bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide characterization and metabolite profiling of Cyathus olla: insights into the biosynthesis of medicinal compounds
Authors: Xie Xiuchao , Zhao Ling , Song Yu , Qiao Yanming , Wang Zhen-Xin , Qi Jianzhao 
Published: June 2024

AbstractCyathus olla, belonging to the genusCyathuswithin the order Agaricales, is renowned for its bird's nest-like fruiting bodies and has been utilized in folk medicine. However, its genome remains poorly understood. To investigate genomic diversity within the genusCyathusand elucidate biosynthetic pathways for medicinal compounds, we generated a high-quality genome assembly ofC. ollawith fourteen chromosomes. The comparative genome analysis revealed variations in both genomes and specific functional genes within the genusCyathus. Phylogenomic and gene family variation analyses provided insights into evolutionary divergence, as well as genome expansion and contraction in individualCyathusspecies and 36 typical Basidiomycota. Furthermore, analysis of LTR-RT and Ka/Ks revealed apparent whole-genome duplication (WGD) events its genome. Through genome mining and metabolite profiling, we identified the biosynthetic gene cluster (BGC) for cyathane diterpenes fromC. olla. Furthermore, we predicted 32 BGCs, containing 41 core genes, involved in other bioactive metabolites. These findings represent a valuable genomic resource that will enhance our understanding ofCyathusspecies genetic diversity. The genome analysis ofC. ollaprovides insights into the biosynthesis of medicinal compounds and establishes a fundamental basis for future investigations into the genetic basis of chemodiversity in this significant medicinal fungus.
Humoral immune response and safety of Sars-Cov-2 vaccine in people with multiple sclerosis
Authors: Hamzavi Seyedeh Sadigheh , Bahrololoom Rosemina , Saeb Sepideh , Marandi Nahid Heydari , Hosseini Marzieh , hesam abadi Alimohammad Keshtvarz , Jamalidoust Marzieh 
Published: June 2024

Abstract
Background
For the past three years, the pandemic has had a major effect on global public health, mainly on those with underlying medical conditions, such as people living with Multiple Sclerosis. Vaccination among this group is of great importance, and the long-term impacts of vaccination and its safety on the health of these patients will continue to be revealed. Therefore, risks related to vaccination and immune response need to be assessed. The objective here was to characterize the immune response, short-term safety, and the effects of multiple variables on these factors after COVID-19 vaccination (mainly Sinopharm) among people with Multiple Sclerosis. We assessed the short-term safety and humoral SARS-COV-2 anti-RBD IgG response using a data collection form and Immunoassay, respectively.

Results
No severe adverse events or MS relapse was observed. Myalgia/body pain (26.7%), low-grade fever (22.2%), and mild headache (15.6%) were the most common adverse events. The use and type of vaccine influenced the frequency of side effects with a p-value < 0.0001. Regarding immune response, patients on rituximab and fingolimod had a lower antibody titer compared to other medications. With a significant difference, hybrid immunity (p-value: 0.047) and type of DMTs (p-value: 0.017) affected the humoral response.

Conclusion
There is a low incidence of serious adverse effects, MS worsening or relapse after COVID-19 vaccination, and mainly, side effects are similar to that of the general population. It appears that treatment with various disease-modifying therapies does not induce or worsen the post-vaccination side effects, although some, including Rituximab and fingolimod, may affect the immunity induced after vaccination.
Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215
Authors: Kellgren Therese , Dwibedi Chinmay , Widerström Micael , Sundell David , Öhrman Caroline , Sjödin Andreas , Monsen Tor , Rydén Patrik , Johansson Anders 
Published: June 2024

Abstract
Background
A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings.

Results
We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination’s role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30–50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2.

