bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a marker within the candidateUn8true loose smut resistance gene for use in barley breeding
Authors: Šķipars Vilnis , Sokolova Elīna , Seile Sanita , Ruņģis Dainis , Legzdiņa Linda 
Published: April 2023

AbstractBreeding for resistance to true loose smut infection caused by the pathogen (Ustilago nuda(Jens.) Rostr.) is an economical and environmentally safe way to limit the effect of this pathogen on barley. However, screening for resistance using natural infection can lead to inconsistent results and artificial inoculation is labour intensive, and can fail, leading to erroneous phenotyping. Marker assisted selection of genes conferring disease resistance can increase the efficiency of breeding programs. A candidate gene forUn8resistance was used to develop a genetic marker which was tested on a recombinant inbred line (RIL) population derived from the resistant ‘CDC Freedom’ and the susceptible ‘Samson’ varieties. The RIL population (98 lines) was phenotyped for resistance to true loose smut by artificial inoculation and genotyped with the newly developed marker. The genotyping results obtained with the marker developed in this study were mostly consistent with true loose smut resistance determined by artificial inoculation. The markers was also tested in additional barley cultivars and breeding material. Repeated analysis of inconsistent results is required to confirm or revise these results, as well as further investigation of the candidate gene to confirm its role in barley true loose smut resistance is being planned.
Loss of myeloid cannabinoid CB1 receptor confers atheroprotection by reducing macrophage proliferation and immunometabolic reprogramming
Authors: Wang Yong , Li Guo , Chen Bingni , Shakir George , Volz Mario , Vorst Emiel P.C. van der , Maas Sanne L. , Muley Carolin , Bartelt Alexander , Li Zhaolong , Sachs Nadja , Maegdefessel Lars , Jahantigh Maliheh Nazari , Hristov Michael , Lacy Michael , Lutz Beat , Weber Christian , Herzig Stephan , Prats Raquel Guillamat , Steffens Sabine 
Published: April 2023

AbstractAlthough the cannabinoid CB1 receptor has been implicated in atherosclerosis, its cell-specific effects in this disease are not well understood. Here, we report that male mice with myeloid-specificCnr1deficiency on atherogenic background developed smaller lesions and necrotic cores than controls, while only minor genotype differences were observed in females. MaleCnr1deficient mice showed reduced arterial monocyte recruitment and macrophage proliferation with less inflammatory phenotype. The sex-specific differences were reproducible in bone marrow derived macrophages and blunted by estradiol. Kinase activity profiling revealed a CB1-dependent regulation of p53 and cyclin-dependent kinases. Transcriptomic profiling further unveiled chromatin modifications, mRNA processing and mitochondrial respiration among the key processes affected by CB1 signaling, which was supported by metabolic flux assays. Chronic administration of the peripherally-restricted CB1 antagonist JD5037 inhibited plaque progression and macrophage proliferation, but only in male mice. Finally,CNR1expression was detectable in human carotid endarterectomy plaques and inversely correlated with proliferation, oxidative metabolism and inflammatory markers, hinting to a possible implication of CB1-dependent regulation in human pathophysiology. In conclusion, impaired CB1 signaling in macrophages is atheroprotective by limiting their arterial recruitment, proliferation and inflammatory reprogramming. The importance of macrophage CB1 signaling seems to be more pronounced in male mice.Abstract FigureGraphical summary(created withBioRender.com)
Cellular energy regulates mRNA translation and degradation in a codon-specific manner
Authors: da Silva Pedro Tomaz , Zhang Yujie , Theodorakis Evangelos , Martens Laura D. , Yépez Vicente A. , Pelechano Vicent , Gagneur Julien 
Published: April 2023

AbstractBackground:Codon optimality is a major determinant of mRNA translation and degradation rates. However, whether and through which mechanisms its effects are regulated remains poorly understood.ResultsHere we show that codon optimality associates with up to 2-fold change in mRNA stability variations between human tissues, and that its effect is attenuated in tissues with high energy metabolism and amplifies with age. Biochemical modeling and perturbation data through oxygen deprivation and ATP synthesis inhibition reveal that cellular energy variations non-uniformly affect the decoding kinetics of different codons.ConclusionsThis new mechanism of codon effect regulation, independent of tRNA regulation, provides a fundamental mechanistic link between cellular energy metabolism and eukaryotic gene expression.
GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples
Authors: Chang Che-Wei , Schmid Karl 
Published: April 2023

