Predicting metabolite-disease associations based on auto-encoder and non-negative matrix factorization.

Metabolism refers to a series of orderly chemical reactions used to maintain life activities in organisms. In healthy individuals, metabolism remains within a normal range. However, specific diseases can lead to abnormalities in the levels of certain metabolites, causing them to either increase or decrease. Detecting these deviations in metabolite levels can aid in diagnosing a disease. Traditional biological experiments often rely on a lot of manpower to do repeated experiments, which is time consuming and labor intensive. To address this issue, we develop a deep learning model based on the auto-encoder and non-negative matrix factorization named as MDA-AENMF to predict the potential associations between metabolites and diseases. We integrate a variety of similarity networks and then acquire the characteristics of both metabolites and diseases through three specific modules. First, we get the disease characteristics from the five-layer auto-encoder module. Later, in the non-negative matrix factorization module, we extract both the metabolite and disease characteristics. Furthermore, the graph attention auto-encoder module helps us obtain metabolite characteristics. After obtaining the features from three modules, these characteristics are merged into a single, comprehensive feature vector for each metabolite-disease pair. Finally, we send the corresponding feature vector and label to the multi-layer perceptron for training. The experiment demonstrates our area under the receiver operating characteristic curve of 0.975 and area under the precision-recall curve of 0.973 in 5-fold cross-validation, which are superior to those of existing state-of-the-art predictive methods. Through case studies, most of the new associations obtained by MDA-AENMF have been verified, further highlighting the reliability of MDA-AENMF in predicting the potential relationships between metabolites and diseases.

In Situ Loading of Ni3ZnC0.7 Nanoparticles with Carbon Nanotubes to 3D Melamine Sponge Derived Hollow Carbon Skeleton toward Superior Microwave Absorption and Thermal Resistance.

The simple and low-cost construction of a 3D network structure is an ideal way to prepare high-performance electromagnetic wave (EMW) absorption materials. Herein, a series of carbon skeleton/carbon nanotubes/Ni3ZnC0.7 composites (CS/CNTs/Ni3ZnC0.7) are successfully prepared by in situ growth of Ni3ZnC0.7 and CNTs on 3D melamine sponge carbon. With the increase of precursor, Ni3ZnC0.7 nanoparticles nucleate and catalyze the generation of CNTs on the surface of the carbon skeleton. The minimum reflection loss (RL) value of the S60min composite (loading time of 60 min) reaches -86.6 dB at 1.6 mm and effective absorption bandwidth (EAB, RL≤-10 dB) is up to 9.3 GHz (8.7-18 GHz). The 3D network sponge carbon with layered micro/nanostructure and hollow skeleton promotes multiple reflection and absorption mechanisms of incident EMW. The N-doping and defects can be equivalent to an electric dipole, providing dipole polarization to increase dielectric relaxation. The uniform Ni3ZnC0.7 nanoparticles and CNTs play a key role in dissipating electromagnetic energy, blocking heat transfer, and enhancing the mechanical properties of the skeleton. Fortunately, the composite displays a quite low thermal conductivity of 0.09075 W m·K-1 and good flexibility, which can provide insulation and quickly recover to its original state after being stressed.

Animal models of heart failure with preserved ejection fraction (HFpEF): from metabolic pathobiology to drug discovery.

Heart failure (HF) with preserved ejection fraction (HFpEF) is currently a preeminent challenge for cardiovascular medicine. It has a poor prognosis, increasing mortality, and is escalating in prevalence worldwide. Despite accounting for over 50% of all HF patients, the mechanistic underpinnings driving HFpEF are poorly understood, thus impeding the discovery and development of mechanism-based therapies. HFpEF is a disease syndrome driven by diverse comorbidities, including hypertension, diabetes and obesity, pulmonary hypertension, aging, and atrial fibrillation. There is a lack of high-fidelity animal models that faithfully recapitulate the HFpEF phenotype, owing primarily to the disease heterogeneity, which has hampered our understanding of the complex pathophysiology of HFpEF. This review provides an updated overview of the currently available animal models of HFpEF and discusses their characteristics from the perspective of energy metabolism. Interventional strategies for efficiently utilizing energy substrates in preclinical HFpEF models are also discussed.

