bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nematocyst sequestration within the family Fionidae (Gastropoda: Nudibranchia) considering ecological properties and evolution
Authors: Ekimova Irina A. , Vorobyeva Olga A. , Mikhlina Anna L. , Schepetov Dimitry M. , Vortsepneva Elena V. , Antokhina Tatiana I. , Malakhov Vladimir V. 
Published: November 2022

AbstractAeolid nudibranchs are well-known for their ability to incorporate cnidarian nematocysts and use them for defense; this process is tightly linked with the feeding preferences of molluscs. As many nudibranch groups show signs of ecology-based adaptive radiation, studies of prey-based defensive mechanisms can provide valuable insight into details of nudibranch evolutionary history. The main goal of this study is to test the correlation of ecological traits, feeding mechanisms, and prey preferences with cnidosac fine morphology and to pinpoint the phylogenetic value of these traits.We study the cnidosac morphology in thirteen species—representatives of the main lineages within the family Fionidaes.l.The morphological analysis includes histological sections, transmission electron microscopy, confocal laser scanning microscopy, and scanning electron microscopy. For phylogenetic study, available molecular data from public repositories were used, and phylogenetic trees were produced based on Bayesian Inference and Maximum likelihood analysis for a concatenated dataset of three molecular markers (COI, 16S, H3). In general, fionid cnidosacs fit the common aeolid pattern, but among different species we detected a high variation in type of obtained nematocysts, their arrangement within cnidophages, and in number of cell types within cnidosacs. We report on presence ofcellules specialein the haemocoel of all studied species, and for the first time, we report on cells with chitinous spindles in the haemocoel of all fionids exceptEubranchus.The function of both these cell types remains unknown. The loss of functional cnidosacs occurred at least three times within Fionidae, and in case of the generaPhestilla, Calma,andFiona,this loss is linked to their non-cnidarian diet. The diversity of cnidosac fine structure within Fionidaes.l.correlates with that of the radular morphology and feeding preferences of each species. Prey shifts between cnidarian and non-cnidarian prey (both through evolutionary shifts and individual variation) rarely occur within Fionidaes.l.;however, microevolutionary shifts between different hydrozoan species within a single genus are more common. Cnidosac morphology demonstrates considerable resulting changes even when switching between similar hydrozoan species, or changing the feeding site on same prey species. These data indicate that cnidosac morphology likely follows microevolutionary prey shifts—in other words, it is affected by switches in prey species and changes in feeding sites with a single prey species. Thus, the cnidosac morphology may be a useful indicator when studying ecological features of particular species.
Automated patient-robot assignment for a robotic rehabilitation gym: a simplified simulation model
Authors: Miller Benjamin A. , Adhikari Bikranta , Jiang Chao , Novak Vesna D. 
Published: November 2022

AbstractBackgroundA robotic rehabilitation gym can be defined as multiple patients training with multiple robots or passive sensorized devices in a group setting. Recent work with such gyms has shown positive rehabilitation outcomes; furthermore, such gyms allow a single therapist to supervise more than one patient, increasing cost-effectiveness. To allow more effective multipatient supervision in future robotic rehabilitation gyms, we propose an automated system that could dynamically assign patients to different robots within a session in order to optimize rehabilitation outcome.MethodsAs a first step toward implementing a practical patient-robot assignment system, we present a simplified mathematical model of a robotic rehabilitation gym. Mixed-integer nonlinear programming algorithms are used to find effective assignment and training solutions for multiple evaluation scenarios involving different numbers of patients and robots (5 patients and 5 robots, 6 patients and 5 robots, 5 patients and 7 robots), different training durations (7 or 12 time steps) and different complexity levels (whether different patients have different skill acquisition curves, whether robots have exit times associated with them). In all cases, the goal is to maximize total skill gain across all patients and skills within a session.ResultsAnalyses of variance across different scenarios show that disjunctive and time-indexed optimization models significantly outperform two baseline schedules: staying on one robot throughout a session and switching robots halfway through a session. The disjunctive model results in higher skill gain than the time-indexed model in the given scenarios, and the optimization duration increases as the number of patients, robots and time steps increases. Additionally, we discuss how different model simplifications (e.g., perfectly known and predictable patient skill level) could be addressed in the future and how such software may eventually be used in practice.ConclusionsThough it involves unrealistically simple scenarios, our study shows that intelligently moving patients between different rehabilitation robots can improve overall skill acquisition in a multi-patient multi-robot environment. While robotic rehabilitation gyms are not yet commonplace in clinical practice, prototypes of them already exist, and our study presents a way to use intelligent decision support to potentially enable more efficient delivery of technologically aided rehabilitation.
CT radiomics-based long-term survival prediction for locally advanced non-small cell lung cancer patients treated with concurrent chemoradiotherapy using features from tumor and tumor organismal environment
Authors: Chen Nai-Bin , Xiong Mai , Zhou Rui , Zhou Yin , Qiu Bo , Luo Yi-Feng , Zhou Su , Chu Chu , Li Qi-Wen , Wang Bin , Jiang Hai-Hang , Guo Jin-Yu , Peng Kang-Qiang , Xie Chuan-Miao , Liu Hui 
Published: November 2022

