bluuebunny/crossref_metadata_2025_split huggingface dataset:
The molecular mechanism of transforming red light signal to (E)‐β‐caryophyllene biosynthesis in Arabidopsis
Authors: Xu Chuanjia , Wang Xin , Mehraliyeva Malakkhanim , Sun Jia , Chen Fangfang , Li Changfu , Xu Zhengqin , Tang Nan , Zhang Yansheng 
Published: January 2025

AbstractIt is known that red light irradiation enhances the biosynthesis of (E)‐β‐caryophyllene in plants. However, the underlying mechanism connecting red light to (E)‐β‐caryophyllene biosynthesis remains elusive. This study reveals a molecular cascade involving the phyB‐PIF4‐MYC2 module, which regulates (E)‐β‐caryophyllene biosynthesis in response to the red light signal in Arabidopsis thaliana. In this module, phyB positively regulates (E)‐β‐caryophyllene biosynthesis under red light, whereas PIF4 negatively regulates it; both regulations require the involvement of MYC2, a transcription factor that can bind directly to the promoter of the TPS21 gene which encodes (E)‐β‐caryophyllene synthase. Importantly, protein–protein and protein‐DNA interaction assays show that PIF4 reduces the binding affinity of MYC2 to the TPS21 promoter through direct interaction with MYC2. We propose that the phyB‐PIF4‐MYC2 module represents a universal mechanism linking red light to sesquiterpene biosynthesis in plants.
Evolutionary dynamics of nitrate uptake, assimilation, and signalling in plants: adapting to a changing environment
Authors: Zhang Xiaojia , Bai Shufeng , Min Hui , Cui Yuxuan , Sun Yibo , Feng Yulong 
Published: January 2025

AbstractNitrogen (N) is a crucial macronutrient for plant growth, with nitrate as a primary inorganic N source for most plants. Beyond its role as a nutrient, nitrate also functions as a signalling molecule, influencing plant morphogenetic development. While nitrate utilization and signalling mechanisms have been extensively studied in model plants, the origin, evolution, and diversification of core components in nitrate uptake, assimilation, and signalling remain largely unexplored. In our investigation, we discovered that deep sea algae living in low nitrate conditions developed a high‐affinity transport system (HATS) for nitrate uptake and a pathway of nitrate primary assimilation (NR‐NiR‐GS‐GOGAT). In contrast, low‐affinity transport systems (LATS) and the plastid GS originated from the ancestors of land and seed plants, respectively. These adaptations facilitated amino acid acquisition as plants conquered terrestrial environments. Furthermore, the intricate nitrate signalling, relying on NRT1.1 and NLP7, evolved stepwise, potentially establishing systematic regulation in bryophytes for self‐regulation under complex terrestrial nitrate environments. As plants underwent terrestrialization, they underwent adaptive changes to thrive in dynamic nitrate environments, continually enhancing their nitrate uptake, assimilation, and signal transduction abilities.
The effect of the COVID‐19 pandemic and school closures on self‐harming and suicidal behaviors in adolescents: A comprehensive meta‐analysis
Authors: Vardi Ilor , Hamdan Sami , Zalsman Gil , Stukalin Yelena 
Published: January 2025

AbstractIntroductionThe COVID‐19 pandemic has significantly affected adolescents' mental health, raising concerns about the potential increase in self‐harming and suicidal behaviors (SIB). This study aimed to evaluate the pandemic's impact on SIB among adolescents and explore the effects of school closures and psychiatric vulnerabilities to inform future interventions.MethodsA systematic review and meta‐analysis were conducted using PubMed, resulting in 420 studies, of which 36 studies (comprising 53 samples) met the inclusion criteria, encompassing 1,754,106 adolescents. Effect sizes were calculated using proportion effect size. Heterogeneity across studies was assessed using Q‐statistics and I², while Egger's test was applied to evaluate publication bias. Differences between clinical and community samples, as well as the influence of psychiatric symptoms or disorders, were examined.ResultsClinical samples demonstrated higher rates of SIB compared to community samples, with adolescents having psychiatric symptoms or disorders being more vulnerable. Overall, the pandemic was associated with a decline in SIB rates compared to pre‐pandemic levels. Suicidal ideation decreased by 4.14% in combined samples and by 7.13% in community samples. Self‐harm rates fell by 5.38% and 6.62% in combined and community samples, respectively. In contrast, clinical samples showed a distinct trend, with suicidal ideation decreasing by 29.39%, while self‐harm rates increased by 32.51% and suicide attempts rose by 22.41%.ConclusionThe COVID‐19 pandemic's impact on adolescents' SIB varied significantly across population types and levels of psychiatric vulnerability. While general declines were observed, the pronounced increases in self‐harm and suicide attempts among clinical samples highlight the need for tailored mental health interventions. Addressing these disparities is essential for future mental health strategies and crisis preparedness.
A comparison of phylogenomic inference pipelines for low‐coverage whole‐genome sequencing in Formica ants
Authors: Zhang Junxia , Lin Long , Mu Yannan , Brelsford Alan , Purcell Jessica 
Published: January 2025