IDH1/MDH1 deacetylation promotes acute liver failure by regulating NETosis.

BACKGROUND: Acute liver failure (ALF) is a life-threatening disease, but its pathogenesis is not fully understood. NETosis is a novel mode of cell death. Although the formation of neutrophil extracellular traps (NETs) has been found in various liver diseases, the specific mechanism by which NETosis regulates the development of ALF is unclear. In this article, we explore the role and mechanism of NETosis in the pathogenesis of ALF. METHODS: Clinically, we evaluated NETs-related markers in the liver and peripheral neutrophils of patients with ALF. In in vitro experiments, HL-60 cells were first induced to differentiate into neutrophil-like cells (dHL-60 cells) with dimethyl sulfoxide (DMSO). NETs were formed by inducing dHL-60 cells with PMA. In in vivo experiments, the ALF model in mice was established with LPS/D-gal, and the release of NETs was detected by immunofluorescence staining and western blotting. Finally, the acetylation levels of IDH1 and MDH1 were detected in dHL-60 cells and liver samples by immunoprecipitation. RESULTS: Clinically, increased release of NETs in liver tissue was observed in patients with ALF, and NETs formation was detected in neutrophils from patients with liver failure. In dHL-60 cells, mutations at IDH1-K93 and MDH1-K118 deacetylate IDH1 and MDH1, which promotes the formation of NETs. In a mouse model of ALF, deacetylation of IDH1 and MDH1 resulted in NETosis and promoted the progression of acute liver failure. CONCLUSIONS: Deacetylation of IDH1 and MDH1 reduces their activity and promotes the formation of NETs. This change aggravates the progression of acute liver failure.

Follow-up Value of Hip Medial Ultrasound in Infants and Children With Developmental Dysplasia of the Hip Treated With Reduction and Spica Casting.

OBJECTIVE: Closed or open reduction and spica casting are common treatments for children aged 6 to 18 months, as well as infants aged 0 to 6 months whose harness treatment for developmental dysplasia of the hip (DDH) was unsuccessful. The study aimed to quantify the distance between the femoral head and the acetabulum after closed or open reduction and evaluate the dynamic docking progression of the femoral head using serial hip medical ultrasound. METHODS: We retrospectively reviewed the medical records and hip medial ultrasound images of a consecutive series of patients with DDH who underwent spica casting after reduction and compared images obtained immediately after reduction and at follow-up. The first cast (stage I) was maintained for 2 to 3 months and scheduled for outpatient repeat ultrasound in 4 to 8 weeks. Then the second cast was placed (stage II), lasting for another 2 to 3 months. The triradiate cartilage-femoral head distance (TFD) was measured in the acetabulum coronal mid-sectional plane. The Wilcoxon signed-rank test was used to compare the TFD values. RESULTS: This study included 49 patients. All patients underwent hip medial ultrasound 0 to 3 days after stage I (time 1) and 4 to 8 weeks (time 2) postoperatively, with 24 patients reviewed again 0 to 7 days after stage II. The TFD values in time 1 and time 2 were 6.0 (5.0, 9.0) mm and 5.0 (3.6, 7.0) mm, respectively. There was a statistically significant difference between times 1 and 2 regarding TFD values in 49 close-reduction hips (6.0 vs 5.0 mm, P < 0.001). Similar findings were also observed in 13 open-reduction hips (6.0 vs 5.0 mm, P = 0.023). CONCLUSIONS: Hip medial ultrasonography during the period of cast immobilization after reduction in children with DDH can objectively and quantitatively show the dynamic change of the distance between the femoral head and the acetabulum, and can be used to assess reduction of the hip and progression of femoral head docking. LEVEL OF EVIDENCE: Level II-prognostic study.

Kinematic and Joint Compliance Modeling Method to Improve Position Accuracy of a Robotic Vision System.

