Mrakia polaris sp. nov. and Mrakia amundsenii sp. nov. (Mrakiaceae, Cystofilobasidiales), two novel psychrophilic yeast species isolated from Arctic habitats.

Four yeast strains belonging to the basidiomycetous yeast genus Mrakia were isolated from diverse habitats in the Ny-Ålesund region (Svalbard, High Arctic): two from vascular plants, one from seawater and one from freshwater. Phylogenetic analysis, based on the ITS region and the D1/D2 domain of the 28S rRNA gene, identified these four strains as representing two novel species within the genus Mrakia. The names Mrakia polaris sp. nov. (MycoBank number: MB 852063) and Mrakia amundsenii sp. nov. (MycoBank number: MB 852064) are proposed. These two new species show distinct psychrophilic adaptations, as they exhibit optimal growth at temperatures between 10 and 15°C, while being unable to grow at 25°C. The holotype of M. polaris sp. nov. is CPCC 300345T, and the holotype of M. amundsenii sp. nov. is CPCC 300572T.

Predicting Microwave Ablation Early Efficacy in Pulmonary Malignancies via Δ Radiomics Models.

OBJECTIVE: This study aimed to explore the value of preoperative and postoperative computed tomography (CT)-based radiomic signatures and Δ radiomic signatures for evaluating the early efficacy of microwave ablation (MWA) for pulmonary malignancies. METHODS: In total, 115 patients with pulmonary malignancies who underwent MWA treatment were categorized into response and nonresponse groups according to relevant guidelines and consensus. Quantitative image features of the largest pulmonary malignancies were extracted from CT noncontrast scan images preoperatively (time point 0, TP0) and immediately postoperatively (time point 1, TP1). Critical features were selected from TP0 and TP1 and as Δ radiomics signatures for building radiomics models. In addition, a combined radiomics model (C-RO) was developed by integrating radiomics parameters with clinical risk factors. Prediction performance was assessed using the area under the receiver operating characteristic curve (AUC) and decision curve analysis (DCA). RESULTS: The radiomics model using Δ features outperformed the radiomics model using TP0 and TP1 features, with training and validation AUCs of 0.892, 0.808, and 0.787, and 0.705, 0.825, and 0.778, respectively. By combining the TP0, TP1, and Δ features, the logistic regression model exhibited the best performance, with training and validation AUCs of 0.945 and 0.744, respectively. The DCA confirmed the clinical utility of the Δ radiomics model. CONCLUSIONS: A combined prediction model, including TP0, TP1, and Δ radiometric features, can be used to evaluate the early efficacy of MWA in pulmonary malignancies.

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

Value of High-Resolution MRI in the Diagnosis of Brachial Plexus Injury in Infants and Young Children.

Purpose: To investigate the value of high-resolution MRI based on 3D-short inversion time inversion recovery sampling perfection with application-optimized contrasts (3D-STIR SPACE) sequence for the diagnosis of brachial plexus injury in infants and young children. Methods: Physical examination, electromyography (EMG) and MRI data of 26 children with brachial plexus injury were retrospectively analyzed. Sensitivity, specificity, and accuracy were calculated for the three tests. The agreement among these examinations was analyzed with the Kappa test. P<0.05 was considered statistically significant. Results: Of the 26 children, 3 cases had normal MRIs, 23 cases had unilateral brachial plexus injury diagnosed with MRI, and a total of 73 nerve roots and/or sheaths were involved. Among the 23 cases with aberrant MRI findings, there were 19 cases of nerve root thickening (42 nerve roots), 4 cases of nerve root sleeve expansion (5 nerve roots), 17 cases of pseudomeningeal cysts (34 nerve roots), 2 cases of nerve root loosening (2 nerve roots), 8 cases of nerve root dissection (11 nerve roots), 19 cases with increased nerve signal (43 nerve roots), and 9 cases with an increased signal of the muscles on the affected side. As for the diagnosis of brachial plexus injury, the sensitivity and the accuracy of physical examination, EMG and MRI were 0.92, 0.86, and 0.88, respectively. The agreement between MRI and physical examination was substantial (κ=0.780, P=0.000), as did the agreement between MRI and EMG (κ=0.611, P=0.005). Conclusion: High-resolution MRI based on 3D-STIR SPACE sequence plays a role in the diagnosis and evaluation of brachial plexus injury in infants and young children. It can accurately identify the injured nerve and characterize related pathological alterations. Besides EMG and physical examination, it can be used as a valuable tool for screening and monitoring of brachial plexus injury in infants and children.

Preoperative prediction of extramural venous invasion in rectal cancer by dynamic contrast-enhanced and diffusion weighted MRI: a preliminary study.

