bluuebunny/crossref_metadata_2025_split huggingface dataset:
c-Fos regulated by TMPO/ERK axis promotes 5-FU resistance via inducing NANOG transcription in colon cancer
Authors: Gui Yanping , Qian Xiaoping , Ding Youxiang , Chen Qianqian , Fangyu Ye  , Ye Yuting , Hou Yingjian , Yu Jun , Zhao Li 
Published: January 2024

AbstractAcquired drug resistance is one of the most common limitations for the clinical response of colon cancer to 5-Fluorouracil (5-FU)-based chemotherapy. The relevant molecular mechanisms might be diversity, but still not be elucidated clearly. In this study, we aimed to investigate the potential mechanisms of c-Fos, a subfamily of activator protein-1, in 5-FU chemoresistance. We determined that phosphorylated c-Fos promoted colon cancer cells resistance to 5-FU by facilitating the cancer stemness. Mechanically, 5-FU treatment induced autolysosome-dependent degradation of TMPO, which subsequently triggered ERK-mediated phosphorylation of c-Fos. Additionally, c-Fos was found to bind to the promoter of NANOG and phosphorylation of c-Fos at Ser 374 was required for its regulation of NANOG expression. NANOG ablation impaired c-Fos/p-c-Fos induced 5-FU resistance and stemness. Taken together, these findings revealed that TMPO-mediated phosphorylation of c-Fos conferred 5-FU resistance by regulating NANOG expression and promoting cell stemness in colon cancer cells. c-Fos could be as a therapeutic target for colon cancer.
BACH2-mediated CD28 and CD40LG axes contribute to pathogenesis and progression of T-cell lymphoblastic leukemia
Authors: Feng Min , Zhang Bailing , Li Guilan , Yang Yan , Liu Jiangyuan , Zhang Ziting , Zhou Bing , Zhang Han 
Published: January 2024

AbstractT-cell acute lymphoblastic leukemia (T-ALL) is an aggressive subtype of ALL characterized by its high heterogeneity and unfavorable clinical features. Despite improved insights in genetic and epigenetic landscapes of T-ALL, the molecular mechanisms that drive malignant T-cell development remain unclear. BTB and CNC homology 2 (BACH2) is a lymphoid-specific transcription repressor recognized as a tumor suppressor in B-cell malignancies, but little is known about its function and regulatory network in T-ALL. Here we found extremely low levels of BACH2 in T-ALL clinical samples and cell lines compared to normal T cells. Overexpression of BACH2 in T-ALL cells not only induced cell growth retardation but also inhibited cancer progression and infiltration in xenografts. Further RNA sequencing (RNA-seq) analysis revealed significant alterations in regulation of defense and immune responses in T-ALL cells upon BACH2 overexpression. Strikingly, CD28 and CD40LG, two essential stimulatory molecules on T cells, were for the first time identified as novel downstream targets repressed by BACH2 in T-ALL cells. Interestingly, both CD28 and CD40LG were indispensable for T-ALL survival, since largely or completely silencing CD28 and CD40LG led to rapid cell death, whereas partial knockdown of them resulted in cell-cycle arrest and enhanced apoptosis. More importantly, BACH2-mediated CD28 and CD40LG signals contributed to cell migration and dissemination of T-ALL cells to the bone marrow, thus adding a new layer to the BACH2-mediated tumor immunoregulation in T-cell malignancies.
Dietary long-chain fatty acids promote colitis by regulating palmitoylation of STAT3 through CD36-mediated endocytosis
Authors: Wei Yuping , Li Jinting , Li Jiao , Liu Chuan , Guo Xingzhou , Liu Zhengru , Zhang Luyun , Bao Shenglan , Wu Xiaohan , Su Wenhao , Wang Xiaoli , Zhang Jixiang , Dong Weiguo 
Published: January 2024