AbstractA rapid proliferation in the availability of whole genome sequences (WGS), often with relatively low read depth, offers an unprecedented opportunity for phylogenomic advances using publicly available data, but there are several key challenges in applying these data. Using low‐coverage WGS data for the ant species of Formica, we conducted detailed comparisons on two different analytical pipelines (reference‐based vs. de novo genome assembly), four types of datasets (5‐kbp‐window, ultra‐conserved element [UCE], single‐copy ortholog [BUSCO] and mitogenome), and a series of analytical procedures (e.g. concatenation vs. coalescent analyses) to identify which are robust to typical WGS data. The results show that at a shallow scale of phylogenetic relationships of closely related species 5‐kbp‐windows from the reference‐based pipeline and UCEs from the de novo assemblies are more successful than the BUSCOs in recovering informative markers for phylogenetic inference. Compared with concatenation analyses, coalescent analyses often resulted in disparate deeper relationships in the phylogeny. This study also uncovers evident mito‐nuclear discordance and demonstrates genome‐wide gene conflicts in phylogenetic signals, both pointing to possible incomplete lineage sorting and/or hybridization during the early, rapid radiation of Formica ants. Divergence dating analyses show that different types of data and analytical methods could result in inconsistent time estimates, highlighting the potential need for multiple approaches to better understand species divergence. The strengths and weaknesses of different analytical pipelines and strategies are discussed. Findings from this study provide valuable insights for large‐scale phylogenomic projects using WGS data.
FhaA plays a key role in mycobacterial polar elongation and asymmetric growth
Authors: Rossello Jessica , Rivera Bernardina , Anzibar Fialho Maximiliano , Augusto Ingrid , Gil Magdalena , Forrellad Marina Andrea , Bigi Fabiana , Rodríguez Taño Azalia , Urdániz Estefanía , Piuri Mariana , Miranda Kildare , Wehenkel Anne Marie , Alzari Pedro M. , Malacrida Leonel , Durán Rosario 
Published: January 2025

ABSTRACT

Mycobacteria, including pathogens like
Mycobacterium tuberculosis
, exhibit unique growth patterns and cell envelope structures that challenge our understanding of bacterial physiology. This study sheds light on FhaA, a conserved protein in
Mycobacteriales
, revealing its pivotal role in coordinating cell envelope biogenesis and asymmetric growth. The elucidation of the FhaA interactome in living mycobacterial cells reveals its participation in the protein network orchestrating cell envelope biogenesis and cell elongation/division. By manipulating FhaA levels, we uncovered its influence on cell morphology, cell envelope organization, and the localization of peptidoglycan biosynthesis machinery. Notably,
fhaA
deletion disrupted the characteristic asymmetric growth of mycobacteria, highlighting its importance in maintaining this distinctive feature. Our findings position FhaA as a key regulator in a complex protein network, orchestrating the asymmetric distribution and activity of cell envelope biosynthetic machinery. This work not only advances our understanding of mycobacterial growth mechanisms but also identifies FhaA as a potential target for future studies on cell envelope biogenesis and bacterial growth regulation. These insights into the fundamental biology of mycobacteria may pave the way for novel approaches to combat mycobacterial infections addressing the ongoing challenge of diseases like tuberculosis in global health.