Conclusions
This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.
Physiological and transcriptome analysis of changes in endogenous hormone and sugar content during the formation of tender asparagus stems
Authors: He Maolin , Chen Peiran , Li Mengyao , Lei Fengyun , Lu Wei , Jiang Chengyao , Liu Junting , Li Yanwen , Xiao Jiachang , Zheng Yangxia 
Published: June 2024

AbstractAsparagus is a nutritionally dense stem vegetable whose growth and development are correlated with its quality and yield. To investigate the dynamic changes and underlying mechanisms during the elongation and growth process of asparagus stems, we documented the growth pattern of asparagus and selected stem segments from four consecutive elongation stages using physiological and transcriptome analyses. Notably, the growth rate of asparagus accelerated at a length of 25 cm. A significant decrease in the concentration of sucrose, fructose, glucose, and additional sugars was observed in the elongation region of tender stems. Conversely, the levels of auxin and gibberellins(GAs) were elevated along with increased activity of enzymes involved in sucrose degradation. A significant positive correlation existed between auxin, GAs, and enzymes involved in sucrose degradation. The ABA content gradually increased with stem elongation. The tissue section showed that cell elongation is an inherent manifestation of stem elongation. The differential genes screened by transcriptome analysis were enriched in pathways such as starch and sucrose metabolism, phytohormone synthesis metabolism, and signal transduction. The expression levels of genes such as ARF, GA20ox, NCED, PIF4, and otherswere upregulated during stem elongation, while DAO, GA2ox, and other genes were downregulated. The gene expression level was consistent with changes in hormone content and influenced the cell length elongation. Additionally, the expression results of RT-qPCR were consistent with RNA-seq. The observed variations in gene expression levels, endogenous hormones and sugar changes during the elongation and growth of asparagus tender stems offer valuable insights for future investigations into the molecular mechanisms of asparagus stem growth and development and provide a theoretical foundation for cultivation and production practices.
Selenium and its nanoparticles modulate the metabolism of reactive oxygen species and morpho-physiology of wheat (Triticum aestivum L.) to combat oxidative stress under water deficit conditions
Authors: Hasanuzzaman Mirza , Raihan Md. Rakib Hossain , Siddika Ayesha , Bardhan Kirti , Hosen Md. Sarwar , Prasad P. V. Vara 
Published: June 2024

Abstract
Background
Wheat (Triticum aestivum L.) is one of the most important cereal crop species worldwide, but its growth and development are adversely influenced by drought stress. However, the application of trace elements is known to improve plant physiology under water-limited conditions. In this study, the effects of drought stress on wheat plants were investigated, with a focus on potential mitigation by foliar application of selenium nanoparticles (Se(np)) and sodium selenate (Na2SeO4). The experiment was conducted in a net house using a completely randomized design with four replications. The treatments involved three levels of drought stress (mild, moderate, and severe) started at 30 days after sowing (DAS), with foliar sprays of Se(np) and Se (both 25 µM) initiated at 27 DAS and repeated 4 times at 7-day intervals until 55 DAS.

Results
Drought stress significantly reduced plant growth, whereas Se(np) and Se sprays enhanced it. Drought stress induced chlorophyll degradation, increased malondialdehyde and hydrogen peroxide levels, impaired membrane stability, and caused electrolyte leakage. Severe drought stress reduced the levels of antioxidants (e.g., proline, ascorbate, and glutathione by 4.18-fold, 80%, and 45%) and the activities of antioxidant enzymes (ascorbate peroxidase, dehydroascorbate reductase, and others). Conversely, treatment with Se(np) and Se restored these parameters, for example, 1.23-fold higher total chlorophyll content with Se(np) treatment, 26% higher APX activity with Se treatment, 15% lower electrolyte leakage with Se treatment in wheat plants under severe drought stress. This Se-associated enhancement facilitated rapid scavenging of reactive oxygen species and reduced methylglyoxal toxicity, thereby diminishing oxidative stress and positively affecting the morphophysiological and biochemical responses of the plants under drought.