In the field of robotic automation, achieving high position accuracy in robotic vision systems (RVSs) is a pivotal challenge that directly impacts the efficiency and effectiveness of industrial applications. This study introduces a comprehensive modeling approach that integrates kinematic and joint compliance factors to significantly enhance the position accuracy of a system. In the first place, we develop a unified kinematic model that effectively reduces the complexity and error accumulation associated with the calibration of robotic systems. At the heart of our approach is the formulation of a joint compliance model that meticulously accounts for the intricacies of the joint connector, the external load, and the self-weight of robotic links. By employing a novel 3D rotary laser sensor for precise error measurement and model calibration, our method offers a streamlined and efficient solution for the accurate integration of vision systems into robotic operations. The efficacy of our proposed models is validated through experiments conducted on a FANUC LR Mate 200iD robot, showcasing notable improvements in the position accuracy of robotic vision system. Our findings contribute a framework for the calibration and error compensation of RVS, holding significant potential for advancements in automated tasks requiring high precision.

Arrest, Senescence and Death of Shoot Apical Stem Cells in Arabidopsis thaliana.

Shoot stem cells act as the source of the aboveground parts of flowering plants. A precise regulatory basis is required to ensure that plant stem cells show the right status during the stages of proliferation, senescence and cell death. Over the past few decades, the genetic circuits controlling stem cell fate, including the regulatory pathways of establishment, maintenance and differentiation, have been largely revealed. However, the morphological changes and molecular mechanisms of the final stages of stem cells, which are represented by senescence and cell death, have been less studied. The senescence and death of shoot stem cells are under the control of a complex series of pathways that integrate multiple internal and external signals. Given the crucial roles of shoot stem cells in influencing plant longevity and crop yields, researchers have attempted to uncover details of stem cell senescence and death. Recent studies indicate that stem cell activity arrest is controlled by the FRUITFULL-APETALA2 pathway and the plant hormones auxin and cytokinin, while the features of senescent and dead shoot apical stem cells have also been described, with dynamic changes in reactive oxygen species implicated in stem cell death. In this review, we highlight the recent breakthroughs that have enriched our understanding of senescence and cell death processes in plant stem cells.

The nuclear-localized RNA helicase 13 is essential for chloroplast development in Arabidopsis thaliana.

The chloroplast is a semi-autonomous organelle with a double membrane structure, and its structural stability is a prerequisite for its correct function. Chloroplast development is regulated by known nuclear-encoded chloroplast proteins or proteins encoded within the chloroplast itself. However, the mechanism of chloroplast development regulated by other organelles remains largely unknown. Here, we report that the nuclear-localized DEAD-box RNA helicase 13 (RH13) is essential for chloroplast development in Arabidopsis thaliana. RH13 is widely expressed in tissues and localized to the nucleolus. A homozygous rh13 mutant shows abnormal chloroplast structure and leaf morphogenesis. Proteomic analysis showed that the expression levels of photosynthesis-related proteins in chloroplasts were reduced due to loss of RH13. Furthermore, RNA-sequencing and proteomics data revealed decreases in the expression levels of these chloroplast-related genes, which undergo alternative splicing events in the rh13 mutant. Taken together, we propose that nucleolus-localized RH13 is critical for chloroplast development in Arabidopsis.

Current spreading structure of GaN-based vertical-cavity surface-emitting lasers.

Indium tin oxide (ITO) is often used as a current spreading layer in the GaN-based vertical-cavity surface-emitting lasers (VCSELs). However, the absorption coefficient of ITO is significant, which reduces the laser output power, raises the threshold, and makes VCSELs hardly lase in the ultraviolet range. To find a transparent conductive structure that can replace ITO, we propose a periodic p-AlGaN/u-GaN/p-GaN structure. In the simulation of light-emitting diodes, the optimized parameter is obtained with multi-period 10 nm p-Al0.1Ga0.9N/2 nm u-GaN/8 nm p-GaN combined with n-GaN/n-Al0.2Ga0.8N in the n region. Applying the structure to 435 nm VCSELs and comparing it to a common VCSEL with the ITO current spreading layer, it can be found that the new structure reduces the threshold from 9.17 to 3.06 kA/cm2. The laser power increases from 1.33 to 15.4 mW. The optimized structure has a high laser power and a lower threshold, which can be used in future investigations.

