bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change
Authors: Minot Samuel S. , Li Naisi , Sriniva Harini , Ayers Jessica L. , Yu Ming , Koester Sean , Stangis Mary M. , Dominitz Jason , Halberg Richard B. , Grady William M. , Dey Neelendu 
Published: January 2024

Abstract

BACKGROUND & AIMS. The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC). While a robust body of research has identified several different CRC-associated bacterial species, the full scope of the host-microbial dialogue in CRC is unknown. Here we aimed to define the scale and membership of the body of CRC-associated and health-associated gut bacteria in global populations.
METHODS. We perform a microbiome-CRC correlation analysis of deep shotgun metagenomic sequencing data from published global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters significantly enriched in either CRC or in health. We validate predicted microbiome effects in preclinical CRC models and interrogate mechanism via colonic gene expression profiling (including through single-cell RNAseq) and using organoid co-culture systems.
RESULTS. Here we link an unprecedented ~40% of gut bacteria to CRC (split nearly evenly as CRC-associated or health-associated). These microbes encode 2,319 co-abundant genes (CAGs) encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We validate tumorigenicity of previously unimplicated bacteria in preclinical models. Single-cell RNA sequencing disclosed microbiome-induced senescence in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice.
CONCLUSIONS. Our findings suggest that an astounding ~40% of gut bacteria may be carcinogenic or chemoprotective. Many of these had not previously been linked to CRC, thus expanding the scope of “known unknowns” of CRC-associated microbes. These results offer proof-of-principle for gene-level metagenomic analysis enabling wide-ranging discovery of microbiome-induced precancerous effects and cancer prevention opportunities.
Growth reduction of Vibrionaceae and microflora diversification in ice-stored Pacific white shrimp (Penaeus vannamei) treated with low-frequency electric field
Authors: Xu Lijuan , Chen Haiqiang , Liang Zuanhao , Chen Shanshan , Xia Yu , Zhu Siming , Yu Ming 
Published: January 2024

Abstract
A novel storage technique combining low-frequency electric field (LFEF) and ice temperature was applied to extend the shelf life of Pacific white shrimp (Penaeus vannamei). Changes in microbial community composition was investigated in Pacific white shrimp treated with LFEF in combination with ice temperature. LFEF treatment increased diversity of microbial communities and reduced abundance of major spoilage bacteria in Penaeus vannamei. The spoilage microorganisms of shripm samples stored at ice temperature for 11 days included Aliivibrio, Pseudoalteromonas, Photobacterium, Moritella and Psychrobacter. However, Pseudoalteromonas and Psychrobacter were dominant in LFEF-treated samples. Furthermore, due to the modulation of the microbial community by LFEF and ice temperature storage, the microbial structure in shrimp muscle did not tend to be simplistic. In conclusion, LFEF as an auxiliary technology for low temperature preservation is a reliable and potential method for preserving the quality of aquatic products.
The miR-183/96/182 cluster regulates sensory innervation, resident myeloid cells and functions of the cornea through cell-type-specfic target genes
Authors: Gupta Naman , Somayajulu Mallika , Gurdziel Katherine , LoGrasso Giovanni , Aziz Haidy , McClellan Sharon , Pitchaikannu Ahalya , Santra Manoranjan , Shukkur Muhammed , Hazlett Linda , Xu Shunbin 
Published: January 2024

