bluuebunny/crossref_metadata_2025 huggingface dataset:
CircZmMED16 delays plant flowering by negatively regulating starch content through its binding to ZmAPS1
Authors: Tang Xin , Feng Xiaoju , Xu Yang , Yang Bo , Wang Yi , Zhou Yang , Wang Qi , Mao Yan , Xie Wubing , Liu Tianhong , Tang Qi , Liu Yaxi , Wang Yao , Xu Jie , Lu Yanli
Published: January 2025

Circular RNAs (circRNAs), a type of head‐to‐tail closed RNA molecules, have been implicated in various aspects of plant development and stress responses through transcriptome sequencing; however, the precise functional roles of circRNAs in plants remain poorly understood. In this study, we identified a highly expressed circular RNA, circZmMED16, derived from exon 8 of the mediator complex subunit 16 (ZmMED16) across different maize (Zea mays L.) inbred lines using circRNA‐seq analysis. This circRNA is predominantly expressed in maize tassels and functions in the cytoplasm. Overexpression of circZmMED16 resulted in increased expression of ZmMED16/AtMED16 and delayed flowering in both maize and Arabidopsis thaliana, compared with that in wild‐type plants. In contrast, overexpression of the parent gene ZmMED16 did not alter the flowering time of transgenic plants in Arabidopsis, suggesting that circZmMED16 plays a specific role in regulating flowering, distinct from that of linear ZmMED16. To further understand the mechanisms underlying the regulation of flowering time by circZmMED16, we performed RNA pull‐down, dual‐luciferase, RNA interference (RNAi), and ribonuclease protection assays (RPA). These results indicate that circZmMED16 interacts with small subunit 1 of ADP‐glucose pyrophosphorylase (APS1) mRNA in both maize and Arabidopsis. The knockdown of circZmMED16 increased the expression of ZmAPS1, whereas the overexpression of circZmMED16 led to the downregulation of ZmAPS1 RNA and protein. By affecting ZmAPS1 expression, circZmMED16 reduced ADP‐glucose pyrophosphorylase (AGPase) activity and led to delayed flowering. These results revealed a novel regulatory mechanism for circRNAs in flowering time and shed light on their functional and regulatory roles in plants.
Forecasting Solar Energy: Leveraging Artificial Intelligence and Machine Learning for Sustainable Energy Solutions
Authors: Saadati Taraneh , Barutcu Burak
Published: January 2025

Integrating solar energy into power grids is essential for advancing a low‐carbon economy, but accurate forecasting remains challenging due to solar output variability. This study comprehensively reviews solar energy forecasting models, focusing on how Artificial Intelligence (AI) and Machine Learning (ML) enhance forecast accuracy. It examines the current landscape of solar forecasting, identifies limitations in existing models, and underscores the need for more adaptable approaches. The primary goals are to analyze the evolution of AI/ML‐based models, assess their strengths and weaknesses, and propose a structured methodology for selecting and implementing AI/ML models tailored to solar power forecasting. Through comparative analysis, the study evaluates individual and hybrid models across different forecasting scenarios, identifying under‐explored research areas. The findings indicate significant improvements in prediction accuracy through AI/ML advancements, aiding grid management and supporting the low‐carbon transition. Ensemble methods, deep learning techniques, and hybrid models show great promise in enhancing reliability. Combining diverse forecasting approaches with advanced AI/ML techniques results in more reliable solar forecasts. The study suggests that improving model accuracy through these integrated methods offers substantial opportunities for further research, contributing to global sustainability efforts, particularly UN SDGs 7 and 13, and promoting economic growth with minimal environmental impact.
Larger Perfusion Mismatch Volume Is Associated With Longer Hospital Length of Stay in Medium Vessel Occlusion Stroke
Authors: Mei Janet , Salim Hamza Adel , Lakhani Dhairya A. , Balar Aneri , Vagal Vaibhav , Koneru Manisha , Wolman Dylan , Xu Risheng , Urrutia Victor , Marsh Elisabeth Breese , Pulli Benjamin , Hoseinyazdi Meisam , Luna Licia , Deng Francis , Hyson Nathan Z. , Bahouth Mona , Dmytriw Adam A. , Guenego Adrien , Albers Gregory W , Lu Hanzhang , Nael Kambiz , Hillis Argye E. , Llinas Raf , Wintermark Max , Faizy Tobias D. , Heit Jeremy J. , Yedavalli Vivek
Published: January 2025

Background and purpose

Prolonged length of stay (LOS) following a stroke is associated with unfavorable clinical outcomes. Factors predicting LOS in medium vessel occlusion (MeVO), impacting up to 40% of acute ischemic stroke (AIS) cases, remain underexplored. This study aims to investigate the predictors of LOS in AIS‐MeVO.

