bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation optimization and screening of halophilic enzymes and antimicrobial activities of halophilic archaea from the high-altitude, hypersaline Da Qaidam Salt Lake, China
Authors: Ma Xin , Lv Jiaxuan , Ma Xiangrong , Zhu Derui , Long Qifu , Xing Jiangwa 
Published: January 2025

Abstract

Aim
The aim of this study is to increase the diversity of culturable halophilic archaea by comparing various isolation conditions and to explore the application of halophilic archaea for enzyme-producing activities and antimicrobial properties.

Methods and results
We systematically compared the isolation performance of various archaeal and bacterial media by isolating halophilic archaea from the Da Qaidam Salt Lake, a magnesium sulfate subtype hypersaline lake on the Qinghai-Tibet Plateau, China, using multiple enrichment culture and gradient dilution conditions. A total of 490 strains of halophilic archaea were isolated, which belonged to five families and 11 genera within the order Halobacteriales of the class Halobacteria of the phylum Euryarchaeota. The 11 genera consisted of nine known genera and two potentially new genera, the former including Halorubrum, Natranaeroarchaeum, Haloplanus, Haloarcula, Halorhabdus, Halomicrobium, Halobacterium, Natrinema, and Haloterrigene. Halorubrum was the dominant genus with a relative abundance of 78.98%. By comparing different culture conditions, we found that bacterial media 2216E and R2A showed much better isolation performance than all archaeal media, and enrichment culture after 60 d and dilution gradients of 10–1 and 10–2 were best fitted for halophilic archaea cultivation. The screening of 40 halophilic archaeal strains of different species indicated that these halophilic archaea had great extracellular enzyme activities, including amylase (62.5%), esterase (50.0%), protease (27.5%), and cellulase (15.0%), and possessed great antimicrobial activities against human pathogens. A total of 34 strains exhibited antimicrobial activity against four or more pathogens, and 19 strains exhibited antimicrobial activity against all six pathogens.

Conclusions
The diversity of culturable halophilic archaea was significantly increased by enrichment culture and selection of bacterial media, and screening of representative strains showed that halophilic archaea have multiple extracellular enzyme activities and broad-spectrum antimicrobial activity against human pathogens.
Molecular characterization of an endophytic strain of Bacillus subtilis with plant growth-promoting properties from a wild relative of papaya
Authors: Patil Basavaprabhu L , Gopalkrishna Amulya M , G M Sandeep Kumar , R Umamaheswari 
Published: January 2025

Abstract

Aim
Bacillus subtilis is usually found in soil, and their biocontrol and plant growth-promoting capabilities are being explored more recently than ever. However, knowledge about metabolite production and genome composition of endophytic B. subtilis from seeds is limited. In the present study, B. subtilis EVCu15 strain isolated from the seeds of Vasconcellea cundinamarcensis (mountain papaya) was subjected to whole genome sequencing and detailed molecular and functional characterization.

Methods and results
Whole genome sequencing and sequence analysis of the endophytic bacterium from mountain papaya seed revealed that the bacterium was B. subtilis, strain EVCu15. The genomic sequence had more than 98% nucleotide similarity with two published whole genome sequences of B. subtilis strains. Some of the important secondary metabolite gene clusters involved in production of bioactive compounds such as surfactin, fengycin, plipastatin, bacillibactin, bacillaene, subtilomycin, subtilosin A, and bacilysin were identified from the whole genome sequence analysis. Genes encoding several plant growth-promoting metabolites, mostly involved in the nutrient metabolism, were identified in the bacterial genome. These included factors coding for nitrogen, phosphorus, iron, sulfur, potassium, and trehalose metabolism. Genes involved in auxin, riboflavin, acetoin biosynthesis, ACC deaminase activity, and xylan degradation were also identified. Proteomic analysis confirmed the biosynthesis and release of several bioactive secondary metabolites in the endophytic B. subtilis strain EVCu15. Liquid chromatography-mass spectrometry-based profiling for hormones and vitamins identified extracellular secretion of several important plant growth-promoting compounds such as IAA, salicylic acid, zeatin, vitamin D1, D2, E, K1, and pyridoxine. The in vitro and in vivo studies with the endophytic B. subtilis against various plant pathogenic fungi showed moderate to high levels of resistance. The B. subtilis EVCu15 compared to B. amyloliquefaciens showed better control over the root-knot nematode Meloidogyne incognita, in terms of egg hatching inhibition and the mortality of J2 juveniles.

