bluuebunny/crossref_metadata_2025_split huggingface dataset:
Background and clustering characteristics of recent seismicity in Southwestern China
Authors: Liu Yue , Zhuang Jiancang , Guo Yicun , Jiang Changsheng , Tian Qinjian , Zhang Yongxian , Long Feng 
Published: June 2024

SUMMARY
This study analysed seismicity in southwestern China (1 January 2008 to 30 June 2021) using the earthquake catalogue compiled by the China Earthquake Network Center and four different space–time Epidemic-Type Aftershock Sequence models: the 2-D point-source (PS) model, the 2-D finite-source (FS) model, the 3-D PS model and the 3-D FS model. Our objective was to understand the features of the background seismicity and the patterns of earthquake clusters to better evaluate the regional seismic hazard. We carefully investigated the aftershock sequences that followed 7 of the 10 MS ≥ 6.0 earthquakes that have struck this region since the occurrence of the 2008 Wenchuan MS 8.0 earthquake [i.e. the Panzhihua (31 August 2008; MS 6.0), Yaoan (9 July 2009; MS 6.0), Lushan (20 April 2013; MS 7.0), Ludian (3 August 2014; MS 6.5), Jinggu (7 October 2014; MS 6.6), Kangding (11 November 2014; MS 6.3) and Yangbi (21 May 2021; MS 6.4) earthquakes]. Our results revealed the following. (1) The background seismicity level for natural earthquakes is usually stable but can experience sudden change due to major events, such as the 2014 Ludian MS 6.5, and the 2014 Jinggu MS 6.6 events. Such changes in the background rate can reach 50 per cent. (2) Reservoir-induced earthquakes substantially increase the level of regional seismicity, indicating that they cannot be ignored when analysing natural seismicity and evaluating regional earthquake hazards. (3) Events triggered directly by the main shock occur mostly in regions adjacent to areas with large coseismic slip, showing a pattern complementary to the main shock ruptures.
Deep Amplicon Sequencing Reveals Culture Selection of Mycobacterium Tuberculosis by Clinical Samples
Authors: Qu Jiuxin , Liu Wanfei , Chen Shuyan , Wu Chi , Lai Wenjie , Qin Rui , Ye Feidi , Li Yuanchun , Fu Liang , Deng Guofang , Liu Lei , Lin Qiang , Cui Peng 
Published: June 2024

Abstract
The commonly-used drug susceptibility testing (DST) relies on bacterial culture and faces shortcomings such as long turnaround time and clone/subclone selection. We developed a targeted deep amplification sequencing (DAS) method directly applied to clinical specimens. In this DAS panel, we examined 941 drug-resistant mutations associated with 20 anti-tuberculosis drugs with an initial amount of 4 pg DNA and reduced clinical testing time from 20 days to two days. A prospective study was conducted using 115 clinical specimens mainly with Xpert® Mycobacterium tuberculosis/rifampicin (Xpert MTB/RIF) assay positive to evaluate drug-resistant mutation detection. DAS was performed on culture-free specimens, while culture-dependent isolates were used for phenotypic DST, DAS, and whole-genome sequencing (WGS). For in silico molecular DST, our result based on DAS panel revealed the similar accuracy to three published reports based on WGS. For 82 isolates, application of DAS showed better sensitivity (93.03% vs. 92.16%), specificity (96.10% vs. 95.02%), and accuracy (91.33% vs. 90.62%) than Mykrobe software using WGS. Compared to culture-dependent WGS, culture-free DAS provides a full picture of sequence variation at population level, exhibiting in detail the gain-and-loss variants caused by bacterial culture. Our study performs a systematic verification of the advantages of DAS in clinical applications and comprehensively illustrates the discrepancy in Mycobacterium tuberculosis before and after culture.
Ex-combatants and the Truth Commission in Colombia: An Analysis of the Participation of Former Military and Ex-guerrillas
Authors: Ugarriza Juan E , Peralta Laly C 
Published: June 2024

