bluuebunny/crossref_metadata_2025_split huggingface dataset:
A modified system using macrophage-conditioned medium revealed that the indirect effects of anti-inflammatory food-derived compounds improve inflammation-induced suppression of UCP-1 mRNA expression in 10T1/2 adipocytes
Authors: Takahashi Hisako , Morikawa Miori , Ozaki Emi , Numasaki Minami , Morimoto Hiromu , Tanaka Miori , Inoue Hirofumi , Goto Tsuyoshi , Kawada Teruo , Eguchi Fumio , Uehara Mariko , Takahashi Nobuyuki 
Published: March 2024

Abstract
Recently, it has been suggested that brown and beige adipocytes may ameliorate obesity because these adipocytes express uncoupling protein-1 (UCP-1), which generates heat by consuming lipid. However, obesity-induced inflammation suppresses the expression of UCP-1. To improve such conditions, food components with anti-inflammatory properties are attracting attention. In this study, we developed a modified system to evaluate only the indirect effects of anti-inflammatory food-derived compounds by optimizing the conventional experimental system using conditioned medium. We validated this new system using 6-shogaol and 6-gingerol, which have been reported to show the anti-inflammatory effects and to increase the basal expression of UCP-1 mRNA. In addition, we found that the acetone extract of Sarcodon aspratus, an edible mushroom, showed anti-inflammatory effects and rescued the inflammation-induced suppression of UCP-1 mRNA expression. These findings indicate that the system with conditioned medium is valuable for evaluation of food-derived compounds with anti-inflammatory effects on the inflammation-induced thermogenic adipocyte dysfunction.
Photoinduced dehydrogenation of protected piperazines
Authors: Nowaki Kokoro , Maeda Bumpei , Murakami Kei 
Published: March 2024

Abstract
Piperazine represents one of the most important building blocks of pharmaceuticals. Hence, the development of various piperazine derivatives is important. Herein we report photoinduced dehydrogenation of protected piperazines. The reaction proceeded with various alkyl-substituted piperazines. The resulting products have electron-rich olefin moieties that can react with benzyne, carbene, or acyl anhydride.
FGCD: a database of fungal gene clusters related to secondary metabolism
Authors: Zhang Fuyuan , Cao Hongzhe , Si Helong , Zang Jinping , Dong Jingao , Xing Jihong , Zhang Kang 
Published: March 2024

Abstract
Fungal secondary metabolites are not necessary for growth, but they are important for fungal metabolism and ecology because they provide selective advantages for competition, survival and interactions with the environment. These various metabolites are widely used as medicinal precursors and insecticides. Secondary metabolism genes are commonly arranged in clusters along chromosomes, which allow for the coordinate control of complete pathways. In this study, we created the Fungal Gene Cluster Database to store, retrieve, and visualize secondary metabolite gene cluster information across fungal species. The database was created by merging data from RNA sequencing, Basic Local Alignment Search Tool, genome browser, enrichment analysis and the R Shiny web framework to visualize and query putative gene clusters. This database facilitated the rapid and thorough examination of significant gene clusters across fungal species by detecting, defining and graphically displaying the architecture, organization and expression patterns of secondary metabolite gene clusters. In general, this genomic resource makes use of the tremendous chemical variety of the products of these ecologically and biotechnologically significant gene clusters to our further understanding of fungal secondary metabolism.
Database URL: https://www.hebaubioinformatics.cn/FungalGeneCluster/
ThermoPCD: a database of molecular dynamics trajectories of antibody–antigen complexes at physiologic and fever-range temperatures
Authors: Singh Puneet K , Stan Razvan C 
Published: March 2024

Abstract
Progression of various cancers and autoimmune diseases is associated with changes in systemic or local tissue temperatures, which may impact current therapies. The role of fever and acute inflammation-range temperatures on the stability and activity of antibodies relevant for cancers and autoimmunity is unknown. To produce molecular dynamics (MD) trajectories of immune complexes at relevant temperatures, we used the Research Collaboratory for Structural Bioinformatics (RCSB) database to identify 50 antibody:antigen complexes of interest, in addition to single antibodies and antigens, and deployed Groningen Machine for Chemical Simulations (GROMACS) to prepare and run the structures at different temperatures for 100–500 ns, in single or multiple random seeds. MD trajectories are freely available. Processed data include Protein Data Bank outputs for all files obtained every 50 ns, and free binding energy calculations for some of the immune complexes. Protocols for using the data are also available. Individual datasets contain unique DOIs. We created a web interface, ThermoPCD, as a platform to explore the data. The outputs of ThermoPCD allow the users to relate thermally-dependent changes in epitopes:paratopes interfaces to their free binding energies, or against own experimentally derived binding affinities. ThermoPCD is a free to use database of immune complexes’ trajectories at different temperatures that does not require registration and allows for all the data to be available for download.
Database URL: https://sites.google.com/view/thermopcd/home
A case report of percutaneous intramyocardial septal radiofrequency ablation in an adult with re-obstruction after Morrow procedure
Authors: Wang Huiyi , Lei Changhui , Liu Liwen 
Published: March 2024

