bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into ENSO Diversity from an Intermediate Coupled Model. Part II: Role of Nonlinear Dynamics and Stochastic Forcing
Authors: Geng Licheng , Jin Fei-Fei 
Published: August 2023

Abstract
In this study, we investigate how a single leading linear El Niño–Southern Oscillation (ENSO) mode, as studied in Part I, leads to the irregular coexistence of central Pacific (CP) and eastern Pacific (EP) ENSO, a phenomenon known as ENSO spatiotemporal diversity. This diversity is fundamentally generated by deterministic nonlinear pathways to chaos via the period-doubling route and, more prevailingly, the subharmonic resonance route with the presence of a seasonally varying basic state. When residing in the weakly nonlinear regime, the coupled system sustains a weak periodic oscillation with a mixed CP/EP pattern as captured by the linear ENSO mode. With a stronger nonlinearity effect, the ENSO behavior experiences a period-doubling bifurcation. The single ENSO orbit splits into coexisting CP-like and EP-like ENSO orbits. A sequence of period-doubling bifurcation results in an aperiodic oscillation featuring irregular CP and EP ENSO occurrences. The overlapping of subharmonic resonances between ENSO and the seasonal cycle allows this ENSO irregularity and diversity to be more readily excited. In the strongly nonlinear regime, the coupled system is dominated by regular EP ENSO. The deterministic ENSO spatiotemporal diversity is thus confined to a relatively narrow range corresponding to a moderately unstable ENSO mode. Stochastic forcing broadens this range and allows ENSO diversity to occur when the ENSO mode is weakly subcritical. A close relationship among a weakened mean zonal temperature gradient, stronger ENSO activity, and more (fewer) occurrences of EP (CP) ENSO is noted, indicating that ENSO–mean state interaction may yield ENSO regime modulations on the multidecadal time scale.
Multifunctional Smoke- and Gas-Suppressant Systems for Polyurethane Foams
Authors: Grayson S.J. , Hume J. , Smith D.A. 
Published: August 2023

Although many different smoke suppressants and fire retardants for polyurethane foams have been reported, these often increase the evolution of toxic gas on burning. Even where this is not so, as in the case of ‘char-formers’, on which we have reported previously, no previous claim has been made for a system which successfully combines suppression of both smoke and toxic gas.This paper shows that new, multifunctional additive systems comprising a char-forming smoke-and-toxic-gas (STG) suppressant together with a combustion-rate-reducing component and a char-stabilising component can lead to dramatic reductions in evolved toxic gases, particularly carbon monoxide, early in the burning process. As a result, substantial improvements in safety can result from the lengthening of escape times.
Development of clinical and magnetic resonance imaging-based radiomics nomograms for the differentiation of nodular fasciitis from soft tissue sarcoma
Authors: Wang Chunjie , Zhang Zhengyang , Dou Yanping , Liu Yajie , Chen Bo , Liu Qing , Wang Shaowu 
Published: August 2023

Background Accurate differentiation of nodular fasciitis (NF) from soft tissue sarcoma (STS) before surgery is essential for the subsequent diagnosis and treatment of patients. Purpose To develop and evaluate radiomics nomograms based on clinical factors and magnetic resonance imaging (MRI) for the preoperative differentiation of NF from STS. Material and Methods This retrospective study analyzed the MRI data of 27 patients with pathologically diagnosed NF and 58 patients with STS who were randomly divided into training (n = 62) and validation (n = 23) groups. Univariate and multivariate analyses were performed to identify the clinical factors and semantic features of MRI. Radiomics analysis was applied to fat-suppressed T1-weighted (T1W-FS) images, fat-suppressed T2-weighted (T2W-FS) images, and contrast-enhanced T1-weighted (CE-T1W) images. The radiomics nomograms incorporating the radiomics signatures, clinical factors, and semantic features of MRI were developed. ROC curves and AUCs were carried out to compare the performance of the clinical factors, radiomics signatures, and clinical radiomics nomograms. Results Tumor location, size, heterogeneous signal intensity on T2W-FS imaging, heterogeneous signal intensity on CE-T1W imaging, margin definitions on CE-T1W imaging, and septa were independent predictors for differentiating NF from STS ( P < 0.05). The performance of the radiomics signatures based on T2W-FS imaging (AUC = 0.961) and CE-T1W imaging (AUC = 0.938) was better than that based on T1W-FS imaging (AUC = 0.833). The radiomics nomograms had AUCs of 0.949, which demonstrated good clinical utility and calibration. Conclusion The non-invasive clinical radiomics nomograms exhibited good performance in the differentiation of NF from STS, and they have clinical application in the preoperative diagnosis of diseases.
Macrophage heterogeneity in the single-cell era: facts and artifacts
Authors: Hume David A. , Millard Susan M. , Pettit Allison R. 
Published: August 2023

