bluuebunny/crossref_metadata_2025_split huggingface dataset:
BPG4 regulates chloroplast development and homeostasis by suppressing GLK transcription factors and involving light and brassinosteroid signaling
Authors: Tachibana Ryo , Abe Susumu , Marugami Momo , Yamagami Ayumi , Akema Rino , Ohashi Takao , Nishida Kaisei , Nosaki Shohei , Miyakawa Takuya , Tanokura Masaru , Kim Jong-Myong , Seki Motoaki , Inaba Takehito , Matsui Minami , Ifuku Kentaro , Kushiro Tetsuo , Asami Tadao , Nakano Takeshi 
Published: January 2024

AbstractChloroplast development adapts to the environment for performing suitable photosynthesis. Brassinosteroids (BRs), plant steroid hormones, have crucial effects on not only plant growth but also chloroplast development. However, the detailed molecular mechanisms of BR signaling in chloroplast development remain unclear. Here, we identify a regulator of chloroplast development, BPG4, involved in light and BR signaling. BPG4 interacts with GOLDEN2-LIKE (GLK) transcription factors that promote the expression of photosynthesis-associated nuclear genes (PhANGs), and suppresses their activities, thereby causing a decrease in the amounts of chlorophylls and the size of light-harvesting complexes. BPG4 expression is induced by BR deficiency and light, and is regulated by the circadian rhythm. BPG4 deficiency causes increased reactive oxygen species (ROS) generation and damage to photosynthetic activity under excessive high-light conditions. Our findings suggest that BPG4 acts as a chloroplast homeostasis factor by fine-tuning the expression of PhANGs, optimizing chloroplast development, and avoiding ROS generation.
Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming
Authors: Tian Jing , Dungait Jennifer A. J. , Hou Ruixing , Deng Ye , Hartley Iain P. , Yang Yunfeng , Kuzyakov Yakov , Zhang Fusuo , Cotrufo M. Francesca , Zhou Jizhong 
Published: January 2024

AbstractIncreasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.
Neutrophil activation and clonal CAR-T re-expansion underpinning cytokine release syndrome during ciltacabtagene autoleucel therapy in multiple myeloma
Authors: Yang Shuangshuang , Xu Jie , Dai Yuting , Jin Shiwei , Sun Yan , Li Jianfeng , Liu Chenglin , Ma Xiaolin , Chen Zhu , Chen Lijuan , Hou Jian , Mi Jian-Qing , Chen Sai-Juan 
Published: January 2024

AbstractCytokine release syndrome (CRS) is the most common complication of chimeric antigen receptor redirected T cells (CAR-T) therapy. CAR-T toxicity management has been greatly improved, but CRS remains a prime safety concern. Here we follow serum cytokine levels and circulating immune cell transcriptomes longitudinally in 26 relapsed/refractory multiple myeloma patients receiving the CAR-T product, ciltacabtagene autoleucel, to understand the immunological kinetics of CRS. We find that although T lymphocytes and monocytes/macrophages are the major overall cytokine source in manifest CRS, neutrophil activation peaks earlier, before the onset of severe symptoms. Intracellularly, signaling activation dominated by JAK/STAT pathway occurred prior to cytokine cascade and displayed regular kinetic changes. CRS severity is accurately described and potentially predicted by temporal cytokine secretion signatures. Notably, CAR-T re-expansion is found in three patients, including a fatal case characterized by somatic TET2-mutation, clonal expanded cytotoxic CAR-T, broadened cytokine profiles and irreversible hepatic toxicity. Together, our findings show that a latent phase with distinct immunological changes precedes manifest CRS, providing an optimal window and potential targets for CRS therapeutic intervention and that CAR-T re-expansion warrants close clinical attention and laboratory investigation to mitigate the lethal risk.
Single-cell mapping of lipid metabolites using an infrared probe in human-derived model systems
Authors: Bai Yeran , Camargo Carolina M. , Glasauer Stella M. K. , Gifford Raymond , Tian Xinran , Longhini Andrew P. , Kosik Kenneth S. 
Published: January 2024

AbstractUnderstanding metabolic heterogeneity is the key to uncovering the underlying mechanisms of metabolic-related diseases. Current metabolic imaging studies suffer from limitations including low resolution and specificity, and the model systems utilized often lack human relevance. Here, we present a single-cell metabolic imaging platform to enable direct imaging of lipid metabolism with high specificity in various human-derived 2D and 3D culture systems. Through the incorporation of an azide-tagged infrared probe, selective detection of newly synthesized lipids in cells and tissue became possible, while simultaneous fluorescence imaging enabled cell-type identification in complex tissues. In proof-of-concept experiments, newly synthesized lipids were directly visualized in human-relevant model systems among different cell types, mutation status, differentiation stages, and over time. We identified upregulated lipid metabolism in progranulin-knockdown human induced pluripotent stem cells and in their differentiated microglia cells. Furthermore, we observed that neurons in brain organoids exhibited a significantly lower lipid metabolism compared to astrocytes.
Functional neuronal circuits emerge in the absence of developmental activity
Authors: Barabási Dániel L. , Schuhknecht Gregor F. P. , Engert Florian 
Published: January 2024