SummaryLandscape genomics is an emerging field of research that integrates genomic and environmental information to explore the drivers of evolution. Reliable data on the geographical origin of biological samples is a prerequisite for accurate landscape genomics studies. Traditionally, researchers discover potentially questionable samples using visualization-based tools. However, such approaches cannot handle large sample sizes due to overlapping data points on a graph and can hinder reproducible research. To address this shortcoming, we developedGeo-Geneticoutlier(GGoutlieR), an R package of a heuristic framework for detecting and visualizing samples with unusual geo-genetic patterns. Outliers are identified by calculating empirical p-values for each sample, allowing users to identify them in data sets with thousands of samples. The package also provides a plotting function to display the geo-genetic patterns of outliers on a geographical map. GGoutlieR could significantly reduce the amount of data cleaning that researchers need to do before carrying out landscape genomics analyses.
Length of fermentation time affects microbiome composition and biological activity ofPanchgavya
Authors: Gajera Gemini , Funde Snehal , Palep Hanmanthrao , Kothari Vijay 
Published: April 2023

AbstractObjectiveThis study aimed at investigating whether the duration of fermentingPanchgavya(PG) preparation in copper vessel affects its biological activity and microbiome composition.MethodsProphylactic potential of PG against bacterial infection was assessed through anin vivoassay employing the nematode wormCaenorhabditis elegansas a model host. Bacterial diversity of the PG samples was revealed through metagenomic analysis.ResultsDuration of fermentation was found to affect biological activity as well as microbiome composition of the PG samples. PG-samples fermented ≥60 min lost their prophylactic potential, and develop anthelmintic activity. Bacterial phyla whose relative abundance was significantly different between the prophylactic and anthelmintic PG samples were Planctomycetota, Proteabacteria, Bacteroidota, Verrucomicrobiota, Patescibacteria, Acidobacteriota, Chloroflexi, Firmicutes and Campilobacterota.ConclusionThis study validates the prophylactic potential ofPanchgavyaagainst bacterial pathogens, and shows that duration of the fermentation time while preparing PG can have profound effect on its biological activities. Biological activities of PG samples seem to have a correlation with their inherent microbial community. Metagenomic profiling can be an effective tool for standardization of PG formulations.
M-Ionic: Prediction of metal ion binding sites from sequence using residue embeddings
Authors: Shenoy Aditi , Kalakoti Yogesh , Sundar Durai , Elofsson Arne 
Published: April 2023

AbstractMotivationUnderstanding metal-protein interaction can provide structural and functional insights into cellular processes. As the number of protein sequences increases, developing fast yet precise computational approaches to predict and annotate metal binding sites becomes imperative. Quick and resource-efficient pre-trained protein language model (PLM) embeddings have successfully predicted binding sites from protein sequences despite not using structural or evolutionary features (multiple sequence alignments). Using residue-level embeddings from the PLMs, we have developed a sequence-based method (M-Ionic) to identify metal-binding proteins and predict residues involved in metal-binding.ResultsOn independent validation of recent proteins, M-Ionic reports an area under the curve (AUROC) of 0.83 (recall=84.6%) in distinguishing metal-binding from non-binding proteins compared to AUROC of 0.74 (recall =61.8%) of the next best method. In addition to comparable performance to the state-of-the-art method for identifying metal-binding residues (Ca2+, Mg2+, Mn2+, Zn2+), M-Ionic provides binding probabilities for six additional ions (i.e., Cu2+, Po43-, So42-, Fe2+, Fe3+, Co2+). We show that the PLM embedding of a single residue contains sufficient information about its neighbours to predict its binding properties.Availability and ImplementationM-Ionic can be used on your protein of interest using a Google Colab Notebook (https://bit.ly/40FrRbK). GitHub repository (https://github.com/TeamSundar/m-ionic) contains all code and data.Contactarne@bioinfo.seSupplementary informationSupplementary data are available atBioinformaticsonline.
Amine recognizing domain in diverse receptors from bacteria and archaea evolved from the universal amino acid sensor
Authors: Cerna-Vargas Jean Paul , Gumerov Vadim M. , Krell Tino , Zhulin Igor B. 
Published: April 2023

AbstractBacteria contain many different receptor families that sense different signals permitting an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Due to a significant sequence divergence, the signal recognized by sensor domains is only poorly reflected in overall sequence identity. Biogenic amines are of central physiological relevance for microorganisms and serve for example as substrates for aerobic and anaerobic growth, neurotransmitters or osmoprotectants. Based on protein structural information and sequence analysis, we report here the identification of a sequence motif that is specific for amine-sensing dCache sensor domains (dCache_1AM). These domains were identified in more than 13,000 proteins from 8,000 bacterial and archaeal species. dCache_1AM containing receptors were identified in all major receptor families including sensor kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases. The screening of compound libraries and microcalorimetric titrations of selected dCache_1AM domains confirmed their capacity to specifically bind amines. Mutants in the amine binding motif or domains that contain a single mismatch in the binding motif, had either no or a largely reduced affinity for amines, illustrating the specificity of this motif. We demonstrate that the dCache_1AM domain has evolved from the universal amino acid sensing domain, providing novel insight into receptor evolution. Our approach enables precise “wet”-lab experiments to define the function of regulatory systems and thus holds a strong promise to address an important bottleneck in microbiology: the identification of signals that stimulate numerous receptors.
CT Multi-Task Learning with a Large Image-Text (LIT) Model
Authors: Niu Chuang , Wang Ge 
Published: April 2023

