Miracle-dz/UniFAR-FTUs huggingface dataset:
A Predictive Model for the 10-year Overall Survival Status of Patients With Distant Metastases From Differentiated Thyroid Cancer Using XGBoost Algorithm-A Population-Based Analysis

Purpose: To explore clinical and non-clinical characteristics affecting the prognosis of patients with differentiated thyroid cancer with distant metastasis (DTCDM) and establish an accurate overall survival (OS) prognostic model. Patients and methods: Study subjects and related information were obtained from the National Cancer Institute’s surveillance, epidemiology, and results database (SEER). Kaplan‐Meier analysis, log-rank test, and univariate and multivariate Cox analysis were used to screen for factors influencing the OS of patients with DTCDM. Nine variables were introduced to build a machine learning (ML) model, receiver operating characteristic (ROC) was used to evaluate the recognition ability of the model, calibration plots were used to obtain prediction accuracy, and decision curve analysis (DCA) was used to estimate clinical benefit. Results: After applying the inclusion and exclusion criteria, a total of 3,060 patients with DTCDM were included in the survival analysis from 2004 to 2017. A machine learning prediction model was developed with nine variables: age at diagnosis, gender, race, tumor size, histology, regional lymph node metastasis, primary site surgery, radiotherapy, and chemotherapy. After excluding patients who survived <120 months, variables were sub-coded and machine learning was used to model OS prognosis in patients with DTCDM. Patients 6–50 years of age had the highest scores in the model. Other variables with high scores included small tumor size, male sex, and age 51–76. The AUC and calibration curves confirm that the XGBoost model has good performance. DCA shows that our model can be used to support clinical decision-making in a 10-years overall survival model. Conclusion: An artificial intelligence model was constructed using the XGBoost algorithms to predict the 10-years overall survival rate of patients with DTCDM. After model validation and evaluation, the model had good discriminative ability and high clinical value. This model could serve as a clinical tool to help inform treatment decisions for patients with DTCDM.
Low expression and Hypermethylation of ATP2B1 in Intrahepatic Cholangiocarcinoma Correlated With Cold Tumor Microenvironment

Background The efficacy of current therapeutic schedule is limited owing to fibroproliferative tumor microenvironment (TME) of cholangiocarcinoma, compelling a search for new therapeutic targets. Methods Gene expression profiles and methylation profiles were obtained from UCSC Xena. Consensus clustering was performed on the transcriptome data of cholangiocarcinoma to determine the different immune subtypes. The differentially expressed genes (DEGs) between hot tumor and cold tumors were identified. ESTIMATE was used to assess immune score, and the cases were separated into relatively superior and inferior immune score groups. Single-sample gene set enrichment analysis was applied to assess 28 immune cells in the cholangiocarcinoma microenvironment. Unsupervised consensus was applied for methylation profiling to distribute the high and low methylation groups. The correlation between DNA methylation and mRNA expression was investigated, and the relationship between the ATP2B1 gene and the immune microenvironment was explored. Finally, 77 cases of intrahepatic cholangiocarcinoma (ICC) were collected for verification. Results Seven subtypes were related to patient outcomes (P=0.005). The proportions of CD8+ T cells in the “hot” immune type was significantly greater than that in the “cold” immune type (P<0.05). Next, DEGs and DNA methylation-governed genes were intersected, and ATP2B1 was identified as a prognosis factor in ICC (P=0.035). ATP2B1 expression was positively correlated with immune scores (P=0.005, r=0.458), the levels of infiltrating CD8+ T cells (P=0.004, r=0.47), and CD4+ T cells (P=0.027, r=0.37). Immunohistochemistry confirmed that the amounts of CD8+ and CD4+ T cells were significantly higher in ICC tissue samples than in tissues with ATP2B1 overexpression (P<0.05). Conclusions ATP2B1 overexpression can activate immune signals and prompt cold tumor response.
Low IL7R Expression at Diagnosis Predicted Relapse in Adult Acute Myeloid Leukemia Patients With t(8;21)