Methods

We conducted a retrospective analysis of prospectively maintained stroke databases, comprising AIS cases with MeVO in the anterior circulation, assessed by adequate CT perfusion (CTP). Baseline and clinical data were obtained from electronic health records. Alberta Stroke Program Early CT Scores (ASPECTS) were calculated from non‐contrast head CT. The perfusion mismatch volume (time to maximum > 6 s minus relative cerebral blood flow <30%) volume was reported from CTP. Multiple regression was employed to examine the relationship between baseline parameters and hospital LOS.

Results

A total of 133 patients (median age 71 [interquartile range 63–80] years, 59.4% females) were included in the study cohort. The perfusion mismatch volume significantly positively correlated with LOS (r = 0.264, p = 0.004). After adjusting for age, sex, hypertension, diabetes, prior stroke or transient ischemic attack, admission NIHSS, ASPECTS, Tan score, intravenous thrombolysis, mechanical thrombectomy (MT), and hemorrhagic transformation, a larger mismatch volume remained independently associated with longer hospital stays (β = 0.209, 95% confidence interval [CI] 0.006–0.412, p = 0.045). Additional significant determinants of longer hospital stay included admission NIHSS (β = 0.250, 95% CI: 0.060–0.440, p = 0.010) and MT (β = 0.208, 95% CI: 0.006–0.410, p = 0.044). Among patients who underwent MT (n = 83), multiple regression analysis incorporating both perfusion mismatch volume and admission NIHSS revealed that perfusion mismatch volume remained independently associated with LOS (β = 0.248, 95% CI: 0.019–0.471, p = 0.033), while admission NIHSS did not retain significance (β = 0.208, 95% CI: 0.019–0.433, p = 0.071).

Conclusions

In our cohort of AIS patients with MeVO in the anterior circulation, and particularly in those who underwent MT, the perfusion mismatch volume serves as an independent predictor of LOS. These findings offer critical valuable insights in clinical assessments and decision‐making protocols of MT in AIS‐MeVO.
Pimobendan oral solution is bioequivalent to pimobendan chewable tablets in beagle dogs
Authors: Kuhlmann Olaf , Markert Michael
Published: January 2025

Background

Myxomatous mitral valve disease (MMVD) is frequently diagnosed in small breed dogs. Pimobendan oral solution has been developed to improve dosing accuracy in small and toy breed dogs.

Hypothesis/Objectives

Demonstrate bioequivalence of pimobendan oral solution with pimobendan chewable tablets using a pharmacokinetic and a pharmacodynamic study in healthy purpose bred dogs.

Animals

In the pharmacokinetic study, 24 beagle dogs were dosed in a 4‐period crossover design. In the pharmacodynamic study, 4 mongrel and 2 beagle dogs implanted with telemetry probes were included in a 2‐way crossover design.

Methods

Both studies were designed as prospective, randomized crossover trials. Dogs were given single doses of 5 mg/dog of either formulation followed by serial blood sampling for determination of pimobendan and O‐desmethyl‐pimobendan (ODMP; main metabolite). Because of high variability in the pharmacokinetics, the reference scaled average bioequivalence (RSABE) method was applied. For the pharmacodynamic study, animals were dosed with 0.25 mg/kg of either formulation. Baseline corrected left ventricular maximal pressure (LVdP/dtmax) and heart rate were recorded continuously and compared with a predefined bioequivalence threshold.

Results

Pimobendan was verified as a high variability drug. Based on the RSABE method, both formulations were bioequivalent. Pharmacodynamic results supported bioequivalence.