Conclusion
Overall, this study underscores the biocontrol and plant growth-promoting potential of B. subtilis EVCu15, an endophyte isolated from mountain papaya seeds. Genomic analysis revealed a significant proportion of genes linked to biocontrol and plant growth promotion, corroborating its efficacy against M. incognita and various plant pathogens in vitro and in greenhouse studies. Furthermore, the bacterium’s ability to produce diverse bioactive compounds, including proteins, hormones, and vitamins, was confirmed, highlighting its complex interactions within the plant system.
The Effects of Compound Starter Culture and Sugar and Soy Milk on the Quality and Probiotic Activity of Milk-soy Mixed Yogurt
Authors: Jiang Wenxie , Han Sungjun , Wang Lu , Li Xinxin 
Published: January 2025

Abstract

Background
Yogurt has emerged as an essential nutritional food in contemporary diets, and the development of new multi-component yogurt formulations has become a focal point of current research.

Objective
In this study, the effects of fermentation compounds and the addition of sugar, soy milk on the quality and probiotic activity of milk-soy mixed yogurt were studied to determine the optimal formation of mixed yogurt.

Methods
The various fermentation compounds (YO-MIX 883, Lactobacillus Casei complex starter cultures, Lactobacillus Paracasei compound starter cultures), different concentrations of milk-soy additions (0, 25, 50, 75, 100%) and sugar (2, 4, 6, 8%) were tested within each experimental group, and the pH, appropriate acidity, and total viable bacterial count of the fermented milk-soy mixed yogurt were determined throughout the fermentation and refrigeration processes.

Results
The obtained results showed that the Lactobacillus Paracasei complex was particularly effective for the fermentation of soy milk. The mixed yogurt formulation, comprising 50% soy milk and 4∼6% sucrose, exhibited enhanced acidity, superior sensory evaluation scores, and overall improved product quality. It was observed that during refrigeration, an increase in the milk content of yogurt corresponded to a more pronounced post-acidification effect. The optimal formulation for the milk-soy mixed yogurt identified in this research consisted of 0.3% Lactobacillus Paracasei compound fermenter, 6% sucrose, and 40% soy milk. Under these optimal conditions, the mixed yogurt achieved an acidity level of 76°T, a sensory score of 92 points, and a survival rate index of 1.25. Additionally, the yogurt exhibited a distinctive soybean aroma in its aftertaste, contributing to its overall quality. Furthermore, the probiotic survival index of the mixed yogurt containing 40% soy milk, following simulated gastrointestinal fluid digestion, was recorded at 0.767, indicating that the probiotic activity in this yogurt was significantly higher than that of other yogurts.

Conclusion
The obtained results provide a theoretical foundation for the future industrial production of milk-soy mixed yogurt products.
Functional diversity of senescent cells in driving ageing phenotypes and facilitating tissue regeneration
Authors: Nakano Yasuhiro , Johmura Yoshikazu 
Published: January 2025

Abstract
As the global population continues to age, understanding the complex role of cellular senescence and its implications in healthy lifespans has gained increasing prominence. Cellular senescence is defined as the irreversible cessation of cell proliferation, accompanied by the secretion of a range of pro-inflammatory factors, collectively termed the senescence-associated secretory phenotype (SASP), in response to various cellular stresses. While the accumulation of senescent cells has been strongly implicated in the ageing process and the pathogenesis of age-related diseases owing to their pro-inflammatory properties, recent research has also highlighted their essential roles in processes such as tumour suppression, tissue development and repair. This review provides a comprehensive examination of the dual nature of senescent cells, evaluating their deleterious contributions to chronic inflammation, tissue dysfunction and disease, as well as their beneficial roles in maintaining physiological homeostasis. Additionally, we explored the therapeutic potential of senolytic agents designed to selectively eliminate detrimental senescent cells while considering the delicate balance between transient and beneficial senescence and the persistence of pathological senescence. A deeper understanding of these dynamics is critical to develop novel interventions aimed at mitigating age-related dysfunctions and enhancing healthy life expectancies.
Cellular senescence in the cancer microenvironment
Authors: Meguro Satoru , Nakanishi Makoto 
Published: January 2025

