bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pooled‐sample draft genome assembly provides insights into host plant‐specific transcriptional responses of a Solanaceae‐specializing pest, Tupiocoris notatus (Hemiptera: Miridae)
Authors: Goldberg Jay K. , Allan Carson W. , Copetti Dario , Matzkin Luciano M. , Bronstein Judith 
Published: March 2024

AbstractThe assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study, we show that high‐quality genome assemblies can be produced from samples of multiple wild‐caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae: Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30–100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short‐read assembly standards (N50 = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome‐guided differential expression study of host plant‐specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding on Datura wrightii (Solanaceae) and existing RNA‐seq data from Nicotiana attenuata (Solanaceae)‐fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione‐S‐transferases, cytochrome P450s, and UDP‐glucosyltransferases. Together our results show that long‐read sequencing of pooled samples can provide a cost‐effective genome assembly option for small insects and can provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests.
Host size matters for reproduction: Evolution of spawning preference and female reproductive phenotypes in mussel‐symbiotic freshwater bitterling fishes
Authors: Choi Hee‐kyu , Lee Hyuk Je 
Published: March 2024

AbstractBitterling fishes evolve an idiosyncratic symbiosis with freshwater mussels, in which they are obligated to spawn in the gills of mussels for reproduction. In recent years, freshwater mussel populations have been drastically diminishing, due to accelerating anthropogenic impacts, which can be large threats to the risk of bitterling's extinction cascade (i.e. ‘coextinction’). The host mussel size may be an important factor driving the adaptation and evolution of bitterling's reproductive phenotypes. Here we examined the host size preference and morphological adaptation of female bitterling to the host size from 17 localities at the Han River in Korea. Using our developed molecular‐based species identification for bitterling's eggs/larvae inside the mussels, we further determined the spawning patterns of seven bitterling species. Mean length of spawned mussels (N = 453) was significantly larger than that of unspawned mussels (N = 1814), suggesting that bitterling prefers to use larger hosts as a spawning ground. Spawning probability was clearly greater as mussel size increases. Results of our reciprocal transplant experiments do provide some evidence supporting the ‘bitterling's larger host preference’ hypothesis. Interspecific competition appeared to be intense as two fish species often spawned eggs in the same mussel individuals simultaneously. Longer ovipositor and more elongated egg may evolve in females of Tanakia signifer in response to larger host environments. The observed bitterling's spawning preference for large‐sized mussels may evolve perhaps because of the fitness advantage in relation to the offspring survival. Our findings further inform on the development of effective conservation and management strategy for the endangered bitterling fishes.
Proteasome composition in immune cells implies special immune‐cell‐specific immunoproteasome function
Authors: Inholz Katharina , Anderl Janet L. , Klawitter Moritz , Goebel Heike , Maurits Elmer , Kirk Christopher J. , Fan R. Andrea , Basler Michael 
Published: March 2024

AbstractImmunoproteasomes are a special class of proteasomes, which can be induced with IFN‐γ in an inflammatory environment. In recent years, it became evident that certain immune cell types constitutively express high levels of immunoproteasomes. However, information regarding the basal expression of proteolytically active immunoproteasome subunits in different types of immune cells is still rare. Hence, we quantified standard proteasome subunits (β1c, β2c, β5c) and immunoproteasome subunits (LMP2, MECL‐1, LMP7) in the major murine (CD4+ T cells, CD8+ T cells, CD19+ B cells, CD11c+ dendritic cells, CD49d+ natural killer cells, Ly‐6G+ neutrophils) and human immune cell (CD4+ T cells, CD8+ T cells, CD19+ B cells, CD1c+CD141+ myeloid dendritic cells, CD56+ natural killer cells, granulocytes) subsets. The different human immune cell types were isolated from peripheral blood and the murine immune cell subsets from spleen. We found that proteasomes of most immune cell subsets mainly consist of immunoproteasome subunits. Our data will serve as a reference and guideline for immunoproteasome expression and imply a special role of immunoproteasomes in immune cells.
Beishan exploration tunnel surrounding rock discontinuity identification based on structure from motion photogrammetry technology
Authors: Xuan Chengqiang , Zhang Yangsong , Xu Wentao , Li Xiaozhao , Zhang Ning 
Published: March 2024

