Comparing Strain Assessment in Compressed Sensing and Conventional Cine MRI.

The aim of this study is to assess the feasibility of compressed sensing (CS) acceleration methods compared to conventional segmented cine (Seg) cardiac magnetic resonance (CMR) for evaluating left ventricular (LV) function and strain by feature tracking (FT). In this prospective study, 45 healthy volunteers underwent CMR imaging used Seg, threefold (CS3), fourfold (CS4), and eightfold (CS8) CS acceleration. Cine images were scored for quality (1-5 scale). LV volumetric and functional parameters and global longitudinal (GLS), circumferential (GCS), and radial strains (GRS) were quantified. LV volumetric and functional parameters exhibited no differences between Seg and all CS cines (all P > 0.05). The strains were similar for Seg, CS3, and CS4 (all P > 0.05). Similarly, no significant differences were observed in GRS and GCS between Seg and CS8 (all P > 0.05), but the global longitudinal strain was significantly lower for CS8 versus Seg (P < 0.001). Image quality declined with CS acceleration, especially in long-axis views with CS8. CS cine MRI at acceleration factor 4 maintained good image quality and accurate measurements of LV function and strain, although there was a slight reduction in the quality of long-axis images and GLS with CS8. CS acceleration up to a factor of 4 enabled fast CMR evaluations, making it suitable for clinical use.

Role of Up-Regulated Transmembrane Channel-Like Protein 5 in Pancreatic Adenocarcinoma.

BACKGROUND: Pancreatic adenocarcinoma (PAAD) is a malignant tumor responsible for a heavy disease burden. Previously, only one pan-cancer study of Transmembrane channel-like protein 5 (TMC5) showed that TMC5 was highly expressed in PAAD, but the results lacked comprehensive verification, and the mechanism of TMC5 in PAAD was still unclear. METHODS: For exploring the expression and clinical value of TMC5 in PAAD better, we adopted a comprehensive evaluation method, using internal immunohistochemistry (IHC) data combined with microarray and RNA-sequencing data collected from public databases. The single cell RNA-sequencing (scRNA-seq) data were exploited to explore the TMC5 expression in cell populations and intercellular communication. The potential mechanism of TMC5 in PAAD was analyzed from the aspects of immune infiltration, transcriptional regulation, function and pathway enrichment. RESULTS: Our IHC data includes 148 PAAD samples and 19 non-PAAD samples, along with the available microarray and RNA-sequencing data (1166 PAAD samples, 704 non-PAAD samples). The comprehensive evaluation results showed that TMC5 was evidently up-regulated in PAAD (SMD = 1.17). Further analysis showed that TMC5 was over-expressed in cancerous epithelial cells. Furthermore, TMC5 was up-regulated in more advanced tumor T and N stages. Interestingly, we found that STAT3 as an immune marker of Th17 cells was not only positively correlated with TMC5 and up-regulated in PAAD tissues, but also the major predicted TMC5 transcription regulator. Moreover, STAT3 was involved in cancer pathway of PAAD. CONCLUSION: Up-regulated TMC5 indicates advanced tumor stage in PAAD patients, and its role in promoting PAAD development may be regulated by STAT3.

A clinical laboratory-developed LSC17 stemness score assay for rapid risk assessment of patients with acute myeloid leukemia.

Leukemia stem cells (LSCs) are linked to relapse in acute myeloid leukemia (AML). The LSC17 gene expression score robustly captures LSC stemness properties in AML and can be used to predict survival outcomes and response to therapy, enabling risk-adapted, upfront treatment approaches. The LSC17 score was developed and validated in a research setting. To enable widespread use of the LSC17 score in clinical decision making, we established a laboratory-developed test (LDT) for the LSC17 score that can be deployed broadly in clinical molecular diagnostic laboratories. We extensively validated the LSC17 LDT in a College of American Pathologists/Clinical Laboratory Improvements Act (CAP/CLIA)-certified laboratory, determining specimen requirements, a synthetic control, and performance parameters for the assay. Importantly, we correlated values from the LSC17 LDT to clinical outcome in a reference cohort of patients with AML, establishing a median assay value that can be used for clinical risk stratification of individual patients with newly diagnosed AML. The assay was established in a second independent CAP/CLIA-certified laboratory, and its technical performance was validated using an independent cohort of patient samples, demonstrating that the LSC17 LDT can be readily implemented in other settings. This study enables the clinical use of the LSC17 score for upfront risk-adapted management of patients with AML.