Abstract
In this ageing society, the number of patients suffering from age-related diseases, including cancer, is increasing. Cellular senescence is a cell fate that involves permanent cell cycle arrest. Accumulated senescent cells in tissues over time present senescence-associated secretory phenotype (SASP) and make the inflammatory context, disturbing the tumour microenvironment. In particular, the effect of senescent cancer-associated fibroblasts on cancer progression has recently come under the spotlight. Although scientific evidence on the impact of cellular senescence on cancer is emerging, the association between cellular senescence and cancer is heterogeneous and the comprehensive mechanism is still not revealed. Recently, a therapy targeting senescent cells, senotherapeutics, has been reported to be effective against cancer in preclinical research and even clinical trials. With further research, the development of senotherapeutics as a novel cancer therapy is expected.
An unresolving painful condition following a trivial peripheral fracture
Authors: Minisola Salvatore , Colangelo Luciano , Rossi Giuseppe , Gualdi Gianfranco , Pepe Jessica , Cipriani Cristiana 
Published: January 2025

Vignette
A 58-yr-old woman presented to our mineral metabolism center, complaining of localized and continuous pain, which worsened with movements, and weakness of the right foot. The patient reported having had a fracture of the fifth metatarsal bone of the right foot about 4 mo ago. She was initially treated with a cast that she did not tolerate and then with an orthopedic brace. After about 1 mo, she noticed swelling of the right foot and started complaining of continuous pain. The physical examination when came to our center seemed partly improved in respect to the initial one referred by the patient even though she still presented with a mild swelling, reddish skin color, and mild sweating on the right foot. Allodynia and hyperalgesia still persisted but at a lower grade. Main biochemical parameters of calcium metabolism were in the normal range. After excluding other clinical conditions, a diagnosis of complex regional pain syndrome type I was made. She was treated with neridronate iv with resolution of symptoms while continuing with physical therapy and pain relievers. Similar milder episodes were reported by the patient in the following months. However, they were immediately resolved by prompt neridronate infusion. No further complaints have been reported during the next 3 yr follow-up.
The real prevalence and clinical courses of non-metastatic castration-resistant prostate cancer: a retrospective single-institutional study
Authors: Takamori Hajime , Goto Takayuki , Kashima Soki , Yoshino Takayuki , Ogata Takashi , Aizawa Rihito , Nakamura Kiyonao , Sano Takeshi , Sawada Atsuro , Akamatsu Shusuke , Yamasaki Toshinari , Inoue Takahiro , Mizowaki Takashi , Ogawa Osamu , Kobayashi Takashi 
Published: January 2025

Abstract

Background
Non-metastatic castration-resistant prostate cancer (PCa) has become clinically important in PCa management, with treatments aiming to delay metastasis. However, limited data exist on its prevalence and patient characteristics in real-world settings.

Methods
We retrospectively investigated the clinical records of 1929 patients who were treated for localized PCa between 2005 and 2018. From this population, we counted patients who progressed to non-metastatic castration-resistant PCa, and summarized the characteristics of the patients.

Results
Among patients who underwent radical prostatectomy (796 patients), radiation therapy (1021 patients), or primary androgen deprivation therapy (ADT) (112 patients), 0.9%, 0.9%, and 5.4%, respectively, were diagnosed with non-metastatic castration-resistant PCa over a median follow-up of 5.5 years. Including referred cases, a total of 45 non-metastatic castration-resistant PCa patients were analyzed. The median age at non-metastatic castration-resistant PCa diagnosis was 76 years, with a median time of 4.8 years from the initiation of ADT to non-metastatic castration-resistant PCa development. From the initial PCa diagnosis, the median time to non-metastatic castration-resistant PCa was 5.9 years. Median metastasis-free survival was 5.2 years, while overall survival was 6.3 years.