AbstractThe Beishan Exploration Tunnel (BET) is a facility built to develop technologies associated with the safety of China's first high‐level radioactive nuclear waste(HLW) disposal. The surrounding rock discontinuity identification is a key research topic in BET, which could provide essential geological data for future HLW disposal stability and integrity research. This article presents the rock discontinuity identification research progress in BET based on Structure from Motion (SfM) photogrammetry technology. The discontinuity identification algorithm is improved by introducing the region‐growing algorithm to optimize the candidate subplane. This algorithm automatically picks the seed, avoids human intervention, and thus increases the work efficiency of the discontinuity identification. The FCM method is improved by embedding with the CFSFDP algorithm in the discontinuity sets grouping. The CFSFDP algorithm coincides well with the Fisher distribution of discontinuity orientations, which is suitable for the Beishan situation. A parallel scheme is used when implementing the method, which accelerates the discontinuity calculation. This improved rock discontinuity identification method was tested on a slope above the BET and applied in the BET. The discontinuity identification results were compared with the results from the manual field measurement and the open‐source software DSE. The results show that the improved discontinuity identification method obtains reliable discontinuity data and costs less time and human workload than the other two methods. The surrounding rock discontinuity identification research provides a powerful tool for the Beishan HLW disposal geological investigation.
Optimization of hydrogen purification from biomass‐derived syngas via water gas shift reaction integrated with vacuum pressure swing adsorption for energy storage
Authors: Chen Wei‐Hsin , Chen Wei‐Hao , Chein Rei‐Yu , Manatura Kanit , Ghorbani Mohammad 
Published: March 2024

AbstractBiomass is one of the promising sources to produce green H2, which can be considered an energy storage medium. To produce high‐purity H2 from biomass‐derived syngas, this study implemented a two‐stage H2 purification process. In the first stage, a water gas shift reaction (WGSR) was performed to enhance the H2 concentration in the syngas. The Taguchi method was employed to analyze the influence of the operating conditions and maximize the H2 concentration in the water gas shift reaction product. The results suggested that reaction temperature is a more dominant factor for enhancing the H2 concentration than the molar steam/carbon monoxide (S/CO) ratio. In the second stage, vacuum pressure swing adsorption was employed to obtain the high‐concentration H2 using the product from the water gas shift reaction having the optimum H2 concentration. Using the adsorption pressure as the primary parameter, it was found that high H2 purity and recovery could be obtained from vacuum pressure swing adsorption operated at low adsorption pressures. Based on this study's results, the vacuum pressure swing adsorption unit's best outcome occurs during an adsorption pressure of 2 kg·cm−2 and a flow rate of 17 L·min−1. Under these conditions, 93.61% H2 purity, 31.63% H2 recovery, 4.86 mol H2·(kgads·h)−1 productivity, and 448.14 kJ·(kg H2)−1 energy consumption are obtained.
A federated learning privacy framework for missing data inference in environmental crowd sensing
Authors: Marchang Ningrinla 
Published: March 2024

AbstractFederated learning (FL) is an attractive solution which holds promise to efficiently realize intelligent privacy‐preserving IoT systems. It does so by training local models at the IoT devices using locally collected data and aggregating these models at the server. First, user privacy is achieved as no data is shared with the server. Second, the traffic generated reduces significantly as only the model updates are exchanged between the server and the devices. The first part of this study examines the validity of using FL for provisioning user data privacy in the context of missing data inference in environmental MCS. Using a representative machine language (ML) model, namely, neural network (NN), it is found through simulations with the help of an existing dataset that FL performs as good as traditional ML, while maintaining user privacy. The second part of the study is the design of a privacy‐aware framework for FL sharing (sharing of model updates) so as to ensure privacy of model updates. The proposed framework is economical w.r.t. computational and communication overhead as it uses: (a) a single asymmetric key shared among the FL clients with the help of threshold cryptography, and (b) partial homomorphic encryption (PHE) for sharing the model updates. Additionally, security analysis of the framework supports its validity.
Association between Mediterranean‐dietary approaches to stop hypertension intervention for neurodegenerative delay diet and biomarkers of oxidative stress, metabolic factors, disease severity, and odds of disease in rheumatoid arthritis patients
Authors: Safaei Mahdieh , Kheirouri Sorayya , Alizadeh Mohammad , Pirovi Amir‐Hossein 
Published: March 2024