AbstractLarge language models (LLM) not only empower multiple language tasks but also serve as a general interface across different spaces. Up to now, it has not been demonstrated yet how to effectively translate the successes of LLMs in the computer vision field to the medical imaging field which involves high-dimensional and multi-modal medical images. In this paper, we report a feasibility study of building a multi-task CT large image-text (LIT) model for lung cancer diagnosis by combining an LLM and a large image model (LIM). Specifically, the LLM and LIM are used as encoders to perceive multi-modal information under task-specific text prompts, which synergizes multi-source information and task-specific and patient-specific priors for optimized diagnostic performance. The key components of our LIT model and associated techniques are evaluated with an emphasis on 3D lung CT analysis. Our initial results show that the LIT model performs multiple medical tasks well, including lung segmentation, lung nodule detection, and lung cancer classification. Active efforts are in progress to develop large image-language models for superior medical imaging in diverse applications and optimal patient outcomes.
Expression of DNA repair genes is modulated during differentiation of olfactory sensory neurons
Authors: Rowies Fernanda T. , Batalha Caio M.P.F. , Nakahara Thiago S. , Malnic Bettina , de Souza-Pinto Nadja C. 
Published: April 2023

AbstractOlfactory dysfunction is considered a biomarker of several pathological conditions, including age-associated neurodegenerations, glioblastoma and COVID-19. Olfactory sensory neurons (OSNs) are specialized neurons that detect odorants and send olfactory information to the brain through the olfactory bulb. To perform their function, they are in direct contact with the environment, where they are exposed to several environmental toxins such as atmospheric levels of O2and volatile molecules. Nonetheless, very little is known about DNA damage levels and expression of DNA repair pathways in these cells. Here we measured nuclear and mitochondrial DNA damage in olfactory epithelium (OE) and compared with levels detected in olfactory bulb (OB) and temporal cortex (TC), as a non-olfactory related central nervous system region. Surprisingly, DNA damage was lower in OE and OB when compared with TC, both for nuclear and mitochondrial genomes. Accordingly, expression of representative genes for all excision repair pathways was detected in OSNs. Moreover, expression of most evaluated DNA repair genes was lower in mature versus OSN progenitors, suggesting that DNA repair is downregulated during differentiation. Analysis of single cell expression data confirmed that expression of the most differentially expressed DNA repair genes decreased from progenitor to mature OSNs. Finally,in situhybridization data showed that APE1 mRNA levels are lower in the mature OSNs layer of the olfactory epithelium, closest to the nasal cavity lumen. Altogether, we show here that DNA repair pathways are relevant in protecting OSNs against DNA damage accumulation and that differentiation through the OE is accompanied by changes in the expression levels of DNA repair genes.
The shirker’s dilemma and the prospect of cooperation in large groups
Authors: Peña Jorge , Heifetz Aviad , Nöldeke Georg 
Published: April 2023

AbstractCooperation usually becomes harder to sustain as groups become larger because incentives to shirk increase with the number of potential contributors to collective action. But is this always the case? Here we study a binary-action cooperative dilemma where a public good is provided as long as not more than a given number of players shirk from a costly cooperative task. We find that at the stable polymorphic equilibrium, which exists when the cost of cooperation is low enough, the probability of cooperating increases with group size and reaches a limit of one when the group size tends to infinity. Nevertheless, increasing the group size may increase or decrease the probability that the public good is provided at such an equilibrium, depending on the cost value. We also prove that the expected payoff to individuals at the stable equilibrium (i.e., their fitness) decreases with group size. For low enough costs of cooperation, both the probability of provision of the public good and the expected payoff converge to positive values in the limit of large group sizes. However, we also find that the basin of attraction of the stable polymorphic equilibrium is a decreasing function of group size and shrinks to zero in the limit of very large groups. Overall, we demonstrate non-trivial comparative statics with respect to group size in an otherwise simple collective action problem.
Primary cilia promote the differentiation of human neurons through the WNT signaling pathway
Authors: Coschiera Andrea , Yoshihara Masahito , Lauter Gilbert , Ezer Sini , Kere Juha , Swoboda Peter 
Published: April 2023

