bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial associates of the elm leaf beetle: uncovering the absence of resident bacteria and the influence of fungi on insect performance
Authors: Schott Johanna , Rakei Juliette , Remus-Emsermann Mitja , Johnston Paul , Mbedi Susan , Sparmann Sarah , Hilker Monika , Paniagua Voirol Luis R. 
Published: January 2024

ABSTRACT

Microbial symbionts play crucial roles in the biology of many insects. While bacteria have been the primary focus of research on insect-microbe symbiosis, recent studies suggest that fungal symbionts may be just as important. The elm leaf beetle (ELB,
Xanthogaleruca luteola
) is a serious pest species of field elm (
Ulmus minor
). Using culture-dependent and independent methods, we investigated the abundance and species richness of bacteria and fungi throughout various ELB life stages and generations, while concurrently analyzing microbial communities on elm leaves. No persistent bacterial community was found to be associated with the ELB or elm leaves. By contrast, fungi were persistently present in the beetle’s feeding life stages and on elm leaves. Fungal community sequencing revealed a predominance of the genera
Penicillium
and
Aspergillus
in insects and on leaves. Culture-dependent surveys showed a high prevalence of two fungal colony morphotypes closely related to
Penicillium lanosocoeruleum
and
Aspergillus flavus
. Among these, the
Penicillium
morphotype was significantly more abundant on feeding-damaged compared with intact leaves, suggesting that the fungus thrives in the presence of the ELB. We assessed whether the detected prevalent fungal morphotypes influenced ELB’s performance by rearing insects on (i) surface-sterilized leaves, (ii) leaves inoculated with
Penicillium
spores, and (iii) leaves inoculated with
Aspergillus
spores. Insects feeding on
Penicillium
-inoculated leaves gained more biomass and tended to lay larger egg clutches than those consuming surface-sterilized leaves or
Aspergillus
-inoculated leaves. Our results demonstrate that the ELB does not harbor resident bacteria and that it might benefit from associating with
Penicillium
fungi.

IMPORTANCE

Our study provides insights into the still understudied role of microbial symbionts in the biology of the elm leaf beetle (ELB), a major pest of elms. Contrary to expectations, we found no persistent bacterial symbionts associated with the ELB or elm leaves. Our research thus contributes to the growing body of knowledge that not all insects rely on bacterial symbionts. While no persistent bacterial symbionts were detectable in the ELB and elm leaf samples, our analyses revealed the persistent presence of fungi, particularly
Penicillium
and
Aspergillus
on both elm leaves and in the feeding ELB stages. Moreover, when ELB were fed with fungus-treated elm leaves, we detected a potentially beneficial effect of
Penicillium
on the ELB’s development and fecundity. Our results highlight the significance of fungal symbionts in the biology of this insect.
Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds
Authors: Seveso Andrea , Mazurkewich Scott , Banerjee Sanchari , Poulsen Jens-Christian Navarro , Lo Leggio Leila , Larsbrink Johan 
Published: January 2024

ABSTRACT

Lignocellulose is a renewable but complex material exhibiting high recalcitrance to enzymatic hydrolysis, which is attributed, in part, to the presence of covalent linkages between lignin and polysaccharides in the plant cell wall. Glucuronoyl esterases from carbohydrate esterase family 15 (CE15) have been proposed as an aid in reducing this recalcitrance by cleaving ester bonds found between lignin and glucuronoxylan. In the Bacteroidota phylum, some species organize genes related to carbohydrate metabolism in polysaccharide utilization loci (PULs) which encode all necessary proteins to bind, deconstruct, and respond to a target glycan. Bioinformatic analyses identified CE15 members in some PULs that appear to not target the expected glucuronoxylan. Here, five CE15 members from such PULs were investigated with the aim of gaining insights on their biological roles. The selected targets were characterized using glucuronoyl esterase model substrates and with a new synthetic molecule mimicking a putative ester linkage between pectin and lignin. The CE15 enzyme from
Phocaeicola vulgatus
was structurally determined by X-ray crystallography both with and without carbohydrate ligands with galacturonate binding in a distinct conformation than that of glucuronate. We further explored whether these CE15 enzymes could act akin to pectin methylesterases on pectin-rich biomass but did not find evidence to support the proposed activity. Based on the evidence gathered, the CE15 enzymes in the PULs expected to degrade pectin could be involved in cleavage of uronic acid esters in rhamnogalacturonans.