BACKGROUND: To explore the value of the quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion-weighted imaging (DWI) parameters in assessing preoperative extramural venous invasion (EMVI) in rectal cancer. METHODS: Eighty-two rectal adenocarcinoma patients who had underwent MRI preoperatively were enrolled in this study. The differences in quantitative DCE-MRI and DWI parameters including Krans, Kep and ADC values were analyzed between MR-detected EMVI (mrEMVI)-positive and -negative groups. Multivariate logistic regression analysis was performed to build the combined prediction model for pathologic EMVI (pEMVI) with statistically significant quantitative parameters. The performance of the model for predicting pEMVI was evaluated using receiver operating characteristic (ROC) curve. RESULTS: Of the 82 patients, 24 were mrEMVI-positive and 58 were -negative. In the mrEMVI positive group, the Ktrans and Kep values were significantly higher than those in the mrEMVI negative group (P < 0.01), but the ADC values were significantly lower (P < 0.01). A negative correlation was observed between the Ktrans vs ADC values and Kep vs ADC values in patients with rectal cancer. Among the four quantitative parameters, Ktrans and ADC value were independently associated with mrEMVI by multivariate logistic regression analysis. ROC analysis showed that combined prediction model based on quantitative DCE parameters and ADC values had a good prediction efficiency for pEMVI in rectal cancer. CONCLUSION: The quantitative DCE-MRI parameters, Krans, Kep and ADC values play important role in predicting EMVI of rectal cancer, with Ktrans and ADC value being independent predictors of EMVI in rectal cancer.

Application of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry for the Rapid Identification of Yeast Species From Polar Regions.

Protein profiling based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has proved to be a powerful tool for yeast identification. However, it is rarely used in the identification of yeast isolates from polar regions, which may be due to the limited data available for the differentiation of polar yeast species. The present study constructed a supplementary database of MALDI-TOF MS, including 33 yeast species from the Arctic and Antarctica. These yeast species were used to assess the accuracy and practicality of MALDI-TOF MS-based identification compared to the ribosomal DNA [internal transcribed spacer (ITS) and large subunit (LSU) gene regions] sequencing identification. Their dendrogram based on main spectra profiles (MSPs) in the supplementary database was somewhat consistent with their phylogenetic tree. The accuracy of MALDI-TOF MS identification was also compared by the ethanol-formic acid extraction method and the on-plate extraction method. In addition, peptide markers of some yeast species (e.g., Glaciozyma, Phenoliferia, Mrakia, and Vishniacozyma) were identified. It is concluded that the MALDI-TOF MS method can differentiate some closely related yeast species from polar regions, thus is suitable for the identification of polar yeasts.

Modified Look-Locker Inverse-Recovery (MOLLI) Sequence of Quantitative Imaging in Dirty Magnetic Resonance Longitudinal Relaxation Time Diagnostic Value of GE Combined with Longitudinal Relaxation Time Quantitative Imaging for Myocardial Amyloidosis.

The pathological changes of myocarditis include degeneration and necrosis of myocardial cells and infiltration of inflammatory cells in the myocardial interstitium, accompanied by obvious myocardial fibrosis. Myocardial fibrosis is a determinant of ventricular remodeling and an important indicator of the classification of clinical risk factors and has an important value in evaluating the prognosis of heart disease. Cardiac magnetic resonance (CMR) is the "gold standard" for evaluating the shape and function of the heart, and it can show the characteristic pathological changes of myocardial tissue. The traditional gadolinium imaging agent delays the enhanced sequence images to visually show the extent of the affected myocardial fibrosis, but it cannot effectively identify small focal fibrosis or widespread diffuse fibrosis. The CMR longitudinal relaxation time quantitative technique can directly measure the relaxation time (T1) determined by the myocardial tissue and does not depend on the signal strength of the reference tissue and can quantitatively analyze the affected myocardium. In this study, the initial and enhanced quantitative imaging techniques of CMR were used to measure the magnetic value of the myocardium in patients with myocarditis, to explore the diagnostic value of myocardial fibrosis, and to analyze the correlation between cardiac fibrosis and cardiac function.

Saccharomycomorpha psychra n. g., n. sp., a Novel Member of Glissmonadida (Cercozoa) Isolated from Arctic and Antarctica.