ABSTRACTPrimary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell’s immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and a mutant with altered cilia (RFX2 -/-), we discovered an early-differentiation “ciliary time window” during which transient cilia promote axon outgrowth, branching and arborization. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in “mild” impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
Development of indicators of happiness in learning of Thai open university students
Authors: Laosum Thanyasinee 
Published: April 2023

PurposeThis paper aims to develop indicators of happiness in learning of the Thai open university (TOU)'s undergraduate students.Design/methodology/approachSampling for the study was comprised of two groups. Group I comprised eight lecturers who are experts in their disciplines and six students who were purposively sampled. The focus group was used to validate the appropriateness of the indicators. In Group II, 332 students were engaged in a multistage sampling process. The responses were analyzed using descriptive statistics, coefficient correlation, exploratory factor analysis (EFA) and confirmatory factor analysis (CFA).FindingsThe indicators of happiness in learning of undergraduate students of TOU were classified in six categories. These included satisfaction with learning environment (five indicators), learning anxiety (five indicators), satisfaction with learning (five indicators), enthusiasm to learn (six indicators), self-satisfaction (six indicators) and readiness to learn (seven indicators). The six categories explained happiness in learning of undergraduate students of TOU at the 65% and fit empirical data.Practical implicationsThe TOU can use the indicators for the assessment of happiness in learning of its students as well as guidelines for the improvement of its student learning environments.Originality/valueThere have been very few studies on indicators of happiness in learning of TOU students. Most were done at the basic education level. This study disclosed the six factors affecting happiness in learning of TOU students; therefore, it should inspire and draw attention of many in the field of higher education distance learning.
Developing levodopa-modified sol-gel coating with enhanced anticorrosion performance on Mg alloy AZ31
Authors: Li Jiao , Li Tianshu , Yuwono Jodie A. , Meng Guozhe , Feng Zhiyuan 
Published: April 2023

Purpose
This study aims to develop a sol-gel-based coating to provide a long-lasting corrosion protection on AZ31 Mg alloy. Silane-based sol-gel coatings have been successfully applied to Mg alloys for corrosion protection. However, the micro or nano defects formed during condensation and solidification will cause the coating failure during a long-lasting immersion in a saline solution. More durable corrosion-protective sol-gel coatings are needed.

Design/methodology/approach
A sol-gel-based coating was modified on AZ31 Mg alloy by levodopa (DOPA). The long-lasting corrosion protection mechanism was studied by multiple electrochemical testing methods and surface characterization techniques.

Findings
Long-term testing by electrochemical impedance spectroscopy in aqueous 0.1 M NaCl indicated that the modified DOPA@sol-gel coating exhibited significant corrosion protection performance (>14 days). In comparison, the DOPA-free sol-gel coating failed only after three days of testing. The improved corrosion protection is attributed to the self-polymerized DOPA filling to the micro or nano defects in the glassy cross-linked networks of the sol-gel coating, which greatly improves the compactness of the coating.

Originality/value
The method of this study is simple and easy to process, the raw materials are green and the protective effect is excellent, which is of significance for the study of magnesium alloy corrosion protection.
Constructing cultural space and telling cultural stories: a case study of regional cultural heritage preservation in Shichahai, Beijing
Authors: Liu Xiaojuan , Pan Yinrong , Han Yutong 
Published: April 2023

PurposeThere is a wealth of value hidden in regional cultural heritage, but its preservation status is not optimistic. This study introduces a method that focuses on the inherent cultural value of regional cultural heritage to preserve it by value construction and release.Design/methodology/approachBased on the great value of regional cultural heritage due to spatial adjacency and temporal continuity, this paper focuses on its inherent cultural value to explore the preservation path and chooses Shichahai cultural heritage digital resources for a case study. This paper draws lessons from the narrative method of ancient Chinese historiography, constructs a cultural space and tells cultural stories. A linked data organization model for digital resources is created to construct a conceptual cultural space. Then, the space is materialized by linked dataset creation. The authors tell cultural stories discovered from the space, which are presented by various user interfaces using visualization technologies.FindingsA cultural space promotes the development of a fine-grained description of regional cultural heritage and aids in relationship discovery to enhance the value construction ability. Additionally, storytelling via interactive user interfaces is helpful in the utilization and dissemination of knowledge extracted from a cultural space and enhances the value release of regional cultural heritage. In this way, a path with the inherent cultural value of regional cultural heritage as the core is established, and preservation is achieved.Originality/valueThis study focuses on the inherent cultural value of regional cultural heritage and proposes a new path to preserve these resources. This approach will enrich research on the preservation of regional cultural heritage and contribute to the construction and release of its cultural value.