Abstract
Background
Definitive concurrent chemoradiotherapy (CCRT) is the standard treatment for locally advanced non-small cell lung cancer (LANSCLC) patients, but the treatment response and survival outcomes varied among these patients. We aimed to identify pretreatment computed tomography-based radiomics features extracted from tumor and tumor organismal environment (TOE) for long-term survival prediction in these patients treated with CCRT.

Methods
A total of 298 eligible patients were randomly assigned into the training cohort and validation cohort with a ratio 2:1. An integrated feature selection and model training approach using support vector machine combined with genetic algorithm was performed to predict 3-year overall survival (OS). Patients were stratified into the high-risk and low-risk group based on the predicted survival status. Pulmonary function test and blood gas analysis indicators were associated with radiomic features. Dynamic changes of peripheral blood lymphocytes counts before and after CCRT had been documented.

Results
Nine features including 5 tumor-related features and 4 pulmonary features were selected in the predictive model. The areas under the receiver operating characteristic curve for the training and validation cohort were 0.965 and 0.869, and were reduced by 0.179 and 0.223 when all pulmonary features were excluded. Based on radiomics-derived stratification, the low-risk group yielded better 3-year OS (68.4% vs. 3.3%, p < 0.001) than the high-risk group. Patients in the low-risk group had better baseline FEV1/FVC% (96.3% vs. 85.9%, p = 0.046), less Grade ≥ 3 lymphopenia during CCRT (63.2% vs. 83.3%, p = 0.031), better recovery of lymphopenia from CCRT (71.4% vs. 27.8%, p < 0.001), lower incidence of Grade ≥ 2 radiation-induced pneumonitis (31.6% vs. 53.3%, p = 0.040), superior tumor remission (84.2% vs. 66.7%, p = 0.003).

Conclusion
Pretreatment radiomics features from tumor and TOE could boost the long-term survival forecast accuracy in LANSCLC patients, and the predictive results could be utilized as an effective indicator for survival risk stratification. Low-risk patients might benefit more from radical CCRT and further adjuvant immunotherapy.

Trial registration:
retrospectively registered.
Correlation and significance of COX-2, Ki67, VEGF and other immune indexes with the growth of malignant pulmonary nodules
Authors: Guo Haoxin , Xue Wenfei , Zhao Qingtao , Zhao Huanfen , Hu Zhonghui , Zhang Xiaopeng , Duan Guochen 
Published: November 2022

Abstract
Objective
This study intends to explore the factors affecting the growth of pulmonary nodules in the natural process by immunohistochemical method.

Methods
40 cases of pulmonary nodules followed up for more than 3 years were divided into growth group (n = 20) and stable group (n = 20). The expressions of cyclooxygenase-2 (COX-2), Ki67, vascular endothelial growth factor (VEGF), CD44V6, epidermal growth factor receptor (EGFR), double microsome 2 (MDM2) and transforming growth factor (TGF)-β1 in pulmonary nodules were detected by immunohistochemical method so as to explore the relationship between it and the growth of pulmonary nodules.

Results
Compared with stable pulmonary nodules, the positive rates of COX-2, Ki67 and VEGF in the growth group were 85%, 80% and 55%, respectively. There was significant difference between the stable group and the growth group (P < 0.05). The correlation between other indexes and the growth of pulmonary nodules was not statistically significant (Pcd44v6 = 0.104;PEGFR = 0.337; PMDM2 = 0.49; PTGF-β1 = 0.141). In the subgroup of patients with non-invasive lung cancer, there was a correlation between VEGF and the growth of pulmonary nodules (P < 0.05).