AbstractThe complex neuronal circuitry of the brain develops from limited information contained in the genome. After the genetic code instructs the birth of neurons, the emergence of brain regions, and the formation of axon tracts, it is believed that temporally structured spiking activity shapes circuits for behavior. Here, we challenge the learning-dominated assumption that spiking activity is required for circuit formation by quantifying its contribution to the development of visually-guided swimming in the larval zebrafish. We found that visual experience had no effect on the emergence of the optomotor response (OMR) in dark-reared zebrafish. We then raised animals while pharmacologically silencing action potentials with the sodium channel blocker tricaine. After washout of the anesthetic, fish could swim and performed with 75–90% accuracy in the OMR paradigm. Brain-wide imaging confirmed that neuronal circuits came ‘online’ fully tuned, without requiring activity-dependent plasticity. Thus, complex sensory-guided behaviors can emerge through activity-independent developmental mechanisms.
A micro-architectured material as a pressure vessel for green mobility
Authors: Jeong Yoon Chang , Han Seung Chul , Wu Cheng Han , Kang Kiju 
Published: January 2024

AbstractA shellular is a micro-architectured material, composed of a continuous smooth-curved thin shell in the form of a triply periodic minimal surface. Thanks to the unique geometry, a shellular can support external load by co-planar stresses, unlike microlattice, nanolattice, and mechanical metamaterial. That is, the shellular is the only stretching-dominated material with the highest strength at a density of less than 10−2 g/cc. Therefore, it is expected to support internal pressure, too, by the bi-axial tensile stresses like a balloon. For more than 300 years, spherical and cylindrical vessels have been viable yet compromised options for storing pressurized gases. However, emerging green mobility necessitates a safer and more spatially conformable storage solution for hydrogen than spherical and cylindrical vessels these conventional vessels. In this study, we propose to use the shellular as a pressure vessel. Due to the distinct topological nature – periodic micro-cells constituting the triply periodic minimal surface, the alternative pressure vessel can be tailored individually for spatial requirements while ensuring safety with leak-before-break. For a given constituent material and prescribed pressure, the achievable internal volume-per-total weight of a P-surfaced, cold-stretched, double-chambered shellular vessel with a number of cells more than 15 × 15 × 15 can exceed the practical upper bound of both spherical and cylindrical vessels. For the applications, a thin shell with the large surface area of this micro-architecture is ideal for interfacial transfer of heat or mass between its two sub-volumes under internal pressure.
Diagnostic utility of 7T neuromelanin imaging of the substantia nigra in Parkinson’s disease
Authors: Lakhani Dhairya A. , Zhou Xiangzhi , Tao Shengzhen , Patel Vishal , Wen Sijin , Okromelidze Lela , Greco Elena , Lin Chen , Westerhold Erin M. , Straub Sina , Wszolek Zbigniew K. , Tipton Philip W. , Uitti Ryan J. , Grewal Sanjeet S. , Middlebrooks Erik H. 
Published: January 2024

AbstractParkinson’s disease (PD) is a prevalent neurodegenerative disorder that presents a diagnostic challenge due to symptom overlap with other disorders. Neuromelanin (NM) imaging is a promising biomarker for PD, but adoption has been limited, in part due to subpar performance at standard MRI field strengths. We aimed to evaluate the diagnostic utility of ultra-high field 7T NM-sensitive imaging in the diagnosis of PD versus controls and essential tremor (ET), as well as NM differences among PD subtypes. A retrospective case-control study was conducted including PD patients, ET patients, and controls. 7T NM-sensitive 3D-GRE was acquired, and substantia nigra pars compacta (SNpc) volumes, contrast ratios, and asymmetry indices were calculated. Statistical analyses, including general linear models and ROC curves, were employed. Twenty-one PD patients, 13 ET patients, and 18 controls were assessed. PD patients exhibited significantly lower SNpc volumes compared to non-PD subjects. SNpc total volume showed 100% sensitivity and 96.8% specificity (AUC = 0.998) for differentiating PD from non-PD and 100% sensitivity and 95.2% specificity (AUC = 0.996) in differentiating PD from ET. Contrast ratio was not significantly different between PD and non-PD groups (p = 0.07). There was also significantly higher asymmetry index in SNpc volume in PD compared to non-PD cohorts (p < 0.001). NM signal loss in PD predominantly involved the inferior, posterior, and lateral aspects of SNpc. Akinetic-rigid subtype showed more significant NM signal loss compared to tremor dominant subtype (p < 0.001). 7T NM imaging demonstrates potential as a diagnostic tool for PD, including potential distinction between subtypes, allowing improved understanding of disease progression and subtype-related characteristics.
Testing the effectiveness of interactive training on sexual harassment and assault in field science
Authors: Cronin Melissa R. , Zavaleta Erika S. , Beltran Roxanne S. , Esparza Melanie , Payne Allison R. , Termini Valerie , Thompson Joseph , Jones Megan S. 
Published: January 2024