AbstractThis research aimed to examine the association between the following Mediterranean‐DASH Intervention for Neurodegenerative Delay (MIND) dietary pattern and oxidative stress indicators, metabolic factors, disease activity, and the odds of disease in patients with rheumatoid arthritis (RA). In this cross‐sectional study, we included 101 patients with RA and 101 healthy individuals. The MIND diet score was measured using a semi‐quantitative Food Frequency Questionnaire (FFQ) with 147 food items. Total capacity antioxidant (TCA), superoxide dismutase (SOD), glutathione peroxidase (GPX), and malondialdehyde (MDA) serum concentrations were evaluated by ELISA, and the disease severity was measured regarding the disease activity score 28 (DAS‐28) criteria. The average score of the MIND diet was substantially lower in the RA subjects than in the healthy people (p < .001). Individuals with a higher MIND diet score had lower odds of RA than those with a low score (p < .001). There was no remarkable link between the MIND diet and oxidative stress factors (p > .05). A reverse association was found between the MIND diet score and disease activity (p < .05). The MIND diet was significantly and negatively correlated with triglycerides, low‐density lipoprotein cholesterol, total cholesterol, fasting blood glucose, and hemoglobin A1C. There was a positive association between the diet and high‐density lipoprotein cholesterol. The findings indicate that following the MIND diet may decrease disease activity and the odds of RA. Also, high adherence to the MIND diet may improve the lipid profile and blood glucose status in RA patients.
Survival and complications after carotid resection for head and neck squamous cell carcinoma: A systematic review and pooled analysis
Authors: Pace Gian Marco , Morales‐Olavarría Carolina , Costantino Andrea , Festa Bianca Maria , Russo Elena , Iannella Giannicola , Carnevale Claudio , Di Maio Pasquale , Sampieri Claudio , Accorona Remo , De Virgilio Armando 
Published: March 2024

AbstractObjectiveThe aim of this study is to analyze oncologic outcomes and complications rate after common or internal carotid artery (CCA/ICA) resection for head and neck squamous cell carcinoma (HNSCC).MethodsThis study was conducted in conformity with the PRISMA statement. A systematic review and pooled analysis was performed for overall survival (OS), disease specific survival (DSS) (primary outcomes), and perioperative death rate (secondary outcome).ResultsA total of 276 patients (males: 76.7%, n = 191/249) with a median age of 59 years (n = 239/276; 95% CI 55.0–61.7) who underwent CCA/ICA resection for HNSCC were included. The median follow‐up time was 11 months (n = 276). Estimated pooled OS rates (95% CI) at 1 and 2 years were 52.7% (46.9–59.2) and 29.8% (24.3–36.5), respectively. The median OS (95% CI) was 14 months (12–17). Estimated pooled DSS rates (95% CI) at 1 and 2 years were 58.6% (52.7–65.2) and 34.6% (28.5–41.9), respectively. The median DSS (95% CI) was 16 months (14–19). The perioperative death rate was 6.9% (n = 19/276).ConclusionsCCA/ICA resection should be considered as a treatment option for accurately selected patients. Multicentric prospective studies are recommended to develop a predictive score guiding the decision‐making process.
IGF2BP2 modulates autophagy and serves as a prognostic marker in glioma
Authors: Li Ning , Deng Limei , Zhang Yuming , Tang Xilian , Lei Bingxi , Zhang Qingyu 
Published: March 2024

