Chromosome-level genome assemblies reveal genome evolution of an invasive plant Phragmites australis.

Biological invasions pose a significant threat to ecosystems, disrupting local biodiversity and ecosystem functions. The genomic underpinnings of invasiveness, however, are still largely unknown, making it difficult to predict and manage invasive species effectively. The common reed (Phragmites australis) is a dominant grass species in wetland ecosystems and has become particularly invasive when transferred from Europe to North America. Here, we present a high-quality gap-free, telomere-to-telomere genome assembly of Phragmites australis consisting of 24 pseudochromosomes and a B chromosome. Fully phased subgenomes demonstrated considerable subgenome dominance and revealed the divergence of diploid progenitors approximately 30.9 million years ago. Comparative genomics using chromosome-level scaffolds for three other lineages and a previously published draft genome assembly of an invasive lineage revealed that gene family expansions in the form of tandem duplications may have contributed to the invasiveness of the lineage. This study sheds light on the genome evolution of Arundinoideae grasses and suggests that genetic drivers, such as gene family expansions and tandem duplications, may underly the processes of biological invasion in plants. These findings provide a crucial step toward understanding and managing the genetic basis of invasiveness in plant species.

Chromosome-level genome assembly and characterization of the Calophaca sinica genome.

Calophaca sinica is a rare plant endemic to northern China which belongs to the Fabaceae family and possesses rich nutritional value. To support the preservation of the genetic resources of this plant, we have successfully generated a high-quality genome of C. sinica (1.06 Gb). Notably, transposable elements (TEs) constituted ~73% of the genome, with long terminal repeat retrotransposons (LTR-RTs) dominating this group of elements (~54% of the genome). The average intron length of the C. sinica genome was noticeably longer than what has been observed for closely related species. The expansion of LTR-RTs and elongated introns emerged had the largest influence on the enlarged genome size of C. sinica in comparison to other Fabaceae species. The proliferation of TEs could be explained by certain modes of gene duplication, namely, whole genome duplication (WGD) and dispersed duplication (DSD). Gene family expansion, which was found to enhance genes associated with metabolism, genetic maintenance, and environmental stress resistance, was a result of transposed duplicated genes (TRD) and WGD. The presented genomic analysis sheds light on the genetic architecture of C. sinica, as well as provides a starting point for future evolutionary biology, ecology, and functional genomics studies centred around C. sinica and closely related species.

Chinese adaptation and validation of the chronic rhinosinusitis-patient-reported outcome: Assessment of health-related quality-of-life.

BACKGROUND: The chronic rhinosinusitis patient-reported outcome (CRS-PRO) is a recently published disease-specific questionnaire designed for CRS patients, with fewer entries and ease of completion. This study aimed to translate the CRS-PRO questionnaire into Chinese and assess its reliability, validity, and responsiveness to provide Chinese patients with a more concise and efficient subjective assessment instrument. METHODS: The Chinese version of the CRS-PRO was created through forward-backward translations and cultural adaptation. Here, 168 CRS patients (118 patients CRS with nasal polyps [CRSwNP] and 50 patients with CRS without nasal polyps [CRSsNP]) and 43 healthy individuals were enrolled. All participants completed the CRS-PRO, 22-item Sinonasal Outcome Test (SNOT-22), and EuroQol five dimensions questionnaire (EQ-5D) questionnaires preoperatively as well as 3 and 6 months after surgery. RESULTS: The Chinese version of the CRS-PRO demonstrated good internal consistency, with a Cronbach's α of 0.813. It also exhibited a higher criterion validity (r = 0.65, p < 0.05) than the SNOT-22. A moderate association was found between the CRS-PRO and objective indicators such as the Lund-Mackay and endoscopic scores. Furthermore, the CRS-PRO, like the SNOT-22, could clearly distinguish CRS patients from healthy subjects (p < 0.01), as well as between the CRSwNP and CRSsNP subtypes (p < 0.01). Additionally, changes in the CRS-PRO exhibited a larger effect size compared to changes in the SNOT-22 (Cohen's d = 1.05 and 0.93 vs. 0.71 and 0.90 for 3 and 6 months, respectively, all p < 0.01). CONCLUSIONS: The Chinese version of the CRS-PRO is a concise, reliable, and responsive instrument that can be utilized as a novel subjective evaluation tool for future clinical practice.

Quantitative analysis of dual-phase enhanced CT in cervical lymph node metastasis of papillary thyroid carcinoma: a comparative study along with pathological manifestations.