Abstract
Fieldwork is a critical tool for scientific research, particularly in applied disciplines. Yet fieldwork is often unsafe, especially for members of historically marginalized groups and people whose presence in scientific spaces threatens traditional hierarchies of power, authority, and legitimacy. Research is needed to identify interventions that prevent sexual harassment and assault from occurring in the first place. We conducted a quasi-experiment assessing the impacts of a 90-min interactive training on field-based staff in a United States state government agency. We hypothesized that the knowledge-based interventions, social modeling, and mastery experiences included in the training would increase participants’ sexual harassment and assault prevention knowledge, self-efficacy, behavioural intention, and behaviour after the training compared to a control group of their peers. Treatment–control and pre-post training survey data indicate that the training increased participants’ sexual harassment and assault prevention knowledge and prevention self-efficacy, and, to a lesser extent, behavioural intention. These increases persisted several months after the training for knowledge and self-efficacy. While we did not detect differences in the effect of the training for different groups, interestingly, post-hoc tests indicated that women and members of underrepresented racial groups generally scored lower compared to male and white respondents, suggesting that these groups self-assess their own capabilities differently. Finally, participants’ likelihood to report incidents increased after the training but institutional reports remained low, emphasizing the importance of efforts to transform reporting systems and develop better methods to measure bystander actions. These results support the utility of a peer-led interactive intervention for improving workplace culture and safety in scientific fieldwork settings.

Protocol registration
"The stage 1 protocol for this Registered Report was accepted in principle on August 24, 2022. The protocol, as accepted by the journal, can be found at: https://doi.org/10.6084/m9.figshare.21770165.
Exploring health literacy categories among an Iranian adult sample: a latent class analysis
Authors: Yekaninejad Mir Saeed , Hajiheidari Ahmadreza , Alijanzadeh Mehran , Yahaghi Rafat , Karimi Zahra , Rahmani Jalal , Yazdi Nahid , Jafari Elahe , Alijani Hashem , Zamani Narges , Fotuhi Razie , Taherkhani Elham , Buchali Zeinab , Zarenejad Masoume , Mahmoudi Narges , Shahmahdi Najmeh , Poorzolfaghar Leila , Ahmadizade Safie , Shahbazkhania Azam , Potenza Marc N. , Lin Chung-Ying , Pakpour Amir H. 
Published: January 2024

AbstractGeneral and electronic health literacy are important factors engaging in healthy behaviors and maintaining good health. The present study explored demographic factors associated with general and electronic health literacy in the Iranian adult population. Via stratified cluster sampling, trained interviewers visited adult residents in Qazvin Province, Iran between January, and April 2022. The participants (N = 9775; mean age = 36.44 years; 6576 [67.3%] females) completed the Health Literacy Instrument for Adults (HELIA) assessing health literacy and the eHealth Literacy Scale (eHEALS) assessing electronic health literacy. Demographic data, including age, gender, educational level, marital status, and living location (city or rural), were collected. Latent class analysis (LCA) was used to classify the participants into different health literacy/electronic health literacy levels. The relationships between health literacy/electronic health literacy levels and demographic factors were examined using χ2or analysis of variance. The LCA used HELIA scores to suggest five classes of health literacy and eHEALS scores to suggest three classes of electronic health literacy. For general and electronic health literacy, similar relationships were with demographic factors: females as compared with males had better general/electronic health literacy; younger people as compared with older people had better general/electronic health literacy; higher educational level was associated with better general/electronic health literacy; and city residents as compared with rural residents had better general/electronic health literacy. In conclusion, Iranian governmental agencies may wish to target on males, older adults, people with low educational level, and rural residents to improve their health literacy.
A robust microbiome signature for autism spectrum disorder across different studies using machine learning
Authors: Peralta-Marzal Lucia N. , Rojas-Velazquez David , Rigters Douwe , Prince Naika , Garssen Johan , Kraneveld Aletta D. , Perez-Pardo Paula , Lopez-Rincon Alejandro 
Published: January 2024