Abstract
In this spotlight, we review technical issues that compromise single-cell analysis of tissue macrophages, including limited and unrepresentative yields, fragmentation and generation of remnants, and activation during tissue disaggregation. These issues may lead to a misleading definition of subpopulations of macrophages and the expression of macrophage-specific transcripts by unrelated cells. Recognition of the technical limitations of single-cell approaches is required in order to map the full spectrum of tissue-resident macrophage heterogeneity and assess its biological significance.
Genome-wide transcription factor–binding maps reveal cell-specific changes in the regulatory architecture of human HSPCs
Authors: Subramanian Shruthi , Thoms Julie A. I. , Huang Yizhou , Cornejo-Páramo Paola , Koch Forrest C. , Jacquelin Sebastien , Shen Sylvie , Song Emma , Joshi Swapna , Brownlee Chris , Woll Petter S. , Chacon-Fajardo Diego , Beck Dominik , Curtis David J. , Yehson Kenneth , Antonenas Vicki , O'Brien Tracey , Trickett Annette , Powell Jason A. , Lewis Ian D. , Pitson Stuart M. , Gandhi Maher K. , Lane Steven W. , Vafaee Fatemeh , Wong Emily S. , Göttgens Berthold , Alinejad-Rokny Hamid , Wong Jason W. H. , Pimanda John E. 
Published: August 2023

Abstract
Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay among transcription factors (TFs) to regulate differentiation into mature blood cells. A heptad of TFs (FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2) bind regulatory elements in bulk CD34+ HSPCs. However, whether specific heptad-TF combinations have distinct roles in regulating hematopoietic differentiation remains unknown. We mapped genome-wide chromatin contacts (HiC, H3K27ac, HiChIP), chromatin modifications (H3K4me3, H3K27ac, H3K27me3) and 10 TF binding profiles (heptad, PU.1, CTCF, STAG2) in HSPC subsets (stem/multipotent progenitors plus common myeloid, granulocyte macrophage, and megakaryocyte erythrocyte progenitors) and found TF occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type–specific gene expression. Distinct regulatory elements were enriched with specific heptad-TF combinations, including stem-cell–specific elements with ERG, and myeloid- and erythroid-specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. Furthermore, heptad-occupied regions in HSPCs were subsequently bound by lineage-defining TFs, including PU.1 and GATA1, suggesting that heptad factors may prime regulatory elements for use in mature cell types. We also found that enhancers with cell-type–specific heptad occupancy shared a common grammar with respect to TF binding motifs, suggesting that combinatorial binding of TF complexes was at least partially regulated by features encoded in DNA sequence motifs. Taken together, this study comprehensively characterizes the gene regulatory landscape in rare subpopulations of human HSPCs. The accompanying data sets should serve as a valuable resource for understanding adult hematopoiesis and a framework for analyzing aberrant regulatory networks in leukemic cells.
Lipids, lipid-modifying drug target genes and migraine: a Mendelian randomization study
Authors: Bi Yaodan , Zhu Yinchao , Tang Shuai , Huang Yuguang 
Published: August 2023