Conclusion
This study reports the prevalence of non-metastatic castration-resistant PCa at our institution and provides clinical findings of non-metastatic castration-resistant PCa patients by analyzing consecutive localized PCa cases through comprehensive medical chart reviews for every patient.
Cytokine release syndrome induced by dabrafenib and trametinib therapy in BRAF V600E-mutant non-small cell lung cancer
Authors: Sumi Toshiyuki , Ishigooka Taiki , Matsuura Keigo , Ikeda Takumi , Yamada Yuichi , Chiba Hirofumi 
Published: January 2025

Abstract
Non-small cell lung cancer (NSCLC) with BRAF V600E mutations is responsive to targeted therapies, such as dabrafenib and trametinib. However, these treatments can lead to serious adverse events, including cytokine release syndrome (CRS). Herein, we report the case of a 75-year-old man with stage IVB NSCLC and a BRAF V600E mutation who developed severe CRS, manifesting hepatic and renal dysfunction, following treatment with dabrafenib and trametinib. Despite initial fever management, the patient’s renal function deteriorated rapidly, necessitating hemodialysis. Elevated cytokine levels, including interleukin-6, interferon-γ, and tumor necrosis factor α, were detected. The patient was treated with steroid pulse therapy, which resulted in fever resolution, and his renal function gradually improved. Hemodialysis was discontinued as renal function recovered. This case underscores the importance for early recognition and management of CRS in patients receiving targeted therapies. Prompt intervention with steroids may prevent CRS progression and mitigate associated organ dysfunction. Further investigation is required to clarify the mechanisms of CRS in patients receiving targeted therapy, particularly in the absence of prior immune checkpoint inhibitor use.
Revisiting the individual-level correlates of emigration intentions: Evidence from Central America
Authors: Perelló Lucas 
Published: January 2025

Abstract
Central American countries have grappled with various challenges in recent decades, including economic hardship, insecurity, corruption, and democratic backsliding. In theory, these factors—individually and jointly—contribute to migration. This article builds on a rich body of knowledge and revisits the individual-level correlates of emigration intentions in El Salvador, Guatemala, Honduras, and Nicaragua. I employ a comprehensive dataset spanning over a decade of AmericasBarometer surveys by the Latin American Public Opinion Project from 2006 to 2018–19. The empirical results, which rely on probit maximum likelihood estimators, sketch a statistical outline of the correlates of emigration intentions and reveal to what extent they have changed over time. The statistical analysis confirms that multiple factors correlate to emigration intentions. But a closer look reveals that two variables are more consistent over time and across countries: receiving remittances and crime victimization.
Patterns and Predictors of COVID-19 Vaccine Uptake Among U.S. Active Duty Service Members, 2020-2022: Implications for Future Pandemics
Authors: Sercy Erica , Stewart Laveta , Craig-Kuhn Megan Clare , Stern Caryn , Graham Brock , Michel Amber , Parmelee Edward , Pollett Simon , Burgess Timothy , Tribble David R 
Published: January 2025

ABSTRACT

Introduction
Vaccine mandates have been used to minimize the duty days lost and deaths attributable to infectious disease among active duty Service members (ADSMs). In response to the global COVID-19 pandemic, in August 2021, the U.S. DoD issued a COVID-19 vaccine mandate for all ADSMs. This study aimed to investigate COVID-19 vaccine uptake among the ADSM population, as well as factors associated with timing of COVID-19 vaccine receipt.

Materials and Methods
This study included ADSMs on active duty between January 1, 2020, and June 30, 2022. Univariate analyses investigated associations between demographic factors (age, sex, race, ethnicity, branch of service, rank, and state of residence) and COVID-19 diagnosis with the following outcomes: (1) time to primary series initiation in relation to the DoD vaccine mandate, (2) time between doses of the 2-dose primary series, and (3) time between booster eligibility and receipt. This research received an exempt determination by the USU Human Research Protection Program.