Background Acute myeloid leukemia (AML) with t(8;21) needs to be further stratified. In addition to leukemia cells, immune cells in tumor microenvironment participate in tumor initiation, growth and progression. Interleukins (ILs)/interleukin receptors (ILRs) interaction plays important roles in the antitumor immune response. IL7R is reported to be relevant to prognosis in solid tumor and acute lymphoblastic leukemia. However, the prognostic significance of IL7R in t(8;21) AML remains to be clarified. Methods Bone marrows collected from 156 newly diagnosed t(8;21) AML patients were used for testing IL7R transcript level by TaqMan-based real-time quantitative PCR (RQ-PCR), and RNAseq were performed in 15 of them. Moreover, IL7R expression at diagnosis were measured by RQ-PCR and flow cytometry (FCM) simultaneously in other 13 t(8;21) AML patients. Results t(8;21) AML patients had varied IL7R transcript levels and were categorized into low-expression (IL7R-L) and high-expression (IL7R-H) groups; IL7R-L was significantly associated with a lower relapse-free survival (RFS) rate (P=0.0027) and KITD816/D820 mutation (P=0.0010). Furthermore, IL7R-L was associated with a lower RFS rate in KITD816/D820 group (P=0.013) and IL7R-H/KITD816/D820 patients had similar RFS to KITN822/e8/WT patients (P=0.35). GO analysis enrichment showed that down-regulated genes were predominantly involved in the regulation of T cell and leukocyte activation, proliferation and differentiation in IL7R-L group. IL7R-L had significantly lower levels of Granzymes A/B, CCR7, CD28 and CD27 than IL7R-H group (all P<0.05). FCM analysis showed IL7R protein was primarily expressed in CD4+ T and CD8+ T cell subset. A significant association was found between the transcript level of IL7R and the percentage of CD8+ T cells in nucleated cells (P=0.015) but not CD4+ T cells (P=0.47). Conclusion Low IL7R transcript level of bone marrow at diagnosis predicted relapse in t(8;21) AML, which might be caused by the difference in the amount, status and function of T cells.
Diversity of Free-Living and Particle-Attached Prokaryotes in a River-Influenced Coastal Area of the Northern Adriatic Sea

The Northern Adriatic Sea is a key area of the Mediterranean Sea, strongly affected by freshwater inputs, mainly from the Po River, which bring high amounts of nutrients as well as organic and inorganic particles. Free-living and particle-attached prokaryotes were characterized by 16S rRNA gene amplicon sequencing of size-fractionated samples collected during a diatom bloom in this area. The diversity of free-living and particle-attached prokaryotic assemblages was investigated with the aim to understand how the microbial communities are structured in the two fractions and whether specific microbial groups are associated to one lifestyle or the other. The results highlight a diverse prokaryotic community dominated by Proteobacteria, Bacteroidetes, and, remarkably, Firmicutes. Taxa within Firmicutes and Alphaproteobacteria are identified as the main particle-attached indicators by LEfSe, while members of Bacteroidetes and Gammaproteobacteria were representative of the free-living lifestyle, although they were also usually found as particle-attached. Collectively, the results suggest that both the free-living and the particle-attached lifestyles are a complex combination of specialization and adaptation to local conditions.
Aerosol Jet Printing of Hybrid Ti3C2T x /C Nanospheres for Planar Micro-supercapacitors

When utilized in energy devices, the restacking tendency of MXene Ti3C2T x inhibits its electrochemical performance. Using aerosol jet printing (AJP) technology, hybrid Ti3C2T x /C nanospheres are synthesized with C nanoparticle-bonded MXene nanosheets, and the restacking of MXene nanosheets is blocked efficiently. The formation mechanism for hybrid Ti3C2T x /C nanospheres has been hypothesized, and the Ti3C2T x /C is anticipated to assemble and shape along the droplet surface in tandem with the Marangoni flow within the droplet. The planar microsupercapacitor devices generated from these hybrid spherical nanostructures with increased interlayer spacing exhibit exceptional areal capacitance performance. This concept offers a straightforward and effective method for constructing 3D-structured MXene with suppressed self-stacking for diverse high-performance micro energy storage devices.
Demand response potential evaluation for residential air conditioning loads