A novel genus and species within the order Glissmonadida (Cercozoa, Rhizaria), Saccharomycomorpha psychra n. g., n. sp., is described from lichen in the Ny-Ålesund region (High Arctic) and moss in the Fildes peninsula of King George Island (Maritime Antarctica). Cells were spherical and did not appear to present flagella in organic-rich Potato Dextrose Agar medium where they were able to feed osmotrophically. Molecular phylogenetic analyses based on 18S rRNA gene sequence demonstrated that Saccharomycomorpha psychra belong to "clade T" within the order Glissmonadida (Cercozoa, Rhizaria). All three investigated strains could grow at 4 °C and had an optimum growth temperature of 12 °C, 20 °C, and 20 °C, while a maximum growth temperature of 20 °C, 20 °C, and 25 °C, respectively. In conclusion, we established the phenotypic identity of "clade T," which until now was exclusively detected by environmental sequences, and erect a new family Saccharomycomorphidae for "clade T." Nomenclatural, morphological and ecological aspects of this novel species are discussed.

Application of texture analysis based on T2-weighted magnetic resonance images in discriminating Gleason scores of prostate cancer.

OBJECTIVE: To investigate the value of texture analysis in magnetic resonance images for the evaluation of Gleason scores (GS) of prostate cancer. METHODS: Sixty-six prostate cancer patients are retrospective enrolled, which are divided into five groups namely, GS = 6, 3 + 4, 4 + 3, 8 and 9-10 according to postoperative pathological results. Extraction and analysis of texture features in T2-weighted MR imaging defined tumor region based on pathological specimen after operation are performed by texture software OmniKinetics. The values of texture are analyzed by single factor analysis of variance (ANOVA), and Spearman correlation analysis is used to study the correlation between the value of texture and Gleason classification. Receiver operating characteristic (ROC) curve is then used to assess the ability of applying texture parameters to predict Gleason score of prostate cancer. RESULTS: Entropy value increases and energy value decreases as the elevation of Gleason score, both with statistical difference among five groups (F = 10.826, F = 2.796, P < 0.05). Energy value of group GS = 6 is significantly higher than that of groups GS = 8 and 9-10 (P < 0.005), which is similar between three groups (GS = 3 + 4, 8 and 9-10). The entropy and energy values correlate with GS (r = 0.767, r = -0.692, P < 0.05). Areas under ROC curves (AUC) of combination of entropy and energy are greater than that of using energy alone between groups GS = 6 and ≥7. Analogously, AUC of combination of entropy and energy are significantly higher than that of using entropy alone between groups GS≤3 + 4 and ≥4 + 3, as well as between groups GS≤4 + 3 and ≥8. CONCLUSION: Texture analysis on T2-weighted images of prostate cancer can evaluate Gleason score, especially using the combination of entropy and energy rendering better diagnostic efficiency.

Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex.

How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai-Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae).

Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai-Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well-differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (F ST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.

Genetic origin and composition of a natural hybrid poplar Populus × jrtyschensis from two distantly related species.

BACKGROUND: The factors that contribute to and maintain hybrid zones between distinct species are highly variable, depending on hybrid origins, frequencies and fitness. In this study, we aimed to examine genetic origins, compositions and possible maintenance of Populus × jrtyschensis, an assumed natural hybrid between two distantly related species. This hybrid poplar occurs mainly on the floodplains along the river valleys between the overlapping distributions of the two putative parents. RESULTS: We collected 566 individuals from 45 typical populations of P. × jrtyschensis, P. nigra and P. laurifolia. We genotyped them based on the sequence variations of one maternally inherited chloroplast DNA (cpDNA) fragment and genetic polymorphisms at 20 SSR loci. We further sequenced eight nuclear genes for 168 individuals from 31 populations. Two groups of cpDNA haplotypes characteristic of P. nigra and P. laurifolia respectively were both recovered for P. × jrtyschensis. Genetic structures and coalescent tests of two sets of nuclear population genetic data suggested that P. × jrtyschensis originated from hybridizations between the two assumed parental species. All examined populations of P. × jrtyschensis comprise mainly F1 hybrids from interspecific hybridizations between P. nigra and P. laurifolia. In the habitats of P. × jrtyschensis, there are lower concentrations of soil nitrogen than in the habitats occupied by the other two species. CONCLUSIONS: Our extensive examination of the genetic composition of P. × jrtyschensis suggested that it is typical of F1-dominated hybrid zones. This finding plus the low concentration of soil nitrogen in the floodplain soils support the F1-dominated bounded hybrid superiority hypothesis of hybrid zone maintenance for this particular hybrid poplar.

Transcriptome differences between two sister desert poplar species under salt stress.