Removal of anti-nutritional factors of rapeseed protein isolate (RPI) and toxicity assessment of RPI.

We prepared a detoxified rapeseed protein isolate (RPI) by phytase/ethanol treatment based on alkaline extraction and acidic precipitation. Contents of protein, fat, ash, moisture, crude fiber, glucosinolates, phytic acid, and phenolics and color were determined. To evaluate the safety of detoxified RPI, five groups of C57 mice (detoxified RPI [10 and 20 g kg-1]; commercial soybean protein isolate (SPI) [10 g kg-1]; non-detoxified RPI [10 g kg-1]; control) were used in the acute-toxicity test. Bodyweight and pathology parameters were recorded at different time points, followed by macroscopic examination, organ-weight measurement and microstructure examination. After pretreatment of rapeseed meals with phytase (enzyme : substrate ratio, 1 : 5 mg g-1) for 1.5 h and two-time ethanol extraction for precipitated protein, the chemical characteristics in RPI were protein (88.26%), fat (0.57%), ash (2.72%), moisture (1.90%), crude fiber (0.77%), glucosinolates (0 µmol g-1), phytic acid (0.17%), phenolics (0.36%) and whiteness (73.38). Treatment resulted in significant removal of anti-nutritional factors (ANFs) and increased whiteness in detoxified RPI compared with non-detoxified RPI, and lower than in cruciferin-rich canola protein isolate (Puratein®). Experimental-related effects on bodyweight, clinical observations, or clinicopathology, in mice treated with detoxified RPI were not observed except for a decreased thyroid gland/parathyroid gland index in mice treated with non-detoxified RPI. Furthermore, the no-observed-effect level (NOEL) was 10 g kg-1 of detoxified RPI, whereas the no-observed-adverse-effect-level (NOAEL) was the highest fed level of 20 g kg-1 of detoxified RPI. Overall, detoxified RPI prepared by the combined treatment of phytase and ethanol was considered safe under the conditions tested, in which the contents of the main ANFs were reduced significantly.

Spatiotemporal Evolution of Ecosystem Health of China's Provinces Based on SDGs.

In the context of increasing ecological scarcity, maintaining the balance between natural and artificial capital has become a popular research topic in the field of ecosystem health. From the perspective of coordinating natural and artificial capital and maintaining the balance between human systems and the Earth's ecosystem, the Ecosystem Health Index (EHI) was developed on the basis of the Sustainable Development Goals (SDGs). The EHI consists of the Social Progress Index (SPI), Economic Development Index (EDI), Natural Environment Index (NEI), and a pressure adjustment coefficient. Comprehensive indicator assessment models were used to analyze the spatial and temporal evolution of the EHIs in 30 of China's provinces from 2013 to 2019. A three-dimensional judgment matrix was used to classify the 30 provinces into four basic types. The results show the following: (1) From 2013 to 2019, the EHIs of all provinces improved to different degrees, with 19 provinces achieving a healthy state. (2) Spatially, the EHI showed some regional aggregation in 2013. Provinces with high EHIs were concentrated in the west, followed by those in the east, and those in the central provinces had the lowest EHIs. However, the differences between regions had narrowed by 2019. (3) The spatial distribution patterns of the NEI and the EDI varied widely, and most provinces did not reach a high level of coordination between natural and artificial capital. (4) The environmental pressure in all provinces, except Liaoning, decreased over time. In some cases, excessive pressure decreased the pressure-adjusted EHI, regardless of the EHI value. (5) According to the results of the ecosystem health classification in each province, the factors that hinder ecosystem health vary from place to place.

Comparison Between 360° 3-D Transvaginal Ultrasound and Magnetic Resonance Imaging for Assessment of Vaginal Invasion in Cervical Cancer: A Preliminary Report.