IMPORTANCE
The plant cell wall is a highly complex matrix, and while most of its polymers interact non-covalently, there are also covalent bonds between lignin and carbohydrates. Bonds between xylan and lignin are known, such as the glucuronoyl ester bonds that are cleavable by CE15 enzymes. Our work here indicates that enzymes from CE15 may also have other activities, as we have discovered enzymes in PULs proposed to target other polysaccharides, including pectin. Our study represents the first investigation of such enzymes. Our first hypothesis that the enzymes would act as pectin methylesterases was shown to be false, and we instead propose that they may cleave other esters on complex pectins such as rhamnogalacturonan II. The work presents both the characterization of five novel enzymes and can also provide indirect information about the components of the cell wall itself, which is a highly challenging material to chemically analyze in fine detail.
Substrate specificity and ecological significance of PstS homologs in phosphorus uptake in marine
Synechococcus
sp. WH8102
Authors: Ranjit Pramita , Varkey Deepa , Shah Bhumika S. , Paulsen Ian T. 
Published: January 2024

ABSTRACT

Phosphorus, a vital macronutrient, often limits primary productivity in marine environments. Marine
Synechococcus
strains, including WH8102, rely on high-affinity phosphate-binding proteins (PstS) to scavenge inorganic phosphate in oligotrophic oceans. However, WH8102 possesses three distinct PstS homologs whose substrate specificity and ecological roles are unclear. The three PstS homologs were heterologously expressed and purified to investigate their substrate specificity and binding kinetics. Our study revealed that all three PstS homologs exhibited a high degree of specificity for phosphate but differed in phosphate binding affinities. Notably, PstS1b displayed nearly 10-fold higher binding affinity (
K
D
= 0.44 µM) compared to PstS1a (
K
D =
3.3 μM) and PstS2 (
K
D =
4.3 μM). Structural modeling suggested a single amino acid variation in the binding pocket of PstS1b (threonine instead of serine in PstS1a and PstS2) likely contributed to its higher Pi affinity. Genome context data, together with the protein biophysical data, suggest distinct ecological roles for the three PstS homologs. We propose that PstS1b may be involved in scavenging inorganic phosphorus in oligotrophic conditions and that PstS1a may be involved in transporting recycled phosphate derived from organic phosphate cleavage. The role of PstS2 is less clear, but it may be involved in phosphate uptake when environmental phosphate concentrations are transiently higher. The conservation of three distinct PstS homologs in
Synechococcus
clade III strains likely reflects distinct adaptations for P acquisition under varying oligotrophic conditions.

IMPORTANCE

Phosphorus is an essential macronutrient that plays a key role in marine primary productivity and biogeochemistry. However, intense competition for bioavailable phosphorus in the marine environment limits growth and productivity of ecologically important cyanobacteria. In oligotrophic oceans, marine
Synechococcus
strains, like WH8102, utilize high-affinity phosphate-binding proteins (PstS) to scavenge inorganic phosphate. However, WH8102 possesses three distinct PstS homologs, with unclear substrate specificity and ecological roles, creating a knowledge gap in understanding phosphorus acquisition mechanisms in picocyanobacteria. Through genomic, functional, biophysical, and structural analysis, our study unravels the ecological functions of these homologs. Our findings enhance our understanding of cyanobacterial nutritional uptake strategies and shed light on the crucial role of these conserved nutrient uptake systems in adaptation to specific niches, which ultimately underpins the success of marine
Synechococcus
across a diverse array of marine ecosystems.
Methane-carbon budget of a ferruginous meromictic lake and implications for marine methane dynamics on early Earth
Authors: Akam Sajjad A. , Chuang Pei-Chuan , Katsev Sergei , Wittkop Chad , Chamberlain Michelle , Dale Andrew W. , Wallmann Klaus , Heathcote Adam J. , Swanner Elizabeth D. 
Published: January 2024

