Combined Analysis Research Articles

RNAi‐based genetically engineered rice resistant to black‐streaked dwarf virus does not show adverse genetic effects: A multi‐omics analysis

Societal Impact StatementAdvancements in science and technology enable us to address the challenges of the times: hunger, malnutrition, climate change, and dwindling natural resources. One of the most significant innovations in food and agriculture is the advent of genetic engineering, which may help us address the aforementioned challenges. Millions of people could benefit from the application of genetically engineered crops in agriculture and food. However, it is vital that biosafety assessments of unintended effects are carried out to identify any potential risks to humans, the environment, or society.Summary The study compared the extent of siRNA, transcriptomic and metabolomic changes in the leaves of four RNAi‐based genetically engineered rice lines to evaluate whether RNAi‐based genetically engineered rice that is resistant to black‐streaked dwarf virus experiences changes not seen in the non‐genetically engineered counterpart. siRNA, transcriptome, and metabolome profiling were conducted. siRNAs with different lengths and abundance were highly enriched in the transcript of rice; however, relative expression analysis of eight potential off‐target genes revealed that there was no decrease in gene expression in the RNAi‐based genetically engineered lines, meaning that no off‐target phenomena were caused as a result of siRNA derived from invert repeat sequences of rice black‐streaked dwarf virus in this study. This study identified some differentially expressed genes and differentially accumulated metabolites in the RNAi‐based genetically engineered lines; however, they were not enriched in pathways detrimental for humans, animals and the environment. Only 30 differentially expressed genes were significantly enriched in the plant hormone signal transduction pathway via a combined analysis using two‐way orthogonal partial least squares model. These genes belonging to salicylic acid, jasmonic acid, cytokinin, abscisic acid, and brassinosteroid pathway involved in pathways related to virus resistance or infection response were significantly changed. Taken together, there was no off‐target in RNAi‐based genetically engineered rice lines and may have a positive effect on virus resistance overall in this study.

Single-cell N6-methyladenosine-related genes function within the tumor microenvironment to affect the prognosis and treatment sensitivity in patients with gastric cancer

BackgroundGastric cancer (GC) ranks fifth for morbidity and third for mortality worldwide. The N6-methyladenosine (m6A) mRNA methylation is crucial in cancer biology and progression. However, the relationship between m6A methylation and gastric tumor microenvironment (TME) remains to be elucidated.MethodsWe combined single-cell and bulk transcriptome analyses to explore the roles of m6A-related genes (MRG) in gastric TME.ResultsNine TME cell subtypes were identified from 23 samples. Fibroblasts were further grouped into four subclusters according to different cell markers. M6A-mediated fibroblasts may guide extensive intracellular communications in the gastric TME. The m6A-related genes score (MRGs) was output based on six differentially expressed single-cell m6A-related genes (SCMRDEGs), including GHRL, COL4A1, CAV1, GJA1, TIMP1, and IGFBP3. The protein expression level was assessed by immunohistochemistry. We identified the prognostic value of MRGs and constructed a nomogram model to predict GC patients’ overall survival. MRGs may affect treatment sensitivity in GC patients.ConclusionOur study visualized the cellular heterogeneity of TME at the single-cell level, revealed the association between m6A mRNA modification and intracellular communication, clarified MRGs as an independent risk factor of prognosis, and provided a reference for follow-up treatment.

EFFICACY, SAFETY AND IMMUNOGENICITY OF SUBCUTANEOUS INFLIXIMAB (CT-P13 SC) MONOTHERAPY VERSUS COMBINATION THERAPY WITH IMMUNOSUPPRESSANTS – POST HOC ANALYSIS OF LIBERTY-CD AND LIBERTY-UC STUDY