Skin manifestations and submacroscopical features of acromegaly: A case-control study using dermoscopy and high-frequency ultrasound.

BACKGROUND: Although the cutaneous involvement of acromegaly has been recognized, the submacroscopical skin changes and the extent of skin thickening of patients remain unclear. OBJECTIVES: This study aimed at investigating the clinical cutaneous manifestations, dermoscopic features, and skin thickness revealed by high-frequency ultrasound (HFUS) of acromegalic patients. METHODS: A case-control observational study was conducted. Patients with acromegaly and controls were prospectively included and received thorough cutaneous examinations to compare the macroscopical and dermoscopic features. The skin thickness measured by HFUS and its correlation with clinical data were also assessed. RESULTS: Thirty-seven and 26 patients from acromegalic and control group were included, respectively. Clinical skin manifestations were recorded in detail. Under dermoscopy, red structureless area (91.9% vs. 65.4%, p = 0.021), perifollicular orange halo (78.4% vs. 26.9%, p = 0.005), and follicular plug (70.3% vs. 3.9%, p = 0.001) in the facial area, and perifollicular pigmentation (91.9% vs. 23.1%), broom-head hairs (83.8% vs. 3.9%), honeycomb-like pigmentation (97.3% vs. 38.46%), widened dermatoglyphics (81.1% vs. 3.9%) at the extremities (p < 0.001) were more prevalent in acromegaly. The mean skin thickness was 4.10 ± 0.48 mm for acromegaly, and 3.55 ± 0.52 mm for controls (p < 0.001) but no correlation with disease duration, adenoma size, and hormone level was found in acromegaly. CONCLUSIONS: Submacroscopical skin changes under dermoscopy and skin thickness increase assessed by HFUS can provide clinicians with subtle evidences for early detection of acromegaly and objective parameters for accurate assessment of its skin involvement.

The diagnosis interval influences risk factors of mortality in patients with co-existent active tuberculosis and lung cancer: a retrospective study.

BACKGROUND: Previous studies reported that tuberculosis (TB) is associated with an increased risk of lung cancer or the survival and mortality of lung cancer. However, the impact of coexisting TB on the survival of lung cancer patients was controversial. We aimed to identify risk factors on the survival rate of patients with co-existent active TB and lung cancer. METHODS: One hundred seventy-three patients diagnosed with active TB and lung cancer from January 2016 to August 2021 in Shanghai pulmonary hospital were selected and divided into two groups (≤ 6 months, > 6 months) according to the diagnosis interval between active TB and lung cancer (the order of diagnosis is not considered). The clinical characteristics and survival were analyzed. Univariate and multivariate logistic regression analyses were used to identify the risk factors for overall survival (OS). RESULTS: One hundred seventy-three patients were diagnosed with lung cancer and active TB. The study population exhibited a median age of 64 years, with a majority of 81.5% being male, 58.0% of patients had a history of smoking. Among those involved, 93.6% had pulmonary TB, 91.9% were diagnosed with non-small cell lung cancer (NSCLC), 76.9% were Eastern Cooperative Oncology Group (ECOG) 0-2 and 12.7% were ECOG 3-4. We observed better survival in the > 6 months group compared with the ≤ 6 months group (hazard ratio [HR] 0.456, 95% confidence interval [CI]:0.234-0.889, P = 0.017). The 1-, 3-, and 5- year OS rates were 94.2%, 80.3%, and 77.6%, respectively, in the > 6 months group and 88.3%, 63.8%, and 58.5%, respectively, in the ≤ 6 months group. Surgery (HR 0.193, [95% CI, 0.038-0.097]; P = 0.046) and ECOG Performance Status (HR 12.866, [95% CI, 2.730-60.638]; P = 0.001) were independent prognostic factors in the > 6 months group. CONCLUSIONS: Patients diagnosed with lung cancer and active TB for more than half a year have a significantly better prognosis than those diagnosed within half a year. ECOG Performance Status and surgery might possibly affect the outcomes of patients with co-existent active TB and lung cancer.