Conclusions and Clinical Importance

The novel oral solution of pimobendan was found to be bioequivalent, both applying the Food and Drug Administration (FDA) supported RSABE method and based on pharmacodynamic data. Thus, the novel liquid formulation can be used to facilitate accurate dosing of small and toy breed dogs.
Effect of the Duty‐Free and Quota‐Free Market Access Schemes for Least Developed Countries on Income Inequality and Poverty
Authors: Gnangnon Sèna Kimm
Published: January 2025

This paper has examined whether the Duty‐Free and Quota‐Free (DFQF) market access preference schemes provided by Members of the World Trade Organization (WTO) to Least developed countries (LDCs) have been instrumental in reducing income inequality and poverty in these countries. The analysis has used the entropy balancing method over an unbalanced panel dataset of 36 LDCs (treatment group) and 19 countries in the control group, with data spanning the period 1997–2018. The feasible generalized least squares, the within fixed effects and the Seemingly Unrelated Regression estimators have been employed to address empirically the question. The analysis has established that the DFQF schemes have genuinely been instrumental in reducing income inequality and poverty in LDCs, including to a greater extent in non‐African LDCs than in African LDCs. These findings confirm the importance of the DFQF schemes for LDCs.
Collections overlooked: The Chinese ethnic minority collections in an Asian Cold War context at the Department of Anthropology, the Chinese University of Hong Kong
Authors: Ao Chon Hei
Published: January 2025

This article examines the geopolitical influences on the making of the Chinese ethnic minority ethnographic collections at the Department of Anthropology (DOA), the Chinese University of Hong Kong (CUHK) during the Cold War period. These overlooked collections originated from two Taiwanese department founders, Chiao Chien, and Hsieh Jiann, who used Hong Kong as a node to conduct Chinese ethnic minority studies in the 1980s. After analyzing the DOA's Chinese ethnic minority collections, archives, and virtual museum data, and conducting semi‐structured interviews with DOA members, the study postulates why the collections have been overlooked and discloses the collections' association with the Cold War. This article contributes to understanding the origin of an East Asian anthropology department with its understudied collections in an Asian Cold War context and offers a paradigm of “anthropology of anthropology departments” to examine the departmental history from a collections‐based perspective.
Auditing Cause of Death Reporting to Australia and New Zealand's Dialysis and Transplant Registry: A Retrospective Cohort Study
Authors: Tun Ismail Alia N. , Chavan Nehal , Au Eric H. K. , So Sarah
Published: January 2025

Aim

National data registries provide a valuable source of data for epidemiological research but may be subject to inaccuracies. Whilst studies have compared agreement between cause of death (COD) data from Australia and New Zealand's dialysis and transplant registry (ANZDATA) to other databases, no studies have manually compared agreement with electronic medical records (EMR). This study aimed to assess the agreement between COD for dialysis patients in the Western Sydney renal service according to ANZDATA and EMR.

Methods

We conducted a retrospective cohort study on dialysis patients from the Western Renal Service who died between January 1, 2016 and July 31, 2022, inclusive. We matched ANZDATA patient records to our service's EMR, extracted data on COD from EMR and coded COD according to ANZDATA's categorisation system. Agreement between COD from EMR and ANZDATA was assessed using kappa statistics.

Results

There were 709 deaths in the study period. 449 (63.3%) were male and 260 (36.7%) were female. Of the 539 patients with available records, the most common COD categories were cardiovascular (201, 37%) and infection (154, 29%). There was poor agreement between individual COD from EMR and ANZDATA (kappa of 0.39). However, this improved when comparing broader COD categories (kappa of 0.53). Subgroup analysis showed no difference in agreement between males and females or patients who died between 2016–2018 and 2019–2022.

Conclusion

There is poor agreement between ANZDATA and EMR for individual COD. However, agreement improved to moderate using broader categories of COD, suggesting higher accuracy when utilising registry COD data for epidemiological analysis.
Association between 24‐hour movement behaviors and adiposity in children and adolescents: A compositional data meta‐analysis
Authors: Bourke Matthew , Harrison Zoe , Fortnum Kathryn , Thomas George , O'Flaherty Martin , Mulcahy Samantha K. , Gomersall Sjaan R. , Alsop Tahlia , Trost Stewart G. , Koplin Jennifer J. , Bruijns Brianne A. , Phillips Sophie M. , Vanderloo Leigh M. , Tucker Patricia , Hesketh Kylie D. , Kwan Matthew Y. W. , Cairney John
Published: January 2025

Purpose

To quantitatively synthesize published evidence on the association between 24‐hour movement behavior composition with adiposity in children and adolescents aged 3–18 years.