Abstract INTRODUCTION CT-P13 subcutaneous (SC) infliximab formulation demonstrated superiority over placebo in maintenance therapy in Crohn's disease (CD) and Ulcerative Colitis (UC) patients in two parallel 54 weeks studies (LIBERTY-CD and LIBERTY-UC). We performed a post-hoc subgroup analysis comparing patients treated with CT-P13 SC with and without combination immunosuppressants (IS) at baseline in CD and UC. AIMS & METHODS Patients with moderately to severely active CD and UC who responded at W10 to CT-P13 intravenous infliximab 5mg/kg (Weeks 0, 2 and 6) were randomized (2:1) to receive CT-P13 SC 120 mg (CT-P13 SC) or placebo every 2 weeks until W54 as maintenance therapy. IS (azathioprine [AZA], 6-mercaptopurine [6-MP], or methotrexate [MTX]) were allowed if patients maintained stable doses at least 8 weeks prior to W0, and stable doses were maintained up to W54. RESULTS 231 CD and 294 UC patients were randomized to receive CT-P13 SC maintenance therapy. Among them, 71 (30.7%) and 65 (22.1%) patients received CT-P13 SC with IS in CD and UC, respectively (In CD; 63, 4 and 4 patients of AZA, 6-MP, MTX, respectively, In UC; 63, 2 and 0 patients of AZA, 6-MP, MTX, respectively). There were no meaningful differences in efficacy outcomes at Week 54 by CT-P13 concentration tertiles at Week 54 between monotherapy and combination therapy groups in both studies (Table 1). In combined analysis of CD and UC patients, no statistically significant differences were seen in safety profile between monotherapy and combination therapy groups in the maintenance period except for infection rate (Table 2). In combined analysis of CD and UC patients, rate of anti-drug antibody [ADA] positive conversion up to W54 was statistically lower in combination therapy group (70.2% monotherapy vs 47.8% combination therapy [p<0.0001]). CONCLUSION No meaningful differences in efficacy outcomes at W54 were observed between monotherapy and combination therapy of CT-P13 SC in CD and UC patients. Concomitant IS use was associated with less ADA formation, whereas more infections are seen for combination therapy during maintenance period in CD and UC patients. The overall safety profile during maintenance period was otherwise comparable between monotherapy and combination therapy in CD and UC patients. This post-hoc analysis suggests limited benefit of concomitant IS with CT-P13 SC but a higher infection risk. Notably, patients were not randomized according to IS use nor were the studies ‘powered’ to demonstrate differences. Proportion of patients achieving efficacy outcomes at W54 by tertile of Serum concentrations of Infliximab (ng/mL) at W54 (Pharmacokinetic population) Safety results in maintenance period (Safety population)

Systemic inflammation and insulin resistance-related indicator predicts poor outcome in patients with cancer cachexia

BackgroundThe C-reactive protein (CRP)-triglyceride-glucose (TyG) index (CTI), which is a measure representing the level of inflammation and insulin resistance (IR), is related to poor cancer prognosis; however, the CTI has not been validated in patients with cancer cachexia. Thus, this study aimed to explore the potential clinical value of the CTI in patients with cancer cachexia.MethodsIn this study, our prospective multicenter cohort included 1411 patients with cancer cachexia (mean age 59.45 ± 11.38, 63.3% male), which was a combined analysis of multiple cancer types. We randomly selected 30% of the patients for the internal test cohort (mean age 58.90 ± 11.22% 61.4% male). Additionally, we included 307 patients with cancer cachexia in the external validation cohort (mean age 61.16 ± 11, 58.5% male). Receiver operating characteristic (ROC) and calibration curves were performed to investigate the prognostic value of CTI. The prognostic value of the CTI was also investigated performing univariate and multivariate survival analyses.ResultsThe survival curve indicated that the CTI showed a significant prognostic value in the total, internal, and external validation cohorts. Prognostic ROC curves and calibration curves revealed that the CTI showed good consistency in predicting the survival of patients with cancer cachexia. Multivariate survival analysis showed that an elevated CTI increased the risk of death by 22% (total cohort, 95% confidence interval [CI] = 1.13–1.33), 34% (internal test cohort, 95%CI = 1.11–1.62), and 35% (external validation cohort, 95%CI = 1.14–1.59) for each increase in the standard deviation of CTI. High CTI reliably predicted shorter survival (total cohort, hazard ratio [HR] = 1.45, 95%CI = 1.22–1.71; internal test cohort, HR = 1.62, 95%CI = 1.12–2.36; external validation cohort, HR = 1.61, 95%CI = 1.15–2.26). High CTI significantly predicted shorter survival in different tumor subgroups, such as esophageal [HR = 2.11, 95%CI = 1.05–4.21] and colorectal cancer [HR = 2.29, 95%CI = 1.42–3.71]. The mediating effects analysis found that the mediating proportions of PGSGA, ECOG PS, and EORTC QLQ-C30 on the direct effects of CTI were 21.72%, 19.63%, and 11.61%, respectively We found that there was a significant positive correlation between the CTI and 90-day [HR = 2.48, 95%CI = 1.52–4.14] and 180-day mortality [HR = 1.77,95%CI = 1.24–2.55] in patients with cancer cachexia.ConclusionThe CTI can predict the short- and long-term survival of patients with cancer cachexia and provide a useful prognostic tool for clinical practice.