Our goal was to estimate the agreement between 360° 3-D transvaginal ultrasound (TVUS) and magnetic resonance imaging (MRI) of the vaginal invasion in cervical cancer and to discuss the clinical value of 360° 3-D TVUS. A total of 72 patients with untreated cervical cancer were included in the work. The percentage agreement between 2-D TVUS and MRI in assessing vaginal invasion (yes or no) was 77.8% (kappa, 0.400) and that between 360° 3-D TVUS and MRI was 97.2% (kappa, 0.873). The results of 2-D TVUS demonstrated the following agreement with those of MRI: 77.8% for the upper two-thirds of the vagina (kappa, 0.538), 83.3% for the lower third of the vagina (kappa, 0.471). The results of 360° 3-D TVUS demonstrated the following agreement with those of MRI: 95.8% for the upper two-thirds of the vagina (kappa, 0.907), 98.6% for the lower third of the vagina (kappa, 0.961). The results of 360° 3-D TVUS demonstrated good agreement with MRI, which is less costly and more readily available than MRI and should be considered in the pre-treatment work-up for cervical cancer.

Evolution and Efficiency Assessment of Pesticide and Fertiliser Inputs to Cultivated Land in China.

Excessive use of pesticides and fertilisers has been a key issue limiting sustainable agricultural development. China is a typical pesticide- and chemical-fertiliser-dependent agricultural production area. We have matched the target indicators related to sustainable agricultural development (SDG1 and SDG2) and analysed the gap between China and four developed countries in terms of fertiliser and pesticide use intensity and efficiency from 2002 to 2016. We have used an improved Logarithmic Mean Divisia Index model and cluster analysis to identify the factors and effects driving increased pesticide and fertiliser inputs in China, and we discuss the exploratory effects of different provinces in reducing pesticide and fertiliser application and increasing efficiency. The findings reveal that (1) China is a typical pesticide- and fertiliser-dependent agricultural production area. The average combined fertiliser application efficiency in China from 2002 to 2016 was only 28% of that of the Netherlands, and the country's average combined pesticide application efficiency was only 35% of that of the USA. (2) The most important of the three main drivers of the increase in pesticide and fertiliser inputs in China is the value added of the primary industry, contributing 56% for the period 2007-2016. (3) Further analysis at the provincial level according to four types-high-intensity high-yield type, high-intensity low-yield type, low-intensity high-yield type, and low-intensity low-yield type-clarified the provinces that should be focused on at the national level in terms of pesticide and fertiliser application reduction and efficiency increase in the future.

Assessment of fixed-duration therapies for treatment-naïve Waldenström macroglobulinemia.

Comparative data guiding initial therapy for Waldenström macroglobulinemia (WM), an infrequently encountered non-Hodgkin lymphoma, are sparse. We evaluated three commonly used rituximab-based frontline regimens: rituximab-bendamustine (R-Benda); dexamethasone, rituximab, cyclophosphamide (DRC); and bortezomib, dexamethasone, rituximab (BDR) in 220 treatment-naïve patients with WM, seen at Mayo Clinic between November 1, 2000 and October 31, 2019. The median follow-up was 4.5 (95%CI: 4-5) years. The R-Benda cohort (n = 83) demonstrated superior overall response rate (ORR: 98%), in comparison to DRC (n = 92, ORR: 78%) or BDR (n = 45, ORR: 84%) cohorts, p = 0.003. Similarly, longer progression-free survival (PFS) was evident with R-Benda use [median 5.2 vs. 4.3 (DRC) and 1.8 years (BDR), p < 0.001]. The time-to-next therapy (TTNT) favored R-Benda [median, not-reached, 4.4 (DRC) and 2.6 years (BDR), p < 0.001). These endpoints were comparable between the DRC and BDR cohorts. Overall survival (OS) was similar across the three cohorts, p = 0.77. In a subset analysis of 142 patients genotyped for MYD88L265P mutation, the ORR, PFS and TTNT were unaffected by the patients' MYD88 signature within each cohort. In conclusion, ORR, PFS and TTNT with R-Benda are superior compared to DRC or BDR in treatment-naïve patients with active WM. The patient outcomes with any one of these three regimens are unaffected by the MYD88L265P mutation status.

Assessment of the DPP-IV inhibitory activity of a novel octapeptide derived from rapeseed using Caco-2 cell monolayers and molecular docking analysis.