Conclusions
Drought-stressed wheat plants exhibited reductions in physiological processes, including water uptake and photosynthetic activity. However, Se(np) and Se applied at 25 µM mitigated the detrimental effects of drought. The application of Se(np) was notably more effective than the application of Se in mitigating drought stress, indicating the potential of the application of Se(np) as a sustainable agricultural practice under water-limited conditions.
The contribution of Ca and Mg to the accumulation of amino acids in maize: from the response of physiological and biochemical processes
Authors: He Zhaoquan , Shang Xue , Wang Xiukang , Xing Yingying , Zhang Tonghui , Yun Jianying 
Published: June 2024

Abstract
Background
The quality of maize kernels is significantly enhanced by amino acids, which are the fundamental building blocks of proteins. Meanwhile, calcium (Ca) and magnesium (Mg), as important nutrients for maize growth, are vital in regulating the metabolic pathways and enzyme activities of amino acid synthesis. Therefore, our study analyzed the response process and changes of amino acid content, endogenous hormone content, and antioxidant enzyme activity in kernels to the coupling addition of sugar alcohol-chelated Ca and Mg fertilizers with spraying on maize.

Result
(1) The coupled addition of Ca and Mg fertilizers increased the Ca and Mg content, endogenous hormone components (indole-3-acetic acid, IAA; gibberellin, GA; zeatin riboside, ZR) content, antioxidant enzyme activity, and amino acid content of maize kernels. The content of Ca and Mg in kernels increased with the increasing levels of Ca and Mg fertilizers within a certain range from the filling to the wax ripening stage, and significantly positively correlated with antioxidant enzyme activities. (2) The contents of IAA, GA, and ZR continued to rise, and the activities of superoxide dismutase (SOD) and catalase (CAT) were elevated, which effectively enhanced the ability of cells to resist oxidative damage, promoted cell elongation and division, and facilitated the growth and development of maize. However, the malondialdehyde (MDA) content increased consistently, which would attack the defense system of the cell membrane plasma to some extent. (3) Leucine (LEU) exhibited the highest percentage of essential amino acid components and a gradual decline from the filling to the wax ripening stage, with the most substantial beneficial effect on essential amino acids. (4) CAT and SOD favorably governed essential amino acids, while IAA and MDA negatively regulated them. The dominant physiological driving pathway for the synthesis of essential amino acids was “IAA-CAT-LEU”, in which IAA first negatively drove CAT activity, and CAT then advantageously controlled LEU synthesis.

Conclusion
These findings provide a potential approach to the physiological and biochemical metabolism of amino acid synthesis, and the nutritional quality enhancement of maize kernel.
Age-specific differences in association of glycosylated hemoglobin levels with the prevalence of cardiovascular diseases among nondiabetics: the National Health and Nutrition Examination Survey 2005–2018
Authors: Fan Ruihan , Li Shuna , Xue Zihan , Yang Ruida , Lyu Jun , He Hairong 
Published: June 2024

Abstract
Background
Previous research has supported the presence of an association between high glycated hemoglobin (HbA1c) levels and cardiovascular disease (CVD). The objective of the present study was to determine whether increased HbA1c levels are associated with high CVD prevalence among nondiabetics. Furthermore, we aimed to explore the possible interaction of HbA1c levels and age in regard to CVD.

Methods
This cross-sectional study analyzed data of 28,534 adult participants in the National Health and Nutrition Examination Survey 2005–2018. The association between HbA1c and CVD was assessed using univariate and multivariate logistic regression models. Propensity score matching was used to reduce selection bias. Subgroup analysis and restricted cubic spline (RCS) were used to further characterize the association between HbA1c levels and CVD. We modeled additive interactions to further assess the relationship between HbA1c levels and age.

Results
In the multivariate logistic regression model, a positive association was found between CVD and increased HbA1c levels (highest quartile [Q4] vs. lowest quartile [Q1]: odds ratio [OR] = 1.277, 95% confidence interval [CI] = 1.111–1.469, P = 0.001). In the stratified analyses, the adjusted association between HbA1c and CVD was significant for those younger than 55 years (Q4 vs. Q1: OR = 1.437, 95% CI = 1.099–1.880, P = 0.008). RCS did not reveal a nonlinear relationship between HbA1c levels and CVD among nondiabetics (P for nonlinearity = 0.609). Additionally, a high HbA1c level was favorably connected with old age on CVD, with a synergistic impact.