Analysis of Forest Fragmentation and Connectivity Using Fractal Dimension and Succolarity

Forests around the world, vital for ecological, economic, and social functions, are facing increasing threats such as deforestation and habitat fragmentation. This study introduces “succolarity” to analyse forest connectivity and fragmentation directionally in the Romanian Carpathians from 2000 to 2021. Besides traditional indices such as the fractal fragmentation index (FFI), the fractal fragmentation and disorder index (FFDI), the local connected fractal dimension (LCFD), and succolarity, two novel indices are proposed: potential succolarity and delta (Δ) succolarity, which provide nuanced insights into environmental changes and human interventions in forests worldwide. The succolarity tests showed invariance at the image scale and sensitivity to the obstacles in different image scenarios. The combined analysis of succolarity and fractal indices reveals dynamic patterns of connectivity, fragmentation, and spatial disturbance. The directional insights of succolarity highlight and enhance understanding of deforestation patterns. The FFI and FFDI show different levels of fragmentation across mountain groups, while the LCFD details local connectivity. The adaptability of the method makes it globally applicable, supporting biodiversity conservation and landscape management. In conclusion, the integration of succolarity and traditional fractal indices provides a robust methodology for the comprehensive analysis of forest fragmentation. This advancement not only supports the sustainable management of the Romanian Carpathians but also represents a versatile approach applicable to ecosystems worldwide, ensuring the long-term resilience of forested regions.

Combined pH ratiometry and fluorescence lectin-binding analysis (pH-FLBA) for microscopy-based analyses of biofilm pH and matrix carbohydrates.

Bacterial biofilms have a complex and heterogeneous three-dimensional architecture that is characterized by chemically and structurally distinct microenvironments. Confocal microscopy-based pH ratiometry and fluorescence lectin-binding analysis (FLBA) are well-established methods to characterize pH developments and the carbohydrate matrix architecture of biofilms at the microscale. Here, we developed a combined analysis, pH-FLBA, to concomitantly map biofilm pH and the distribution of matrix carbohydrates in bacterial biofilms while preserving the biofilm microarchitecture. As a proof of principle, the relationship between pH and the presence of galactose- and fucose-containing matrix components was investigated in dental biofilms grown with and without sucrose. The pH response to a sucrose challenge was monitored in different areas at the biofilm base using the ratiometric pH-sensitive dye C-SNARF-4. Thereafter, the fucose- and galactose-specific fluorescently labeled lectins Aleuria aurantia lectin (AAL) and Morus nigra agglutinin G (MNA-G) were used to visualize carbohydrate matrix components in the same biofilm areas and their immediate surroundings. Sucrose during growth significantly decreased biofilm pH (P < 0.05) and increased the amounts of both MNA-G- and AAL-targeted matrix carbohydrates (P < 0.05). Moreover, it modulated the biofilm composition towards a less diverse community dominated by streptococci, as determined by 16S rRNA gene sequencing. Altogether, these results suggest that the production of galactose- and fucose-containing matrix carbohydrates is related to streptococcal metabolism and, thereby, pH profiles in dental biofilms. In conclusion, pH-FLBA using lectins with different carbohydrate specificities is a useful method to investigate the association between biofilm pH and the complex carbohydrate architecture of bacterial biofilms.IMPORTANCEBiofilm pH is a key regulating factor in several biological and biochemical processes in environmental, industrial, and medical biofilms. At the microscale, microbial biofilms are characterized by steep pH gradients and an extracellular matrix rich in carbohydrate components with diffusion-modifying properties that contribute to bacterial acid-base metabolism. Here, we propose a combined analysis of pH ratiometry and fluorescence lectin-binding analysis, pH-FLBA, to concomitantly investigate the matrix architecture and pH developments in microbial biofilms, using complex saliva-derived biofilms as an example. Spatiotemporal changes in biofilm pH are monitored non-invasively over time by pH ratiometry, while FLBA with lectins of different carbohydrate specificities allows mapping the distribution of multiple relevant matrix components in the same biofilm areas. As the biofilm structure is preserved, pH-FLBA can be used to investigate the in situ relationship between the biofilm matrix architecture and biofilm pH in complex multispecies biofilms.