The Octapeptide ELHQEEPL, which was identified from the rapeseed protein napin showed prominent Dipeptidyl peptidase-IV (DPP-IV) inhibitory activity. The objective of this study was to investigate the DPP-IV inhibitory activity and transepithelial transport of ELHQEEPL in an approaching intestinal condition using Caco-2 cell monolayers. ELHQEEPL and its degraded fragments EL, HQEEP, and methylated ELHQEEPL were transported across Caco-2 cell monolayers through different pathways. Compared with the nonbiological enzyme inhibition test, the in vitro experiment on Caco-2 cell monolayers showed that the IC50 value of DPP-IV inhibition increased by 43.11% for ELHQEEPL. There was no significant change in DPP-IV gene expression in the Caco-2 cell monolayers upon treatment with ELHQEEPL. Furthermore, molecular docking predicted that the weaker binding between inhibitory peptide and enzyme for the degradation products from ELHQEEPL during transepithelial transport greatly limited its role in inhibiting DPP-IV. PRACTICAL APPLICATIONS: The DPP-IV inhibitory activity of ELHQEEPL was confirmed using Caco-2 cell monolayers as a novel assessment tool, although its potency was reduced by metabolic degradation. In general, this study reported the use of Caco-2 cell monolayers as a tool for comprehensively studying peptides as sources of DPP-IV inhibitors. A Caco-2 cell-based approach with molecular docking can be adapted for the investigation of intestinal absorption and activity attenuation of food peptides being considered for enzymatic action. Moreover, since the Caco-2 cells express a wide range of enzymes, this method can be used for screening for other active food peptides such as for the inhibitors of ACE and a-glucosidase.

Fast and accurate genome comparison using genome images: The Extended Natural Vector Method.

Using numerical methods for genome comparison has always been of importance in bioinformatics. The Chaos Game Representation (CGR) is an effective genome sequence mapping technology, which converts genome sequences to CGR images. To each CGR image, we associate a vector called an Extended Natural Vector (ENV). The ENV is based on the distribution of intensity values. This mapping produces a one-to-one correspondence between CGR images and their ENVs. We define the distance between two DNA sequences as the distance between their associated ENVs. We cluster and classify several datasets including Influenza A viruses, Bacillus genomes, and Conoidea mitochondrial genomes to build their phylogenetic trees. Results show that our ENV combining CGR method (CGR-ENV) compares favorably in classification accuracy and efficiency against the multiple sequence alignment (MSA) method and other alignment-free methods. The research provides significant insights into the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes.

Integrated assessment of CDK1 upregulation in thyroid cancer.

Cyclin-dependent kinase 1 (CDK1) has a unique role in cell cycle regulation, as it is crucial for cell cycle progression and cell division. The aim of the present study was to use a combination of various detection methods to examine the expression and clinical significance of CDK1 in thyroid cancer (THCA). We used in-house tissue microarrays, immunohistochemistry, public RNA-sequencing, gene microarrays, and meta-analyses to conduct a comprehensive analysis of the role of CDK1 in the occurrence and development of THCA. CDK1 protein expression was notably higher in THCA tissues than in non-cancer tissues as evidenced by the in-house tissue microarrays. The expression of CDK1 protein was also significantly higher in pathologic T3-T4 than in T1-T2 samples. The pooled standardized mean difference (SMD) for CDK1 was 0.71 (95% CI, 0.46-0.95) including a total of 931 THCA and 585 non-cancerous thyroid tissue samples. An aggregation of the immunohistochemistry results and the RNA-sequencing/microarray findings gave a pooled SMD for CDK1 expression of 2.13 (95% CI, 1.30-2.96). The final area under curve (AUC) for the summarized receiver operating characteristic (sROC) was 0.7941 using all 1102 cases of THCA and 672 cases of controls. KEGG analysis with the co-expressed genes of CDK1 in THCA demonstrated the top enriched pathways to be the cell cycle, thyroid hormone synthesis, autoimmune thyroid disease, etc. In summary, we reveal the overexpression of CDK1 in THCA based on multiple detection methods that combine independent cohorts. However, further studies are required to elucidate the molecular mechanisms of CDK1 that promotes the biological aggressiveness of THCA cells.

Hydrochemical characteristics and quality assessment of deep groundwater from the coal-bearing aquifer of the Linhuan coal-mining district, Northern Anhui Province, China.