Methods

Systematic literature searches were conducted in five electronic databases to identify papers published between January 2015 and January 2024. A machine learning‐assisted systematic review was conducted to identify studies applying compositional data analysis to examine the association between 24‐hour movement behaviors and adiposity in children and youth. Random effect meta‐analyses were estimated to examine the relative association between each component of the 24‐hour movement behavior composition and body mass index z‐score (zBMI), waist circumference, fat mass percentage, and fat mass index (FMI).

Results

A total of 16 studies reporting on 15,230 children and youth were included in the review. Most studies reported on zBMI (k = 14), followed by waist circumference (k = 5), body fat percentage (k = 3), and FMI (k = 2). Spending more time sleeping and engaged in moderate‐to‐vigorous intensity physical activity (MVPA) relative to other behaviors was associated with lower adiposity, while spending more time sedentary and engaged in light‐intensity physical activity was associated with higher adiposity.

Conclusion

These results provide support for most recommendations of the 24‐hour movement behavior guidelines, including getting an adequate amount of sleep, limiting sedentary time, and engaging in MVPA, to improve adiposity outcomes.
A comparison of MRI and intraoperative measurements to determine interspinous spacer device size
Authors: Nelson Charles , Liao Chuanhong , Malik Tariq
Published: January 2025

Purpose

To determine whether preoperative magnetic resonance imaging (MRI) can reliably determine intraoperative measurements in the Vertiflex Interspinous Spacer (ISS) procedure.

Methods

Patients who underwent Vertiflex ISS with Lumbar Spinal Stenosis (LSS) and a preoperative MRI available in picture archiving and communication system (PACS) between January 2013 to February 2023 were identified retrospectively from the University of Chicago Medical Center Database. An experienced board‐certified pain specialist and well‐trained 2nd‐year medical student independently performed measurements of the interspinous space where Vertiflex ISSs of various sizes are inserted. MRI measurements were taken blinded to intraoperative measurement and ISS implant size used in the procedure. Pearson's correlation, paired T‐test, intraclass correlation coefficients (ICC), absolute agreement, and 2‐way random effects model were used to determine the relationships between MRI, intraoperative measurement, and ISS size.

Results

A total of 79 patients who underwent the Vertiflex ISS procedure were included in the study. Median Vertiflex ISS size was 10 mm (10–12), mean intraoperative measurement was 11.40 mm (±1.23), and mean MRI measurement was 11.24 mm (±1.44). Mean differences were not significant in intraoperative and MRI measurements (p = 0.271). Pearson's correlation between ISS size and intraoperative measurement was 0.807 (p < 0.001), representing the current best practice model. Pearson's correlation was 0.668 (p < 0.001) between MRI measurement and ISS size and 0.542 (p < 0.001) between MRI and intraoperative measurement. ICC showed good agreement and moderate reliability (0.698) between intraoperative and MRI measurements. Observer interrater ICC agreement of the MRI interspinous space measurement was 0.95 (p < 0.001).

Conclusions

Measuring interspinous space on MRI yielded, on average, a value smaller than the intraoperative measurement in Vertiflex ISS procedures, but the mean differences were not significant. Good agreement and moderate reliability were found between observer MRI and surgeon intraoperative measurements, suggesting MRI can evaluate the intraoperative space for the Vertiflex ISS procedure. Preoperative MRI measurement may help decrease complications by aiding in surgical decision‐making through providing a reference for intraoperative measurements. Further prospective study is necessary to determine if preoperative MRI measurement can predict and potentially replace the need for intraoperative measurement.
Phenotypic Plasticity of Grain Size‐Related Traits in Main‐Crop and Ratoon Rice
Authors: Zhao Qiong , Wang Tian , Pei Fa‐Jing , Chen Ying , Chang Xiao‐Yu , Mi Jia‐Ming , Zhang Yuan‐Ming
Published: January 2025