Density-based lipoprotein depletion improves extracellular vesicle isolation and functional analysis

BackgroundBlood plasma is the main source of extracellular vesicles (EVs) in clinical studies aiming to identify biomarkers and to investigate pathophysiological processes, especially regarding EV roles in inflammation and thrombosis. However, EV isolation from plasma has faced the fundamental issue of lipoprotein contamination, representing an important bias since lipoproteins are highly abundant and modulate cell signaling, metabolism, and thromboinflammation. ObjectivesHere, we aimed to isolate plasma EVs after depleting lipoproteins, thereby improving sample purity and EV thromboinflammatory analysis. MethodsDensity-based gradient ultracentrifugation (G-UC) was used for lipoprotein depletion before EV isolation from plasma through size-exclusion chromatography (SEC) or serial centrifugation (SC). Recovered EVs were analyzed by size, concentration, cellular source, ultrastructure, and bottom-up proteomics. ResultsG-UC efficiently separated lipoproteins from the plasma, allowing subsequent EV isolation through SEC or SC. Combined analysis from EV proteomics, cholesterol quantification, and apoB-100 detection confirmed the significant reduction in lipoproteins from isolated EVs. Proteomic analysis identified similar gene ontology and cellular components in EVs, regardless of lipoprotein depletion, which was consistent with similar EV cellular sources, size, and ultrastructure by flow cytometry and transmission electron microscopy. Importantly, lipoprotein depletion increased the detection of less abundant proteins in EV proteome and enhanced thromboinflammatory responses of platelets and monocytes stimulated in vitro with EV isolates. ConclusionCombination of G-UC+SEC significantly reduced EV lipoprotein contamination without interfering in EV cellular source, gene ontology, and ultrastructure, allowing the recovery of highly pure EVs with potential implications for functional assays and proteomic and lipidomic analyses.

Mechanism and implications of the post-seismic deformation following the 2021 Mw 7.4 Maduo (Tibet) earthquake

SUMMARY A major earthquake shook the Chinese county of Maduo, located in the Songpan-Ganzi terrane on the Tibetan Plateau, on 21 May 2021. Here, we investigate the post-seismic deformation process of this event, with the aim to understand the fault geometry, friction behaviour and regional rheology. To keep the self-consistency between co- and post-seismic deformation models, we first constrain the fault geometry and coseismic slip model of this event, which are directly used in modelling the post-seismic deformation. The coseimsic slip model reveals that the majority of coseismic slip is confined at the middle (3–15 km) of the brittle layer, leading to significant shallow slip deficit. Secondly, we obtain the post-seismic deformation in the first 450 d following the 2021 Maduo earthquake using the GPS and InSAR displacement time-series data. Thirdly, a combined model incorporating afterslip and viscoelastic relaxation is built to explain the observed post-seismic deformation. Our results suggest that the viscoelastic relaxation effect should be considered in the observation period, in order to avoid the unphysical deep afterslip in the ductile lower crustal layer. Combined analysis on viscosities inferred from this study and previous studies suggests a weak lower crust with steady-state viscosity of 1018–1019 Pa s beneath the Songpan-Ganzi terrane, which may give rise to the distributed shear deformation and the development of subparallel secondary faults within the terrane. Besides, the inferred afterslip on uppermost patches of the middle fault segment suggests a rate-strengthening frictional behaviour that may be related to the coseismic slip deficit and rupture arrest of the Maduo earthquake.

Stock movement prediction: A multi‐input LSTM approach

AbstractGenerally, the nonlinear and non‐stationary financial time series becomes an obstacle in the process of stock movement prediction. But the recent theories of machine learning and deep learning have provided with some new solutions. Based on LSTM (long short‐term memory), we propose a hybrid model of wavelet transform (WT) and multi‐input LSTM to predict the trend of SSE composite index. It can mine valid data in time series and support different types of data as input. The whole model is divided into two stages. In the first stage, we adopt the level 1 decomposition with db4 mother wavelet to eliminate noise. In the second stage, combinative and qualitative analysis was made base on the data from Chinese stock market, US stock market, and technical indicators as input. According to the result, the proposed model, with the accuracy of 72.19%, performs better than single‐input LSTM, decision tree, random forest, Support Vector Machine (SVM), and XGBoost.