AbstractGlioma, a malignant brain tumor originating from neural glial cells, presents significant treatment challenges. However, the underlying mechanisms of glioma development are not fully understood, and effective targets are lacking. This study provides insights into the role of insulin‐like growth factor 2 messenger RNA‐binding protein 2 (IGF2BP2) in glioma progression and its therapeutic potential. Our analysis illustrated that elevated IGF2BP2 expression associated with significantly shorter survival among patients with low‐grade glioma (LGG) in The Cancer Genome Atlas (TCGA) database. IGF2BP2 depletion led to compromised cell viability, G0/G1 phase arrest, and reduced colony‐formation ability. Furthermore, ultrastructural analysis and mCherry‐GFP‐LC3 reporter assay revealed an increased abundance of autophagosomes upon IGF2BP2 knockdown. Western blot analysis corroborated these findings by showing reduced p62 levels coupled with increased LC3‐ІІ/LC3‐I ratio upon IGF2BP2 knockdown. A multicolor immunohistochemistry assay demonstrated the positive correlation between IGF2BP2 and p62 expression in glioma patient samples. Additionally, our analysis suggested a link between IGF2BP2 expression and drug‐resistant markers in TCGA‐LGG samples, and Cell Counting Kit‐8 cell viability assay revealed that knockdown of IGF2BP2 sensitized cells to temozolomide treatment. This comprehensive exploration unveils the role of IGF2BP2 in glioma progression, shedding light on autophagy modulation and chemosensitization strategies for glioma therapy.
The gut microbiota‐aromatic hydrocarbon receptor (AhR) axis mediates the anticolitic effect of polyphenol‐rich extracts from Sanghuangporus
Authors: Zhong Shi , Sun Yu‐Qing , Huo Jin‐Xi , Xu Wen‐Yi , Yang Ya‐Nan , Yang Jun‐Bo , Wu Wei‐Jie , Liu Yong‐Xin , Wu Chong‐Ming , Li You‐Gui 
Published: March 2024

AbstractInflammatory bowel disease (IBD) is a significant global health concern. The gut microbiota plays an essential role in the onset and development of IBD. Sanghuangporus (SH), a traditional Chinese medicinal mushroom, has excellent anti‐inflammatory effects and is effective at modulating the gut microbiota. Despite these attributes, the specific anticolitic effects of SH and the mechanisms through which the gut microbiota mediates its benefits remain unclear. Herein, we demonstrated that polyphenol‐rich extract from SH effectively alleviated the pathological symptoms of dextran sodium sulfate (DSS)‐induced colitis in mice by modulating the gut microbiota. Treatment with SH distinctly enriched Alistipes, especially Alistipes onderdonkii, and its metabolite 5‐hydroxyindole‐3‐acetic acid (5HIAA). Oral gavage of live A. onderdonkii or 5HIAA potently mitigated DSS‐induced colitis in mice. Moreover, both 5HIAA and SH significantly activated the aromatic hydrocarbon receptor (AhR), and the administration of an AhR antagonist abrogated their protective effects against colitis. These results underscore the potent efficacy of SH in diminishing DSS‐induced colitis through the promotion of A. onderdonkii and 5HIAA, ultimately activating AhR signaling. This study unveils potential avenues for developing therapeutic strategies for colitis based on the interplay between SH and the gut microbiota.
GINS1 promotes ZEB1‐mediated epithelial‐mesenchymal transition and tumor metastasis via β‐catenin signaling in hepatocellular carcinoma
Authors: Liang Junjie , Yao Nan , Deng Bo , Li Jinying , Jiang Yuchuan , Liu Tongzheng , Hu Youzhu , Cao Mingrong , Hong Jian 
Published: March 2024

AbstractGINS1 regulates DNA replication in the initiation and elongation phases and plays an important role in the progression of various malignant tumors. However, the role of GINS1 in hepatocellular carcinoma (HCC) remains largely unclear. In this study, we investigated the role and underlying mechanisms of GINS1 in contributing to HCC metastasis. We found that GINS1 was significantly upregulated in HCC tissues and cell lines, especially in HCC tissues with vascular invasion and HCC cell lines with highly metastatic properties. Additionally, high expression of GINS1 was positively correlated with the progressive clinical features of HCC patients, including tumor number (multiple), tumor size (>5 cm), advanced tumor stage, vascular invasion and early recurrence, suggesting that GINS1 upregulation was greatly involved in HCC metastasis. Moreover, Kaplan−Meier survival analysis revealed that high GINS1 expression predicted a poor prognosis. Both in vitro and in vivo, silencing of GINS1 inhibited proliferation, migration, invasion and metastasis, while overexpression of GINS1 induced opposite effects. Mechanistically, we found that ZEB1 was a crucial regulator of GINS1‐induced epithelial‐mesenchymal transition (EMT), and GINS1 promoted EMT and tumor metastasis through β‐catenin signaling. Overall, the present study demonstrated that GINS1 promoted ZEB1‐mediated EMT and tumor metastasis via β‐catenin signaling in HCC.
Open‐label, single‐center, clinical study evaluating the safety, tolerability and clinical effects of pentosan polysulfate sodium in subjects with mucopolysaccharidosis I
Authors: Bratkovic Drago , Gravance Curtis , Ketteridge David , Krishnan Ravi , Navuru Divya , Sheehan Michael , Skerrett Donna , Imperiale Michael 
Published: March 2024