Abstract
The conserved miR-183/96/182 cluster (miR-183C) is expressed in both corneal resident myeloid cells (CRMCs) and sensory nerves (CSN) and modulates corneal immune/inflammatory responses. To uncover cell type-specific roles of miR-183C in CRMC and CSN and their contribute to corneal physiology, myeloid-specific miR-183C conditional knockout (MS-CKO), and sensory nerve-specific CKO (SNS-CKO) mice were produced and characterized in comparison to the conventional miR-183C KO. Immunofluorescence and confocal microscopy of flatmount corneas, corneal sensitivity, and tear volume assays were performed in young adult naïve mice; 3’RNA sequencing (Seq) in the trigeminal ganglion (TG), cornea and CRMCs. Our results showed that, similar to conventional KO mice, the numbers of CRMCs were increased in both MS-CKO and SNS-CKO vs age- and sex-matched WT control littermates, suggesting intrinsic and extrinsic regulations of miR-183C on CRMCs. In the miR-183C KO and SNS-CKO, but not the MS-CKO mice, CSN density was decreased in the epithelial layer of the cornea, but not the stromal layer. Functionally, corneal sensitivity and basal tear volume were reduced in the KO and SNS-CKO, but not the MS-CKO mice. Tear volume in males is consistently higher than female WT mice. Bioinformatic analyses of the transcriptomes revealed a series of cell-type specific target genes of miR-183C in TG sensory neurons and CRMCs. Our data elucidate that miR-183C imposes intrinsic and extrinsic regulation on the establishment and function of CSN and CRMCs by cell-specific target genes. miR-183C modulates corneal sensitivity and tear production through its regulation of corneal sensory innervation.
Bacterial association with metals enables in vivo monitoring of microbiota using magnetic resonance imaging
Authors: Goldhawk Donna , Donnelly Sarah , Nassar Moayyad , Hassan Salvan , Gelman Neil , Thiessen Jonathan , Thompson R. , Prato Frank , Burton Jeremy 
Published: January 2024

Abstract

Bacteria constitute a significant part of the biomass of the human microbiota, but their interactions are complex and difficult to replicate outside the host. Exploiting the superior resolution of magnetic resonance imaging (MRI) to examine signal parameters of selected human isolates may allow tracking of their dispersion throughout the body. We investigated longitudinal and transverse MRI relaxation rates and found significant differences between several bacterial strains. Common commensal strains of lactobacilli display notably high MRI relaxation rates, partially explained by elevated cellular manganese content, while other species contain more iron than manganese. Lactobacillus crispatus show particularly high values, 4-fold greater than any other species; up to 60-fold greater signal than relevant tissue background; and a linear relationship between relaxation rate and fraction of live cells. Different bacterial strains have detectable, repeatable MRI relaxation rates that in the future may enable monitoring of their persistence in the human body for enhanced molecular imaging.
Pollution load estimation and influencing factors analysis in the Tuhai River Basin in Shandong Province of China based on improved output coefficient method
Authors: Wang Xi , Zhang Xiaoyu , Gao Xiaomei , Dong Shifan , Zhang Yushuo , Xu Weiying 
Published: January 2024

Abstract
Estimating the pollution loads in the Tuhai River is essential for developing a water quality standard scheme. This study utilized the improved output coefficient method to estimate the total pollution loads in the river basin while analyzing the influencing factors based on the STIRPAT (Stochastic Impacts by Regression on Population, Affluence, and Technology) model. Findings indicated that the projected point source pollution loads for total phosphorus, COD, and ammonia nitrogen would amount to 3937.22 t, 335523.25 t, and 13946.92 t in 2021, respectively. Among these, COD pollution would pose the greatest concern. The primary contributors to the pollution loads were rural scattered life, large-scale livestock and poultry breeding, and surface runoff. Per capita GDP emerged as the most influential factor affecting the pollution loads, followed by cultivated land area, while the urbanization rate demonstrated the least impact.
Hierarchical First-order and Second-order Topological States in Symmetry-Controllable Grain Boundary
Authors: Kim Hyo Won , Jang Won-Jun , Noh Heeyoon , Kang Seoung-Hun , Ko Wonhee , Park Moon Jip 
Published: January 2024

Abstract

The discovery of topological states localized at the boundaries and dislocations is of paramount importance in the physics of topological phases. Structural imperfections can be a promising testbed to engineer the symmetries and the concomitant topological states, as they genuinely exist in solid-state matters. Here, we present the direct evidence of hierarchical first-order and second-order topological states in symmetry–enforced grain boundaries (GB) of 1T′–MoTe2. Guided by exerted scanning tunneling microscope (STM)–tip press and pulse, we construct two distinct types of GBs, which are differentiated by the underlying symmorphic and nonsymmorphic symmetries. The GBs with the nonsymmorphic rotation symmetry harbor the first-order topological edge state protected by nonsymmorphic band degeneracy. On the other hand, the edge state of the symmorphic GBs attains the band gap. More interestingly, the gapped edge state realizes the second-order topological phase, shown by the additional corner states at the GB ends. We anticipate our experiment will pioneer the material platform for the hierarchical realization of the first-order and higher-order topology.
The risk of micro/nanoplastics to human sperm and the intervention against their toxicity using magnetic Fe3O4 nanoparticles
Authors: Chen Ying , Cheng Cheng , Xu Wenqing , Cui Yanfan , Tian Yan , Jiang Yulin , Yuan Yangyang , Qian Ruirui , Wang Yujie , Zheng Liping , Chen Houyang , Luo Tao 
Published: January 2024