AbstractThe Western diet, characterized by its high content of long-chain fatty acids (LCFAs), is widely recognized as a significant triggering factor for inflammatory bowel disease (IBD). While the link between a high-fat diet and colitis has been observed, the specific effects and mechanisms remain incompletely understood. Our study provides evidence that the diet rich in LCFAs can disrupt the integrity of the intestinal barrier and exacerbate experimental colitis in mice. Mechanistically, LCFAs upregulate the signal transducer and activator of transcription-3 (STAT3) pathway in the inflammatory model, and STAT3 knockout effectively counters the pro-inflammatory effects of LCFAs on colitis. Specifically, palmitic acid (PA), a representative LCFA, enters intestinal epithelial cells via the cluster of differentiation 36 (CD36) pathway and participates in the palmitoylation cycle of STAT3. Inhibiting this cycle using pharmacological inhibitors like 2-Bromopalmitate (2-BP) and ML349, as well as DHHC7 knockdown, has the ability to alleviate inflammation induced by PA. These findings highlight the significant role of dietary LCFAs, especially PA, in the development and progression of IBD. Diet adjustments and targeted modulation offer potential therapeutic strategies for managing this condition.
Synthesis of degradable polymers via 1,5-shift radical isomerization polymerization of vinyl ether derivatives with a cleavable bond
Authors: Uchiyama Mineto , Imai Masato , Kamigaito Masami 
Published: January 2024

AbstractWe report a novel method for synthesizing degradable polymers based on 1,5-shift radical isomerization polymerizations of vinyl ethers with transferable atoms or groups and in-between acid-cleavable ether linkages in the side chains. In particular, vinyl ethers with side chains composed of thiocyano and p-methoxybenzyl ether groups underwent radical isomerization polymerizations via 1,5-shifts, in which a vinyl ether radical abstracted the cyano group intramolecularly to generate a thiyl radical and result in a polymer with a p-methoxybenzyl ether linkage in the main chain. The obtained polymer was easily degraded into low molecular-weight products with HCl solution. Furthermore, the copolymerization with vinyl acetate proceeded via 1,5-shift isomerization to introduce cleavable linkages in the main chains of the copolymers, which were similarly degraded.
Body composition assessment in 6-month-old infants: A comparison of two- and three-compartment models using data from the Baby-bod study
Authors: Herath Manoja P. , Beckett Jeffrey M. , Jayasinghe Sisitha , Byrne Nuala M. , Ahuja Kiran D. K. , Hills Andrew P. 
Published: January 2024

Abstract
Background/Objectives
An appreciation of infant body composition is helpful to understand the ‘quality’ of growth in early life. Air displacement plethysmography (ADP) using PEA POD and the deuterium dilution (DD) technique are commonly used body composition approaches in infants. We evaluated the comparability of body composition assessed using both techniques with two-compartment (2C) and three-compartment (3C) models in 6-month-old infants.

Subjects/Methods
Infant fat mass (FM) and percent fat mass (%FM) obtained from a 2C model using PEA POD (2C-PP) and a 2C model using the deuterium dilution technique (2C-DD) were compared to those derived from a 3C model, and to each other, using Bland-Altman analysis and Deming regression.

Results
Measurements were available from 68 infants (93% Caucasian, 53% male). The mean biases were not significant between any of the method comparisons. However, significant constant and proportional biases were identified in 2C-DD vs 3C and 2C-PP vs 2C-DD, but not in the 2C-PP vs 3C comparison. Furthermore, we observed significant associations between the mean differences and infants’ percent total body water (%TBW).