Abstract

Background
Some patients with hypertrophic cardiomyopathy (HCM) re-occur with drug-refractory symptoms but are not eligible for re-operation after the Morrow procedure. Traditional treatment options are limited. We present the first case of the use of ultrasound-guided percutaneous intramyocardial septal radiofrequency ablation (PIMSRA) for the treatment of a patient with HCM combined with congenital anatomically corrected malposition of the great arteries (MGA) after Morrow procedure.

Case summary
A 61-year-old male patient with congenital MGA, who had been treated with the Morrow procedure for HCM, had worsening symptoms in recent years that were difficult to control medically. He was diagnosed with occult obstructive HCM by stress echocardiography. After multi-disciplinary discussion, this patient was treated with PIMSRA. The post-operative clinical outcome was remarkable, with a significant decrease in septal thickness and disappearance of the left anterior branch conduction block.

Conclusion
Percutaneous intramyocardial septal radiofrequency ablation is feasible and can be one of the options for the treatment of patients with HCM, especially those who cannot choose Morrow procedure. However, it still needs a large sample of clinical trials to validate its clinical effectiveness.
May Measurement Month 2021: an analysis of blood pressure screening results from Hungary
Authors: Nemcsik János , Páll Dénes , Nemes-Nagy Zsuzsanna , Pataki-Turi Lívia , Kovács Tibor , Beaney Thomas , Kiru Gaia , Kerr Gabriele , Poulter Neil , Járai Zoltán 
Published: March 2024

Abstract
Elevated blood pressure (BP) is the most important risk factor for cardiovascular diseases (CVDs), which are still the leading cause of mortality in Hungary. Therefore, screening programmes identifying subjects with hypertension have an important role in CVD prevention. In 2017, the International Society of Hypertension initiated May Measurement Month (MMM) aimed at raising awareness of elevated BP. Hungary joined the MMM campaigns in 2017, 2019, and 2021, and a summary of the results from 2021 is presented here. An opportunistic cross-sectional survey of volunteers aged ≥18 was carried out in September 2021. Measurement of BP, the definition of hypertension, and statistical analysis followed the standard MMM protocol. In Hungary, 30 sites were set up in primary and secondary care facilities, in pharmacies, and in malls. Both cities and villages were involved in all regions. A total of 1414 individuals were screened, and 558 subjects (39.5%) had hypertension. Out of 1065 participants not on antihypertensive medication, 209 (19.6%) had elevated BP. Among treated individuals (n = 349), 206 (59.0%) had controlled BP (&lt;140/90 mmHg). Almost 40% of the participants had hypertension. Among untreated participants, one in five had elevated BP, while among patients on antihypertensive medication, 41% had uncontrolled BP. These results confirm the importance of screening of hypertension in untreated individuals and that efforts are required to adequately control BP in treated hypertensive patients.
Seedling microbiota engineering using bacterial synthetic community inoculation on seeds
Authors: Arnault Gontran , Marais Coralie , Préveaux Anne , Briand Martial , Poisson Anne-Sophie , Sarniguet Alain , Barret Matthieu , Simonin Marie 
Published: March 2024

Abstract
Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple and effective seedling microbiota engineering method using SynCom inoculation on seeds. The method was successful using a wide diversity of SynCom compositions and bacterial strains that are representative of the common bean seed microbiota. First, this method enables the modulation of seed microbiota composition and community size. Then, SynComs strongly outcompeted native seed and potting soil microbiota and contributed on average to 80% of the seedling microbiota. We showed that strain abundance on seed was a main driver of an effective seedling microbiota colonization. Also, selection was partly involved in seed and seedling colonization capacities since strains affiliated to Enterobacteriaceae and Erwiniaceae were good colonizers while Bacillaceae and Microbacteriaceae were poor colonizers. Additionally, the engineered seed microbiota modified the recruitment and assembly of seedling and rhizosphere microbiota through priority effects. This study shows that SynCom inoculation on seeds represents a promising approach to study plant microbiota assembly and its consequence on plant fitness.
The Microcystis-microbiome interactions: origins of the colonial lifestyle
Authors: Piccini Claudia , Martínez de la Escalera Gabriela , Segura Angel M , Croci Carolina , Kruk Carla 
Published: March 2024