AbstractLysosomal enzyme deficiency in mucopolysaccharidosis (MPS) I results in glycosaminoglycan (GAG) accumulation leading to pain and limited physical function. Disease‐modifying treatments for MPS I, enzyme replacement, and hematopoietic stem cell therapy (HSCT), do not completely resolve MPS I symptoms, particularly skeletal manifestations. The GAG reduction, anti‐inflammatory, analgesic, and tissue remodeling properties of pentosan polysulfate sodium (PPS) may provide disease‐modifying treatment for musculoskeletal symptoms and joint inflammation in MPS I following ERT and/or HSCT. The safety and efficacy of PPS were evaluated in four subjects with MPS I aged 14–19 years, previously treated with ERT and/or HSCT. Subjects received doses of 0.75 mg/kg or 1.5 mg/kg PPS via subcutaneous injections weekly for 12 weeks, then every 2 weeks for up to 72 weeks. PPS was well tolerated at both doses with no serious adverse events. MPS I GAG fragment (UA‐HNAc [1S]) levels decreased at 73 weeks. Cartilage degradation biomarkers serum C‐telopeptide of crosslinked collagen (CTX) type I (CTX‐I) and type II (CTX‐II) and urine CTX‐II decreased in all subjects through 73 weeks. PROMIS scores for pain interference, pain behavior, and fatigue decreased in all subjects through 73 weeks. Physical function, measured by walking distance and dominant hand function, improved at 49 and 73 weeks. Decreased GAG fragments and cartilage degradation biomarkers, and positive PROMIS outcomes support continued study of PPS as a potential disease‐modifying treatment for MPS I with improved pain and function outcomes.
Story untold: A phenomenological study of the lived experiences impacting the career development of Black women in rehabilitation counselor education
Authors: Peterson Gemarco J. , Brooks Michael 
Published: March 2024

AbstractThis transcendental phenomenological study described the lived experiences impacting career development among Black women in counselor education specializing in rehabilitation counseling. Womanism centralize their voices in this inquiry, while social cognitive career theory enabled more culturally informed interpretation of their experiences. The findings facilitate correct placement of this group into the literature on employment, career development, and counselor education, and can inform policy changes, curriculum, and interventions to promote diversity and equity in the field.
Clinical implications of hepatitis B virus core antigen‐mediated immunopathologic T cell responses in chronic hepatitis B
Authors: Wang Li‐Tzu , Chen Yu‐Hong , Cheng Yang , Fan Hsiu‐Lung , Chen Teng‐Wei , Shih Yu‐Lueng , Hsieh Tsai‐Yuan , Huang Wen‐Yen , Huang Wei‐Chen 
Published: March 2024

AbstractHepatitis B virus (HBV) infection significantly impacts Asian populations. The influences of continuous HBV antigen and inflammatory stimulation to T cells in chronic hepatitis B (CHB) remain unclear. In this study, we first conducted bioinformatics analysis to assess T‐cell signaling pathways in CHB patients. In a Taiwanese cohort, we examined the phenotypic features of HBVcore‐specific T cells and their correlation with clinical parameters. We used core protein overlapping peptides from the Taiwan prevalent genotype B HBV to investigate the antiviral response and the functional implication of HBV‐specific T cells. In line with Taiwanese dominant HLA‐alleles, we also evaluated ex vivo HBVcore‐specific T cells by pMHC‐tetramers targeting epitopes within HBV core protein. Compared to healthy subjects, we disclosed CD8 T cells from CHB patients had higher activation marker CD38 levels but showed an upregulation in the inhibitory receptor PD‐1. Our parallel study showed HBV‐specific CD8 T cells were more activated with greater PD‐1 expression than CMV‐specific subset and bulk CD8 T cells. Moreover, our longitudinal study demonstrated a correlation between the PD‐1 fluctuation pattern of HBVcore‐specific CD8 T cells and liver inflammation in CHB patients. Our research reveals the HBV core antigen‐mediated immunopathologic profile of CD8 T cells in chronic HBV infection. Our findings suggest the PD‐1 levels of HBVcore‐specific CD8 T cells can be used as a valuable indicator of personal immune response for clinical application in hepatitis management.