Mucus Hypersecretion in Chronic Obstructive Pulmonary Disease and Its Treatment.

Most patients diagnosed with chronic obstructive pulmonary disease (COPD) present with hallmark features of airway mucus hypersecretion, including cough and expectoration. Airway mucus function as a native immune system of the lung that severs to trap particulate matter and pathogens and allows them to clear from the lung via cough and ciliary transport. Chronic mucus hypersecretion (CMH) is the main factor contributing to the increased risk of morbidity and mortality in specific subsets of COPD patients. It is, therefore, primarily important to develop medications that suppress mucus hypersecretions in these patients. Although there have been some advances in COPD treatment, more work remains to be done to better understand the mechanism underlying airway mucus hypersecretion and seek more effective treatments. This review article discusses the structure and significance of mucus in the lungs focusing on gel-forming mucins and the impacts of CMH in the lungs. Furthermore, we summarize the article with pharmacological and nonpharmacological treatments as well as novel and interventional procedures to control CMH in COPD patients.

Is Hip Medial Ultrasound More Accurate Than Radiography for Determining the Status of Hip Reduction in Children Treated With a Spica Cast? A Retrospective Diagnostic Accuracy Study.

BACKGROUND: Developmental dysplasia of the hip (DDH) is the most common hip abnormality in children. Closed or open reduction and cast immobilization are the most commonly used treatments for patients aged 6 to 18 months with dislocation; they are also used in children younger than 6 months when brace treatment is not effective. During cast immobilization, surgeons need reliable and timely imaging methods to assess the status of hip reduction to ensure successful treatment and avoid complications. Several methods are used, but they have disadvantages. We developed and, in this study, evaluated a hip medial ultrasound method to evaluate the status of hip reduction in children treated with a spica cast. QUESTION/PURPOSE: Is hip medial ultrasound more accurate than radiography for determining the status of hip reduction in children treated with a spica cast? METHODS: Between November 2017 and December 2020, we treated 136 patients with closed or open reduction and spica casting for DDH in our department. These children were 3 to 18 months old at the time of surgical reduction and had a specific medical history, physical examination findings, or AP radiographic evidence of unilateral or bilateral DDH. None had a concomitant femoral/acetabular osteotomy procedure in these hips. All patients underwent hip medial ultrasound, AP radiography, and MRI under sedation within 2 to 7 days after open or closed reduction. The examination time was from the second day after reduction to enable the patient to recover from anesthesia. MRI was performed within 7 days after reduction because of a few long appointment times, and ultrasound and AP radiography were always performed 1 or 2 days before MRI. Based on that, 65% (88 of 136 [88 hips]) of patients were excluded due to the absence of MRI, ultrasound, or AP radiography; 3% (4 of 136 [4 hips]) of patients were excluded because of concurrent congenital spina bifida, Larson syndrome, or Prader-Willi syndrome; and 1% (1 of 136 [1 hip]) of patients were excluded because the patient underwent MRI before ultrasound. A total of 32% (43 of 136 [43 hips]) of patients were eligible for analysis in this cross-sectional diagnostic study, and these 43 patients underwent AP radiography, ultrasound, and MRI. In this retrospective study, the mean age at the time of surgery was 10 ± 4 months (male:female ratio 5:38; unilateral DDH: 34; bilateral DDH: 9). To ensure the independence of