ABSTRACT∞
The Colombian Truth Commission (2018 to 2022) provides a unique opportunity to delve into the participation of ex-military personnel and former guerrillas within truth-seeking bodies. While existing literature highlights the importance of their involvement in facilitating the assumption of responsibilities, rebuilding relations with their victims and undergoing personal transformation, it tends to overlook their potential contribution to truth and memory. After conducting interviews with former Commissioners, staff, soldiers and ex-guerrillas over a two-year period, our research reveals that former fighters maintained confrontational attitudes toward their previous adversaries. They primarily focused on promoting historical memory narratives rather than making substantial contributions to uncovering the truth. Conversely, the Commission took a moral stance in supporting the victims but failed to prevent conflicting narratives from hindering the path to reconciliation. The Colombian experience underscores the need for strategies to ensure that truth-seeking and memory spaces play a constructive role postconflict, and to accommodate perpetrators’ contributions to historical clarification without condoning their actions.
Period Integrals of Hypersurfaces via Tropical Geometry
Authors: Yamamoto Yuto 
Published: June 2024

Abstract
Let $\left \{ Z_{t} \right \}_{t}$ be a one-parameter family of complex hypersurfaces of dimension $d \geq 1$ in a toric variety. We compute asymptotics of period integrals for $\left \{ Z_{t} \right \}_{t}$ by applying the method of Abouzaid–Ganatra–Iritani–Sheridan, which uses tropical geometry. As integrands, we consider Poincaré residues of meromorphic $(d+1)$-forms on the ambient toric variety, which have poles along the hypersurface $Z_{t}$. The cycles over which we integrate them are spheres and tori, which correspond to tropical $(0, d)$-cycles and $(d, 0)$-cycles on the tropicalization of $\left \{ Z_{t} \right \}_{t}$, respectively. In the case of $d=1$, we explicitly write down the polarized logarithmic Hodge structure of Kato–Usui at the limit as a corollary. Throughout this article, we impose the assumption that the tropicalization is dual to a unimodular triangulation of the Newton polytope.
Circle Actions on Oriented Manifolds With 3 Fixed Points
Authors: Jang Donghoon 
Published: June 2024

Abstract
Let the circle group act on a compact oriented manifold $M$ with a non-empty discrete fixed point set. Then the dimension of $M$ is even. If $M$ has one fixed point, $M$ is the point. In any even dimension, such a manifold $M$ with two fixed points exists, a rotation of an even dimensional sphere. Suppose that $M$ has three fixed points. Then the dimension of $M$ is a multiple of 4. Under the assumption that each isotropy submanifold is orientable, we show that if $\dim M=8$, then the weights at the fixed points agree with those of an action on the quaternionic projective space $\mathbb{H}\mathbb{P}^{2}$, and show that there is no such 12-dimensional manifold $M$.
Communicating through Protocols: The Case of Diplomatic Credential Ceremonies
Authors: Berkowitz Roni , Heimann Gadi , Kampf Zohar 
Published: June 2024

Abstract
This study questions to what extent state agents invest efforts in building interpersonal relations with their counterparts. It is based on data collected during two years of ethnographic fieldwork at the Israeli president’s residence, where we observed credential ceremonies involving ambassadors from twenty-three states and interviewed the president’s advisors. We consider the credential ceremony an extreme case study regulated by highly formalized protocol, including the strictest guidelines existing in the world of diplomacy. We assume that if relation-building between statespersons takes place in the most unexpected spaces of international politics, we can detect it in all sites of diplomacy. Adopting a relational practice approach, we identified two methods of positive signaling for relationship building: preplanned by the organizers “from above,” directed at the individual-as-state-representative, and conveyed by participants “from below,” targeting the individual-as-guest/host. We conclude by discussing the implications of the prevalence of interpersonal relation-building in international politics, the role of diplomatic protocols as a communicative resource that affects the diplomatic environment, and how the concept of affordances provides a fresh look at one of the most fundamental debates in the field of IR: the relationship between agency and structure.
Transcriptomics reveal a unique phago-mixotrophic response to low nutrient concentrations in the prasinophyte Pterosperma cristatum
Authors: Charvet Sophie , Bock Nicholas A , Kim Eunsoo , Duhamel Solange 
Published: June 2024