Abstract
Species of the Microcystis genus are the most common bloom-forming toxic cyanobacteria worldwide. They belong to a clade of unicellular cyanobacteria whose ability to reach high biomasses during blooms is linked to the formation of colonies. Colonial lifestyle provides several advantages under stressing conditions of light intensity, ultraviolet light, toxic substances and grazing. The progression from a single-celled organism to multicellularity in Microcystis has usually been interpreted as individual phenotypic responses of the cyanobacterial cells to the environment. Here, we synthesize current knowledge about Microcystis colonial lifestyle and its role in the organism ecology. We then briefly review the available information on Microcystis microbiome and propose that changes leading from single cells to colonies are the consequence of specific and tightly regulated signals between the cyanobacterium and its microbiome through a biofilm-like mechanism. The resulting colony is a multi-specific community of interdependent microorganisms.
Macrophage pyroptosis induced by Candida albicans
Authors: Zhang Feng-yuan , Lian Ni , Li Min 
Published: March 2024

Abstract
Candida albicans (C. albicans) is a prevalent opportunistic pathogen that causes mucocutaneous and systemic infections, particularly in immunocompromised individuals. Macrophages play a crucial role in eliminating C. albicans in local and bloodstream contexts, while also regulating antifungal immune responses. However, C. albicans can induce macrophage lysis through pyroptosis, a type of regulated cell death. This process can enable C. albicans to escape from immune cells and trigger the release of IL-1β and IL-18, which can impact both the host and the pathogen. Nevertheless, the mechanisms by which C. albicans triggers pyroptosis in macrophages and the key factors involved in this process remain unclear. In this review, we will explore various factors that may influence or trigger pyroptosis in macrophages induced by C. albicans, such as hypha, ergosterol, cell wall remodeling, and other virulence factors. We will also examine the possible immune response following macrophage pyroptosis.
Identification and characterization of novel dual-function antioxidant and umami peptides from protein hydrolysates of Huangjiu lees
Authors: Zhang Rongbin , Zhou Zhilei , Ji Zhongwei , Ren Qingxi , Liu Shuangping , Xu Yuezheng , Mao Jian 
Published: March 2024

Abstract

Objectives
Lees are the major by-product of Huangjiu brewing and are prone to decomposition due to abundant protein residues. This study aims to convert the lees into high-value peptides with umami and antioxidant difunctionals.

Materials and Methods
Herein, a one-step hydrolysis method combined with flavorzyme followed by amylase pretreatment was developed and optimized. The target peptide fraction was collected and evaluated after ultrafiltration and ethanol precipitation, and then identified by nano-high-performance liquid chromatography–tandem mass spectrometry. The target peptides were filtered through virtual screening, sensory, and radical scavenging verification.

Results
The results show that 80 U/g amylase and 3500 U/g flavorzyme synergistic hydrolysis at 50 °C for 3 h performed best for umami intensity and antioxidant activity. A total of 5266 peptides was identified from the 80% ethanol precipitation fraction, finally secreened 7 umami peptides. The umami recognition threshold of the 7 peptides ranged from 0.38 to 0.66 mmol/L in water. Among them, DPDGW and DNPNW exhibited good DPPH antioxidant ability with IC50 values of 0.6982 mg/mL and 0.4315 mg/mL, respectively. Additionally, molecular docking studies indicated that all umami peptides tend to interact with the T1R3 receptor through hydrogen bonds and van der Waals forces, involving key residues such as ASN68, SER104, HIS145, SER276, VAL277, GLU301, ALA302, THR305, and HIS387.