Residential air conditioning loads with energy storage characteristics can quickly participate in the demand response, making it an important demand response resource. It can improve resource utilisation and the flexibility of power grid operation through the effective regulation. However, the degree of residential air conditioning to participate in demand response is affected by the outdoor temperature, users' comfort settings, thermal storage and insulation properties of buildings. Moreover, the difficulty of assessing the demand response potential is further increased by the uncertainty of the influencing factors. To guide the residential air conditioners to participate in the power grid operation, the aggregated air conditioner model is established to describe the relationship among the total power, the external environment, and the indoor temperature. The demand response potential model is established from the amount and the duration of demand response. The effects of outdoor temperature, indoor temperature adjustment and the number of air conditioners participating in the response are quantitatively evaluated. Finally, the accuracy of the aggregated model and demand response potential model are verified by numerical simulation.
A Multi-Scale Approach to Model K+ Permeation Through the KcsA Channel

K+ channels allow a very efficient passage of K+ ions through the membrane while excluding Na+ ions, and these properties are essential for life. The 3D structure of the KcsA K+ channel, solved more than 20 years ago, allows to address many relevant aspects of K+ permeation and selectivity mechanisms at the molecular level. Recent crystallographic data and molecular dynamics (MD) studies suggest that no water is normally present inside the selectivity filter (SF), which can instead accommodate four adjacent K+ ions. Using a multi-scale approach, whereby information taken from a low-level simulation approach is used to feed a high-level model, we studied the mechanism of K+ permeation through KcsA channels. More specifically, we used MD to find stable ion configurations under physiological conditions. They were characterized by two adjacent K+ ions occupying the more central positions of the SF (sites S2 and S3), while the other two K+ ions could be found at the external and internal entrances to the SF. Sites S1 and S4 were instead not occupied by K+. A continuum Bikerman–Poisson–Boltzmann model that takes into account the volume of the ions and their dehydration when entering the SF fully confirmed the MD results, showing peaks of K+ occupancy at S2, S3, and the external and internal entrances, with S1 and S4 sites being virtually never occupied by K+. Inspired by the newly found ion configuration in the SF at equilibrium, we developed a simple kinetic permeation model which, fed with kinetic rate constants assessed from molecular meta-dynamics, reproduced the main permeation properties of the KcsA channel found experimentally, including sublinear current-voltage and saturating conductance-concentration relationships. This good agreement with the experimental data also implies that the ion configuration in the SF we identified at equilibrium would also be a key configuration during permeation.
Developing a Conceptual Partner Matching Framework for Digital Green Innovation of Agricultural High-End Equipment Manufacturing System Toward Agriculture 5.0: A Novel Niche Field Model Combined With Fuzzy VIKOR

Digital green innovation (DGI) is the core factor that affects the digitalization and decarbonization strategy of agricultural high-end equipment manufacturing (AHEM) system. Although AHEM enterprises actively cooperate with academic research institutes to develop agricultural high-end equipment, there are many obstacles in the process of DGI. Moreover, the integration of digital technology and green innovation from the perspective of partner matching for the AHEM system has not been fully introduced in current literature. Hence, this study aimed to (i) establish a suitable framework system for the AHEM system in general, (ii) quantify the selection of DGI by academic research institutions based on niche theory, and (iii) propose an extended niche field model combined with fuzzy VIKOR model. First, a theoretical framework consisting of three core elements of technology superposition, mutual benefit, and mutual trust, and technological complementarity was constructed based on niche intensity and niche overlap degree. DGI ability superposition of technology, mutual trust, and technical complementarity are beneficial for transferring DGI knowledge from academic research institutes to the AHEM industry. Second, triangle fuzzy number and prospect theory combined with the VIKOR method were introduced into the field theory to construct the complementary field model of DGI resources. The niche field model has been successfully applied to practical cases to illustrate how the model can be implemented to solve the problem of DGI partner selection. Third, the results of a case study show that the criteria framework and the niche field model can be applied to real-world partner selection for AHEM enterprises. This study not only puts forward the standard framework of niche fitness evaluation based on niche theory but also establishes the niche domain model of innovation partner selection management based on niche theory. The standard framework and novel niche field model can help enterprises to carry out digital green innovation in the development of high-end agricultural equipment. The study has the following theoretical and practical implications: (i) constructing a criteria framework based on niche theory; (ii) developing a novel niche field model for DGI partner selection of AHEM enterprises; and (iii) assisting AHEM enterprises to perform DGI practice.
Inhibition of Osteoblast Differentiation by JAK2V617F Megakaryocytes Derived From Male Mice With Primary Myelofibrosis

