bluuebunny/crossref_metadata_2025_split huggingface dataset:
The MHC Class II Immunopeptidome of Lymph Nodes in Health and in Chemically Induced Colitis
Authors: Fugmann Tim , Sofron Adriana , Ritz Danilo , Bootz Franziska , Neri Dario 
Published: December 2016

Abstract
We recently described a mass spectrometry–based methodology that enables the confident identification of hundreds of peptides bound to murine MHC class II (MHCII) molecules. In this article, we describe its application to the characterization of MHCII-bound peptides isolated from lymph nodes (LNs) of C57BL/6 mice. More than 1000 peptides could be identified in individual analyses, allowing a direct comparison of the MHCII peptidome in different types of normal LNs or in animals with colitis. The peptide length distribution and consensus sequences in axillary, brachial, inguinal, and mesenteric LNs were virtually identical, and a substantial portion of identified peptides corresponded to proteins found in all LNs. However, skin-specific proteins Sbsn and Dmkn and intestine-specific proteins Dmbt1, Krt19, and Maoa, among others, were exclusively identified in skin-draining and mesenteric LNs, respectively. Differences in peptide-presentation patterns were also observed when comparing healthy mice and mice with dextran sodium sulfate–induced colitis. Peptides derived from a subset of proteins (including IgE, Bank1, chondroitin sulfate synthase 2, Cmip, and Fth1) were exclusively identified in mice with colitis, revealing changes in the peptidome associated with the inflammatory process, as well as activation and clonal expansion of B cells.
TTLL12 Inhibits the Activation of Cellular Antiviral Signaling through Interaction with VISA/MAVS
Authors: Ju Lin-Gao , Zhu Yuan , Lei Pin-Ji , Yan Dong , Zhu Kun , Wang Xiang , Li Qing-Lan , Li Xue-Jing , Chen Jian-Wen , Li Lian-Yun , Wu Min 
Published: December 2016

Abstract
Upon virus infection, host cells use retinoic-acid–inducible geneI I (RIG-I)–like receptors to recognize viral RNA and activate type I IFN expression. To investigate the role of protein methylation in the antiviral signaling pathway, we screened all the SET domain–containing proteins and identified TTLL12 as a negative regulator of RIG-I signaling. TTLL12 contains SET and TTL domains, which are predicted to have lysine methyltransferase and tubulin tyrosine ligase activities, respectively. Exogenous expression of TTLL12 represses IFN-β expression induced by Sendai virus. TTLL12 deficiency by RNA interference and CRISPR-gRNA techniques increases the induced IFN-β expression and inhibits virus replication in the cell. The global gene expression profiling indicated that TTLL12 specifically inhibits the expression of the downstream genes of innate immunity pathways. Cell fractionation and fluorescent staining indicated that TTLL12 is localized in the cytosol. The mutagenesis study suggested that TTLL12’s ability to repress the RIG-I pathway is probably not dependent on protein modifications. Instead, TTLL12 directly interacts with virus-induced signaling adaptor (VISA), TBK1, and IKKε, and inhibits the interactions of VISA with other signaling molecules. Taken together, our findings demonstrate TTLL12 as a negative regulator of RNA-virus–induced type I IFN expression by inhibiting the interaction of VISA with other proteins.
On the Creative Edge: The Artistic Side of One Library
Authors: Fletcher Mary 
Published: December 2016

Libraries can go beyond being places of information to become places of inspiration. Years ago, at the Avon Free Public Library in Connecticut, we began offering creative art for children. These sessions were so successful that a room in the library was redesigned exclusively for creating art. Today, we have one of the first creative art studios located in a public library in the country.
Autonomous Sensing Architected Materials
Authors: Utzeri Mattia , Cebeci Hülya , Kumar Shanmugam 
Published: September 2024