Conclusion
The high expression of COX-2, Ki67 and VEGF proteins may be significantly related to the growth of pulmonary nodules, and VEGF may be an important factor affecting the growth of malignant pulmonary nodules. This study intends to provide a research direction for further searching for the essential causes of the growth of pulmonary nodules.
SIRPα-Fc fusion protein IMM01 exhibits dual anti-tumor activities by targeting CD47/SIRPα signal pathway via blocking the “don’t eat me” signal and activating the “eat me” signal
Authors: Yu Jifeng , Li Song , Chen Dianze , Liu Dandan , Guo Huiqin , Yang Chunmei , Zhang Wei , Zhang Li , Zhao Gui , Tu Xiaoping , Peng Liang , Liu Sijin , Bai Xing , Song Yongping , Jiang Zhongxing , Zhang Ruliang , Tian Wenzhi 
Published: November 2022

AbstractA novel recombinant SIRPα-Fc fusion protein, IMM01, was constructed and produced using an in-house developed CHO-K1 cell expression system, and the anti-tumor mechanism of IMM01 targeting the CD47-SIRPα pathway was explored. The phagocytosis and in vitro anti-tumor activity of IMM01 were evaluated by antibody-dependent cellular phagocytosis (ADCP), antibody-dependent cell-mediated cytotoxicity (ADCC), and complement-dependent cytotoxicity (CDC) assays. In vivo mouse tumor model studies were used to explore therapeutic efficacy as well as the mechanism of action. An in vitro binding assay revealed that IMM01 has a strong binding affinity to CD47 with an EC50 of 0.4967 nM. IMM01 can induce strong ADCP and moderate ADCC, but not CDC. IMM01-induced strong phagocytosis against tumor cells was attributed to dual activities of blocking the "don’t eat me" signal and activating the "eat me" signal, and IMM01 exhibits strong and robust in vivo anti-tumor activities either as monotherapy on hematological malignancies, or in combination therapy with PD-L1 monoclonal antibody (mAb), PD-1 mAb, and HER-2 mAb on solid tumors. Finally, IMM01 demonstrated a favorable safety profile with no human RBC binding activity or hemagglutination induction. IMM01 inhibits the growth of tumor cells by the following three possible mechanisms: (1) directly activating macrophages to phagocytize tumor cells; (2) activated macrophages degrade phagocytized tumor cells and present tumor antigens to T cells through MHC molecules to activate T cells; (3) activated macrophages can convert "cold tumors" into "hot tumors" and increase the infiltration of immune cells through chemotaxis by secreting some cytokines and chemokines.
ARPC1B promotes mesenchymal phenotype maintenance and radiotherapy resistance by blocking TRIM21-mediated degradation of IFI16 and HuR in glioma stem cells
Authors: Gao Zijie , Xu Jianye , Fan Yang , Zhang Zongpu , Wang Huizhi , Qian Mingyu , Zhang Ping , Deng Lin , Shen Jie , Xue Hao , Zhao Rongrong , Zhou Teng , Guo Xing , Li Gang 
Published: November 2022

Abstract
Background
Intratumoral heterogeneity is the primary challenge in the treatment of glioblastoma (GBM). The presence of glioma stem cells (GSCs) and their conversion between different molecular phenotypes contribute to the complexity of heterogeneity, culminating in preferential resistance to radiotherapy. ARP2/3 (actin-related protein-2/3) complexes (ARPs) are associated with cancer migration, invasion and differentiation, while the implications of ARPs in the phenotype and resistance to radiotherapy of GSCs remain unclear.

Methods
We screened the expression of ARPs in TCGA-GBM and CGGA-GBM databases. Tumor sphere formation assays and limiting dilution assays were applied to assess the implications of ARPC1B in tumorigenesis. Apoptosis, comet, γ-H2AX immunofluorescence (IF), and cell cycle distribution assays were used to evaluate the effect of ARPC1B on radiotherapy resistance. Immunoprecipitation (IP) and mass spectrometry analysis were used to detect ARPC1B-interacting proteins. Immune blot assays were performed to evaluate protein ubiquitination, and deletion mutant constructs were designed to determine the binding sites of protein interactions. The Spearman correlation algorithm was performed to screen for drugs that indicated cell sensitivity by the expression of ARPC1B. An intracranial xenograft GSC mouse model was used to investigate the role of ARPC1B in vivo.