AbstractIntroductionMigraine, a prevalent headache disorder with unclear mechanisms and limited treatments, may be influenced by dyslipidemia and genetic factors. Statins and emerging lipid-modifying agents show potential but lack evidence for migraine management. Mendelian Randomization analysis offers insights into causal relationships and therapeutic targets. This study aims to explore genetically predicted lipid traits, drug targets, and their association with migraine risk.MethodWe conducted Mendelian randomization (MR) analyses utilizing genetic variants associated with lipid traits and variants in genes encoding the protein targets of various classes of lipid-lowering drugs. The specific drug classes investigated included HMGCR, PCSK9, NPC1L1, ABCG5/ABCG8, LDLR, LPL, ANGPTL3, APOB, CETP, and APOC3. To determine the effects on migraine risk, we meta-analyzed MR estimates for regional variants using data from two large sample sets. The genetic variants were weighted based on their associations with specific lipid traits, such as low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), Apolipoprotein A1, and Apolipoprotein B. To obtain association weights, we utilized data from lipid genetics consortia. For lipid-modifying drug targets that exhibited suggestive significance, we further employed expression quantitative trait locus (eQTL) data. Additionally, we performed colocalization analysis to assess genetic confounding.ResultThe use of genetic proxies for HMGCR inhibition demonstrated a significant association with a decreased risk of migraine in the FinnGen dataset (OR = 0.64, 95% CI: 0.46–0.88,p = 0.0006) and a nearly significant association in the Choquet dataset (OR = 0.78, 95% CI: 0.60–1.01,p = 0.06). When pooling the estimates, the overall effect size showed a reduced risk of migraine (OR = 0.73, 95% CI: 0.60–0.89,p = 0.0016). Similarly, genetic mimicry of LPL enhancement was associated with a lower risk of migraine in the FinnGen dataset (OR = 0.82, 95% CI: 0.69–0.96,p = 0.01) and the Choquet dataset (OR = 0.91, 95% CI: 0.83–0.99,p = 0.03). Pooling the estimates showed a consistent effect size (OR = 0.89, 95% CI: 0.83–0.96,p = 0.002). Sensitivity analyses yielded no statistically significant evidence of bias arising from pleiotropy or genetic confounding.ConclusionIn the study, it was observed that among the 10 lipid-lowering drug targets investigated, LPL and HMGCR showed significant associations with migraine risk. These findings indicate that LPL and HMGCR have the potential to serve as candidate drug targets for the treatment or prevention of migraines.
2023 BMC Ecology and Evolution image competition: the winning images
Authors: Harman Jennifer , Hipsley Christy A. , Jacobus Luke M. , Liberles David A. , Settele Josef , Traulsen Arne 
Published: August 2023

AbstractIn 2023, researchers from around the world entered the BMC Ecology and Evolution photography competition. As a result, we received a spectacular collection of photographs that capture the wonder of nature, those looking to understand it and glimpses into long lost worlds. This editorial celebrates the winning images selected by the Editor of BMC Ecology and Evolution and senior members of the journal’s editorial board.
Complete mitochondrial genome of Agrostis stolonifera: insights into structure, Codon usage, repeats, and RNA editing
Authors: Li Jiaxing , Chen Yinglong , Liu Yaling , Wang Chen , Li Ling , Chao Yuehui 
Published: August 2023

Abstract
Background
Plants possess mitochondrial genomes that are large and complex compared to animals. Despite their size, plant mitochondrial genomes do not contain significantly more genes than their animal counterparts. Studies into the sequence and structure of plant mitochondrial genomes heavily imply that the main mechanism driving replication of plant mtDNA, and offer valuable insights into plant evolution, energy production, and environmental adaptation.

Results
This study presents the first comprehensive analysis of Agrostis stolonifera’s mitochondrial genome, characterized by a branched structure comprising three contiguous chromosomes, totaling 560,800 bp with a GC content of 44.07%. Annotations reveal 33 unique protein-coding genes (PCGs), 19 tRNA genes, and 3 rRNA genes. The predominant codons for alanine and glutamine are GCU and CAA, respectively, while cysteine and phenylalanine exhibit weaker codon usage biases. The mitogenome contains 73, 34, and 23 simple sequence repeats (SSRs) on chromosomes 1, 2, and 3, respectively. Chromosome 1 exhibits the most frequent A-repeat monomeric SSR, whereas chromosome 2 displays the most common U-repeat monomeric SSR. DNA transformation analysis identifies 48 homologous fragments between the mitogenome and chloroplast genome, representing 3.41% of the mitogenome’s total length. The PREP suite detects 460 C-U RNA editing events across 33 mitochondrial PCGs, with the highest count in the ccmFn gene and the lowest in the rps7 gene. Phylogenetic analysis confirms A. stolonifera’s placement within the Pooideae subfamily, showing a close relationship to Lolium perenne, consistent with the APG IV classification system. Numerous homologous co-linear blocks are observed in A. stolonifera’s mitogenomes and those of related species, while certain regions lack homology.