the results, the study was limited to one hip per patient (in patients with bilateral DDH, the right hip was evaluated). The reduction of 43 hips (left:right ratio 26:17; closed:open reduction ratio 30:13) was evaluated by MRI, hip medial ultrasound, and radiography. Children with spica casts were placed in the supine position, which is necessary to expose the perineum for ultrasound. We used a broad-spectrum, microconvex, and intracavitary probe. The acetabular medial wall was identified by the triradiate cartilage of the ischial tuberosity and the pubis superior, and the femoral head was identified by the femoral neck. Then, the acetabulum coronal midsectional plane was used to determine the positions of the femoral head and acetabulum and to measure the triradiate cartilage-femoral distance. MRI examinations were performed using a 1.5-T MRI system with an eight-channel body coil. Each reviewer evaluated each reduction independently. Additionally, to further assess the hip medial ultrasound method's reliability and reproducibility, we investigated the interobserver and intraobserver agreement in evaluating the reduction using hip medial ultrasound. Using ultrasound or radiography, the reviewers classified hips as reduced, uncertain status, or dislocated. MRI was considered the gold standard for assessing hip reduction, and the reviewers classified hips as reduced or dislocated by MRI. Patients with hips with an uncertain reduction status according to ultrasound or radiography were retained in the analysis. Thus, the test results of radiography and ultrasound were classified into three classifications (positive, negative, or uncertain) in the present study. The test was considered positive or negative when patients were assessed with dislocation or without dislocation, respectively. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of ultrasound and radiography were calculated and compared. We combined uncertain and positive into the positive classification to be conservative in the statistical choices. The specificity, sensitivity, PPV, and NPV were analyzed based on this premise. Furthermore, a subgroup analysis was conducted by sex. MRI evaluation revealed that 41 hips were reduced and two hips were dislocated. RESULTS: The sensitivity, specificity, PPV, and NPV of ultrasound were 100% (95% CI 16% to 100%), 95% (95% CI 84% to 99%), 50% (95% CI 7% to 93%), and 100% (95% CI 91% to 100%), respectively. The sensitivity, specificity, PPV, and NPV of radiography were 50% (95% CI 1% to 99%), 68% (95% CI 52% to 82%), 7% (95% CI 0% to 34%), and 97% (95% CI 82% to 100%), respectively. Ultrasound showed a higher specificity (95% versus 68%; p < 0.001) and PPV (50% versus 7%; p = 0.02) than radiography. The sensitivity, specificity, PPV, and NPV of ultrasound were 100% (95% CI 16% to 100%), 94% (95% CI 81% to 99%), 50% (95% CI 7% to 93%), and 100% (95% CI 90% to 100%), respectively, for female patients (with only five male patients, we could not perform these analyses in this group). The sensitivity, specificity, PPV, and NPV of radiography were 50% (95% CI 1% to 99%), 64% (95% CI 46% to 79%), 7% (95% CI 0% to 34%), and 96% (95% CI 79% to 100%), respectively, for female patients. The κ values for intra- and interobserver reliability both were 1.0. CONCLUSION: Hip medial ultrasound can directly visualize the femoral head and acetabulum. Hip medial ultrasound is more reliable than radiography as a preliminary evaluation method and does not involve irradiation. We recommend using hip medial ultrasound during outpatient follow-up visits for patients younger than 2 years treated with hip reduction and cast immobilization. LEVEL OF EVIDENCE: Level III, diagnostic study.

Saikosaponins regulate bile acid excretion in mice liver and ileum by activating farnesoid X receptor and bile acid transporter.