Results
In total, 1,799,466 ADSMs were included, with 90% receiving ≥1 COVID-19 vaccine dose during the study period and 77% initiating the primary series prior to the mandate. Over 80% of ADSMs received a complete primary series, with 96% of those adhering to the recommended regimen. The history of COVID-19 diagnosis was associated with the later receipt of all doses.

Conclusions
COVID-19 vaccine uptake was high among all ADSMs, with the majority initiating the primary series before the mandate. The high vaccine uptake among ADSMs shown here may be used as a guide to both military and civilian pandemic policy and outreach efforts related to enhanced vaccine uptake.
The Hidden Politics of (Public) Music Theory
Authors: Boyd Clifton 
Published: January 2025

Abstract
In this brief essay, I seek to identify and contribute to a growing body of literature that advocates for a healthy suspicion of the political aims of music theory (academic, public, and otherwise), which at times hides its aim to harm and oppress. I describe how (public) music theory can have explicit politics, implicit politics, and, most relevant to this discussion, hidden politics. I conclude by reflecting on how we professional music theorists might continue our work in and on public music theory in ways that align with broader disciplinary goals of dismantling structural inequities.
Flow and intuition: a systems neuroscience comparison
Authors: Kotler Steven , Parvizi-Wayne Darius , Mannino Michael , Friston Karl 
Published: January 2025

Abstract
This paper explores the relationship between intuition and flow from a neurodynamics perspective. Flow and intuition represent two cognitive phenomena rooted in nonconscious information processing; however, there are clear differences in both their phenomenal characteristics and, more broadly, their contribution to action and cognition. We propose, extrapolating from dual processing theory, that intuition serves as a rapid, nonconscious decision-making process, while flow facilitates this process in action, achieving optimal cognitive control and performance without [conscious] deliberation. By exploring these points of convergence between flow and intuition, we also attempt to reconcile the apparent paradox of the presence of enhanced intuition in flow, which is also a state of heightened cognitive control. To do so, we utilize a revised dual-processing framework, which allows us to productively align and differentiate flow and intuition (including intuition in flow). Furthermore, we draw on recent work examining flow from an active inference perspective. Our account not only heightens understanding of human cognition and consciousness, but also raises new questions for future research, aiming to deepen our comprehension of how flow and intuition can be harnessed to elevate human performance and wellbeing.
Petrogenesis and Geochemistry of Upper Paleozoic Komatiites (Mashhad, NE Iran)
Authors: Mobasheri Mohsen , Arndt Nicholas , Cordier Carole , Sobolev Alexander , Ghasemi Habibollah , Marchesi Claudio , Sabzehei Mossaieb , Garrido Carlos J 
Published: January 2025

Abstract
Upper Paleozoic, probably Permian, komatiites have been found in the Paleo-Tethys suture zone in NE Iran. These rocks are divided into three groups: (i) differentiated and undifferentiated komatiite lava flows, (ii) komatiitic basalts, and (iii) ultramafic–mafic pillow lavas. The rocks have a wide range of textures including random olivine spinifex, layered olivine spinifex, random and string-beef pyroxene spinifex, micrographic intergrowths of plagioclase and clinopyroxene, and cumulate textures. MgO contents range from 7.1 wt % in basalts and gabbros in differentiated flows to 38.0 wt % in cumulates, flow margins and samples with olivine spinifex textures. The MgO content of the parental melt is estimated using the Fo content of olivine (89–91) to be between 20 and 25 wt %, and the higher MgO content in spinifex samples (30 to 36 wt %) is attributed to accumulation of olivine. The rocks have low Al2O3/TiO2 and are relatively depleted in heavy rare earth elements. They, therefore, are classified as Al-depleted komatiite, the first report of this magma type in a Phanerozoic locality. These characteristics are attributed to the presence of garnet in the source during mantle melting and melt extraction. The rocks also have relatively low contents of the more incompatible trace elements indicating derivation from a depleted source. Our study indicates that the parental magma formed by 10% to (about) 20% partial melting in a mantle plume at pressures of about 4 to 5 GPa (depths of 120–150 km). Ascent of the plume into the Late Paleozoic subduction zone at the margin of the Paleo-Tethys Ocean is a possible petrogenetic model for the generation of these komatiites.