Abstract
Constitutive mixoplankton—plastid–bearing microbial eukaryotes capable of both phototrophy and phagotrophy—are ubiquitous in marine ecosystems and facilitate carbon transfer to higher trophic levels within aquatic food webs, which supports enhanced sinking carbon flux. However, the regulation of the relative contribution of photosynthesis and prey consumption remains poorly characterized. We investigated the transcriptional dynamics behind this phenotypic plasticity in the prasinophyte green alga Pterosperma cristatum. Based on what is known of other mixoplankton species that cannot grow without photosynthesis (obligate phototrophs), we hypothesized that P. cristatum uses phagotrophy to circumvent the restrictions imposed on photosynthesis by nutrient depletion, to obtain nutrients from ingested prey, and to maintain photosynthetic carbon fixation. We observed an increase in feeding as a response to nutrient depletion, coinciding with an upregulation of expression for genes involved in essential steps of phagocytosis including prey recognition, adhesion and engulfment, transport and maturation of food vacuoles, and digestion. Unexpectedly, genes involved in the photosynthetic electron transfer chain, pigment biosynthesis, and carbon fixation were downregulated as feeding increased, implying an abatement of photosynthesis. Contrary to our original hypothesis, our results therefore suggest that depletion of inorganic nutrients triggered an alteration of trophic behavior from photosynthesis to phagotrophy in P. cristatum. While this behavior distinguishes P. cristatum from other groups of constitutive mixoplankton, its physiological response aligns with recent discoveries from natural microbial communities. These findings indicate that mixoplankton communities in nutrient-limited oceans can regulate photosynthesis against bacterivory based on nutrient availability.
Intracellular symbiont Symbiodolus is vertically transmitted and widespread across insect orders
Authors: Wierz Jürgen C , Dirksen Philipp , Kirsch Roy , Krüsemer Ronja , Weiss Benjamin , Pauchet Yannick , Engl Tobias , Kaltenpoth Martin 
Published: June 2024

Abstract
Insects engage in manifold interactions with bacteria that can shift along the parasitism–mutualism continuum. However, only a small number of bacterial taxa managed to successfully colonize a wide diversity of insects, by evolving mechanisms for host-cell entry, immune evasion, germline tropism, reproductive manipulation, and/or by providing benefits to the host that stabilize the symbiotic association. Here, we report on the discovery of an Enterobacterales endosymbiont (Symbiodolus, type species Symbiodolus clandestinus) that is widespread across at least six insect orders and occurs at high prevalence within host populations. Fluorescence in situ hybridization in several Coleopteran and one Dipteran species revealed Symbiodolus’ intracellular presence in all host life stages and across tissues, with a high abundance in female ovaries, indicating transovarial vertical transmission. Symbiont genome sequencing across 16 host taxa revealed a high degree of functional conservation in the eroding and transposon-rich genomes. All sequenced Symbiodolus genomes encode for multiple secretion systems, alongside effectors and toxin-antitoxin systems, which likely facilitate host-cell entry and interactions with the host. However, Symbiodolus-infected insects show no obvious signs of disease, and biosynthetic pathways for several amino acids and cofactors encoded by the bacterial genomes suggest that the symbionts may also be able to provide benefits to the hosts. A lack of host-symbiont cospeciation provides evidence for occasional horizontal transmission, so Symbiodolus’ success is likely based on a mixed transmission mode. Our findings uncover a hitherto undescribed and widespread insect endosymbiont that may present valuable opportunities to unravel the molecular underpinnings of symbiosis establishment and maintenance.
Disruption of the cell division protein ftsK gene changes elemental selenium generation, selenite tolerance, and cell morphology in Rahnella aquatilis HX2
Authors: Xu Qiaolin , Gao Shanshan , Zhang Sasa , Li Kui , Guo Yanbin 
Published: June 2024

Abstract

Aims
Some studies have indicated that the alterations in cellular morphology induced by selenite [Se(Ⅳ)] may be attributed to its inhibitory effects on cell division. However, whether the genes associated with cell division are implicated in Se(Ⅳ) metabolism remains unclear.

Methods and Results
The ftsK gene in Rahnella aquatilis HX2 was mutated with an in-frame deletion strategy. The ftsK mutation strongly reduced the tolerance to selenite [Se(Ⅳ)] and the production of red elemental selenium [Se(0)] in R. aquatilis HX2, and this effect could not be attributed solely to the inhibition of cell growth. Deleting the ftsK gene also resulted in a significant decrease in bacterial growth of R. aquatilis HX2 during both exponential and stationary phases. The deletion of ftsK inhibited cell division, resulting in the development of elongated filamentous cells. Furthermore, the loss-of-function of FtsK significantly impacted the expression of seven genes linked to cell division and Se(Ⅳ) metabolism by at least 2-fold, as unveiled by real-time quantitative PCR (RT-qPCR) under Se(Ⅳ) treatment.