Conclusions
Increased HbA1c levels were associated with high CVD prevalence among nondiabetics. However, we still need to carefully explain the effect of age on the relationship between HbA1c and CVD in nondiabetic population. Given the correlations of HbA1c with CVDs and CV events, HbA1c might be a useful indicator for predicting CVDs and CV events in the nondiabetic population.
Unusual Cutibacterium acnes splenic abscess with bacteremia in an immunocompetent man: phylotyping and clonal complex analysis
Authors: Roudeau Angèle , Corvec Stéphane , Heym Beate , d’Epenoux Louise Ruffier , Lidove Olivier , Zeller Valérie 
Published: June 2024

Abstract
Background
Cutibacterium acnes is an anaerobic bacterium mostly implicated in cutaneous and body-implant infections. Splenic abscess is a rare entity and C. acnes abscesses have only exceptionally been reported. We describe a spontaneous splenic C. acnes abscess in an immunocompetent man with no predisposing factors or identified portal of entry. His isolates were subjected to single-locus sequence typing (SLST) to explore their genetic relatedness and better understand this rare infection.

Case presentation
A splenic abscess was diagnosed on a computed-tomography scan in a 74-year-old man with chronic abdominal pain. No risk factor was identified. Abscess-drained pus and post-drainage blood cultures grew C. acnes. SLST of abscess and blood isolates showed that they belonged to the same C. acnes SLST type C1 found in normal skin and rarely in inflammatory skin disease. Specific virulence factors could not be identified.

Conclusion
C. acnes abscesses are extremely rare and can develop in immunocompetent patients without an identifiable portal of entry. Molecular typing of clinical isolates can help confirm infection (versus contamination) and enables genetic background comparisons. Further research is needed to understand C. acnes tropism and virulence.
Usefulness of the mini nutritional assessment short-form for evaluating nutritional status in patients with nontuberculous mycobacterial pulmonary disease: a prospective cross-sectional study
Authors: Chung Eunki , Park Youngmok , Lee Hye-Jeong , Kang Young Ae 
Published: June 2024

Abstract
Background
Although the Mini Nutritional Assessment (MNA) is recognized as a useful tool for evaluating nutritional status in patients with various diseases, its applicability in patients with nontuberculous mycobacterial pulmonary disease (NTM-PD) remains undetermined.

Methods
We designed a prospective cross-sectional study to investigate whether the MNA Short-Form (MNA-SF) score can serve as a screening tool to assess the nutritional status of patients with NTM-PD. The MNA-SF was conducted upon patient enrollment, and correlation analyses were performed to compare MNA-SF scores with other nutritional measurements and disease severity. Multivariable logistic regression analyses were conducted to evaluate the association between MNA-SF scores and NTM-PD severity.

Results
The 194 patients with NTM-PD included in the analysis had a median age of 65.0 (59.0–69.0) years; 59.3% (n = 115) had low MNA-SF scores (< 12). The low MNA-SF group exhibited a lower body mass index (19.7 vs. 22.4 kg/m2, p < 0.001) and fat-free mass index (14.7 vs. 15.6 kg/m2, p < 0.001) than the normal MNA-SF group, as well as higher incidences of sarcopenia (20.0% vs. 6.3%, p = 0.008) and adipopenia (35.7% vs. 5.1%, p < 0.001). However, no significant differences in calorie and protein intakes were observed between the two groups. Low MNA-SF scores were associated with radiographic severity (adjusted odds ratio 2.72, 95% confidence interval 1.38–5.36) but not with forced vital capacity.

Conclusions
The MNA-SF can effectively assess the nutritional status of patients with NTM-PD and can serve as an important clinical indicator in NTM-PD where treatment timing is determined by clinical judgment.
The elevated lactate dehydrogenase to albumin ratio is a risk factor for developing sepsis-associated acute kidney injury: a single-center retrospective study
Authors: Fang Yipeng , Zhang Yuan , Zhang Xin 
Published: June 2024

Abstract
Background
There is no evidence to determine the association between the lactate dehydrogenase to albumin ratio (LAR) and the development of sepsis-associated acute kidney injury (SAKI). We aimed to investigate the predictive impact of LAR for SAKI in patients with sepsis.