Abstract
Micro/nanoplastics (MNPs) are novel hazardous materials that pose multiple environmental challenges. Polystyrene (PS)-MNPs (especially those with sizes less than 10 µm) reduce male fertility in murine models. More importantly, microplastics contaminate male reproductive tissues, but whether MNPs truly affect male reproduction in humans is poorly understood. In this study, we aimed to evaluate the risk of human sperm exposure to NMPs and explore interventions for their toxicity. Using a coculture system, we exposed human sperm to synthetic PS-MNPs, environmental MNPs from disposable paper cups, and a combination of PS-MNPs and bisphenol A (a commonly used plastic additive). In addition, this study examined the ability of magnetic Fe3O4 nanoparticles to prevent the toxicity of PS-MNPs to human sperm. The results showed that human semen contains approximately 3.6 µg/mL PS-MNPs with sizes less than 10 µm. PS-MNPs of 25–100 nm can penetrate human sperm, while those of 0.5–10 µm can bind to the sperm surface. Only 25-nm PS-NPs significantly affect human sperm functions and physiological parameters at semen-relevant concentration. The 25-nm PS-NPs also exhibited synergistic toxicity with bisphenol A on human sperm. However, environmental MNPs released from disposable paper cups do not pose a significant hazard to human sperm. Furthermore, magnetic Fe3O4 nanoparticles could aggregate and coprecipitate with 25-nm PS-NPs to eliminate their adverse effects on human sperm. Here, we demonstrated the potential risk of PS-MNPs to male reproduction in humans and provided an effective intervention strategy against their toxicity.
Insights into the Epidemiology, Survival, and Prognostic Factors of T-Lymphoblastic Lymphoma in a Multicenter Retrospective Study: Evaluation of Chidamide as a Promising Therapeutic Avenue
Authors: Huang Yilan , Chen Feili , Huang Ling , Yang Yong , Zhou Shengsheng , Wu Jingsong , Zhao Zhenyu , Li ChengPing , Cheng Shuqin , Zhang Hongyu , Shi Keqian , Wei Xiaolei , Yang Hui , Jiang Yirong , Guo Hanguo , Jiang Xinmiao , Wei Xiaojuan , Liu Sichu , Lin Caidi , Liang Zhanli , Wang Ning , Pan Lu , Li Wenyu 
Published: January 2024

Abstract
Objective
The primary objective of this retrospective multicenter study was to elucidate the epidemiological characteristics, survival outcomes and prognostic factors of T-cell lymphoblastic lymphoma (T-LBL) patients in real-world settings. Furthermore, a secondary aim was to comprehensively evaluate the clinical management strategies, and therapeutic effectiveness of the combination therapy involving Chidamide and chemotherapy.
Methods
The study analyzed a cohort of 118 newly diagnosed T-LBL patients from multiple clinical centers between 2009 and 2022, among whom 17 patients received Chidamide. A comprehensive assessment of patient demographics, treatment schedules, treatment response, prognostic indicators, and prognostic factors was conducted.
Results
The 5-year progression-free survival (PFS) and overall survival (OS) rates for the entire cohort were 44.4% and 50.4%. The combination therapy of Chidamide and chemotherapy demonstrated promising outcomes, yielding an 88.2% overall response rate (ORR) and a 70.6% complete remission rate (CRR), indicating its effectiveness and safety for T-LBL treatment. The median PFS and the median OS were considerably longer in the Chidamide group (123.7 months and NE) than the reference group. In addition, the study revealed that peripheral blood neutrophil-to-lymphocyte ratio (NLR) ≥ 4.07 was an independent prognostic factor negatively impacting patients' PFS and OS, with risk ratios of 3.26 (95% CI 1.79–5.95, p < 0.001) and 3.78 (95% CI 1.95–7.30, p < 0.001).
Conclusion
This retrospective multicenter analysis provides compelling evidence that Chidamide, used in conjunction with chemotherapy, is an efficacious treatment modality for T-LBL. Moreover, peripheral blood NLR serves as a valuable independent prognostic factor for predicting T-LBL patient outcomes.
Exploring the cost and emissions impacts, feasibility, and scalability of battery-electric ships
Authors: Park Won Young , Moon Hee Seung , Hendrickson Thomas , Phadke Amol , Popovich Natalie 
Published: January 2024