Grain size and weight of main‐crop are larger than those of ratoon rice, indicating that increasing grain size and weight of ratoon rice is an effective way to increase rice yield. Thus, grain length (GL), grain width (GW), and thousand‐grain weight (TGW) of main‐crop and ratoon rice in 159 indica rice accessions were used to associate with 2 017 495 SNP markers to detect quantitative trait nucleotides (QTNs) and their interactions with meteorological factors (QMIs), such as temperature and sunlight hours. Around 59 QMIs identified for temperature and 80 QMIs identified for sunlight hours, first, candidate gene LOC_Os02g40840 for GW and LOC_Os04g45480 for TGW were found to interact with temperature, while LOC_Os01g19970 for GL, LOC_Os02g39360 and LOC_Os07g05720 for GW, and LOC_Os07g49460 for TGW were found to interact with sunlight hours. Based on the results of previous studies, LOC_Os04g45480 exhibits high expression levels in the main‐crop under higher temperature, thereby enhancing the accumulation of the auxin receptor TIR1. TIR1, in turn, promotes starch accumulation in the endosperm, explaining why TGW is heavier in main‐crop than in ratoon rice. Finally, the analysis of best linear unbiased prediction values revealed 1 (LOC_Os08g10350) and 3 (LOC_Os02g50860, LOC_Os08g28680, and LOC_Os08g29160) candidate genes responsible for GW and TGW, respectively. In addition, we discussed the four available and six unavailable candidate genes in ratoon rice breeding. This study provides new method and genes for studying differences in grain size‐related traits between main‐crop and ratoon rice.
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

It 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

Nitrogen (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

Introduction

The 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.

Methods

A 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.

Results

Clinical 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%.

Conclusion

The 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

A 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.
Direct optical absorption detection of metal vapor in mechanically stimulated gas emission
Authors: Kamiyama Brandon E. , Glumac Nick G.
Published: January 2025

Optical absorption spectroscopy has been used to detect neutral atomic emission from surfaces undergoing deformation at high strain rates due to shock waves induced by high explosive detonation. Magnesium and zinc alloys are investigated, and four atomic species Mg, Zn, Pb, and Sn are detected in single-shot absorption spectra. This technique offers the potential to study mechanically stimulated gas emission with quantification of the spatial and temporal variations of the emission event.
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

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

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

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

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.
Enumeration of Maximum Matchings of Graphs
Authors: Wu Tingzeng , Zeng Xiaolin , Lü Huazhong
Published: January 2025

Counting maximum matchings in a graph is of great interest in statistical mechanics, solid-state chemistry, theoretical computer science, mathematics, among other disciplines. However, it is a challengeable problem to explicitly determine the number of maximum matchings of general graphs. In this paper, using Gallai–Edmonds structure theorem, we derive a computing formula for the number of maximum matchings in a graph. According to the formula, we obtain an algorithm to enumerate maximum matchings of a graph. In particular, the formula implies that computing the number of maximum matchings of a graph is converted to computing the number of perfect matchings of some induced subgraphs of the graph.
QATCH: Automatic Evaluation of SQL-centric Tasks on Proprietary Data
Authors: Papicchio Simone , Papotti Paolo , Cagliero Luca
Published: January 2025

Tabular Representation Learning (TRL) and Large Language Models (LLMs) have become established for tackling Question Answering (QA) and Semantic Parsing (SP) tasks on tabular data. State-of-the-art models are pre-trained and evaluated on large open-domain datasets. However, the performance on existing QA and SP benchmarks is not necessarily representative of that achieved on proprietary data as the characteristics of the input and the complexity of the posed queries show high variability. To tackle this challenge, our goal is to allow end-users to evaluate TRL and LLM performance on their own proprietary data. We present
QATCH
(Query-Aided TRL Checklist), a toolbox to automatically generate a testing checklist tailored to QA and SP. QATCH provides a testing suite highlighting models’ strengths and weaknesses on relational tables unseen at training time. The proposed toolbox relies on a SQL query generator that crafts tests of varying types and complexity including, amongst others, tests on null values, projection, selections, joins, group by, and having clauses. QATCH also supports a set of general cross-task performance metrics providing more insights into SQL-related model capabilities than currently used metrics. The empirical results, achieved by state-of-the-art TRL models and LLMs, show substantial performance
differences (1) between existing benchmarks and proprietary data, (2) across queries of different 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.
Probabilistic Temporal Reasoning using Superposition Semantics
Authors: Maggi Fabrizio M. , Montali Marco , Peñaloza Rafael
Published: January 2025