Conclusions
The unique features and complexities of the A. stolonifera mitochondrial genome, along with its similarities and differences to related species, provide valuable insights into plant evolution, energy production, and environmental adaptation. The findings from this study significantly contribute to the growing body of knowledge on plant mitochondrial genomes and their role in plant biology.
Genetic-based dissection of resistance to bacterial leaf streak in rice by GWAS
Authors: Zhu Xiaoyang , Chen Lei , Zhang Zhanying , Li Jinjie , Zhang Hongliang , Li Zichao , Pan Yinghua , Wang Xueqiang 
Published: August 2023

Abstract
Background
Rice is the second-largest food crop in the world and vulnerable to bacterial leaf streak disease. A thorough comprehension of the genetic foundation of agronomic traits was essential for effective implementation of molecular marker-assisted selection.

Results
Our study aimed to evaluate the vulnerability of rice to bacterial leaf streak disease (BLS) induced by the gram-negative bacterium Xanthomonas oryzae pv. oryzicola (Xoc). In order to accomplish this, we first analyzed the population structure of 747 accessions and subsequently assessed their phenotypes 20 days after inoculation with a strain of Xoc, GX01. We conducted genome-wide association studies (GWAS) on a population of 747 rice accessions, consisting of both indica and japonica subpopulations, utilizing phenotypic data on resistance to bacterial leaf streak (RBLS) and sequence data. We identified a total of 20 QTLs associated with RBLS in our analysis. Through the integration of linkage mapping, sequence analysis, haplotype analysis, and transcriptome analysis, we were able to identify five potential candidate genes (OsRBLS1—OsRBLS5) that possess the potential to regulate RBLS in rice. In order to gain a more comprehensive understanding of the genetic mechanism behind resistance to bacterial leaf streak, we conducted tests on these genes in both the indica and japonica subpopulations, ultimately identifying superior haplotypes that suggest the potential utilization of these genes in breeding disease-resistant rice varieties.

Conclusions
The findings of our study broaden our comprehension of the genetic mechanisms underlying RBLS in rice and offer significant insights that can be applied towards genetic improvement and breeding of disease-resistant rice in rapidly evolving environmental conditions.
Artificial intelligence in estimating fractional flow reserve: a systematic literature review of techniques
Authors: Farhad Arefinia , Reza Rabiei , Azamossadat Hosseini , Ali Ghaemian , Arash Roshanpoor , Mehrad Aria , Zahra Khorrami 
Published: August 2023

Abstract
Background
Fractional Flow Reserve (FFR) is the gold standard for the functional evaluation of coronary arteries, which is effective in selecting patients for revascularization, avoiding unnecessary procedures, and reducing treatment costs. However, its use is limited due to invasiveness, high cost, and complexity. Therefore, the non-invasive estimation of FFR using artificial intelligence (AI) methods is crucial.

Objective
This study aimed to identify the AI techniques used for FFR estimation and to explore the features of the studies that applied AI techniques in FFR estimation.

Methods
The present systematic review was conducted by searching five databases, PubMed, Scopus, Web of Science, IEEE, and Science Direct, based on the search strategy of each database.

Results
Five hundred seventy-three articles were extracted, and by applying the inclusion and exclusion criteria, twenty-five were finally selected for review. The findings revealed that AI methods, including Machine Learning (ML) and Deep Learning (DL), have been used to estimate the FFR.

