V–U) sandstone-hosted and black shale-hosted deposits of assumed Permian to Triassic age are documented in the Midcontinent copper belt from western Texas to southern Idaho, including (1) Cu–Ag sediment-hosted deposits in western Colorado, southeastern Utah, and northern Arizona and (2) the Montpelier and Lake Alice sandstone-hosted Cu–Ag deposits in southeastern Idaho and western Wyoming, respectively.
A maximum force perspective on black hole thermodynamics, quantum pressure, and near-extremality
Authors: Ong Yen Chin 
Published: November 2023

AbstractI re-examined the notion of the thermodynamic force constructed from the first law of black hole thermodynamics. In general relativity, the value of the charge (or angular momentum) at which the thermodynamic force equals the conjectured maximum force $$F=1/4$$

F
=
1
/
4

is found to correspond to $$Q^2/M^2=8/9$$

Q
2

/

M
2

=
8
/
9

(respectively, $$a^2/M^2=8/9$$

a
2

/

M
2

=
8
/
9

), which is known in the literature to exhibit some special properties. This provides a possible characterization of near-extremality. In addition, taking the maximum force conjecture seriously amounts to introducing a pressure term in the first law of black hole thermodynamics. This resolves the factor of two problem between the proposed maximum value $$F=1/4$$

F
=
1
/
4

and the thermodynamic force of Schwarzschild spacetime $$F=1/2$$

F
=
1
/
2

. Surprisingly it also provides another indication for the instability of the inner horizon. For a Schwarzschild black hole, under some reasonable assumptions, this pressure can be interpreted as being induced by the quantum fluctuation of the horizon position, effectively giving rise to a diffused “shell” of characteristic width $$\sqrt{M}$$

M

. The maximum force can therefore, in some contexts, be associated with inherently quantum phenomena, despite the fact that it is free of $$\hbar $$
ħ
. Some implications are discussed as more questions are raised.
The importance of nodal plane orientation diversity for earthquake focal mechanism stress inversions
Authors: Lundstern Jens-Erik , Beaucé Eric , Teran Orlando J. 
Published: November 2023

Abstract

Inversions of earthquake focal mechanisms are among the most accessible and reliable methods for determining crustal stress. However, the use of this method varies widely, and the assumptions that underpin it are often violated, potentially compromising stress estimates. We investigate the consequences of violating the little-studied assumption that the focal mechanisms have diverse orientations. Our approach is to employ data-informed synthetic mechanisms, with nodal plane orientations defined by recent earthquake lineaments in the Midland Basin, western Texas, and rakes consistent with slip in the mapped stress field. Using both the traditional stress inversion method that assumes constant shear stress magnitudes on the causative faults as well as a recently published variable shear stress method, we show that low fault plane diversity can cause maximum horizontal stress (
S
Hmax
) orientation and relative principal stress magnitude (faulting regime) estimates to differ markedly from the true values. This problem is compounded for catalogues with even modest amounts of noise (≤15°) or few (e.g. 20) mechanisms. Significantly, traditional approaches for quantifying uncertainty such as the bootstrap can severely underestimate the true uncertainty under these circumstances. To remedy this, we provide simple tools to quantify nodal plane orientation diversity and stress inversion reliability.
Choral: Object-oriented Choreographic Programming
Authors: Giallorenzo Saverio , Montesi Fabrizio , Peressotti Marco 
Published: November 2023

Choreographies are coordination plans for concurrent and distributed systems, which define the roles of the involved participants and how they are supposed to work together. In the paradigm of choreographic programming, choreographies are programs that can be compiled into executable implementations.In this article, we present Choral, the first choreographic programming language based on mainstream abstractions. The key idea in Choral is a new notion of data type, which allows for expressing that data is distributed over different roles. We use this idea to reconstruct the paradigm of choreographic programming through object-oriented abstractions. Choreographies are classes, and instances of choreographies are objects with states and behaviours implemented collaboratively by roles.Choral comes with a compiler that, given a choreography, generates an implementation for each of its roles. These implementations are libraries in pure Java, whose types are under the control of the Choral programmer. Developers can then modularly compose these libraries in their programs, to participate correctly in choreographies. Choral is the first incarnation of choreographic programming offering such modularity, which finally connects more than a decade of research on the paradigm to practical software development.The integration of choreographic and object-oriented programming yields other powerful advantages, where the features of one paradigm benefit the other in ways that go beyond the sum of the parts. On the one hand, the high-level abstractions and static checks from the world of choreographies can be used to write concurrent and distributed object-oriented software more concisely and correctly. On the other hand, we obtain a much more expressive choreographic language from object-oriented abstractions than in previous work. This expressivity allows for writing more reusable and flexible choreographies. For example, object passing makes Choral the first higher-order choreographic programming language, whereby choreographies can be parameterised over other choreographies without any need for central coordination. We also extend method overloading to a new dimension: specialisation based on data location. Together with subtyping and generics, this allows Choral to elegantly support user-defined communication mechanisms and middleware.
Glimpses on Brazilian and Indian Gondwana II
Authors: Petri Setembrino 
Published: November 2023

This publication comprises original research articles of a group of Indian and Brazilian paleobotanists and palynologists. These papers are results of the Project of International Scientific Cooperation entitled “Palaeobotanical Studies in Brazilian and Indian sedimentary basins with special reference to the marine dinoflagellate-cysts, Gondwana Flora and their applications” sponsored by Brazil-CNPq 490829/2007-4 and by India-DST RPO 24/2007, coordinated from the Brazilian side by Dr. Mary Elizabeth Cerruti Bernardes-de-Oliveira (Instituto de Geociências/USP) and from the Indian side by Dr. Naresh Chandra Mehrotra (Birbal Sahni Institute of Palaeosciences).