Temporal logics over finite traces have recently seen wide application in a number of areas, from business process modelling, monitoring, and mining to planning and decision making. However, real-life dynamic systems contain a degree of uncertainty which cannot be handled with classical logics. We thus propose a new probabilistic temporal logic over finite traces using superposition semantics, where all possible evolutions are possible, until observed. We study the properties of the logic and provide automata-based mechanisms for deriving probabilistic inferences from its formulas. We then study a fragment of the logic with better computational properties. Notably, formulas in this fragment can be discovered from event log data using off-the-shelf existing declarative process discovery techniques.
A Scientist in Russia: My Story
Authors: Stishov Sergei M.
Published: January 2025

Born on December 12, 1937, I remember the first bombing of Moscow by the Germans in 1941. My schooling began in 1944, and I soon became interested in chemistry, setting up a kind of makeshift chemical laboratory behind a high cupboard in my house. I enrolled in Moscow University in 1955 and published my first scientific paper in 1959. After entering graduate school in 1960, I produced dense silica with a rutile structure, a natural analog of which was later named stishovite. I received my doctorate in 1961 and got a job at the Institute of Crystallography in 1962, where I worked until 1993. My first visit to the West was in 1976. I was became a Fairchild Distinguished Scholar at Caltech in 1989–1990 and a member of the USSR Academy of Sciences in 1990. I was a Miller Professor at the University of California, Berkeley and an Orson Anderson Distinguished Scholar at Los Alamos National Laboratory. From 1993 to 2022, I was director of the Institute for High Pressure Physics. During that time, I was awarded the P. Bridgman Gold Medal and the Gold Medal of P. Kapitsa.
CT, MRI, and FDG PET/CT in the Assessment of Lymph Node Involvement in Pediatric Hodgkin Lymphoma: An Expert Consensus Definition by an International Collaboration on Staging Evaluation and Response Criteria Harmonization for Children, Adolescent, and Young Adult Hodgkin Lymphoma (SEARCH for CAYAHL)
Authors: Stoevesandt Dietrich , Steglich Jonas , Bartelt Jörg M. , Kurch Lars , McCarten Kathleen M. , Flerlage Jamie E. , Georgi Thomas W. , Mauz-Körholz Christine , Cho Steve Y. , Körholz Dieter , Kluge Regine , Kelly Kara M. , Pelz Tanja , Vordermark Dirk , Hoppe Bradford S. , Dieckmann Karin , Voss Stephan D.
Published: January 2025

An international consensus definition of lymph node involvement at CT, MRI, and fluorodeoxyglucose PET/CT in pediatric Hodgkin lymphoma allows more robust comparisons between clinical trials, particularly those that include involved node or involved site radiation therapy.
Impact of Multimodal Prompt Elements on Diagnostic Performance of GPT-4V in Challenging Brain MRI Cases
Authors: Schramm Severin , Preis Silas , Metz Marie-Christin , Jung Kirsten , Schmitz-Koep Benita , Zimmer Claus , Wiestler Benedikt , Hedderich Dennis M. , Kim Su Hwan
Published: January 2025

Textual descriptions of radiologic image findings play a critical role in GPT-4 with vision–based differential diagnosis, underlining the importance of radiologist experts even in multimodal large language models.
Contrast-enhanced US of High-Risk Indeterminate Focal Liver Observations Categorized as LR-4 or LR-M at CT/MRI
Authors: Lyshchik Andrej , Kuon Yeng Escalante Cristina , Siu Xiao Tania , Piscaglia Fabio , Kono Yuko , Medellin-Kowalewski Alexandra , Rodgers Shuchi K. , Planz Virginia , Kamaya Aya , Fetzer David T. , Berzigotti Annalisa , Radu Iuliana-Pompilia , Sidhu Paul S. , Wessner Corinne E. , Bradigan Kristen , Eisenbrey John R. , Forsberg Flemming , Wilson Stephanie R. ,   for the CEUS LI-RADS Trial Group, Yusuf Gibran T. , Suddle Abid , Rafailidis Vasileios D. , Mulazzani Lorenzo , Granito Alessandro , Terzi Eleonora , Forgione Antonella , Giamperoli Alice , Stefanini Bernardo , Finch Lisa , Singal Amit
Published: January 2025