Abstract

The United States’ ambitious greenhouse gas (GHG) emission reduction goals, along with targets set by the International Maritime Organization, create an opportunity to explore battery-electric options for the shipping sector. In this study, we generate a life cycle model of costs and GHG emissions from shipping electrification. We estimate that electrifying 6,323 domestic ships under 1,000 gross tonnage would reduce U.S. domestic maritime sector GHG emissions by up to 75% by 2035 from 2022 levels. By 2035, electrifying up to 85% of these 6,323 ships will become cost effective versus internal combustion ships if they cover 99% of historical trips and charge from a deeply decarbonized grid. We also find that charging demands from electrifying these ships will be concentrated at just 20 of 150 major ports nationwide. Further research is recommended to identify optimal locations based on vessel needs and local grid emissions.
Small molecules with hydantoin-containing and spiro-like structures promote devernalization in Arabidopsis
Authors: Shirakawa Makoto , Otsuka Nana , Yamaguchi Ryoya , Sawa Hikaru , Kadofusa Naoya , Kato Nanako , Sato Ayato , Ito Toshiro 
Published: January 2024

Abstract

Monocarpic plants flower only once and then produce seeds. Many monocarpic plants require a cold treatment known as vernalization before they flower. This requirement delays flowering until the plant is exposed to warm temperatures in the spring. Exposure to high temperature following vernalization causes devernalization, which cancels the vernalized state, resulting in delayed flowering and the resumption of vegetative growth. In this study, we screened over 16,000 chemical compounds and identified five small molecules (devernalizers; DVRs) that induce devernalization at room temperature without requiring a high-temperature treatment. Treatment with DVRs reactivated the expression of FLOWERING LOCUS C (FLC), a master repressor of flowering, and delayed flowering time. Three of the DVRs share two structures: a hydantoin-like region and a spiro-like carbon. Treatment with DVR06, which has a simple chemical structure that includes these structures, delayed flowering time, and reduced the amount of repressive histone modification at FLC. Our extensive chemical screening revealed that hydantoin and spiro are key chemical signatures that reduce repressive histone modifications and promote devernalization in plants.
The Universal Zero Markup Drug Policy and Gastric Cancer Hospitalization Expenses: An Analysis of Trends and Influencing Factors in Shanghai from 2014 to 2021
Authors: Gu Yichun , Hao Jiajun , He Da , Sun Hui , Cui Xin , Tian Wenqi , Zhang Yulin , Jin Chunlin , Wang Haiyin 
Published: January 2024

Abstract
Background
The increasing hospitalization expenses for Gastric Cancer (GC) cause a serious economic burden on society. Although the Chinese government has implemented the Universal Zero Markup Drug Policy (UZMDP) to control the growth of hospitalization expenditures, they remain a rising trend. It’s crucial to identify the factors influencing the hospitalization expenses of GC patients. This study aimed to analyze the trends and factors influencing hospitalization expenses of GC patients in Shanghai from 2014 to 2021.
Methods
Study data were sourced from the Health Network of Shanghai Economic Information Center. We employed interrupted time series analysis (ITSA) to analyze the trends in various medical expenditures before and after the implementation of UZMDP. The degree of association between various medical expenditures and hospitalization expenditures of GC patients was calculated by using the new gray relational analysis (GRA). Furthermore, we used multiple linear regression to identify the influencing factors of hospitalization expenses for GC patients.
Results
Our study included a total of 23,335 participants. The ITSA results showed an increasing trend in hospitalization expenses following the implementation of UZMDP. Drug expenses decreased instantaneously with the implementation of UZMDP, but subsequently began to trend upwards. After UZMDP, the expenses of medical consumables, examinations, and healthcare services all showed an upward trend. The new GRA indicated that the influencing factors of hospitalization expenses were drug expenses, consumable expenses, healthcare service expenses, and examination expenses in sequence. Multiple linear regression analysis showed that GC patients aged 60 or below had lower hospitalization expenses (Coefficient=-780.06, P = 0.0398). However, factors influencing increased hospitalization expenses included longer length of stay (Coefficient = 1753.01, P < 0.001), surgeries (Coefficient = 29047.26, P < 0.001), and hospitalization in the tertiary hospitals (Coefficient = 25485.19, P < 0.001) or secondary hospitals (Coefficient = 17755.12, P < 0.001).
Conclusions
Hospitalization expenses of GC patients in Shanghai have been rising annually from 2014 to 2021. Despite the implementation of the UZMDP policy, drug expenses remain a major factor in escalating hospitalization expenses. The hospitalization expenses of GC patients are significantly influenced by several factors, including the demographic characteristics of patients, the severity of diseases, and the levels of hospitals. These findings provide a scientific basis for effectively managing the hospitalization expenses of GC.
Variations in reproductive output in alpine populations of Ranunculus acris
Authors: Vassvik Linn , Nielsen Anders , Östman Silje Andrea Hjortland , Vandvik Vigdis , Halbritter Aud 
Published: January 2024