Abstract
The greenhouse gas methane (CH4) contributed to a warm climate that maintained liquid water and sustained Earth’s habitability in the Precambrian despite the faint young sun. The viability of methanogenesis (ME) in ferruginous environments, however, is debated, as iron reduction can potentially outcompete ME as a pathway of organic carbon remineralization (OCR). Here, we document that ME is a dominant OCR process in Brownie Lake, Minnesota (midwestern United States), which is a ferruginous (iron-rich, sulfate-poor) and meromictic (stratified with permanent anoxic bottom waters) system. We report ME accounting for ≥90% and &gt;9% ± 7% of the anaerobic OCR in the water column and sediments, respectively, and an overall particulate organic carbon loading to CH4 conversion efficiency of ≥18% ± 7% in the anoxic zone of Brownie Lake. Our results, along with previous reports from ferruginous systems, suggest that even under low primary productivity in Precambrian oceans, the efficient conversion of organic carbon would have enabled marine CH4 to play a major role in early Earth’s biogeochemical evolution.
Effects of electromagnetic field on a radiating star
Authors: Jaryal Suresh C. , Chatterjee Ayan , Kumar Akshay 
Published: January 2024

AbstractIn this paper we study the shear free spherical symmetric gravitational collapse of a charged radiating star. All the physical quantities including pressure, density are regular. Energy conditions are satisfied throughout the interior of the matter configuration. The luminosity is time independent and mass is radiated linearly. The causal and non causal temperature remain greater than that of the uncharged collapsing scenario.
Isotropization and complexity shift of gravitationally decoupled charged anisotropic sources
Authors: Albalahi Abeer M. , Yousaf Z. , Ali Akbar , Khan S. 
Published: January 2024

AbstractThis article focuses on investigating the role of decoupling in isotropizing anisotropic, self-gravitational charged sources with spherical symmetry through a well-known gravitational technique, known as minimal geometric deformation (MGD). This technique separates the given system into two gravitational systems: the Einstein-Maxwell system and the gravitational system governed by additional source. We employ novel approaches, including the zero complexity factor and isotropization techniques, to construct various charged compact star models using the Tolman IV as the seed source within the framework of the MGD scheme. The term complexity factor emerges as one of the structure-defining scalar quantities resulting from the orthogonal splitting of the Riemann–Christoffel curvature tensor, as proposed by Herrera (Phys Rev D 97(4):044010, 2018). This scalar function, denoted as $$Y_{TF}$$

Y

TF

, is associated with the fundamental structural characteristics of self-gravitational compact configurations. Our approach is innovative in that it derives the deformation functions by imposing the requirement of $$Y_{TF}=0$$

Y

TF

=
0

and employs isotropization techniques for electrically charged anisotropic configurations.
Flat and bent branes in Born–Infeld-like scalar field models
Authors: Andrade I. , Marques M. A. , Menezes R. 
Published: January 2024

AbstractIn this work, we investigate the presence of thick branes modeled by a single scalar field with Born–Infeld-like dynamics. We consider the 4-dimensional metric being Minkowski, de Sitter or anti-de Sitter. We obtain the field equations and the conditions to get a first order formalism compatible with them. To illustrate our procedure, some specific models are presented. They support localized warp factor and have their properties controlled by the 4-dimensional cosmological constant. In particular, a hybrid brane may arise, with a thick or thin profile depending on the extra dimension being inside or outside a compact space.
Completeness, Recall, and Negation in Open-world Knowledge Bases: A Survey
Authors: Razniewski Simon , Arnaout Hiba , Ghosh Shrestha , Suchanek Fabian 
Published: January 2024