Conclusion
This study shows that AI methods can be used non-invasively to estimate FFR, which can help physicians diagnose and treat coronary artery occlusion and provide significant clinical performance for patients.
Molecular surveillance of arboviruses in Nigeria
Authors: Shaibu Joseph Ojonugwa , Akinyemi Kabiru Olusegun , Uzor Oshilonyah Henry , Audu Rosemary Ajuma , Bola Oriowo Oyefolu Akeeb 
Published: August 2023

AbstractArboviral infections are fast becoming a global public health concern as a result of its high fatality rate and sporadic spread. From the outbreak of Zika virus in the Americas, the endemicity of Yellow fever in West Africa and South America, outbreaks of West Nile virus in South Africa to the year-round and national risk of Dengue fever in Mainland China and India. The war against emerging and re-emerging viral infection could probably lead to the next pandemic. To be above the pending possible arboviral pandemic, consistent surveillance of these pathogens is necessary in every society. This study was aimed at conducting a surveillance for Yellow fever virus, Zika virus, Chikungunya virus, Dengue virus and Rift Valley fever virus in four states in Nigeria using molecular techniques. A cross-sectional study involving 1600 blood samples collected from febrile patients in Lagos, Kwara, Ondo and Delta States between 2018 and 2021 was conducted using Real time polymerase chain reaction for detection of the pathogens. Extraction and purification of viral RNA were done using Qiagen Viral RNA Mini Kit. Samples were analyzed using One Step PrimeScript III RT-PCR mix (Takara Bio) alongside optimized primers and probes designed in-house. Positive samples were sequenced on MinION platform (Nanopore technologies). Bioinformatic and phylogenetic analysis were performed with DNASTAR Lasergene 17.3. All the RNA extracted from samples collected from the four states were negative for ZIKV RNA, RVFV RNA, CHIKV RNA and DENV RNA. However, twelve of the samples (2%) tested positive for YFV RNA. Three full genomes of sizes 10,751 bp, 10,500 bp and 10,715 bp were generated and deposited in GenBank with accession numbers: ON323052, ON323053 and ON323054 respectively. Phylogenetic analysis shows clustering within lineage 3 of West African genotype. This result shows an active spread of Yellow fever in Delta State, Nigeria. However, there is no emergence of a new genotype There is a need for an intense surveillance of Yellow fever virus in Nigeria to avert a major outbreak.
Anticipated benefits and challenges of implementing group care in Suriname’s maternity and child care sector: a contextual analysis
Authors: Martens Nele , Hindori-Mohangoo Ashna D. , Hindori Manodj P. , Damme Astrid Van , Beeckman Katrien , Reis Ria , Crone Mathilde R. , van der Kleij Rianne RMJJ 
Published: August 2023

Abstract
Background
Suriname is a uppermiddle-income country with a relatively high prevalence of preventable pregnancy complications. Access to and usage of high-quality maternity care services are lacking. The implementation of group care (GC) may yield maternal and child health improvements. However, before introducing a complex intervention it is pivotal to develop an understanding of the local context to inform the implementation process.

Methods
A context analysis was conducted to identify local needs toward maternity and postnatal care services, and to assess contextual factor relevant to implementability of GC. During a Rapid Qualitative Inquiry, 63 online and face-to-face semi-structured interviews were held with parents, community members, on-and off-site healthcare professionals, policy makers, and one focus group with parents was conducted. Audio recordings were transcribed in verbatim and analysed using thematic analysis and Framework Method. The Consolidated Framework for Implementation Research served as a base for the coding tree, which was complemented with inductively derived codes.

Results
Ten themes related to implementability, one theme related to sustainability, and seven themes related to reaching and participation of the target population in GC were identified. Factors related to health care professionals (e.g., workload, compatibility, ownership, role clarity), to GC, to recipients and to planning impact the implementability of GC, while sustainability is in particular hampered by sparse financial and human resources. Reach affects both implementability and sustainability. Yet, outer setting and attitudinal barriers of health professionals will likely affect reach.

Conclusions
Multi-layered contextual factors impact not only implementability and sustainability of GC, but also reach of parents. We advise future researchers and implementors of GC to investigate not only determinants for implementability and sustainability, but also those factors that may hamper, or facilitate up-take. Practical, attitudinal and cultural barriers to GC participation need to be examined. Themes identified in this study will inspire the development of adaptations and implementation strategies at a later stage.