Past studies described interactions between normal megakaryocytes, the platelet precursors, and bone cell precursors in the bone marrow. This relationship has also been studied in context of various mutations associated with increased number of megakaryocytes. The current study is the first to examine the effects of megakaryocytes from transgenic mice carrying the most common mutation that causes primary myelofibrosis (PMF) in humans (JAK2V617F) on bone cell differentiation. Organ level assessments of mice using micro-computed tomography showed decreased bone volume in JAK2V617F males, compared to matching controls. Tissue level histology revealed increased deposition of osteoid (bone matrix prior mineralization) in these mutated mice, suggesting an effect on osteoblast differentiation. Mechanistic studies using a megakaryocyte-osteoblast co-culture system, showed that both wild type or JAK2V617F megakaryocytes derived from male mice inhibited osteoblast differentiation, but JAK2V617F cells exerted a more significant inhibitory effect. A mouse mRNA osteogenesis array showed increased expression of Noggin, Chordin, Alpha-2-HS-glycoprotein, Collagen type IV alpha 1 and Collagen type XIV alpha 1 (mostly known to inhibit bone differentiation), and decreased expression of alkaline phosphatase, Vascular cell adhesion molecule 1, Sclerostin, Distal-less homeobox 5 and Collagen type III alpha 1 (associated with osteogenesis) in JAK2V617F megakaryocytes, compared to controls. This suggested that the mutation re-programs megakaryocytes to express a cluster of genes, which together could orchestrate greater suppression of osteogenesis in male mice. These findings provide mechanistic insight into the effect of JAK2V617F mutation on bone, encouraging future examination of patients with this or other PMF-inducing mutations.
Gut Microbiota Structure and Metabolites, Before and After Treatment in Early Rheumatoid Arthritis Patients: A Pilot Study

Rheumatoid Arthritis (RA) is a chronic systemic autoimmune disease. Modifications of gut microbiota seem to be associated with the disease, but the impact of gut microbiota on therapies’ outcome remains unclear. A role of T cells in RA pathogenesis has been addressed, particularly on the Th17/Treg cells balance. Our study aimed to evaluate in early RA (ERA) patients compared to a control group, fecal gut microbiota composition, short-chain fatty acids concentrations, and the levels of circulating Th17/Treg and their own cytokines, before and after 3 months of standard treatment (Methotrexate (MTX) plus glucocorticoids). Fecal microbiota characterization was carried out on 19 ERA patients and 20 controls matched for sex and age. Significant decreased biodiversity levels, and a partition on the base of the microbiota composition, between the ERA patients at baseline compared to controls, were observed. The co-occurrent analysis of interactions revealed a characteristic clustered structure of the microbial network in controls that is lost in ERA patients where an altered connection between microbes and clinical parameters/metabolites has been reported. Microbial markers such as Acetanaerobacterium elongatum, Cristiansella massiliensis, and Gracilibacter thermotolerans resulted significantly enriched in control group while the species Blautia gnavus emerged to be more abundant in ERA patients. Our results showed an alteration in Th17/Treg balance with higher Th17 levels and lower Treg levels in ERA group respect to control at baseline, those data improved after therapy. Treatment administration and the achievement of a low disease activity/remission appear to exert a positive pressure on the structure of intestinal microbiota with the consequent restoration of biodiversity, of the structure of microbial network, and of the abundance of taxa that became closer to those presented by the subject without the disease. We also found an association between Blautia gnavus and ERA patients characterized by a significant reduction of propionic acid level. Furthermore significant differences highlighted at baseline among controls and ERA patients are no more evident after treatment. These data corroborate the role played by gut microbiota in the disease and suggest that therapy aimed to restore gut microbiota would improve treatment outcome.
Identification and Functional Prediction of Poplar Root circRNAs Involved in Treatment With Different Forms of Nitrogen