PURPOSE: This study aimed to investigate the diagnostic value of dual-phase enhanced computed tomography (CT) in the cervical lymph node metastasis (LNM) of papillary thyroid carcinoma (PTC) by analyzing the dual-phase enhanced Hounsfield units (HUs) of lymph node and sternocleidomastoid muscle, and the ratio and difference. METHODS: The CT arterial-phase and venous-phase imaging data of 143 metastasis-positive lymph nodes (MPLNs) in 88 cases and 172 metastasis-negative lymph nodes (MNLNs) in 128 cases with PTC were retrospectively analyzed. All lymph nodes were confirmed by surgical pathology. The arterial-phase HU of lymph nodes (ANHU), venous-phase HU of lymph nodes (VNHU), arterial-phase HU of the sternocleidomastoid muscle (AMHU) and venous-phase HU of the sternocleidomastoid muscle (VMHU) were measured, and their difference and ratio (ANHU-AMHU, ANHU/AMHU, VNHU-VMHU, VNHU/VMHU) were calculated. The cutoff values and corresponding diagnostic efficacy for diagnosing LNM in PTC were sought by performing the receiver operating characteristic curves. The maximum pathological diameter (MPD) measured on pathological sections of lymph nodes was compared with the maximum transverse diameter (MTD) and maximum sagittal diameter (MSD) and their average values on CT images. RESULTS: The ANHU, and VNHU of MPLNs and MNLNs were 111.89 ± 33.26 and 66.12 (56.81-76.86) (P < 0.001), and 99.07 ± 23.27 and 75.47 ± 13.95 (P < 0.001), respectively. The area under the curve, sensitivity, and specificity of the arterial-phase three parameters (ANHU, ANHU-AMHU, ANHU/AMHU) for diagnosing LNM were (0.877-0.880), (0.755-0.769), and (0.901-0.913), respectively, and the venous-phase three parameters (VNHU, VNHU-VMHU, VNHU/VMHU) were (0.801-0.817), (0.650-0.678), and (0.826-0.901), respectively. Compared with MPD, MTD (Z = -2.686, P = 0.007) and MSD (Z = -3.539, P < 0.001) were significantly different, while (MTD + MSD)/2 was not statistically different (Z = -0.038b, P = 0.969). CONCLUSION: In the differential diagnosis of cervical LNM of PTC by dual-phase enhanced CT angiography, the arterial phase had higher diagnostic efficacy.

Study on Creepage Control for PLS-160 Wheel-Rail Adhesion Test Rig Based on LADRC.

Aiming at the problem of low control accuracy caused by nonlinear disturbances in the operation of the PLS-160 wheel-rail adhesion test rig, a linear active disturbance rejection controller (LADRC) suitable for the wheel-rail adhesion test rig was designed. The influence of nonlinear disturbances during the operation of the test rig on the control accuracy was analyzed based on SIMPACK. The SIMAT co-simulation platform was established to verify the control performance of the LADRC designed in this paper. The simulation results show that the speed and creepage errors of the test rig under the control of the LADRC met the adhesion test technical indicators under four different conditions. Compared with the traditional PID controller, the creepage overshoot and response time with the LADRC were reduced by 1.27% and 60%, respectively, under the constant creepage condition, and the stability recovery time was shorter under the condition of a sudden decrease in the adhesion coefficient. The LADRC designed in this paper shows better dynamic and anti-interference performance; therefore, it is more suitable for a follow-up study of the PLS-160 wheel-rail adhesion test rig.

Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.).

BACKGROUND: Pectin methylesterase (PME) is one of pectin-modifying enzyme that affects the pectin homeostasis in cell wall and regulates plant growth and diverse biological processes. The PME genes have been well explored and characterized in different plants. Nevertheless, systematic research on the soybean (Glycine max L.) PME genes remain lacking. RESULTS: We identified 127 Glycine max PME genes (GmPME) from the soybean Wm82.a2.v1 genome, which unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis classified the GmPME genes into four clades (Group I, Group II, Group III and Group IV). GmPME gene members in the same clades displayed similar gene structures and motif patterns. The gene family expansion analysis demonstrated that segmental duplication was the major driving force to acquire novel GmPME genes compared to the tandem duplication events. Further synteny and evolution analyses showed that the GmPME gene family experienced strong purifying selective pressures during evolution. The cis-element analyses together with the expression patterns of the GmPME genes in various tissues suggested that the GmPME genes broadly participate in distinct biological processes and regulate soybean developments. Importantly, based on the transcriptome data and quantitative RT-PCR validations, we examined the potential roles of the GmPME genes in regulating soybean flower bud development and seed germination. CONCLUSION: In conclusion, we provided a comprehensive characterization of the PME genes in soybean, and our work laid a foundation for the functional study of GmPME genes in the future.