Conclusion
This study shows that Huangjiu lees is a potential resource for flavor and bioactive peptide development, which provides a reference for other waste protein recycling.
A Small Genome amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba
Authors: Tekle Yonas I , Tefera Hanna 
Published: March 2024

Abstract
This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea’s significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into noncoding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic data sets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.
The 1444 Sunday law of London
Authors: Kirkland Justin S 
Published: March 2024

Abstract
On Sunday 3 May 1444, the London Common Council issued a law that prohibited certain professions from selling their goods on Sundays. While there were numerous laws created during the middle ages that prohibited commerce and work on holy days, the 1444 London law is unique in that it was stricter than the canon law of the church. This article analyses the 1444 London law in order to gain a better insight into mid fifteenth-century London and late medieval religion. It suggests that the 1444 law was created as a response to ideas originally found in canon law and confessors’ manuals. These orthodox sources allowed certain activities that were, seemingly, objectionable to some in 1440s London.
Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion
Authors: Nelson Amelia R , Fegel Timothy S , Danczak Robert E , Caiafa Marcos V , Roth Holly K , Dunn Oliver I , Turvold Cosette A , Borch Thomas , Glassman Sydney I , Barnes Rebecca T , Rhoades Charles C , Wilkins Michael J 
Published: March 2024

Abstract
Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning—the combustion of logging residue on the forest floor—is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.
Validation of a Method for Surveillance of Nanoparticles in Mussels Using Single-Particle Inductively Coupled Plasma-Mass Spectrometry
Authors: Bruvold Are , Valdersnes Stig , Loeschner Katrin , Bienfait André Marcel 
Published: March 2024

Abstract

Background
Determining the concentration of nanoparticles (NPs) in marine organisms is important for evaluating their environmental impact and to assess potential food safety risks to human health.

Objective
The current work aimed at developing an in-house method based on single-particle inductively coupled plasma-mass spectrometry (SP-ICP-MS) suitable for surveillance of NPs in mussels.

Methods
A new low-cost and simple protease mixture was utilized for sample digestion, and novel open-source data processing was used, establishing detection limits on a statistical basis using false-positive and false-negative probabilities. The method was validated for 30 and 60 nm gold NPs spiked to mussels as a proxy for seafood.

Results
Recoveries were 76–77% for particle mass concentration and 94–101% for particle number concentration. Intermediate precision was 8–9% for particle mass concentration and 7–8% for particle number concentration. The detection limit for size was 18 nm, for concentration 1.7 ng/g, and 4.2 × 105 particles/g mussel tissue.

Conclusion
The performance characteristics of the method were satisfactory compared with numeric Codex criteria. Further, the method was applied to titanium-, chromium- and copper-based particles in mussels.

Highlights
The method demonstrates a new practical and cost-effective sample treatment, and streamlined, transparent, and reproducible data treatment for the routine surveillance of NPs in mussels.
False-positive MDA findings in HRMS-based screening of putrefied postmortem blood samples—Identification of the interference as N-acetyltyramine
Authors: Stammer Viviane C , Wissenbach Dirk K , Peters Frank T 
Published: March 2024

Abstract
An unidentified compound in putrefied postmortem blood samples showed identical accurate mass and chromatographic behavior as 3,4-methylenedioxyamphetamine (MDA) and led to false-positive preliminary screening results. The aim of the study was to identify this unknown interference. Postmortem blood samples were analyzed after protein precipitation on a QExactive Focus high-resolution mass spectrometer (Thermo Fisher, Germany) coupled to a RP C18 column (Macherey-Nagel, Germany). Based on the analysis of mass spectrometry (MS) adducts and isotope ratios using fullscan (m/z 134–330) information, the empiric formula of the protonated molecule [M + H]+ of the unknown compound was found to be C10H14O2N (+ 0.6 ppm). Product ion spectra recorded using normalized collision energy 22% showed a base peak of C8H9O1 (+ 1.5 ppm) and a low-abundant water loss to C7H9 (+ 1.9 ppm), neutral losses of C2H2O and NH3 were found. Based on fullscan and MS-MS information and under consideration of the observed order of neutral losses, the compound was presumptively identified as N-acetyltyramine. This assumption was supported by SIRIUS software showing a SIRIUS score of 99.43% for N-acetyltyramine. Finally, the putative structure annotation was confirmed by a reference compound. The described false-positive MDA findings could be attributed to the presence of N-acetyltyramine in putrefied blood samples. Being an isomer of MDA, N-acetyltyramine could not be distinguished by high-resolution data of the protonated molecules. The presented results once again highlight that false-positive findings may occur even in hyphenated high-resolution mass spectrometry (HRMS) when using full-scan information only.