Theory and experiment on the terahertz vibrational spectrum of ferulic acid

Ferulic acid (FA, C10H10O4), a type of hydroxycinnamic acid derivative, has beneficial pharmacological effects and biological activities and is known for its high application value in medicine, health care, and cosmetic products. The vibration spectrum of FA ranging from 0.3 THz to 2.0 THz has been investigated by terahertz time-domain spectroscopy. The characteristic absorption peaks located at 0.937, 1.159, 1.464, 1.694, and 1.910 THz are obtained experimentally. To understand the origin of the characteristic absorption peaks of FA, density functional theory calculations based on isolated molecule and crystalline structure are separately performed to differentiate the intramolecular and intermolecular vibrational modes. Combined analysis of the experimental and theoretical results informs that the characteristic absorption peak at 1.464 THz comes from intramolecular interaction, and the ones at 0.937, 1.159, 1.694, and 1.910 THz originate from intermolecular collective vibrational modes.

P712 Effectiveness of switching from intravenous to subcutaneous infliximab in Inflammatory Bowel Disease patients: A combined analysis of real-world evidence

Abstract Background Since approval, numerous inflammatory bowel disease (IBD) patients have been treated with subcutaneous (SC) infliximab (IFX), but real-life data based on a large multi-national population of patients switching from intravenous (IV) to SC IFX is lacking. Methods The ASSEMBLE project is an initiative to combine multi-national real-world cohort datasets and analyse the effectiveness and safety of SC IFX therapy. In the ASSEMBLE-1 analysis, three studies from France and the United Kingdom1-3 were integrated to assess the clinical outcomes up to 6 months (6M) after switching from IV to SC IFX. Clinical remission was defined as Harvey-Bradshaw Index (HBI) or modified HBI (mHBI) &amp;lt;5 for Crohn’s disease (CD) and Simple Clinical Colitis Activity Index (SCCAI) or partial Mayo score (PMS) &amp;lt;3 for ulcerative colitis (UC). Treatment persistence was assessed by Kaplan-Meier survival analysis. Results The data of 428 patients were pooled from the three datasets (70.6% CD, 29.4% UC). 85.4% of patients were in clinical remission before switching with median HBI or mHBI of 1 (IQR 0,2) for CD and median SCCAI of 2 (IQR 1,3) or PMS of 0 (IQR 0,0) for UC. 59.6% of patients were treated with the standard dose of IV IFX (5 mg/kg Q8W) before switching and 54.0% of patients were on concomitant immunomodulator therapy. Patients were switched to SC IFX 120 mg Q2W (94.4%) or 120 mg QW (5.6%) regimen. After switching, the overall clinical remission rates were 83.4% and 84.7% at 3M and 6M, respectively. CD patients were associated with higher remission rate (89.8%) than UC patients (71.9%) at 6M (p&amp;lt;0.001). The disease activity scores and the levels of fecal calprotectin and C-reactive protein of the overall population were maintained stable after switching (Table 1). High persistence was observed in both CD (97.3% at 3M, 94.8% at 6M) and UC patients (96% at 3M, 94.1% at 6M), with no significant difference between indications (p=0.47 at 3M and p=0.78 at 6M). Perianal CD patients (n=89) did not have a significantly worse treatment persistence rate than non-perianal CD patients (p=0.30). The most common reasons leading to drug discontinuation were lost to follow-up, consent withdrawal, worsening of disease activity, and worsening of perianal disease (3 cases for each). Two patients discontinued due to injection-site pain. Conclusion This pooled analysis of ASSEMBLE-1 confirms that switching from IV to SC IFX is effective and safe for CD and UC patients in clinical practice and that the clinical remission is well maintained up to 6M after switching, with no new concerns in safety profiles. [1] Smith et al. J Crohns Colitis 2022 [2] Buisson et al. Clin Gastroenterol Hepatol 2023 [3] Rahmany et al. Gastroenterology 2023.

Zinc speciation in highly weathered tropical soils affected by large scale vegetable production