Results
We concluded that ARPC1B was significantly upregulated in MES-GBM/GSCs and was correlated with a poor prognosis. Both in vitro and in vivo assays indicated that knockdown of ARPC1B in MES-GSCs reduced tumorigenicity and resistance to IR treatment, whereas overexpression of ARPC1B in PN-GSCs exhibited the opposite effects. Mechanistically, ARPC1B interacted with IFI16 and HuR to maintain protein stability. In detail, the Pyrin of IFI16 and RRM2 of HuR were implicated in binding to ARPC1B, which counteracted TRIM21-mediated degradation of ubiquitination to IFI16 and HuR. Additionally, the function of ARPC1B was dependent on IFI16-induced activation of NF-κB pathway and HuR-induced activation of STAT3 pathway. Finally, we screened AZD6738, an ataxia telangiectasia mutated and rad3-related (ATR) inhibitor, based on the expression of ARPC1B. In addition to ARPC1B expression reflecting cellular sensitivity to AZD6738, the combination of AZD6738 and radiotherapy exhibited potent antitumor effects both in vitro and in vivo.

Conclusion
ARPC1B promoted MES phenotype maintenance and radiotherapy resistance by inhibiting TRIM21-mediated degradation of IFI16 and HuR, thereby activating the NF-κB and STAT3 signaling pathways, respectively. AZD6738, identified based on ARPC1B expression, exhibited excellent anti-GSC activity in combination with radiotherapy.
Neoantigen-specific TCR-T cell-based immunotherapy for acute myeloid leukemia
Authors: Zhou Weijun , Yu Jinyi , Li Yilu , Wang Kankan 
Published: November 2022

AbstractNeoantigens derived from non-synonymous somatic mutations are restricted to malignant cells and are thus considered ideal targets for T cell receptor (TCR)-based immunotherapy. Adoptive transfer of T cells bearing neoantigen-specific TCRs exhibits the ability to preferentially target tumor cells while remaining harmless to normal cells. High-avidity TCRs specific for neoantigens expressed on AML cells have been identified in vitro and verified using xenograft mouse models. Preclinical studies of these neoantigen-specific TCR-T cells are underway and offer great promise as safe and effective therapies. Additionally, TCR-based immunotherapies targeting tumor-associated antigens are used in early-phase clinical trials for the treatment of AML and show encouraging anti-leukemic effects. These clinical experiences support the application of TCR-T cells that are specifically designed to recognize neoantigens. In this review, we will provide a detailed profile of verified neoantigens in AML, describe the strategies to identify neoantigen-specific TCRs, and discuss the potential of neoantigen-specific T-cell-based immunotherapy in AML.
Beneficial effect of the short-chain fatty acid propionate on vascular calcification through intestinal microbiota remodelling
Authors: Yan Jianlong , Pan Yanbin , Shao Wenming , Wang Caiping , Wang Rongning , He Yaqiong , Zhang Min , Wang Yongshun , Li Tangzhiming , Wang Zhefeng , Liu Wenxing , Wang Zhenmin , Sun Xin , Dong Shaohong 
Published: November 2022

Abstract
Background
Vascular calcification is a major cause of the high morbidity and mortality of cardiovascular diseases and is closely associated with the intestinal microbiota. Short-chain fatty acids (SCFAs) are derived from the intestinal microbiota and can also regulate intestinal microbiota homeostasis. However, it remains unclear whether exogenous supplementation with propionate, a SCFA, can ameliorate vascular calcification by regulating the intestinal microbiota. This study was conducted to explore the roles of propionate and the intestinal microbiota in the process of vascular calcification.

Methods
In total, 92 patients were enrolled consecutively as the observational cohort to analyse the relationship between SCFAs and vascular calcification in both blood and faecal samples. A rat model of vascular calcification was induced by vitamin D3 and nicotine (VDN) to validate the effect of propionate. Differences in the intestinal microbiota were analysed by 16S ribosomal RNA gene sequencing. Faecal microbiota transplantation and Akkermansia muciniphila transplantation experiments were performed to evaluate the functions of the intestinal microbiota.