AbstractIntegrating autonomous sensing materials into future applications necessitates developing advanced multiscale multiphysics predictive models. This study introduces an experimentally informed predictive framework for autonomous sensing architected materials, combining theoretical and computational methodologies. By incorporating stress‐dependent electrical resistivity through anisotropic piezoresistive constitutive effects, alongside considering material, geometric, and contact nonlinearities, the proposed multiscale model captures the architecture‐dependent piezoresistive responses of lattice composites produced via additive manufacturing of polyetherimide (PEI)/carbon nanotube (CNT) nanoengineered feedstock. The PEI/CNT composite exhibits exceptional strength (105 MPa), stiffness (3368 MPa), and strain sensitivity (gauge factor ≈13), translating into remarkable piezoresistive characteristics for the PEI/CNT lattice composites, surpassing existing works (gauge factor ≈3 to 11). This multiscale finite element model accurately predicts both macroscopic piezoresistive responses and the influence of architectural and topological variations on electric current paths, validated via infrared thermography analysis. Additionally, an Ashby chart for the gauge factor of PEI/CNT lattice composites suggests their prediction through a scaling law similar to mechanical properties, underscoring the tunable strain and damage sensitivity of these materials. The combined experimental, theoretical, and numerical findings offer critical insights into optimizing piezoresistive composites through architected design, with profound implications for smart orthopedics, structural health monitoring, sensors, batteries, and other multifunctional applications.
Cognitive, Social, and Emotional‐Behavioral Outcomes in Children and Adolescents With Beckwith–Wiedemann Syndrome
Authors: Butti Niccolò , Urgesi Cosimo , Mussa Alessandro , Montirosso Rosario 
Published: September 2024

ABSTRACTAlthough Beckwith–Wiedemann syndrome spectrum (BWSp) is not usually associated with intellectual disability, recent evidences calls for further investigation of cognitive development and academic skills in children with BWSp. Moreover, research has documented social difficulties and emotional‐behavioral problems associated with BWSp. Nevertheless, a full characterization of socio‐emotional development in BWSp is still lacking. In the current study, cognitive and socio‐emotional development was assessed in 29 children with BWSp aged 5–18 years, using a test of nonverbal intelligence, a neuropsychological battery covering multiple domains, academic skills tests, and questionnaires evaluating autistic traits and emotional‐behavioral problems. As expected, most participants showed adequate performance in cognitive tests. However, the findings also highlighted greater difficulties in language than visuospatial processing, strengths in social perception, as well as slowness in reading and mental calculation. The assessment of emotional‐behavioral difficulties indicated a prevalent phenotype characterized by increased anxiety, low self‐esteem, social withdrawal and a tendency to control externalizing reactions, but no associations with autistic traits, cognitive outcomes, and the clinical score proposed by the recent Consensus statement. Increased social perception and internalization problems likely result from coping strategies with social and care‐related stress. Overall, the findings of this study inform clinical management and genetic counseling for children and adolescents with BWSp.
Identification of dilated cardiomyopathy‐linked key genes by bioinformatics methods and evaluating the impact of tannic acid and monosodium glutamate in rats
Authors: Karadas Habibe , Tosun Hilal , Ceylan Hamid 
Published: September 2024

AbstractDilated cardiomyopathy (DCM) is the most common type of myocardial dysfunction, affecting mostly young adults, but its therapeutic diagnosis and biomarkers for prognosis are lacking. This study aimed to investigate the possible effect of the common food additive monosodium glutamate (MSG) and tannic acid (TA), a phenolic compound, on the key molecular actors responsible for DCM. DCM‐related publicly available microarray datasets (GSE120895, GSE17800, and GSE19303) were downloaded from the comprehensive Gene Expression Omnibus (GEO) database, and analyzed to identify differentially expressed genes (DEGs). By integrating DEGs and gene‐disease validity curation results, overlapping genes were screened and identified as hub genes. Protein‐protein interaction (PPI) network and ontology analysis were performed to make sense of the identified biological data. Finally, mRNA expression changes of identified hub genes in the heart tissues of rats treated with MSG and TA were measured by the qPCR method. Six upregulated (IGF1, TTN, ACTB, LMNA, EDN1, and NPPB) DEGs were identified between the DCM and healthy control samples as the hub genes. qPCR results revealed that the mRNA levels of these genes involved in DCM development increased significantly in rat heart tissues exposed to MSG. In contrast, this increase was remarkably alleviated by TA treatment. Our results provide new insights into critical molecular mechanisms that should be focused on in future DCM studies. Moreover, MSG may play a critical role in DCM formation, and TA may be used as a promising therapeutic agent in DCM.
Elucidating the protective mechanism of ganoderic acid DM on breast cancer based on network pharmacology and in vitro experimental validation
Authors: Swallah Mohammed Sharif , Bondzie‐Quaye Precious , Yu Xin , Fetisoa Monia Ravelonandrasana , Shao Chang‐Sheng , Huang Qing 
Published: September 2024