There is little information available about the hydrochemical characteristics of deep groundwater in the Linhuan coal-mining district, Northern Anhui Province, China. In this study, we report information about the physicochemical parameters, major ions, and heavy metals of 17 groundwater samples that were collected from the coal-bearing aquifer. The results show that the concentrations of total dissolved solids, electrical conductivity, and potassium and sodium (K(+) + Na(+)) in most of the groundwater samples exceeded the guidelines of the World Health Organization (WHO) and the Chinese National Standards for Drinking Water Quality (GB 5749-2006). The groundwater from the coal-bearing aquifer was dominated by the HCO3·Cl-K + Na and HCO3·SO4-K + Na types. Analysis with a Gibbs plot suggested that the major ion chemistry of the groundwater was primarily controlled by weathering of rocks and that the coal-bearing aquifer in the Linhuan coal-mining district was a relatively closed system. K(+) and Na(+) originated from halite and silicate weathering reactions, while Ca(2+) and Mg(2+) originated from the dissolution of calcite, dolomite, and gypsum or anhydrite. Ion exchange reactions also had an influence on the formation of major ions in groundwater. The concentrations of selected heavy metals decreased in the order Mn > Zn > Cr > Cu > Ni > Pb. In general, the heavy metal concentrations were low; however, the Cr, Mn, and Ni concentrations in some of the groundwater samples exceeded the standards outlined by the WHO, the GB 5749-2006, and the Chinese National Standards for Groundwater (GB/T 14848-93). Analysis by various indices (% Na, SAR, and EC), a USSL diagram, and a Wilcox diagram showed that both the salinity and alkalinity of the groundwater were high, such that the groundwater could not be used for irrigating agricultural land without treatment. These results will be significant for water resource exploiting and utilization in coal mine area.

[Precision medicine-oriented safety assessment strategy for traditional Chinese medicines: disease-syndrome-based toxicology].

Drug toxicity is commonly divided into intrinsic and idiosyncratic types. The former can be generally uncovered in the preclinical safety evaluation stage by conventional toxicological experiments, while the latter is usually found only in the clinical evaluation stage, which is the main cause of severe adverse reactions and withdrawal of post-marketing drugs. Assessment and prediction of idiosyncratic toxicity is a challenging problem worldwide, and is an essential in the development of translational toxicology and precision medicine. Since traditional Chinese medicines (TCMs) have been applied for thousands of years with long experience in clinical efficacy and safety, idiosyncratic toxicity is regarded as an important factor for traditional "non-toxic" medicines and is associated with multiple individual states including different diseases, syndromes, habitus, etc. However, these individual conditions related to disease are often difficult to be resolved in conventional toxicological experiments, leading to insufficient translation of the experimental results into clinical application. We took an approach of systematic analysis of the differences and similarities in toxic property, medication rule and evaluating requirement between TCMs and chemical synthetic medicines. We present a novel and clinic-associated safety assessment strategy, namely as "disease-syndrome-based toxicology", for TCMs. The strategy is able to access the relativity, susceptibility and controllability of the toxicity of TCMs. The new strategy provides a theoretical and methodological guidance to practice and development of the TCM in favor of precision medicine.

Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique.

Genome wide analysis of DNA methylation provides important information in a variety of diseases, including cancer. Here, we describe a simple method, Digital Restriction Enzyme Analysis of Methylation (DREAM), based on next generation sequencing analysis of methylation-specific signatures created by sequential digestion of genomic DNA with SmaI and XmaI enzymes. DREAM provides information on 150,000 unique CpG sites, of which 39,000 are in CpG islands and 30,000 are at transcription start sites of 13,000 RefSeq genes. We analyzed DNA methylation in healthy white blood cells and found methylation patterns to be remarkably uniform. Inter individual differences > 30% were observed only at 227 of 28,331 (0.8%) of autosomal CpG sites. Similarly, > 30% differences were observed at only 59 sites when we comparing the cord and adult blood. These conserved methylation patterns contrasted with extensive changes affecting 18-40% of CpG sites in a patient with acute myeloid leukemia and in two leukemia cell lines. The method is cost effective, quantitative (r ( 2) = 0.93 when compared with bisulfite pyrosequencing) and reproducible (r ( 2) = 0.997). Using 100-fold coverage, DREAM can detect differences in methylation greater than 10% or 30% with a false positive rate below 0.05 or 0.001, respectively. DREAM can be useful in quantifying epigenetic effects of environment and nutrition, correlating developmental epigenetic variation with phenotypes, understanding epigenetics of cancer and chronic diseases, measuring the effects of drugs on DNA methylation or deriving new biological insights into mammalian genomes.