Conclusions
While no significant between-method mean differences were found in body composition estimates, some comparisons revealed significant constant and proportional biases and notable associations between the mean differences and %TBW were observed. Our results emphasise the importance of method choice, ensuring methodological uniformity in long-term studies, and carefully considering and regulating multiple pre-analytical variables, such as the hydration status of the participants.
Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance
Authors: Tung Angela , Sperry Megan M. , Clawson Wesley , Pavuluri Ananya , Bulatao Sydney , Yue Michelle , Flores Ramses Martinez , Pai Vaibhav P. , McMillen Patrick , Kuchling Franz , Levin Michael 
Published: January 2024

AbstractInformation for organismal patterning can come from a variety of sources. We investigate the possibility that instructive influences for normal embryonic development are provided not only at the level of cells within the embryo, but also via interactions between embryos. To explore this, we challenge groups of embryos with disruptors of normal development while varying group size. Here, we show that Xenopus laevis embryos are much more sensitive to a diverse set of chemical and molecular-biological perturbations when allowed to develop alone or in small groups, than in large groups. Keeping per-embryo exposure constant, we find that increasing the number of exposed embryos in a cohort increases the rate of survival while incidence of defects decreases. This inter-embryo assistance effect is mediated by short-range diffusible signals and involves the P2 ATP receptor. Our data and computational model emphasize that morphogenesis is a collective phenomenon not only at the level of cells, but also of whole bodies, and that cohort size is a crucial variable in studies of ecotoxicology, teratogenesis, and developmental plasticity.
Accelerating process development for 3D printing of new metal alloys
Authors: Guirguis David , Tucker Conrad , Beuth Jack 
Published: January 2024

AbstractAddressing the uncertainty and variability in the quality of 3D printed metals can further the wide spread use of this technology. Process mapping for new alloys is crucial for determining optimal process parameters that consistently produce acceptable printing quality. Process mapping is typically performed by conventional methods and is used for the design of experiments and ex situ characterization of printed parts. On the other hand, in situ approaches are limited because their observable features are limited and they require complex high-cost setups to obtain temperature measurements to boost accuracy. Our method relaxes these limitations by incorporating the temporal features of molten metal dynamics during laser-metal interactions using video vision transformers and high-speed imaging. Our approach can be used in existing commercial machines and can provide in situ process maps for efficient defect and variability quantification. The generalizability of the approach is demonstrated by performing cross-dataset evaluations on alloys with different compositions and intrinsic thermofluid properties.
Thermal responses of dissolved organic matter under global change
Authors: Hu Ang , Jang Kyoung-Soon , Tanentzap Andrew J. , Zhao Wenqian , Lennon Jay T. , Liu Jinfu , Li Mingjia , Stegen James , Choi Mira , Lu Yahai , Feng Xiaojuan , Wang Jianjun 
Published: January 2024

AbstractThe diversity of intrinsic traits of different organic matter molecules makes it challenging to predict how they, and therefore the global carbon cycle, will respond to climate change. Here we develop an indicator of compositional-level environmental response for dissolved organic matter to quantify the aggregated response of individual molecules that positively and negatively associate with warming. We apply the indicator to assess the thermal response of sediment dissolved organic matter in 480 aquatic microcosms along nutrient gradients on three Eurasian mountainsides. Organic molecules consistently respond to temperature change within and across contrasting climate zones. At a compositional level, dissolved organic matter in warmer sites has a stronger thermal response and shows functional reorganization towards molecules with lower thermodynamic favorability for microbial decomposition. The thermal response is more sensitive to warming at higher nutrients, with increased sensitivity of up to 22% for each additional 1 mg L-1 of nitrogen loading. The utility of the thermal response indicator is further confirmed by laboratory experiments and reveals its positive links to greenhouse gas emissions.
Efficient biological carbon export to the mesopelagic ocean induced by submesoscale fronts
Authors: Guo Mingxian , Xing Xiaogang , Xiu Peng , Dall’Olmo Giorgio , Chen Weifang , Chai Fei 
Published: January 2024