AbstractGanoderma lucidum, a popular medicinal fungus, has been utilized to treat a variety of diseases. It possesses a unique therapeutic and pharmacological reputation in suppressing cancer/tumor progression, especially breast cancer, due to its embedded rich bioactive chemical constituents, mainly triterpenoids (ganoderic acids). The most prevalent malignant tumor in women with a high mortality and morbidity rate is breast cancer. Ganoderic acids A, D, DM, F, and H are evidenced in previous research to have breast cancer–preventive properties by exhibiting autophagic and apoptosis, anti‐proliferative, and anti‐angiogenesis effects. However, the anti‐breast cancer mechanism remains unclear. The putative targets of the ganoderic acids were further determined using bioinformatics techniques and molecular docking calculation. Finally, the key targets were verified in vitro. A total of 53 potential target proteins associated with 202 pathways were predicted to be related to breast cancer. The potential targets were narrowed down to six key targets (AKT1, PIK3CA, epidermal growth factor receptor [EGFR], STAT1, ESR1, and CTNNB1), using different algorithms of the CytoHubba plugin, which were further validated using molecular docking analysis. The ganoderic acid DM (GADM) and the targets (PIK3CA and EGFR) with the strongest interactions were validated via MDA‐MB‐231 and MCF7 cells. The expression level of PIK3CA in both MDA‐MB‐231 and MCF7 cells was dose‐dependently suppressed by GADM, whereas EGFR expression was unexpectedly increased, which warrants further investigation. These data indicated that the network pharmacology–based prediction of GADM targets for treating human breast cancer could be reliable.
Annexin A1 protects periodontal ligament cells against lipopolysaccharide‐induced inflammatory response and cellular senescence: An implication in periodontitis
Authors: Luo Shuwen , Zhang Lin , Li Xiaoyu , Tong Chunshi 
Published: September 2024

AbstractPeriodontitis is an inflammatory condition that affects the tooth‐supporting structures, triggered by the host's immune response toward the bacterial deposits around the teeth. Annexin A1 (AnxA1), a vital member of the annexin superfamily, is known for its diverse physiological functions, particularly its anti‐inflammatory and anti‐senescence properties. We hypothesized that AnxA1 has a protective effect against lipopolysaccharide (LPS)‐induced inflammatory responses and cellular damage in periodontal ligament cells (PDLCs). In this study, we demonstrate that LPS stimulation significantly reduced telomerase activity in PDLCs, a decline that was dose‐dependently reversed by AnxA1. Importantly, AnxA1 protected the cells from LPS‐induced cellular senescence and the downregulation of human telomerase reverse transcriptase (hTERT) expression. In line with this, AnxA1 suppressed the LPS‐induced expression of p21 and p16 at both the mRNA and protein levels. Furthermore, AnxA1 demonstrated potent anti‐inflammatory effects by inhibiting the secretion of interleukin 6 (IL‐6), interleukin 8 (IL‐8), and monocyte chemoattractant protein‐1 (MCP‐1). It also mitigated LPS‐induced oxidative stress by reducing the levels of phosphorylated Foxo3a (Ser253) and restored sirtuin 1 (SIRT1) expression. Notably, SIRT1 silencing abolished AnxA1's protective effects on Foxo3a phosphorylation and cellular senescence, suggesting that SIRT1 mediates AnxA1's actions. In conclusion, AnxA1 protected PDLCs against LPS‐triggered inflammation and cell senescence by activating SIRT1 signal pathway. These findings indicate that AnxA1 could serve as a promising therapeutic strategy for the treatment of periodontitis.
Risk factors investigation for different outcomes between unilateral and bilateral chronic rhinosinusitis with nasal polyps patients
Authors: Wang Jianwei , Zhang Yu , Chen Ying , Xu Xinjun , Yang Yujuan , Yin Jiali , Guo Jing , Yu Pengyi , Liu Zhen , Liu Huifang , Zuo Ting , Zhao Hongfei , Hao Yan , Zhang Bei , Song Xicheng 
Published: September 2024