BACKGROUND: Populus euphratica Oliv and P. pruinosa Schrenk (Salicaceae) both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P. pruinosa occurs in deserts in which there is underground water close to the surface. We therefore hypothesized that these two sister species may have evolved divergent regulatory and metabolic pathways during their interaction with different salt habitats and other stresses. To test this hypothesis, we compared transcriptomes from callus exposed to 24 h of salt stress and control callus samples from both species and identified differentially expressed genes (DEGs) and alternative splicing (AS) events that had occurred under salt stress. RESULTS: A total of 36,144 transcripts were identified and 1430 genes were found to be differentially expressed in at least one species in response to salt stress. Of these DEGs, 884 and 860 were identified in P. euphratica and P. pruinosa, respectively, while 314 DEGs were common to both species. On the basis of parametric analysis of gene set enrichment, GO enrichment in P. euphratica was found to be significantly different from that in P. pruinosa. Numerous genes involved in hormone biosynthesis, transporters and transcription factors showed clear differences between the two species in response to salt stress. We also identified 26,560 AS events which were mapped to 8380 poplar genomic loci from four libraries. GO enrichments for genes undergoing AS events in P. euphratica differed significantly from those in P. pruinosa. CONCLUSIONS: A number of salt-responsive genes in both P. euphratica and P. pruinosa were identified and candidate genes with potential roles in the salinity adaptation were proposed. Transcriptome comparisons of two sister desert poplar species under salt stress suggest that these two species may have developed different genetic pathways in order to adapt to different desert salt habitats. The DEGs that were found to be common to both species under salt stress may be especially important for future genetic improvement of cultivated poplars or other crops through transgenic approaches in order to increase tolerance of saline soil conditions.

Barcoding poplars (Populus L.) from western China.

BACKGROUND: Populus is an ecologically and economically important genus of trees, but distinguishing between wild species is relatively difficult due to extensive interspecific hybridization and introgression, and the high level of intraspecific morphological variation. The DNA barcoding approach is a potential solution to this problem. METHODOLOGY/PRINCIPAL FINDINGS: Here, we tested the discrimination power of five chloroplast barcodes and one nuclear barcode (ITS) among 95 trees that represent 21 Populus species from western China. Among all single barcode candidates, the discrimination power is highest for the nuclear ITS, progressively lower for chloroplast barcodes matK (M), trnG-psbK (G) and psbK-psbI (P), and trnH-psbA (H) and rbcL (R); the discrimination efficiency of the nuclear ITS (I) is also higher than any two-, three-, or even the five-locus combination of chloroplast barcodes. Among the five combinations of a single chloroplast barcode plus the nuclear ITS, H+I and P+I differentiated the highest and lowest portion of species, respectively. The highest discrimination rate for the barcodes or barcode combinations examined here is 55.0% (H+I), and usually discrimination failures occurred among species from sympatric or parapatric areas. CONCLUSIONS/SIGNIFICANCE: In this case study, we showed that when discriminating Populus species from western China, the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions. Meanwhile, combining the ITS region with chloroplast regions may improve the barcoding success rate and assist in detecting recent interspecific hybridizations. Failure to discriminate among several groups of Populus species from sympatric or parapatric areas may have been the result of incomplete lineage sorting, frequent interspecific hybridizations and introgressions. We agree with a previous proposal for constructing a tiered barcoding system in plants, especially for taxonomic groups that have complex evolutionary histories (e.g. Populus).

[Study on the correlation between knee osteoarthritis imaging and effects of arthroscope].

OBJECTIVE: To explore the indications of arthroscope for the treatment of knee osteoarthritis and investigate the correlation between knee osteoarthritis imaging and effects of arthroscope. METHODS: From 2005.8 to 2008.4, 86 patients with knee osteoarthritis underwent arthroscope examination and treatment. Among the patients, 44 patients were male, and 42 patients were female, ranging in age from 46 to 67 years, averaged 56.3 years. Arthrodial cartilage of knee was graded by ICRS MR, and by Kellgern Laqrence X-ray. All the patients were followed up, and the duration ranged from 12 to 30 months. The Lysholm score was evaluated at the follow-up time. RESULTS: Among 86 knees in 86 cases, cartilage injury degree of knees was graded as follows: grade 4 in 30 cases, grade 3 in 22 cases, grade 2 in 20 cases, grade 1 in 12 cases, grade 0 in 2 cases, mean grade (2.77 +/- 1.138). Postoperative Lysholm score ranged from 59 to 100, averaged (95.17 +/- 7.556), Kendall's correlation coefficient was -0.089, P = 0.317. There was no correlations between cartilage injury degree and Lysholm score. X-ray of knees was graded as follows: grade 4 in 0 cases, grade 3 in 24 cases, grade 2 in 38 cases, grade 1 in 17 cases, grade 0 in 7 cases, mean grade was (2.13 +/- 0.67), the Kendall's correlation coefficient was -0.851 with negative correlations (P = 0.036) between postoperative Lysholm score and K/L grade. CONCLUSION: There is no correlation between the grade of knee cartilage injury confirmed by MRI (1.5T) and effects of arthroscopy, and the grade is not a gold standard as an operation indication in arthroscope procedure. The K/L grade in X-ray had important effects.