Agriculture in highly weathered tropical soils often requires considerable application of lime and fertilizers to ensure satisfactory plant nutrient levels. The consequences of these continue long-term applications is not well understood may induce changes in soil chemical properties, the abundance, and speciation of potentially toxic trace element and as well as of micronutrients in agriculture soils. In this study, we evaluated the adsorption (at pH 5) and speciation of Zn in tropical soils (both agricultural and native vegetation) as a function of fertilization and contact time using chemical fractionation analyses and X-ray absorption spectroscopy. The soils overall had high Zn adsorption capacities (∼ 700 mg kg-1), but the agricultural soil was approximately 30 % higher than of the soil under native vegetation, and the proportion of Zn in the mobile fraction was 35 % in native vegetation and 21 % in agricultural soils. Zn speciation via linear combination analysis showed a strong relationship with soil mineralogical composition and reveled that Zn associated with organic matter decreased while Zn associated with P increased after the conversion of soils from native vegetation to highly fertilized soil. Aluminosilicate soil minerals were identified as major sinks of soil Zn, accounting for 34 % of total Zn retention regardless of soil origin and land use. Association of Zn with phosphate (i.e., hopeite) was observed in the agricultural soil samples, which might be an unexpected Zn-bearing mineral in highly weathered tropical soils and could have impacts on Zn plant nutrition.

New insights into the physiological effects of structural environmental enrichment on black sea bream (Acanthopagrus schlegelii) based on a combined analysis of transcriptomics and metabolomics

Environmental enrichment (EE) has been generally accepted as an effective and promising way to enhance the performance and improve the welfare of animals kept in captivity. Evidence for the effects of EE on fish has accumulated rapidly, but little is known about its underlying mechanisms. In this study, black sea bream (Acanthopagrus schlegelii) were reared under enriched and enrichment-free conditions for 30 (post-larval) and 60 (juvenile) days. Physiological, transcriptome, and metabolome data were compared to investigate potential rearing improvements, physiological responses to acute stress, and the underlying mechanisms. The results showed that fish reared under enriched conditions had significantly better growth performance, a higher survival rate, and lower basal cortisol levels. Meanwhile, the cortisol, lactic acid, malondialdehyde (MDA), and total antioxidant capacity (T-AOC) levels in fish subjected to acute stress suggested that EE-reared individuals presented greater stress resistance. However, the effect of EE may decrease with the extension of treatment time for larger fish. The transcriptome analysis showed that energy-related pathways (including oxidative phosphorylation, the citrate cycle, and glycolysis/gluconeogenesis) as well as protein folding, sorting, and degradation-related pathways (protein processing in the endoplasmic reticulum and proteasome pathways); replication and repair related pathways (including pathways involved in nucleotide excision repair, base excision repair, mismatch repair, and homologous recombination); and immune-related pathways (complement and coagulation cascades pathway and the IL-17 signaling pathway) were significantly altered in the EE-reared individuals. In addition, integrated analysis of metabolome and transcriptome data revealed marked enrichment of transcription-associated metabolites involved in cortisol synthesis and secretion, taste transduction, olfactory transduction, and protein digestion and absorption pathways. Our results suggested that EE may influence the growth, fitness, and stress resistance of A. schlegelii by regulating a series of biological processes including energy metabolism, cortisol synthesis, antioxidant enzyme activities, protein folding, DNA replication and repair, and complement and coagulation cascades.

Determination of growth and developmental stages in hand-wrist radiographs : Can fractal analysis in combination with artificial intelligence be used?

The goal of this work was to assess the classification of maturation stage using artificial intelligence (AI) classifiers. Hand-wrist radiographs (HWRs) from 1067 individuals aged between 7and 18years were included. Fifteen regions of interest were selected for fractal dimension (FD) analysis. Five predictive models with different inputs were created (model1: only FD; model2: FD and Chapman sesamoid stage; model3: FD, age, and sex; model4: FD, Chapman sesamoid stage, age, and sex; model5: Chapman sesamoid stage, age, and sex). The target diagnoses were accelerating growth velocity, very high growth velocity, and decreasing growth velocity. Four AI algorithms were applied: multilayer perceptron (MLP), support vector machine (SVM), gradient boosting machine (GBM) and C5.0 decision tree classifier. All AI algorithms except for C5.0 yielded similar overall predictive accuracies for the five models. In order from lowest to highest, the predictive accuracies of the models were as follows: model1 < model3 < model2 < model5 < model4. The highest overall F1 score, which was used instead of accuracy especially for models with unbalanced data, was obtained for models1,2, and3 based on SVM, for model4 based on MLP, and for model5 based on C5.0. Adding Chapman sesamoid stage, chronologic age, and sex as additional inputs to the FD values significantly increased the F1 score. Applying FD analysis to HWRs is not sufficient to predict maturation stage in growing patients but can be considered agrowth rate prediction method if combined with the Chapman sesamoid stage, age, and sex.