Contrast-enhanced US Liver Imaging Reporting and Data System (LI-RADS) could resolve some indeterminate liver observations (categorized as LR-4 and LR-M at CT or MRI), having a particularly high clinical effect for observations measuring at least 20 mm.
Anodic Dissolution of the Aluminum Current Collector in Lithium-ion Cells with LiFSI, LiPF6, and LiBF4
Authors: Scheer Kilian M. , Tulloch Meredith , Hamam Ines , Abraham Jeffin James , Johnson Michel B. , Metzger Michael
Published: January 2025

Anodic dissolution (often referred to as corrosion) of the positive electrode aluminum current collector can be a limiting factor for the performance, lifetime, and safety of lithium-ion cells. The superior performance of lithium bis(fluorosulfonyl)imide (LiFSI) salt, especially in high-temperature lithium-ion cells, motivates this study of the Al current collector corrosion in electrolytes with and without LiFSI. With pure lithium hexafluorophosphate (LiPF6) and lithium tetrafluoroborate (LiBF4) or LiFSI blends of these salts, only minor Al corrosion currents were found in cyclic voltammetry (CV), open-circuit voltage storage, cycling experiments, and ultra-high precision coulometry; however severe corrosion was found with pure LiFSI. Importantly, there is a discrepancy between the results of CV experiments and actual NMC532/graphite pouch cell cycling in terms of the magnitudes and onset voltages of Al corrosion. For the latter, severe anodic dissolution was only observed when using LiFSI above 4.2 V, but for the former severe corrosion currents were already observed at 3.8 V vs Li+/Li when using bare Al foil in CV experiments. This discrepancy is likely due to proton scavenging by H+/Li+ exchange and/or solvent-mediated hydrogenation of layered oxide positive electrode materials - two mechanisms that are absent in cells with bare Al electrodes.
Secondhand vape exposure regulation of CFTR and immune function in cystic fibrosis
Authors: Wisniewski Benjamin L. , Shrestha Mahesh , Bojja Dinesh , Shrestha Chandra L. , Lee Chris S. , Ozuna Hazel , Rayner Rachael E. , Bai Shasha , Cormet-Boyaka Estelle , Reynolds Susan D. , Kopp Benjamin T.
Published: January 2025

New research reveals that e-cigarettes pose a serious health risk for individuals with cystic fibrosis (CF). Exposure to electronic cigarette (e-cig) vapors decreases CF transmembrane conductance regulator (CFTR) function and undermines the effectiveness of CFTR modulators, potentially worsening inflammation and metabolic responses. This highlights an urgent need for awareness around e-cig use, especially among caregivers and peers of those with CF. E-cigarettes may further complicate the management of this chronic lung disease.
Leveraging Attention Mechanisms in Neural Networks for High‐Order Accuracy in Particle‐in‐Cell Simulations
Authors: Chen Jian-Nan , Zhang Jun-Jie
Published: January 2025

This paper introduces a novel approach to enhance the accuracy of charge density calculations in particle‐in‐cell (PIC) simulations by leveraging attention mechanisms in neural networks (NNs). We propose a three‐network architecture comprising a 1st‐order‐pre‐trainer, a 2nd‐order‐improver, and a discriminator network. The 1st‐order‐pre‐trainer is initially trained on a large dataset to predict charge densities from particle positions and charges. Subsequently, it is fine‐tuned with the 2nd‐order‐improver and discriminator network using a smaller dataset to achieve near 2nd‐order accuracy. Our approach substitutes the traditional particle interpolation process in JefiPIC with a meticulously trained NN. The results demonstrate that PIC simulations enhanced by NNs can simulate plasmas and electromagnetic (EM) fields with significantly enhanced accuracy, achieving an absolute accuracy improvement exceeding 10% when compared to a 1st‐order PIC simulator and a relative accuracy improvement of over 50% in comparison to other direct training techniques. Furthermore, our method has the potential to diminish the reliance on acquiring real labels, which are often difficult to observe. This work highlights the potential of integrating artificial intelligence (AI) techniques to improve the precision and efficiency of PIC simulations, paving the way for future advancements in plasma and nuclear physics research.