IMPORTANCE

Mycobacterium tuberculosis
, the bacterium responsible for tuberculosis, remains a global health concern. Unlike most well-studied model bacilli, mycobacteria possess a distinctive and complex cell envelope, as well as an asymmetric polar growth mode. However, the proteins and mechanisms that drive cell asymmetric elongation in these bacteria are still not well understood. This study sheds light on the role of the protein FhaA in this process. Our findings demonstrate that FhaA localizes at the septum and asymmetrically to the poles, with a preference for the fast-growing pole. Furthermore, we showed that FhaA is essential for population heterogeneity and asymmetric polar elongation and plays a role in the precise subcellular localization of the cell wall biosynthesis machinery. Mycobacterial asymmetric elongation results in a physiologically heterogeneous bacterial population which is important for pathogenicity and response to antibiotics, stressing the relevance of identifying new factors involved in these still poorly characterized processes.
SLO co-opts host cell glycosphingolipids to access cholesterol-rich lipid rafts for enhanced pore formation and cytotoxicity
Authors: Sanduja Pooja , Schmieder Stefanie S. , Baddal Buket , Tian Songhai , Velarde Jorge J. , Lencer Wayne I. , Dong Min , Wessels Michael R. 
Published: January 2025

ABSTRACT

Streptolysin O (SLO) is a virulence determinant of group A
Streptococcus
(
S. pyogenes
), the agent of streptococcal sore throat and severe invasive infections. SLO is a member of a family of bacterial pore-forming toxins known as cholesterol-dependent cytolysins, which require cell membrane cholesterol for pore formation. While cholesterol is essential for cytolytic activity, accumulating data suggest that cell surface glycans may also participate in the binding of SLO and other cholesterol-dependent cytolysins to host cells. Here, we find that unbiased CRISPR screens for host susceptibility factors for SLO cytotoxicity identified genes encoding enzymes involved in the earliest steps of glycosphingolipid (GSL) biosynthesis. Targeted knockouts of these genes conferred relative resistance to SLO cytotoxicity in two independent human cell lines. Inactivation of
ugcg
, which codes for UDP-glucose ceramide glucosyltransferase, the enzyme catalyzing the first glycosylation step in GSL biosynthesis, reduced the clustering of SLO on the cell surface. This result suggests that binding to GSLs serves to cluster SLO molecules at lipid rafts where both GSLs and cholesterol are abundant. SLO clustering and susceptibility to SLO cytotoxicity were restored by reconstituting the GSL content of
ugcg
knockout cells with ganglioside GM1, but susceptibility to SLO cytotoxicity was not restored by a GM1 variant that lacks an oligosaccharide head group required for SLO binding, nor by a variant with a “kinked” acyl chain that prevents efficient packing of the ganglioside ceramide moiety with cholesterol. Thus, SLO appears to co-opt cell surface glycosphingolipids to gain access to lipid rafts for increased efficiency of pore formation and cytotoxicity.

IMPORTANCE

Group A
Streptococcus
is a global public health concern as it causes streptococcal sore throat and less common but potentially life-threatening invasive infections. Invasive infections have been associated with bacterial strains that produce large amounts of a secreted toxin, streptolysin O (SLO), which belongs to a family of pore-forming toxins produced by a variety of bacterial species. This study reveals that SLO binds to a class of molecules known as glycosphingolipids on the surface of human cells and that this interaction promotes efficient binding of SLO to cholesterol in the cell membrane and enhances pore formation. Understanding how SLO damages human cells provides new insight into streptococcal infection and may inform new approaches to treatment and prevention.
Draft genome sequence of
Streptomyces
sp. CC302I with non-canonical biosynthetic gene clusters for codon-readthrough activity
Authors: Trejo-Alarcon Luisa M. , Cruz-Morales Pablo , Licona-Cassani Cuauhtémoc 
Published: January 2025

ABSTRACT

Streptomyces
sp. CC302I was isolated from a highly oligothrophic environment. High-throughput screening shows high codon-readthrough activity for the isolate with no canonical biosynthetic gene cluster responsible. Here, we report the whole-genome assembly of
Streptomyces
sp. CC302I and a preliminary identification of biosynthetic gene clusters encoded in the genome.
Thermalization in Krylov basis
Authors: Alishahiha Mohsen , Vasli Mohammad Javad 
Published: January 2025