Abstract
Plant reproduction is affected both directly by small-scale abiotic heterogeneity in the alpine topography (abiotic), and indirectly through flower density and plant-pollinator interactions (biotic). In this study we investigated how different abiotic and biotic factors influence reproductive output in alpine populations of Ranunculus acris over a two-year period. We used ten snowmelt gradients in an alpine area at Finse, southern Norway, where each gradient contained three stages representing three different times of snowmelt. Reproductive output, measured as both seed mass and number of seeds, in alpine R. acris was affected by different factors, varying between years and timing of snowmelt. Higher temperatures during seed maturation resulted in higher reproductive output in both years, with a lower output later in the growing season. We also found a negative correlation between seed mass and R. acris density in the surrounding vegetation in the second year, when flower density was substantially higher than in the first year. We found no signs of pollen limitation, suggesting that pollinators did not limit reproductive output. Our study shows that reproductive output in R. acris is affected by both abiotic and biotic factors, and since timing and length of the flowering period in alpine environments are expected to change due to climate change, this could have further implications for plants in this study system.
Stochastic Properties of Musical Timeseries
Authors: Geisel Theo , Nelias Corentin 
Published: January 2024

Abstract

Musical sequences are correlated dynamical processes that may differ depending on musical styles. We aim to quantify the correlations through power spectral analysis of pitch sequences in a large corpus of musical compositions as well as improvised performances. Using a multitaper method we extend the power spectral estimates down to the smallest possible frequencies optimizing the tradeoff between bias and variance. The power spectral densities reveal a characteristic behavior; they typically follow inverse power laws (1/f β -noise), yet only down to a cutoff frequency, where they end in a plateau (white noise). Correspondingly the pitch autocorrelation function exhibits slow power law decays only up to a cutoff time, beyond which the correlations vanish. We determine cutoff times between 4 and 100 quarter note units for the compositions and improvisations of the corpus, serving as a measure for the degree of persistence and predictability in music. The histogram of exponents β for the power law regimes has a pronounced peak near β = 1 for classical compositions, but is much broader for jazz improvisations.
Syntalos: A software for precise simultaneous multi-modal data acquisition and closed-loop interventions
Authors: Klumpp Matthias , Embray Lee , Simon Justus , Heimburg Filippo , Groh Alexander , Draguhn Andreas , Both Martin 
Published: January 2024

Abstract

Complex experimental protocols often require multi-modal data acquisition with precisely aligned timing, as well as state- and behavior-dependent interventions. Tailored solutions are mostly restricted to individual experimental setups and lack flexibility and interoperability. We present an integrated software solution, called ‘Syntalos’, for simultaneous acquisition of data from an arbitrary number of sources, including multi-channel electrophysiological recordings and different live imaging devices, as well as closed-loop, real-time interventions with different actuators. Precisely matching timestamps for all inputs are ensured by continuous statistical analysis and correction of individual devices’ timestamps. New data sources can be integrated with minimal programming skills. Data is stored in a comprehensively structured format to facilitate pooling or sharing data between different laboratories. Syntalos enables precisely synchronized multi-modal recordings as well as closed-loop interventions for multiple experimental approaches. Preliminary experiments with different research questions show the successful performance and easy-to-learn structure of the software suite.