General-purpose knowledge bases (KBs) are a cornerstone of knowledge-centric AI. Many of them are constructed pragmatically from web sources and are thus far from complete. This poses challenges for the consumption as well as the curation of their content. While several surveys target the problem of completing incomplete KBs, the first problem is arguably to know whether and where the KB is incomplete in the first place, and to which degree.
In this survey, we discuss how knowledge about completeness, recall, and negation in KBs can be expressed, extracted, and inferred. We cover (i) the logical foundations of knowledge representation and querying under partial closed-world semantics; (ii) the estimation of this information via statistical patterns; (iii) the extraction of information about recall from KBs and text; (iv) the identification of interesting negative statements; and (v) relaxed notions of relative recall.
This survey is targeted at two types of audiences: (1) practitioners who are interested in tracking KB quality, focusing extraction efforts, and building quality-aware downstream applications; and (2) data management, knowledge base, and semantic web researchers who wish to understand the state-of-the-art of knowledge bases beyond the open-world assumption. Consequently, our survey presents both fundamental methodologies and the results that they have produced, and gives practice-oriented recommendations on how to choose between different approaches for a problem at hand.
Hematocrit Is Associated with Cancer-Related Fatigue in Colorectal Cancer Survivors: A Longitudinal Analysis
Authors: Kiebach Joann , de Vries-ten Have Judith , van Duijnhoven Fränzel J.B. , Kok Dieuwertje E. , van Lanen Anne-Sophie , Kouwenhoven Ewout A. , de Wilt Johannes H.W. , Schrauwen Ruud W.M. , Kampman Ellen , Winkels Renate M. , Wesselink Evertine 
Published: January 2024

Abstract

Background:
Cancer-related fatigue (CRF) is a frequent symptom in colorectal cancer survivors. It is unknown to what extent anemia may contribute to CRF in colorectal cancer survivors. This study aimed to investigate the association between hematocrit, as marker for anemia, and CRF among colorectal cancer survivors from diagnosis until two years thereafter.

Methods:
The study population included 1,506 newly diagnosed colorectal cancer survivors at any stage of disease from a prospective cohort study. Hematocrit and CRF (EORTC QLQ-C30) were assessed at diagnosis, six months, and two years after diagnosis. Multivariable logistic regression or multivariable linear mixed models were used to assess the associations of hematocrit with CRF prevalence, or CRF severity over time, respectively.

Results:
A low hematocrit (levels &lt;40% men/&lt;36% women) was present in a third of the survivors at diagnosis and six months thereafter, and among 16% two years after diagnosis. The prevalence of CRF was 15% at diagnosis, peaked at 27% at six months, and was 14% two years after diagnosis. Hematocrit was associated with the prevalence of CRF at diagnosis [OR, 0.92; confidence interval (CI), 0.88–0.95], 6 months (OR, 0.89; 95% CI, 0.86–0.92), and 2 years (OR, 0.91; CI, 0.87–0.96) after diagnosis. Lower hematocrit was associated with higher severity of CRF over time (beta-coefficient = 1.3; CI, 1.5–1.1).

Conclusions:
Lower hematocrit levels were longitudinally associated with a higher prevalence and severity of CRF in colorectal cancer.

Impact:
Our findings emphasize the importance of long-term anemia monitoring and a potential role of anemia in CRF among colorectal cancer survivors.
LRRC75A-AS1 Drives the Epithelial–Mesenchymal Transition in Cervical Cancer by Binding IGF2BP1 and Inhibiting SYVN1-Mediated NLRP3 Ubiquitination
Authors: Sui Hongying , Shi Caixia , Yan Zhipeng , Chen Jinyang , Man Lin , Wang Fang 
Published: January 2024

Abstract
Cervical cancer severely affects women’s health with increased incidence and poor survival for patients with metastasis. Our study aims to investigate the mechanism by which lncRNA LRRC75A-AS1 regulates the epithelial–mesenchymal transition (EMT) of cervical cancer through modulating m6A and ubiquitination modification. In this study, tumor tissues were collected from patients to analyze the expression of LRRC75A-AS1 and SYVN1. Migratory and invasive capacities of HeLa and CaSki cells were evaluated with wound healing and transwell assays. CCK-8 and EdU incor-poration assays were employed to examine cell proliferation. The interaction between LRRC75A-AS1, IGF2BP1, SYVN1, and NLRP3 was evaluated through RNA immunoprecipitation, RNA pull-down, FISH, and coimmunoprecipitation assays, respectively. MeRIP-qPCR was applied to analyze the m6A modification of SYVN1 mRNA. A subcutaneous tumor model of cervical cancer was established. We showed LRRC75A-AS1 was upregulated in tumor tissues, and LRRC75A-AS1 enhanced EMT through activating NLRP3/IL1β/Smad2/3 signaling in cervical cancer. Furthermore, LRRC75A-AS1 inhibited SYVN1-mediated NLRP3 ubiquitination by destabilizing SYVN1 mRNA. LRRC75A-AS1 competitively bound to IGF2BP1 protein and subsequently impaired the m6A modification of SYVN1 mRNA and its stability. Knockdown of LRRC75A-AS1 repressed EMT and tumor growth via inhibiting NLRP3/IL-1β/Smad2/3 signaling in mice. In conclusion, LRRC75A-AS1 competitively binds to IGF2BP1 protein to destabilize SYVN1 mRNA, subsequently suppresses SYVN1-mediated NLRP3 ubiquitination degradation and activates IL1β/Smad2/3 signaling, thus promoting EMT in cervical cancer.
Implication: LRRC75A-AS1 promotes cervical cancer progression, and this study suggests LRRC75A-AS1 as a new therapeutic target for cervical cancer.
Long Memory in Average Monthly Temperatures and Precipitations in Guatemala
Authors: Gil-Alana Luis A. , Castillo Marlon J. 
Published: January 2024