Abstract
We study thermalization in closed non-integrable quantum systems using the Krylov basis. We demonstrate that for thermalization to occur, the matrix representation of typical local operators in the Krylov basis should exhibit a specific tridiagonal form with all other elements in the matrix being exponentially small, reminiscent of the eigenstate thermalization hypothesis. Within this framework, we propose that the nature of thermalization, whether weak or strong, can be examined by the infinite time average of the Krylov complexity. Moreover, we analyze the variance of Lanczos coefficients as another probe for the nature of thermalization. One observes that although the variance of Lanczos coefficients may capture certain features of thermalization, it is not as effective as the infinite time average of complexity.
Primal Logic of Information
Authors: Gurevich Yuri , Blass Andreas 
Published: January 2025

Primal logic arose in access control; it has a remarkably efficient (linear time) decision procedure for its entailment problem. But primal logic is a general logic of information. In the realm of arbitrary items of information (infons), conjunction, disjunction, and implication may seem to correspond (set-theoretically) to union, intersection, and relative complementation. But, while infons are closed under union, they are not closed under intersection or relative complementation.
It turns out that there is a systematic transformation of propositional intuitionistic calculi to the original (propositional) primal calculi; we call it Flatting. We extend Flatting to quantifier rules, obtaining arguably the right quantified primal logic, QPL. The QPL entailment problem is exponential-time complete, but it is polynomial-time complete in the case, of importance to applications (at least to access control), where the number of quantifiers is bounded.
Clinical Diagnosis and Management Challenges of Harlequin Ichthyosis in a Preterm Neonate: A Case Report From Uganda
Authors: Turyasiima Munanura , Mohamed Djamila Magan , Yusuf Hamdi Mohamed , Nakalema Gloria , Akot Balbina Gillian , Kyoshabire Joan , Mutagamba Shabirih , Kimono Grace Gladys , Duca Jimmy Emmy , Makongwa Ibrahimu 
Published: January 2025

Introduction: Harlequin ichthyosis is a rare autosomal recessive genetic disorder resulting from mutations in the ABCA12 gene. It is marked by distinctive skin abnormalities, including armor‐like thickened scales separated by deep fissures. This condition is infrequently reported in the African population.Clinical Findings: This report presents the case of a preterm neonate, born at 28 weeks of gestation, exhibiting dysmorphic features and severe generalized hyperkeratosis. The defining skin abnormalities included deep fissures across the head and trunk, bilateral eyelid ectropion, eclabium, underdeveloped auricles, and limbs enveloped in thick hyperkeratotic plaques with constricting bands and hypoplastic digits.Diagnosis, Interventions, and Outcomes: The diagnosis of harlequin ichthyosis was established based on the characteristic clinical presentation. Supportive care included routine neonatal management and conservative treatment for prematurity‐related respiratory distress syndrome. However, specific therapies, such as systemic retinoids, could not be administered due to their unavailability in the clinical setting. Unfortunately, the neonate passed away on the fifth day of life due to respiratory complications.Conclusion: Harlequin ichthyosis remains associated with a high mortality rate, especially in resource‐limited settings. Contributing factors include inadequate prenatal diagnostic services, restricted access to essential treatments, and insufficient neonatal care infrastructure, all of which exacerbate poor outcomes in developing countries.
Identifying and Targeting Key Driver Genes for Collagen Production within the 11q13/14 Breast Cancer Amplicon
Authors: Araiza-Olivera Daniela , Prudnikova Tatiana Y. , Uribe-Alvarez Cristina , Cai Kathy Q. , Franco-Barraza Janusz , Dones Jesus M. , Raines Ronald T. , Chernoff Jonathan 
Published: January 2025