Results
The results of the observational cohort study revealed that the levels of SCFAs (particularly propionate) in both blood and faecal samples independently correlated negatively with calcification scores (P < 0.01). To verify the activities of propionate, it was provided to VDN-treated rats, and oral or rectal propionate delivery reshaped the intestinal microbiota, resulted in elevated SCFA production, improved intestinal barrier function and alleviated inflammation, ultimately ameliorating vascular calcification. Furthermore, we demonstrated that transplantation of the propionate-modulated intestinal microbiota induced beneficial outcomes similar to those with oral or rectal propionate administration. Interestingly, linear discriminant analysis (LDA) effect size (LEfSe) revealed that oral or rectal propionate administration and propionate-modulated intestinal microbiota transplantation both enriched primarily Akkermansia. Subsequently, we demonstrated that Akkermansia supplementation could ameliorate VDN-induced vascular calcification in rats.

Conclusions
Propionate can significantly ameliorate vascular calcification in VDN-treated rats, and this effect is mediated by intestinal microbiota remodelling. The findings in our study indicate that the intestinal tract-vessel axis is a promising target for alleviating vascular calcification.
Urease and β-glucosidase activity enhanced the transformation of functional groups of humin amended by straw and straw-derived biochar
Authors: Liu Xinwei , An Qi , Song Xiangyun , Hussain Qaiser , Cui Liqiang , Wang Chengji , Wang Yan , Cui Dejie 
Published: November 2022

Abstract
Background
Organic materials carbon is mainly sequestrated in humin. However, the carbon (C) stability of humin with organic materials amendments in different types of soils is mainly affected by organic materials or soil types as well as the enzymatic reaction is important for understanding the C sequestration mechanism of soil.

Results
In this study, straw and straw-derived biochar were incorporated into three different types of soils. Using 13C nuclear magnetic resonance (NMR) spectroscopy, the structural composition of humin (Hu) was analyzed, along with the urease and β-glucosidase activities. The results showed that biochar amendment enhanced aryl C to 49.63%–76.55% while straw amendments increased O-alkyl C of Hu to 33.99%–51.70%. Two-way ANOVA analysis revealed significant differences in the impact of soil types and treatments on enzyme activities and functional groups of humin. A significant positive correlation was found between β-glucosidase activity and O-alkyl C, phenolic C, and methoxyl C of humin. In addition, urease activity showed a significant positive correlation with alkyl C of humin. Compared to tobacco straw, tobacco straw-biochar amendment increased β-glucosidase activity for 22.01 mg kg−1 d−1, 26.01 mg kg−1 d−1 and 14.01 mg kg−1 d−1 in three types of soils, respectively.

Conclusions
These results showed that β-glucosidase contributed to the transformation of humin functional groups and was influenced by organic materials and soil types, especially the organic materials types. The findings imply that straw or straw-derived biochar application stimulates urease and β-glucosidase activities, which improves the alternation of functional groups of humin in different types of soil.

Graphical Abstract
Development and psychometric analysis of a new tool to assess food literacy in diabetic patients
Authors: Bastami Fatemeh , Mardani Mahnaz , Rezapour Pouria 
Published: November 2022

Abstract
Background
One of the factors affecting self-care in diabetic patients is food literacy, which helps said patients in following a healthy diet. Thus, it is crucial to analyze food literacy in diabetic patients through suitable and reliable instruments.

Objective
The current study aimed to design a questionnaire for food literacy assessment in diabetic patients and analyze its psychometric features.

Method
The present study was a cross-sectional descriptive analysis carried out in 2021. Firstly, the concepts of food literacy in diabetic patients were identified and the questionnaire was deigned based on them. Secondly, its face and content validities and its reliability were analyzed. Finally, the construct validity was analyzed by exploratory factor analysis. The study was carried out on 300 diabetic participants chosen at random via stratified cluster sampling from Health service centers. The exploratory factor analysis was carried out by extracting the main factors and using varimax rotation with eigenvalue values more than 1.

Results
A five-pronged structure accounted for 52.745% of food literacy variance. This included the ability to read food facts, practical ability to group foods, the ability to identify the caloric content of different foods, the ability to understand the effect of food on health, and the ability to prepare a healthy meal. Items with an impact score below 1.5 were discarded. Additionally, items with CVR scores below 0.62 and CVI scores below 0.79 were deleted too. The Kaiser-Meyer-Okin measurement was 0.836 (p < 0.001). Alpha Cronbach Scale dimension was 0.610–0.951.

Conclusion
The results of this study showed that the exploratory dimensions of the current study were consistent with health literacy measurements, such as functional, interactive, and critical food literacy. This scale has acceptable reliability and validity. Health professionals can use this scale to analyze and improve food literacy in diabetic patients. This is a new instrument and thus far no questionnaire has been made to evaluate food literacy in diabetic patients.