Combinatorial analysis: mathematics investigations by high school students at the Federal Institute of Tocantins

This article is based on a study on mathematical research carried out with 2nd grade high school students at the Federal Institute of Tocantins. The investigation is placed in a qualitative perspective, based on Ponte's typology (2009). The objective of the research was to develop and apply activities that would enable students to develop mathematical investigation regarding the study of Combinatorial Analysis. The purpose was to investigate the impact of this experience on students, trying to understand not only the way they formulate questions and hypotheses, how they design and consolidate the choice of information, analyze the data they collected and also the disseminated results obtained. During the completion of the task, there was the role of teacher guiding the tasks and as it unfolded, conclusions were perceived which ensure that it is advantageous, both for teachers and learners and even though the activities carried out surprisingly promoted non-mechanized learning.

Blood pressure variability supersedes heart rate variability as a real-world measure of dementia risk

Blood pressure variability (BPV) and heart rate variability (HRV) have been associated with Alzheimer’s Disease and Related Dementias (ADRD) in rigorously controlled studies. However, the extent to which BPV and HRV may offer predictive information in real-world, routine clinical care is unclear. In a retrospective cohort study of 48,204 adults (age 54.9 ± 17.5 years, 60% female) receiving continuous care at a single center, we derived BPV and HRV from routinely collected clinical data. We use multivariable Cox models to evaluate the association of BPV and HRV, separately and in combination, with incident ADRD. Over a median 3 [2.4, 3.0] years, there were 443 cases of new-onset ADRD. We found that clinically derived measures of BPV, but not HRV, were consistently associated with incident ADRD. In combined analyses, only patients in both the highest quartile of BPV and lowest quartile of HRV had increased ADRD risk (HR 2.34, 95% CI 1.44–3.81). These results indicate that clinically derived BPV, rather than HRV, offers a consistent and readily available metric for ADRD risk assessment in a real-world patient care setting. Thus, implementation of BPV as a widely accessible tool could allow clinical providers to efficiently identify patients most likely to benefit from comprehensive ADRD screening.

Double Negativity of MRI-Detected and Pathologically-Diagnosed Extramural Venous Invasion is a Favorable Prognostic Factor for Rectal Cancer.

Extramural venous invasion (EMVI) is a prognostic factor in rectal cancer. There are two types: EMVI detected by magnetic resonance imaging (MRI) (mr-EMVI) and EMVI detected by pathology (p-EMVI). They have been separately evaluated, but they have not yet been concurrently evaluated. We therefore evaluate both mr-EMVI and p-EMVI in rectal cancer at the same time and clarify their association with prognosis. Included were the 186 consecutive patients who underwent complete radical resection of tumors ≤ stage III at Wakayama Medical University Hospital, Japan, between 2010 and 2018. All underwent preoperative MRI examination, and were reassessed for EMVI by a radiologist. Surgically resected specimens were then reassessed for EMVI by a pathologist. We assessed the correlation between positivity of mr-EMVI and p-EMVI and prognosis, and the clinicopathological background behind them. Patients with double negativity for mr-EMVI and p-EMVI had better prognosis than patients with mr-EMVI or p-EMVI positivity (p < 0.0001). Positivity for mr-EMVI or p-EMVI was a poor independent prognostic factor in multivariate analysis. Combined analysis of mr-EMVI and p-EMVI may enable prediction of postoperative prognosis of rectal cancer. Patients with double negativity of mr-EMVI and p-EMVI had better prognosis than patients with some form of positivity. Stated differently, patients with positivity of mr-EMVI, p-EMVI, or both had a poorer prognosis than those with double negativity. Postoperative adjuvant chemotherapy may improve poor prognosis. Combined evaluation of mr-EMVI and p-EMVI may be used to predict clinical outcomes and may be an effective prognostic predictor of rectal cancer.

Comprehensive analysis of m6A modification in lipopolysaccharide-induced acute lung injury in mice