AbstractOceanic submesoscale processes are ubiquitous in the North Pacific Subtropical Gyre (NPSG), where the biological carbon pump is generally ineffective. Due to difficulties in collecting continuous observations, however, it remains uncertain whether episodic submesoscale processes can drive significant changes in particulate organic carbon (POC) export into the mesopelagic ocean. Here we present observations from high-frequency Biogeochemical-Argo floats in the NPSG, which captured the enhanced POC export fluxes during the intensifying stages of a submesoscale front and a cyclonic eddy compared to their other life stages. A higher percentage of POC export flux was found to be transferred to the base of mesopelagic layer at the front compared to that at the intensifying eddy and the mean of previous studies (37% vs. ~10%), suggesting that the POC export efficiency was significantly strengthened by submesoscale dynamics. Such findings highlight the importance of submesoscale fronts for carbon export and sequestration in subtropical gyres.
Cochaperones convey the energy of ATP hydrolysis for directional action of Hsp90
Authors: Vollmar Leonie , Schimpf Julia , Hermann Bianca , Hugel Thorsten 
Published: January 2024

AbstractThe molecular chaperone and heat shock protein Hsp90 is part of many protein complexes in eukaryotic cells. Together with its cochaperones, Hsp90 is responsible for the maturation of hundreds of clients. Although having been investigated for decades, it still is largely unknown which components are necessary for a functional complex and how the energy of ATP hydrolysis is used to enable cyclic operation. Here we use single-molecule FRET to show how cochaperones introduce directionality into Hsp90’s conformational changes during its interaction with the client kinase Ste11. Three cochaperones are needed to couple ATP turnover to these conformational changes. All three are therefore essential for a functional cyclic operation, which requires coupling to an energy source. Finally, our findings show how the formation of sub-complexes in equilibrium followed by a directed selection of the functional complex can be the most energy efficient pathway for kinase maturation.
Differential perovskite hemispherical photodetector for intelligent imaging and location tracking
Authors: Feng Xiaopeng , Li Chenglong , Song Jinmei , He Yuhong , Qu Wei , Li Weijun , Guo Keke , Liu Lulu , Yang Bai , Wei Haotong 
Published: January 2024

AbstractAdvanced photodetectors with intelligent functions are expected to take an important role in future technology. However, completing complex detection tasks within a limited number of pixels is still challenging. Here, we report a differential perovskite hemispherical photodetector serving as a smart locator for intelligent imaging and location tracking. The high external quantum efficiency (~1000%) and low noise (10−13 A Hz−0.5) of perovskite hemispherical photodetector enable stable and large variations in signal response. Analysing the differential light response of only 8 pixels with the computer algorithm can realize the capability of colorful imaging and a computational spectral resolution of 4.7 nm in a low-cost and lensless device geometry. Through machine learning to mimic the differential current signal under different applied biases, one more dimensional detection information can be recorded, for dynamically tracking the running trajectory of an object in a three-dimensional space or two-dimensional plane with a color classification function.
Influence of radiation on borosilicate glass leaching behaviors
Authors: Qin Kemian , Zhang Buyun , Jin Zhaoxuan , Wang Yuchuan , Pan Yuhe , Sun Yuqian , Bai Kai , Zhu Shikun , Wang Tieshan , Peng Haibo 
Published: January 2024

AbstractVitrification is widely recognized as a promising method for the geological disposal of high-level radioactive waste (HLW) worldwide. To ensure the safe disposal of radioactive waste, the borosilicate glass that vitrifies HLW must exhibit exceptional water resistance to prevent the possibility of groundwater corrosion and subsequent radioactive leaks. Radiation might change the water resistance of borosilicate glass. A series of zirconium-containing borosilicate glass with an irradiation dose of 0.3 dpa were utilized to examine the radiation effect on glass-water interaction. Scanning electron microscopy (SEM), Time-of-Flight Secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), Inductively Coupled Plasma Optical Emission spectroscopy (ICP-OES) and Fourier transform infrared spectroscopy (FTIR) were used to investigate the leaching behavior of the non- and irradiated samples. The depth profile of the leached samples implied the interdiffusion dominated glass-water interaction. The results from FTIR and ICP-OES indicated that, after irradiation, the initial leaching rate increased by threefold. Additionally, the impact of different zirconium contents on the water resistance of borosilicate glass was also presented.
Affinity-optimizing enhancer variants disrupt development
Authors: Lim Fabian , Solvason Joe J. , Ryan Genevieve E. , Le Sophia H. , Jindal Granton A. , Steffen Paige , Jandu Simran K. , Farley Emma K. 
Published: January 2024