AbstractAutism spectrum disorder (ASD) is a highly complex neurodevelopmental disorder characterized by deficits in sociability and repetitive behaviour, however there is a great heterogeneity within other comorbidities that accompany ASD. Recently, gut microbiome has been pointed out as a plausible contributing factor for ASD development as individuals diagnosed with ASD often suffer from intestinal problems and show a differentiated intestinal microbial composition. Nevertheless, gut microbiome studies in ASD rarely agree on the specific bacterial taxa involved in this disorder. Regarding the potential role of gut microbiome in ASD pathophysiology, our aim is to investigate whether there is a set of bacterial taxa relevant for ASD classification by using a sibling-controlled dataset. Additionally, we aim to validate these results across two independent cohorts as several confounding factors, such as lifestyle, influence both ASD and gut microbiome studies. A machine learning approach, recursive ensemble feature selection (REFS), was applied to 16S rRNA gene sequencing data from 117 subjects (60 ASD cases and 57 siblings) identifying 26 bacterial taxa that discriminate ASD cases from controls. The average area under the curve (AUC) of this specific set of bacteria in the sibling-controlled dataset was 81.6%. Moreover, we applied the selected bacterial taxa in a tenfold cross-validation scheme using two independent cohorts (a total of 223 samples—125 ASD cases and 98 controls). We obtained average AUCs of 74.8% and 74%, respectively. Analysis of the gut microbiome using REFS identified a set of bacterial taxa that can be used to predict the ASD status of children in three distinct cohorts with AUC over 80% for the best-performing classifiers. Our results indicate that the gut microbiome has a strong association with ASD and should not be disregarded as a potential target for therapeutic interventions. Furthermore, our work can contribute to use the proposed approach for identifying microbiome signatures across other 16S rRNA gene sequencing datasets.
The prognostic evaluation of ALBI score in endoscopic treatment of esophagogastric varices hemorrhage in liver cirrhosis
Authors: Liu Yuhua , Wu Shengnan , Cai Shanshan , Xie Bushan 
Published: January 2024

AbstractTo analyze the independent risk factors for recurrent bleeding and death within 1 year after endoscopic treatment of esophagogastric varices hemorrhage (EGVB) in patients with liver cirrhosis, and to validate the predictive value of ALBI score for recurrent bleeding and death within 1 year after endoscopic treatment of EGVB in patients with liver cirrhosis. A total of 338 patients with EGVB who received endoscopic treatment for the first time in the Department of Gastroenterology, First Affiliated Hospital of Nanchang University from January 1, 2016 to March 1, 2020 were selected. A database was established to analyze the patients’ demographic data, surgical variables and postoperative outcomes. All patients were contacted and followed up to verify the predictive value of ALBI score for recurrent bleeding and mortality. 130 patients had rebleeding within 1 year after surgery (38.5%). 66 patients died within 1 year after surgery (19.5%). Patients with ALBI grade 3 had significantly higher rebleeding and mortality rates than those with grades 1 and 2. The AUC was used to compare the predictive value of the four scores for rebleeding and mortality within one year after endoscopic surgery. Both ALBI scores had the largest AUC. The ALBI score has certain predictive value for rebleeding and mortality within 1 year after endoscopic therapy in patients with cirrhotic EGVB.
Validated assays for the quantification of C9orf72 human pathology
Authors: Salomonsson S. E. , Maltos A. M. , Gill K. , Aladesuyi Arogundade O. , Brown K. A. , Sachdev A. , Sckaff M. , Lam K. J. K. , Fisher I. J. , Chouhan R. S. , Van Laar V. S. , Marley C. B. , McLaughlin I. , Bankiewicz K. S. , Tsai Y.-C. , Conklin B. R. , Clelland C. D. 
Published: January 2024

AbstractA repeat expansion mutation in the C9orf72 gene is the leading known genetic cause of FTD and ALS. The C9orf72-ALS/FTD field has been plagued by a lack of reliable tools to monitor this genomic locus and its RNA and protein products. We have validated assays that quantify C9orf72 pathobiology at the DNA, RNA and protein levels using knock-out human iPSC lines as controls. Here we show that single-molecule sequencing can accurately measure the repeat expansion and faithfully report on changes to the C9orf72 locus in what has been a traditionally hard to sequence genomic region. This is of particular value to sizing and phasing the repeat expansion and determining changes to the gene locus after gene editing. We developed ddPCR assays to quantify two major C9orf72 transcript variants, which we validated by selective excision of their distinct transcriptional start sites. Using validated knock-out human iPSC lines, we validated 4 commercially available antibodies (of 9 tested) that were specific for C9orf72 protein quantification by Western blot, but none were specific for immunocytochemistry. We tested 15 combinations of antibodies against dipeptide repeat proteins (DPRs) across 66 concentrations using MSD immunoassay, and found two (against poly-GA and poly-GP) that yielded a 1.5-fold or greater signal increase in patient iPSC-motor neurons compared to knock-out control, and validated them in human postmortem and transgenic mouse brain tissue. Our validated DNA, RNA and protein assays are applicable to discovery research as well as clinical trials.