Advantages of Short-term Personalized Vestibular Rehabilitation at Home Guided by Professional Therapist for Treatment of Decompensated Vestibular Vertigo.

OBJECTIVE: Patients suffered a lot from decompensated vestibular vertigo. Pharmacotherapy and vestibular rehabilitation training have been proven to be effective in prompting vestibular compensation. Routine rehabilitation training is faced with the challenges of patients' compliance, completion, the average recuperation time and so on. This study is aimed to investigate advantages of short-term personalized vestibular rehabihitation at home guided by professional therapist. METHODS: A short-term personalized vestibular rehabilitation program (ST-PVR) was designed for patients with decompensated vestibular vertigo in this study. RESULTS: Patients experiencing the ST-PVR program showed significant improvement of Self-Rating Anxiety Scale (SAS), Dizziness Handicap Inventory (DHI), Activities-Specific Balance Confidence Scale (ABC) scores by the second follow-up (at 2nd week after treatment, P<0.05). However-improvement in the medication group occurred slightly later, DHI for 1 month and SAS for 2 months after treatment (P<0.05). Also, the improvement in the onset time of unilateral weakness (UW) at 2nd week after treatment in the personalized vestibular rehabilitation (PVR) group was faster than that in the medication group. CONCLUSION: In general, the short-term PVR program showed great advantages by prompting vestibular compensation quickly and putting forward future direction for clinical treatment on decompensated vestibular vertigo.

Genome-Wide Identification and Characterization of TALE Superfamily Genes in Soybean (Glycine max L.).

The three-amino-acid-loop-extension (TALE) superfamily genes broadly existed in plants, which played important roles in plant growth, development and abiotic stress responses. In this study, we identified 68 Glycine max TALE (GmTALE) superfamily members. Phylogenetic analysis divided the GmTALE superfamily into the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Moreover, the KNOX subfamily could be further categorized into three clades (KNOX Class I, KNOX Class II and KNOX Class III). The GmTALE genes showed similarities in the gene structures in the same subfamily or clade, whose coding proteins exhibited analogous motif and conserved domain compositions. Besides, synteny analyses and evolutionary constraint evaluations of the TALE members among soybean and different species provided more clues for GmTALE superfamily evolution. The cis-element analyses in gene promoter regions and relevant gene expression profiling revealed different regulating roles of GmTALE genes during soybean plant development, saline and dehydration stresses. Genome-wide characterization, evolution, and expression profile analyses of GmTALE genes can pave the way for future gene functional research and facilitate their roles for applications in genetic improvement on soybean in saline and dehydration stresses.

Genome-wide identification and characterization of GRAS genes in soybean (Glycine max).

BACKGROUND: GRAS proteins are crucial transcription factors, which are plant-specific and participate in various plant biological processes. Thanks to the rapid progress of the whole genome sequencing technologies, the GRAS gene families in different plants have been broadly explored and studied. However, comprehensive research on the soybean (Glycine max) GRAS gene family is relatively lagging. RESULTS: In this study, 117 Glycine max GRAS genes (GmGRAS) were identified. Further phylogenetic analyses showed that the GmGRAS genes could be categorized into nine gene subfamilies: DELLA, HAM, LAS, LISCL, PAT1, SCL3, SCL4/7, SCR and SHR. Gene structure analyses turned out that the GmGRAS genes lacked introns and were relatively conserved. Conserved domains and motif patterns of the GmGRAS members in the same subfamily or clade exhibited similarities. Notably, the expansion of the GmGRAS gene family was driven both by gene tandem and segmental duplication events. Whereas, segmental duplications took the major role in generating new GmGRAS genes. Moreover, the synteny and evolutionary constraints analyses of the GRAS proteins among soybean and distinct species (two monocots and four dicots) provided more detailed evidence for GmGRAS gene evolution. Cis-element analyses indicated that the GmGRAS genes may be responsive to diverse environmental stresses and regulate distinct biological processes. Besides, the expression patterns of the GmGRAS genes were varied in various tissues, during saline and dehydration stresses and during seed germination processes. CONCLUSIONS: We conducted a systematic investigation of the GRAS genes in soybean, which may be valuable in paving the way for future GmGRAS gene studies and soybean breeding.