AbstractEnhancers control the location and timing of gene expression and contain the majority of variants associated with disease1–3. The ZRS is arguably the most well-studied vertebrate enhancer and mediates the expression ofShhin the developing limb4. Thirty-one human single-nucleotide variants (SNVs) within the ZRS are associated with polydactyly4–6. However, how this enhancer encodes tissue-specific activity, and the mechanisms by which SNVs alter the number of digits, are poorly understood. Here we show that the ETS sites within the ZRS are low affinity, and identify a functional ETS site, ETS-A, with extremely low affinity. Two human SNVs and a synthetic variant optimize the binding affinity of ETS-A subtly from 15% to around 25% relative to the strongest ETS binding sequence, and cause polydactyly with the same penetrance and severity. A greater increase in affinity results in phenotypes that are more penetrant and more severe. Affinity-optimizing SNVs in other ETS sites in the ZRS, as well as in ETS, interferon regulatory factor (IRF), HOX and activator protein 1 (AP-1) sites within a wide variety of enhancers, cause gain-of-function gene expression. The prevalence of binding sites with suboptimal affinity in enhancers creates a vulnerability in genomes whereby SNVs that optimize affinity, even slightly, can be pathogenic. Searching for affinity-optimizing SNVs in genomes could provide a mechanistic approach to identify causal variants that underlie enhanceropathies.
Impact of tumor microenvironment on efficacy of anti-CD19 CAR T cell therapy or chemotherapy and transplant in large B cell lymphoma
Authors: Locke Frederick L. , Filosto Simone , Chou Justin , Vardhanabhuti Saran , Perbost Regis , Dreger Peter , Hill Brian T. , Lee Catherine , Zinzani Pier L. , Kröger Nicolaus , López-Guillermo Armando , Greinix Hildegard , Zhang Wangshu , Tiwari Gayatri , Budka Justin , Marincola Francesco M. , To Christina , Mattie Mike , Schupp Marco , Cheng Paul , Bot Adrian , Shen Rhine , Bedognetti Davide , Miao Harry , Galon Jérôme 
Published: January 2024

AbstractThe phase 3 ZUMA-7 trial in second-line large B cell lymphoma demonstrated superiority of anti-CD19 CAR T cell therapy (axicabtagene ciloleucel (axi-cel)) over standard of care (SOC; salvage chemotherapy followed by hematopoietic transplantation) (NCT03391466). Here, we present a prespecified exploratory analysis examining the association between pretreatment tumor characteristics and the efficacy of axi-cel versus SOC. B cell gene expression signature (GES) and CD19 expression associated significantly with improved event-free survival for axi-cel (P = 0.0002 for B cell GES; P = 0.0165 for CD19 expression) but not SOC (P = 0.9374 for B cell GES; P = 0.5526 for CD19 expression). Axi-cel showed superior event-free survival over SOC irrespective of B cell GES and CD19 expression (P = 8.56 × 10–9 for B cell GES high; P = 0.0019 for B cell GES low; P = 3.85 × 10–9 for CD19 gene high; P = 0.0017 for CD19 gene low). Low CD19 expression in malignant cells correlated with a tumor GES consisting of immune-suppressive stromal and myeloid genes, highlighting the inter-relation between malignant cell features and immune contexture substantially impacting axi-cel outcomes. Tumor burden, lactate dehydrogenase and cell-of-origin impacted SOC more than axi-cel outcomes. T cell activation and B cell GES, which are associated with improved axi-cel outcome, decreased with increasing lines of therapy. These data highlight differences in resistance mechanisms to axi-cel and SOC and support earlier intervention with axi-cel.
Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines
Authors: Valencia E. Michael , Maki Katherine A. , Dootz Jennifer N. , Barb Jennifer J. 
Published: January 2024

AbstractShotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.