Conclusions
These findings suggest that FtsK is associated with Se(Ⅳ) tolerance and Se(0) generation and is a key player in coordinating bacterial growth and cell morphology in R. aquatilis HX2.
Exploring coaggregation mechanisms involved in biofilm formation in drinking water through a proteomic-based approach
Authors: Afonso Ana C , Simões Manuel , Saavedra Maria José , Simões Lúcia , Lema Juan M , Trueba-Santiso Alba 
Published: June 2024

Abstract

Aim
Coaggregation, a highly specific cell–cell interaction mechanism, plays a pivotal role in multispecies biofilm formation. While it has been mostly studied in oral environments, its occurrence in aquatic systems is also acknowledged. Considering biofilm formation’s economic and health-related implications in engineered water systems, it is crucial to understand its mechanisms. Here, we hypothesized that traceable differences at the proteome level might determine coaggregation ability.

Methods and Results
Two strains of Delftia acidovorans, isolated from drinking water were studied. First, in vitro motility assays indicated more swarming and twitching motility for the coaggregating strain (C+) than non-coaggregating strain (C−). By transmission electronic microscopy, we confirmed the presence of flagella for both strains. By proteomics, we detected a significantly higher expression of type IV pilus twitching motility proteins in C+, in line with the motility assays. Moreover, flagellum ring proteins were more abundant in C+, while those involved in the formation of the flagellar hook (FlE and FilG) were only detected in C−. All the results combined suggested structural and conformational differences between stains in their cell appendages.

Conclusion
This study presents an alternative approach for identifying protein biomarkers to detect coaggregation abilities in uncharacterized strains.
Molecular and aflatoxigenicity analyses of Aspergillus flavus isolates indigenous to grain corn in Malaysia; potentials for biological control
Authors: Yazid Siti Nur Ezzati , Selamat Jinap , Ismail Siti Izera , Sanny Maimunah , Samsudin Nik Iskandar Putra 
Published: June 2024

Abstract

Aims
The present work aimed to distinguish the indigenous Aspergillus flavus isolates obtained from the first (pioneer) grain corn farms in Terengganu, Malaysia, into aflatoxigenic and non-aflatoxigenic by molecular and aflatoxigenicity analyses, and determine the antagonistic capability of the non-aflatoxigenic isolates against aflatoxigenic counterparts and their aflatoxin production in vitro.

Methods and results
Seven A. flavus isolates previously obtained from the farms were characterized molecularly and chemically. All isolates were examined for the presence of seven aflatoxin biosynthesis genes, and their aflatoxigenicity was confirmed using high performance liquid chromatography with fluorescence detector. Phylogenetic relationships of all isolates were tested using ITS and β-tubulin genes. Of the seven isolates, two were non-aflatoxigenic, while the remaining were aflatoxigenic based on the presence of all aflatoxin biosynthesis genes tested and the productions of aflatoxins B1 and B2. All isolates were also confirmed as A. flavus following phylogenetic analysis. The indigenous non-aflatoxigenic isolates were further examined for their antagonistic potential against aflatoxigenic isolates on 3% grain corn agar. Both non-aflatoxigenic isolates significantly reduced AFB1 production of the aflatoxigenic isolates.

Conclusion
The indigenous non-aflatoxigenic A. flavus strains identified in the present work were effective in controlling the aflatoxin production by the aflatoxigenic A. flavus isolates in vitro and can be utilized for in situ testing.
Analysis of ddRAD-seq data provides new insights into the genomic structure and patterns of diversity in Italian donkey populations
Authors: Criscione Andrea , Chessari Giorgio , Cesarani Alberto , Ablondi Michela , Asti Vittoria , Bigi Daniele , Bordonaro Salvatore , Ciampolini Roberta , Cipolat-Gotet Claudio , Congiu Michele , De Palo Pasquale , Landi Vincenzo , Macciotta Nicolò Pietro Paolo , Matassino Donato , Portolano Baldassare , Riggio Silvia , Sabbioni Alberto , Sardina Maria Teresa , Senczuk Gabriele , Tumino Serena , Vasini Matteo , Ciani Elena , Mastrangelo Salvatore 
Published: June 2024