AVNet: A retinal artery/vein classification network with category-attention weighted fusion.

BACKGROUND AND OBJECTIVE: Automatic artery/vein (A/V) classification in retinal images is of great importance in detecting vascular abnormalities, which may provide biomarkers for early diagnosis of many systemic diseases. It is intuitive to apply popular deep semantic segmentation network for A/V classification. However, the model is required to provide powerful representation ability since vessel is much more complex than general objects. Moreover, deep network may lead to inconsistent classification results for the same vessel due to the lack of structured optimization objective. METHODS: In this paper, we propose a novel segmentation network named AVNet, which effectively enhances the classification ability of the model by integrating category-attention weighted fusion (CWF) module, significantly improving the pixel-level A/V classification results. Then, a graph based vascular structure reconstruction (VSR) algorithm is employed to reduce the segment-wise inconsistency, verifying the effect of the graph model on noisy vessel segmentation results. RESULTS: The proposed method has been verified on three datasets, i.e. DRIVE, LES-AV and WIDE. AVNet achieves pixel-level accuracies of 90.62%, 90.34%, and 93.16%, respectively, and VSR further improves the performance by 0.19%, 1.85% and 0.64%, achieving the state-of-the-art results on these three datasets. CONCLUSION: The proposed method achieves competitive performance in A/V classification task.

Are Meniere's disease patients with otolith organ impairment more likely to have balance dysfunction?

Background: Patients with Meniere's disease (MD) may present with peripheral vestibular end organ dysfunction and balance dysfunction. Objective: This study aimed to compare the results of vestibular evoked myogenic potential (VEMP) tests with those of the sensory organization test (SOT) in patients with MD to determine whether they are correlated. Material and methods: In total, 132 patients with unilateral MD were evaluated using an audiometric test, the SOT, a caloric test and VEMP tests. Results: Cervical VEMP and ocular VEMP tests were conducted in 132 patients with MD, and the response rates of the affected side were lower than those of the unaffected side. The composite score, C5ES, and C6ES of the SOT were significantly decreased in patients with no VEMP responses compared to those with VEMP responses. Conclusions and significance: MD patients with no VEMP responses are more likely to develop balance impairment than those with VEMP responses. MD patients with otolith organ impairment may therefore have balance disorders, and should exercise caution to prevent falls and subsequent injuries.

BTS-DSN: Deeply supervised neural network with short connections for retinal vessel segmentation.

BACKGROUND AND OBJECTIVE: The condition of vessel of the human eye is an important factor for the diagnosis of ophthalmological diseases. Vessel segmentation in fundus images is a challenging task due to complex vessel structure, the presence of similar structures such as microaneurysms and hemorrhages, micro-vessel with only one to several pixels wide, and requirements for finer results. METHODS: In this paper, we present a multi-scale deeply supervised network with short connections (BTS-DSN) for vessel segmentation. We used short connections to transfer semantic information between side-output layers. Bottom-top short connections pass low level semantic information to high level for refining results in high-level side-outputs, and top-bottom short connection passes much structural information to low level for reducing noises in low-level side-outputs. In addition, we employ cross-training to show that our model is suitable for real world fundus images. RESULTS: The proposed BTS-DSN has been verified on DRIVE, STARE and CHASE_DB1 datasets, and showed competitive performance over other state-of-the-art methods. Specially, with patch level input, the network achieved 0.7891/0.8212 sensitivity, 0.9804/0.9843 specificity, 0.9806/0.9859 AUC, and 0.8249/0.8421 F1-score on DRIVE and STARE, respectively. Moreover, our model behaves better than other methods in cross-training experiments. CONCLUSIONS: BTS-DSN achieves competitive performance in vessel segmentation task on three public datasets. It is suitable for vessel segmentation. The source code of our method is available at: https://github.com/guomugong/BTS-DSN.

Degree sums and dense spanning trees.

Finding dense spanning trees (DST) in unweighted graphs is a variation of the well studied minimum spanning tree problem (MST). We utilize established mathematical properties of extremal structures with the minimum sum of distances between vertices to formulate some general conditions on the sum of vertex degrees. We analyze the performance of various combinations of these degree sum conditions in finding dense spanning subtrees and apply our approach to practical examples. After briefly describing our algorithm we also show how it can be used on variations of DST, motivated by variations of MST. Our work provide some insights on the role of various degree sums in forming dense spanning trees and hopefully lay the foundation for finding fast algorithms or heuristics for related problems.