Methods
A total of 4,087 patients with sepsis from the Medical Information Mart for Intensive Care IV (MIMIC IV) database were included. Logistic regression analysis was used to identify the association between LAR and the risk of developing SAKI, and the relationship was visualized using restricted cubic spline (RCS). The clinical predictive value of LAR was evaluated by ROC curve analysis. Subgroup analysis was used to search for interactive factors.

Results
The LAR level was markedly increased in the SAKI group (p < 0.001). There was a positive linear association between LAR and the risk of developing SAKI (p for nonlinearity = 0.867). Logistic regression analysis showed an independent predictive value of LAR for developing SAKI. The LAR had moderate clinical value, with an AUC of 0.644. Chronic kidney disease (CKD) was identified as an independent interactive factor. The predictive value of LAR for the development of SAKI disappeared in those with a history of CKD but remained in those without CKD.

Conclusions
Elevated LAR 12 h before and after the diagnosis of sepsis is an independent risk factor for the development of SAKI in patients with sepsis. Chronic comorbidities, especially the history of CKD, should be taken into account when using LAR to predict the development of AKI in patients with sepsis.
A systematic review and meta-analysis of neuroimaging studies examining synaptic density in individuals with psychotic spectrum disorders
Authors: Husain Muhammad Omair , Jones Brett , Arshad Usman , Ameis Stephanie H. , Mirfallah Giselle , Schifani Christin , Rodak Terri , Aiken Madina , Shafique Mudassar , Ahmed Fatima , Voineskos Aristotle , Husain Muhammad Ishrat , Foussias George 
Published: June 2024

Abstract
Background
Psychotic disorders have long been considered neurodevelopmental disorders where excessive synaptic pruning and cortical volume loss are central to disease pathology. We conducted a systematic review of the literature to identify neuroimaging studies specifically examining synaptic density across the psychosis spectrum.

Methods
PRISMA guidelines on reporting were followed. We systematically searched MEDLINE, Embase, APA PsycINFO, Web of Science and The Cochrane Library from inception to December 8, 2023, and included all original peer-reviewed articles or completed clinical neuroimaging studies of any modality measuring synaptic density in participants with a diagnosis of psychosis spectrum disorder as well as individuals with psychosis-risk states. The NIH quality assessment tool for observational cohort and cross-sectional studies was used for the risk of bias assessment.

Results
Five studies (k = 5) met inclusion criteria, comprising n = 128 adults (psychotic disorder; n = 61 and healthy volunteers; n = 67 and specifically measuring synaptic density via positron emission tomography (PET) imaging of the synaptic vesicle glycoprotein 2 A (SV2A). Three studies were included in our primary meta-analysis sharing the same outcome measure of SV2A binding, volume of distribution (VT). Regional SV2A VT was reduced in psychotic disorder participants in comparison to healthy volunteers, including the occipital lobe (Mean Difference (MD)= -2.17; 95% CI: -3.36 to -0.98; P < 0.001 ), temporal lobe (MD: -2.03; 95% CI: -3.19 to -0.88; P < 0.001 ), parietal lobe (MD:-1.61; 95% CI: -2.85 to -0.37; P = 0.01), anterior cingulate cortex (MD= -1.47; 95% CI: -2.45 to -0.49; P = 0.003), frontal cortex (MD: -1.16; 95% CI: -2.18 to -0.15; P = 0.02), amygdala (MD: -1.36; 95% CI: -2.20 to -0.52, p = 0.002), thalamus (MD:-1.46; 95% CI:-2.46 to -0.46, p = 0.004) and hippocampus (MD= -0.96; 95% CI: -1.59 to -0.33; P = 0.003).

Conclusions
Preliminary studies provide in vivo evidence for reduced synaptic density in psychotic disorders. However, replication of findings in larger samples is required prior to definitive conclusions being drawn.

PROSPERO
CRD42022359018.