BackgroundN6-Methyladenosine (m6A) methylation is the most prevalent post-transcriptional modification in mRNA, and plays significant roles in various diseases. Nevertheless, the precise functions of m6A modification in the formation of ALI remain unclear. In this study we explore the transcriptome distribution of m6A methylation and its probable roles of in ALI.MethodsLipopolysaccharide (LPS) was utilized to establish an ALI mouse model. Real-time qPCR, Western blotting and m6A dot blot were utilized to assess m6A methylation level and the expression of m6A methylation enzymes. MeRIP-Seq and RNA-seq were utilized to explore differential m6A modifications and differentially expressed genes in ALI mice. The hub genes and enriched pathways were assessed by Real-time qPCR and Western blotting.ResultsOur findings showed that overall m6A methylation level was increased in ALI mice lung tissues, accompanied by lower levels of METTL3 and FTO. Notably, the protein expression of these methylases were different in various cells. There were 772 differently expressed m6A peaks in ALI as compared to the control group, with 316 being hypermethylated and 456 being hypomethylated. GO and KEGG analyses demonstrated these differentially methylated genes were associated with the calcium signaling pathway and cAMP signaling pathway. Furthermore, we identified 50 genes with distinct m6A peaks and mRNA expressions by combined analysis of MeRIP-Seq and RNA-Seq. KEGG analysis also demonstrated that these overlapped genes were closely associated with the calcium signaling pathway, cGMP-PKG signaling pathway, etc. Besides, Western blotting results demonstrated that the protein expression of Fibronectin leucine-rich transmembrane protein 3 (Flrt3) as well as the calcium signaling pathway and cGMP-PKG signaling pathway, increased significantly after ALI.Conclusionsm6A modification was paramount in the pathogenesis of ALI, and provided a foundation for the further investigation in the prevention and treatment of ALI.

Nitrogen degradation performance and microbial dynamic analysis for the efficient combination of partial denitrification and anammox (PD/A) process

The coupling partial denitrification and anammox (PD/A) is a promising technology for deep-level nitrogen removal, and the quickly effective startup remains a huge challenge in real application. In this study, the stability of nitrite (NO2--N) accumulation was investigated in the PD sequential batch reactor (PSBR), and the nitrogen removal performance in response to nitrogen loading rate (NLR) was compared in another independent anammox SBR (ASBR), where the combined PD/A operation was subsequently carried out based on the optimal operating conditions. In the PSBR, nitrate removal efficiency (NRE) maintained around 89–90% with a mean nitrate-to-nitrite transformation ratio (NTR) of 84.43%, and the total proportion of functional bacteria (e.g., Terrimonas, norank_f_A4b, Ellin6067, Defluviicoccus, etc) accounted for 40.98% after long-term acclimation. In the ASBR, increased NLR (0.22 → 0.70 kgN/(m3·d)) depressed the anammox activity owing to the sludge disintegration and adverse nitrogen contribution, however, the dominant Candidatus_Brocadia enriched from 0.50% to 2.05% and realized the efficient retention of functional bacteria, which also laid a good foundation for the rapid startup of PD/A process. As NLR controlled around 0.18 - 0.25 kgN/(m3·d), the total nitrogen removal (ReTN) climbed from 33.88% to 98% with anammox contribution soaring up to 65%, since the higher tight-bound extracellular polymeric substances (T-EPS) production and protein/polysaccharide (PN/PS) ratio accelerated the re-formation of anammox granular sludge. In the end, the potential significances and challenges of PD/A process were further summarized for the mainstream wastewater treatment.

Anatomical and Functional Study of the Ostrich (Struthio camelus) Lung through Macroscopic Analysis in Combination with Optical and Electron Microscopy Techniques.

The Ostrich occupies a unique position as the largest bird on the planet. Like other ratites, it has been reputed to have a phylogenetically primitive lung. We used macroscopy, light microscopy, transmission and scanning electron microscopy as well as silicon rubber casting to elucidate the functional design of its lung and compare it with what is already documented for the avian species. The neopulmonic region was very small and poorly developed. The categories of the secondary bronchi (SB) present and their respective numbers included laterodorsal (8-10), lateroventral (4-5), medioventral (4-6) and posterior (16-24). The lateral aspects of the laterodorsals were covered with a transparent collapsible membrane internally lined with a squamous to cuboidal epithelium. The bulk of these SB were in close proximity to intercostal spaces and the intercostal muscles and were thought to be important in the propulsion of gases. The lung parenchyma was rigid, with the atria well supported by septa containing smooth muscles, connective tissue interparabronchial septa were absent, and blood capillaries were supported by epithelial bridges. There were two categories of epithelia bridges: the homogenous squamous type comprising two leaflets of type I cells and the heterogeneous type consisting of a type I pneumocyte and type II cell. Additional type two cells were found at the atrial openings as well as the walls of the infundibulae and the air capillaries. The atria were shallow and opened either directly into several air capillaries or into a few infundibulae. The presence of numerous type II cells and the absence of interparabronchial connective tissue septa may imply that the ostrich lung could be capable of some degree of compliance.