Abstract
In this paper, we perform a fractional integration analysis of the average monthly temperature and precipitation data in 17 departments of Guatemala. Two analyses are performed, the first with the original data and the second with the anomalies based on the period January 1994–December 1999. The results indicate that there is a significant positive time trend in temperatures in the departments of Guatemala (0.0045°C month−1), Quetzaltenango (0.0040°C month−1), Escuintla (0.0034°C month−1), and Huehuetenango (0.0047°C month−1), whereas in the case of precipitation no time trend was observed. An important relevant result is that the departments of El Progreso, Baja Verapaz, and Guatemala occupy the second, third and fourth highest levels of persistence for both temperatures and precipitation, with Sacatepéquez and Quiché displaying the first places for temperature and precipitation, respectively, thus making these five departments the ones that are most vulnerable to climate change since a shock would take a long time to disappear.
Atmospheric Rivers are Responsible for Cyclicity in Sierra Nevada Precipitation
Authors: Williams A. P. , Anchukaitis K. J. , Varuolo-Clarke A. M. 
Published: January 2024

Abstract
Cool-season (November–March) precipitation contributes critically to California’s water resources and flood risk. In the Sierra Nevada, approximately half of cool-season precipitation is derived from a small proportion of storms classified as atmospheric rivers (ARs). The frequency and intensity of ARs are highly variable from year to year and unreliable climate teleconnections limit forecasting. However, previous research provides intriguing evidence of cycles with biennial (2.2 years) and decadal (10–20 years) periodicities in Sierra Nevada cool-season precipitation, suggesting it is not purely stochastic. To identify the source of this cyclicity, we decompose daily precipitation records (1949–2022) into contributions from ARs versus non-ARs, as well as into variations in frequency and intensity. We find that the biennial and decadal spectral peaks in Sierra Nevada precipitation totals are entirely due to precipitation delivered by ARs, and primarily due to variations in the frequency of days with AR precipitation. While total non-AR precipitation correlates with sea surface temperature (SST) and atmospheric pressure patterns associated with the El Niño–Southern Oscillation, AR precipitation shows no consistent remote teleconnections at any periodicity. Supporting this finding, atmospheric simulations forced by observed SSTs do not reproduce the biennial or decadal precipitation variations identified in observations. These results, combined with the lack of long-term stable cycles in previously published tree-ring reconstructions, suggest that the observed biennial and decadal quasi-cyclicity in Sierra Nevada precipitation is unreliable as a forecasting tool.

Significance Statement
In California’s Sierra Nevada, where most of the state’s above-ground water resources originate, cool-season precipitation totals exhibited year-to-year and decadal cyclicity over the past century. Long-range forecasts are notoriously unskillful in this region, so nonrandom cycles would be intriguing to water managers challenged to simultaneously minimize flood and drought risk. Over 1949–2022, precipitation cycles were driven by variations in the number of atmospheric river (AR) storms per year even though ARs account for just half of total precipitation. These findings bring us a step closer to understanding the causes of precipitation cyclicity, but we find no evidence that the cycles were underpinned by larger-scale ocean–atmosphere circulations so we caution against relying on continued cycles into the future.