AbstractBackgroundStudies involving chronic rhinosinusitis with nasal polyps (CRSwNP) have mostly focused on bilateral cases, making unilateral CRSwNP inadequately recognized. This study examined the differences in clinical characteristics, outcomes, and risk factors for poor outcomes between unilateral and bilateral CRSwNP to facilitate a better assessment in the two groups.MethodsDemographic information, tissue and blood cells, endoscopic scores, Lund‐Mackay scores, recurrence rates, and disease control conditions were compared between 310 unilateral and 596 bilateral CRSwNP patients. Furthermore, the stepwise regression multivariate Cox proportional hazard models were performed to generate risk factors for poor outcomes in the two groups.ResultsBilateral cases exhibited higher rates of smoking, AR, and asthma comorbidities, along with higher numbers of tissue eosinophils and blood inflammatory cells when compared to unilateral patients. Endoscopic nasal polyp score, total computed tomography (CT) score (with scores for each sinus cavity), and adjusted CT scores were significantly higher in the bilateral group, except for a markedly higher adjusted maxillary score in the unilateral group. Furthermore, significantly higher proportions of bilateral patients experienced nasal polyp recurrence, uncontrolled status, and most disease control‐related symptoms at follow‐up. The primary risk factors for poor outcomes were asthma, tissue eosinophils, and total CT score in the bilateral group and blood basophils in the unilateral group.ConclusionsBilateral CRSwNP patients experience worse disease severity and outcomes than their unilateral counterparts. Primarily, asthma, tissue eosinophils, and total CT score were risk factors for poor outcomes in bilateral CRSwNP patients, with blood basophils in unilateral cases.
Tristetraprolin affects invasion‐associated genes expression and cell motility in triple‐negative breast cancer model
Authors: Hubiernatorova Anastasiia , Novak Josef , Vaskovicova Michaela , Sekac David , Kropyvko Serhii , Hodny Zdenek 
Published: September 2024

AbstractTristetraprolin (TTP) is an RNA‐binding protein that negatively regulates its target mRNAs and has been shown to inhibit tumor progression and invasion. Tumor invasion requires precise regulation of cytoskeletal components, and dysregulation of cytoskeleton‐associated genes can significantly alter cell motility and invasive capability. Several genes, including SH3PXD2A, SH3PXD2B, CTTN, WIPF1, and WASL, are crucial components of the cytoskeleton reorganization machinery and are essential for adequate cell motility. These genes are also involved in invasion processes, with SH3PXD2A, SH3PXD2B, WIPF1, and CTTN being key components of invadopodia—specialized structures that facilitate invasion. However, the regulation of these genes is not well understood. This study demonstrates that ectopic expression of TTP in MDA‐MB‐231 cells leads to decreased mRNA levels of CTTN and SH3PXD2A, as well as defects in cell motility and actin filament organization. Additionally, doxorubicin significantly increases TTP expression and reduces the mRNA levels of cytoskeleton‐associated genes, enhancing our understanding of how doxorubicin may affect the transcriptional profile of cells. However, doxorubicin affects target mRNAs differently than TTP ectopic expression, suggesting it may not be the primary mechanism of doxorubicin in breast cancer (BC) treatment. High TTP expression is considered as a positive prognostic marker in multiple cancers, including BC. Given that doxorubicin is a commonly used drug for treating triple‐negative BC, using TTP as a prognostic marker in this cohort of patients might be limited since it might be challenging to understand if high TTP expression occurred due to the favorable physiological state of the patient or as a consequence of treatment.
Expression analysis of genes including Zfhx4 in mice and zebrafish reveals a temporospatial conserved molecular basis underlying craniofacial development
Authors: Liu Shujie , Xu Lin , Kashima Makoto , Narumi Rika , Takahata Yoshifumi , Nakamura Eriko , Shibuya Hirotoshi , Tamura Masaru , Shida Yuki , Inubushi Toshihiro , Nukada Yuko , Miyazawa Masaaki , Hata Kenji , Nishimura Riko , Yamashiro Takashi , Tasaki Junichi , Kurosaka Hiroshi 
Published: September 2024

AbstractBackgroundEmbryonic craniofacial development involves several cellular and molecular events that are evolutionarily conserved among vertebrates. Vertebrate models such as mice and zebrafish have been used to investigate the molecular and cellular etiologies underlying human craniofacial disorders, including orofacial clefts. However, the molecular mechanisms underlying embryonic development in these two species are unknown. Therefore, elucidating the shared mechanisms of craniofacial development between disease models is crucial to understanding the underlying mechanisms of phenotypes in individual species.ResultsWe selected mice and zebrafish as model organisms to compare various events during embryonic craniofacial development. We identified genes (Sox9, Zfhx3 and 4, Cjun, and Six1) exhibiting similar temporal expression patterns between these species through comprehensive and stage‐matched gene expression analyses. Expression analysis revealed similar gene expression in hypothetically corresponding tissues, such as the mice palate and zebrafish ethmoid plate. Furthermore, loss‐of‐function analysis of Zfhx4/zfhx4, a causative gene of human craniofacial anomalies including orofacial cleft, in both species resulted in deformed skeletal elements such as the palatine and ethmoid plate in mice and zebrafish, respectively.ConclusionsThese results demonstrate that these disease models share common molecular mechanisms, highlighting their usefulness in modeling craniofacial defects in humans.
Carbon Nitride‐Supported Zinc Oxide Nanocomposite for the Electrochemical Detection of Dopamine and the Development of Disposable Sensors
Authors: Saha Chandan , Ghosh Sarit K , Kumari Pooja , Perla Venkata K , Singh Harishchandra , Mallick Kaushik 
Published: September 2024