Abstract
With more than 150 recognized breeds, donkeys assume relevant economic importance, especially in developing countries. Even if the estimated number of heads worldwide is 53M, this species received less attention than other livestock species. Italy has traditionally been considered one of the cradles of European donkey breeding, and despite a considerable loss of biodiversity, today still counts nine autochthonous populations. A total of 220 animals belonging to nine different populations were genotyped using the double-digest restriction site associated DNA (ddRAD) sequencing to investigate the pattern of diversity using a multi-technique approach. A total of 418,602,730 reads were generated and successfully demultiplexed to obtain a medium-density SNP genotypes panel with about 27K markers. The diversity indices showed moderate levels of variability. The genetic distances and relationships, largely agree with the breeding history of the donkey populations under investigation. The results highlighted the separation of populations based on their genetic origin or geographical proximity between breeding areas, showed low to moderate levels of admixture, and indicated a clear genetic difference in some cases. For some breeds, the results also validate the success of proper management conservation plans. Identified runs of homozygosity islands, mapped within genomic regions related to immune response and local adaptation, are consistent with the characteristics of the species known for its rusticity and adaptability. This study is the first exhaustive genome-wide analysis of the diversity of Italian donkey populations. The results emphasized the high informativeness of genome-wide markers retrieved through the ddRAD approach. The findings take on great significance in designing and implementing conservation strategies. Standardized genotype arrays for donkey species would make it possible to combine worldwide datasets to provide further insights into the evolution of the genomic structure and origin of this important genetic resource.
diABZI and poly(I:C) inhibit osteoclastic bone resorption by inducing IRF7 and IFIT3
Authors: Huang Yingkang , Zhang Mingchao , Zhang Jun , Liu Siying , Li Dapei , Qiao Zigang , Yao Haiping , Shi Qin , Zhou Xiaozhong , Ma Feng 
Published: June 2024

Abstract
Type I interferons (IFN-I) are pleiotropic factors endowed with multiple activities that play important roles in innate and adaptive immunity. Although many studies indicate that IFN-I inducers exert favorable effects on broad-spectrum antivirus, immunomodulation, and anti-tumor activities by inducing endogenous IFN-I and IFN-stimulated genes, their function in bone homeostasis still needs further exploration. Here, our study demonstrates 2 distinct IFN-I inducers, diABZI and poly(I:C), as potential therapeutics to alleviate osteolysis and osteoporosis. First, IFN-I inducers suppress the genes that control osteoclast (OC) differentiation and activity in vitro. Moreover, diABZI alleviates bone loss in Ti particle-induced osteolysis and ovariectomized -induced osteoporosis in vivo by inhibiting OC differentiation and function. In addition, the inhibitory effects of IFN-I inducers on OC differentiation are not observed in macrophages derived from Ifnar1−/−mice, which indicate that the suppressive effect of IFN-I inducers on OC is IFNAR-dependent. Mechanistically, RNAi-mediated silencing of IRF7 and IFIT3 in OC precursors impairs the suppressive effect of the IFN-I inducers on OC differentiation. Taken together, these results demonstrate that IFN-I inducers play a protective role in bone turnover by limiting osteoclastogenesis and bone resorption through the induction of OC-specific mediators via the IFN-I signaling pathway.
Das House Kapital: A Long-Run Theory of House Prices and Housing Wealth
Authors: Grossmann Volker , Larin Benjamin , Steger Thomas 
Published: June 2024

Abstract
Over the last 70 years, many advanced countries have experienced growing real house prices and an increasing housing wealth-to-income ratio. To explain these long-run patterns, this paper introduces a novel multi-sector growth model where housing services are produced using non-reproducible land and reproducible structures. Land is also employed in the non-housing sector. First, we identify two fundamental mechanisms driving the long-run increase in the real house price: (i) technological progress in the construction sector lags behind the technological progress of the rest of the economy and (ii) housing production is more land-intensive than non-housing production. Second, we study transitional dynamics for the US, UK, France, and Germany. Our calibrated model explains most of the observed increase in the housing wealth-to-income ratio since 1950. Counterfactual experiments identify initially low stocks of residential structures and non-residential capital as key exogenous drivers for this increase. The associated investment incentives led to a long-lasting construction boom and steadily increasing land scarcity, boosting residential land prices.