Circular RNAs (circRNAs) are a class of noncoding RNA molecules with ring structures formed by covalent bonds and are commonly present in organisms, playing an important regulatory role in plant growth and development. However, the mechanism of circRNAs in poplar root responses to different forms of nitrogen (N) is still unclear. In this study, high-throughput sequencing was used to identify and predict the function of circRNAs in the roots of poplar exposed to three N forms [1 mM NO3− (T1), 0.5 mM NH4NO3 (T2, control) and 1 mM NH4+ (T3)]. A total of 2,193 circRNAs were identified, and 37, 24 and 45 differentially expressed circRNAs (DECs) were screened in the T1-T2, T3-T2 and T1-T3 comparisons, respectively. In addition, 30 DECs could act as miRNA sponges, and several of them could bind miRNA family members that play key roles in response to different N forms, indicating their important functions in response to N and plant growth and development. Furthermore, we generated a competing endogenous RNA (ceRNA) regulatory network in poplar roots treated with three N forms. DECs could participate in responses to N in poplar roots through the ceRNA regulatory network, which mainly included N metabolism, amino acid metabolism and synthesis, response to NO3− or NH4+ and remobilization of N. Together, these results provide new insights into the potential role of circRNAs in poplar root responses to different N forms.
Molecular Pathways and Key Genes Associated With Breast Width and Protein Content in White Striping and Wooden Breast Chicken Pectoral Muscle

Growth-related abnormalities affecting modern chickens, known as White Striping (WS) and Wooden Breast (WB), have been deeply investigated in the last decade. Nevertheless, their precise etiology remains unclear. The present study aimed at providing new insights into the molecular mechanisms involved in their onset by identifying clusters of co-expressed genes (i.e., modules) and key loci associated with phenotypes highly related to the occurrence of these muscular disorders. The data obtained by a Weighted Gene Co-expression Network Analysis (WGCNA) were investigated to identify hub genes associated with the parameters breast width (W) and total crude protein content (PC) of Pectoralis major muscles (PM) previously harvested from 12 fast-growing broilers (6 normal vs. 6 affected by WS/WB). W and PC can be considered markers of the high breast yield of modern broilers and the impaired composition of abnormal fillets, respectively. Among the identified modules, the turquoise (r = -0.90, p < 0.0001) and yellow2 (r = 0.91, p < 0.0001) were those most significantly related to PC and W, and therefore respectively named “protein content” and “width” modules. Functional analysis of the width module evidenced genes involved in the ubiquitin-mediated proteolysis and inflammatory response. GTPase activator activity, PI3K-Akt signaling pathway, collagen catabolic process, and blood vessel development have been detected among the most significant functional categories of the protein content module. The most interconnected hub genes detected for the width module encode for proteins implicated in the adaptive responses to oxidative stress (i.e., THRAP3 and PRPF40A), and a member of the inhibitor of apoptosis family (i.e., BIRC2) involved in contrasting apoptotic events related to the endoplasmic reticulum (ER)-stress. The protein content module showed hub genes coding for different types of collagens (such as COL6A3 and COL5A2), along with MMP2 and SPARC, which are implicated in Collagen type IV catabolism and biosynthesis. Taken together, the present findings suggested that an ER stress condition may underly the inflammatory responses and apoptotic events taking place within affected PM muscles. Moreover, these results support the hypothesis of a role of the Collagen type IV in the cascade of events leading to the occurrence of WS/WB and identify novel actors probably involved in their onset.