AbstractThe carbon nitride‐supported zinc oxide (CNZO) nanocomposite was synthesized through a high‐temperature synthesis method, resulting in zinc oxide nanoparticles with an average size of ~44 nm, dispersed on a carbon nitride matrix. X‐ray diffraction confirmed the formation of the hexagonal wurtzite phase of zinc oxide, with a space group of P63mc. X‐ray photoelectron spectroscopy and Fourier‐transform infrared analysis further verified the presence of both zinc oxide and carbon nitride. The CNZO nanocomposite served as a catalyst for the electrochemical detection of dopamine, achieving limit of detection and sensitivity of 2.66 μM and 6.23 μA μM−1 cm−2 respectively, using square wave voltammetry technique. Cyclic voltammetry experiments demonstrated excellent electroactivity of the CNZO nanocomposite in a neutral pH environment. An electrochemical paper‐based analytical device (EPAD) was designed and successfully employed for the electrochemical analysis of dopamine in pharmaceutical samples using CNZO nanocomposites. Additionally, CNZO was used as an active material in the development of a disposable dopamine sensor based on an extended gate field‐effect transistor (EG‐FET). This sensor exhibited a sensitivity and limit of detection 18.22 μA μM−1 cm−2 and 0.36 μM, respectively, with a correlation coefficient of 0.99.
A novel framework for assessing the joint and relative impacts of precipitation and groundwater on ecological drought processes in Northwest China
Authors: Jiang Tiangliang , Qu Yanping , Su Xiaoling , Chu Jiangdong , Han Yu 
Published: September 2024

AbstractEcological drought has emerged as a critical research topic within eco‐hydrology, driven by the increased drought risk associated with global warming. This study aims to unravel the hydrological processes driving ecological drought in Northwest China by (1) constructing standardized indices for precipitation, groundwater storage anomaly, and ecological water deficit to detect variation across different hydrological components; (2) developing a framework to assess the joint and relative impacts of precipitation and groundwater variations on ecological drought; and (3) identifying the primary hydrological drivers of ecological drought across different regions. The results indicate that the joint impact of precipitation and groundwater on ecological drought variation dominates approximately 60% of the area, primarily in arid and semi‐arid regions. The average contribution of this joint impact to the alleviation of ecological drought ranges between 0.26 and 0.43 across all seasons. Notably, groundwater scarcity, rather than precipitation variation, is the primary driver of ecological drought in regions such as southern Shaanxi, southeastern Gansu, and southern Qinghai, accounting for 12.7% to 21.8% of the total area. These insights into the complex hydrological processes underlying ecological drought have significant implications for water resource management and ecosystem conservation in drought‐prone regions. This research provides valuable information for mitigating drought impacts and protecting vulnerable ecosystems in Northwest China and similar regions worldwide.
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Authors: Chen Yance , Dai Yue , Bodepudi Srikrishna Chanakya , Liu Xinyu , Ma Yuan , Xing Shiyu , Di Dawei , Tian Feng , Ming Xin , Liu Yingjun , Pang Kai , Xue Fei , Zhang Yunyan , Yu Zexin , Dan Yaping , Penkov Oleksiy V. , Zhang Yishu , Qi Dianyu , Fang Wenzhang , Xu Yang , Gao Chao 
Published: September 2024

A silicon‐integrated MXene X‐ray detector exhibits high sensitivity and an ultra‐low detection limit, enabling clear and precise single‐pixel X‐ray imaging
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Authors: Zhao Heping , Li Yuewei , Mi Chao , Zi Yingzhu , Bai Xue , Haider Asif Ali , Cun Yangke , Huang Anjun , Liu Yue , Qiu Jianbei , Song Zhiguo , Liao Jiayan , Zhou Ji , Yang Zhengwen 
Published: September 2024

A novel strategy explores the reversible modulation of visible and NIR luminescence in rare earth ion‐doped photochromic bismuth‐based glasses for information encryption and multi‐dimensional optical storage.
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