Abstract
Breast cancers of the Integrative Cluster 2 (IntClust-2) type, characterized by amplification of a small portion of chromosome 11, have a median survival of only 5 years. Several cancer-relevant genes occupy this portion of chromosome 11, and it is thought that overexpression of a combination of driver genes in this region is responsible for the poor outcome of women in this group. In this study, we used a gene editing method to knock out, one by one, each of the 198 genes that are located within the amplified region of chromosome 11 and determined how much each of these genes contributed to the survival of breast cancer cells. In addition to well-known drivers such as CCND1 and PAK1, we identified two different genes (SERPINH1 and P4HA3) that encode proteins involved in collagen synthesis and organization. Using both in vitro and in vivo functional analyses, we determined that P4HA3 and/or SERPINH1 provide a critical driver function for IntClust-2 basic processes, such as viability, proliferation, and migration. Inhibiting these enzymes via genetic or pharmacologic means reduced collagen synthesis and impeded oncogenic signaling transduction in cell culture models, and a small-molecule inhibitor of P4HA3 was effective in treating 11q13 tumor growth in an animal model. As collagen has a well-known association with tissue stiffness and aggressive forms of breast cancer, we believe that the two genes we identified provide an opportunity for a new therapeutic strategy in IntClust-2 breast cancers.
Implications: Breast cancers with 11q13/14 chromosomal amplifications may be vulnerable to inhibitors of collagen synthesis.
Deep Learning–Enabled Assessment of Right Ventricular Function Improves Prognostication After Transcatheter Edge-to-Edge Repair for Mitral Regurgitation
Authors: Lachmann Mark , Fortmeier Vera , Stolz Lukas , Tokodi Márton , Kovács Attila , Hesse Amelie , Leipert Antonia , Rippen Elena , Alvarez Covarrubias Héctor Alfonso , von Scheidt Moritz , Tervooren Jule , Roski Ferdinand , Fett Michelle , Gerçek Muhammed , Schuster Tibor , Harmsen Gerhard , Yuasa Shinsuke , Mayr N. Patrick , Kastrati Adnan , Schunkert Heribert , Joner Michael , Xhepa Erion , Laugwitz Karl-Ludwig , Hausleiter Jörg , Rudolph Volker , Trenkwalder Teresa 
Published: January 2025

BACKGROUND:
Right ventricular (RV) function has a well-established prognostic role in patients with severe mitral regurgitation (MR) undergoing transcatheter edge-to-edge repair (TEER) and is typically assessed using echocardiography-measured tricuspid annular plane systolic excursion. Recently, a deep learning model has been proposed that accurately predicts RV ejection fraction (RVEF) from 2-dimensional echocardiographic videos, with similar diagnostic accuracy as 3-dimensional imaging. This study aimed to evaluate the prognostic value of the deep learning–predicted RVEF values in patients with severe MR undergoing TEER.

METHODS:
This multicenter registry study analyzed the associations between the predicted RVEF values and 1-year mortality in patients with severe MR undergoing TEER. To predict RVEF, 2-dimensional apical 4-chamber view videos from preprocedural transthoracic echocardiographic studies were exported and processed by a rigorously validated deep learning model.

RESULTS:

Good-quality 2-dimensional apical 4-chamber view videos could be retrieved for 1154 patients undergoing TEER between 2017 and 2023. Survival at 1 year after TEER was 84.7%. The predicted RVEF values ranged from 26.6% to 64.0% and correlated only modestly with tricuspid annular plane systolic excursion (Pearson
R
=0.33;
P
<0.001). Importantly, predicted RVEF was superior to tricuspid annular plane systolic excursion levels in predicting 1-year mortality after TEER (area under the curve, 0.687 versus 0.625;
P
=0.029). Furthermore, Kaplan-Meier survival analysis revealed that patients with reduced RV function (n=723; defined as a predicted RVEF of <45%) had significantly worse 1-year survival rates than patients with preserved RV function (n=431; defined as a predicted RVEF of ≥45%; 80.3% [95% CI, 77.4%–83.3%] versus 92.1% [95% CI, 89.5%–94.7%]; hazard ratio for 1-year mortality, 2.67 [95% CI, 1.82–3.90];
P
<0.001).

CONCLUSIONS:
Deep learning–enabled assessment of RV function using standard 2-dimensional echocardiographic videos can refine the prognostication of patients with severe MR undergoing TEER. Thus, it can be used to screen for patients with RV dysfunction who might benefit from intensified follow-up care.