Radix Bupleuri exerts effective hepatoprotective and cholagogic effects through its Saikosaponins (SSs) component. Therefore, we attempted to determine the mechanism of saikosaponins used to promote bile excretion by studying their effects on intrahepatic bile flow, focusing on the synthesis, transport, excretion, and metabolism of bile acids. C57BL/6N mice were continuously gavaged with saikosaponin a (SSa), saikosaponin b2 (SSb2 ), or saikosaponin D (SSd) (200 mg/kg) for 14 days. Liver and serum biochemical indices were determined using Enzyme-linked immunosorbent assay (ELISA) kits. In addition, an ultra-performance liquid chromatography-mass spectrometer (UPLC-MS) was used to measure the levels of the 16 bile acids in the liver, gallbladder, and cecal contents. Furthermore, SSs pharmacokinetics and docking between SSs and farnesoid X receptor (FXR)-related proteins were analyzed to investigate the underlying molecular mechanisms. Administration of SSs and Radix Bupleuri alcohol extract (ESS) did not cause significant changes in alanine aminotransferase (ALT), aspartate aminotransferase (AST), or alkaline phosphatase (ALP) levels. Saikosaponin-regulated changes in bile acid (BA) levels in the liver, gallbladder, and cecum were closely related to genes involved in BA synthesis, transport, and excretion in the liver. Pharmacokinetic studies indicated that SSs were characterized by rapid elimination (t1/2 as 0.68-2.47 h), absorption (Tmax as 0.47-0.78 h), and double peaks in the drug-time curves of SSa and SSb2 . A molecular docking study revealed that SSa, SSb2 , and SSd docked well with the 16 protein FXR molecules and target genes (<-5.2 kcal/mol). Collectively, saikosaponins may maintain BA homeostasis in mice by regulating FXR-related genes and transporters in the liver and intestine.

An Improved In-Motion Coarse Alignment Method for SINS/GPS Integration with Initial Velocity Error Suppression.

The integrated system with the strapdown inertial navigation system (SINS) and the global positioning system (GPS) is the most popular navigation mode. It has been used in many navigation fields. Before the integrated system works properly, it must determine the initial attitude for SINS. In SINS/GPS-integrated systems, the navigational velocity can be used to carry out the initial alignment when the system is installed in the in-motion vehicle. However, the initial velocity errors are not considered in the current popular in-motion alignment methods for SINS/GPS integration. It is well-known that the initial velocity errors must exist when the initial velocity is obtained from the GPS outputs. In this paper, an improved method was proposed to solve this problem. By analyzing the original observation vectors in the in-motion coarse alignment method, an average operation was used to construct the intermediate vectors, and the new observation vector can be calculated by subtracting the intermediate vector from the original observation vector. Then, the initial velocity errors can be eliminated from the newly constructed observation vector. Thus, the interferences of the initial velocity errors for the initial alignment process can be suppressed. The simulation and field tests are designed to verify the performance of the proposed method. The tests results showed that the proposed method can obtain the higher accurate results than the current methods when the initial velocity is considered. Additionally, the results of the proposed method were similar to the current methods when the initial velocity errors were not considered. This shows that the initial velocity errors were eliminated effectively by the proposed method, and the alignment accuracy were not decreased.

Global survey of alternative splicing and gene modules associated with fertility regulation in a thermosensitive genic male sterile wheat.

Thermosensitive genic male sterile (TGMS) wheat lines are the core of two-line hybrid systems. Understanding the mechanism that regulates male sterility in TGMS wheat lines is helpful for promoting wheat breeding. Several studies have obtained information regarding the mechanisms associated with male sterility at the transcriptional level, but it is not clear how the post-transcriptional process of alternative splicing might contribute to controlling male sterility. In this study, we performed genome-wide analyses of alternative splicing during the meiosis stage in TGMS line BS366 using PacBio and RNA-Seq hybrid sequencing. Cytological observations indicated that cytoskeleton assembly in pollen cells, calcium deposition in pollen and tapetal cells, and vesicle transport in tapetal cells were deficient in BS366. According to our cytological findings, 49 differentially spliced genes were isolated. Moreover, 25 long non-coding RNA targets and three bHLH transcription factors were identified. Weighted gene co-expression network analysis detected four candidate differentially spliced genes that had strong co-relation with the seed setting percentage, which is the direct representation of male sterility in BS366. In this study, we obtained comprehensive data regarding the alternative splicing-mediated regulation of male sterility in TGMS wheat. The candidates identified may provide the molecular basis for an improved understanding of male sterility.

Identification of the yield traits related haplotype combinations of transcription factor genes TaHDZ34 in common wheat.

A predominant objective in wheat breeding is improving yield-related traits. The homeodomain-leucine zipper (HD-Zip) transcription factor plays a significant role in plant growth and development. In this study, we cloned all homeologs of TaHDZ34, which is a member of the HD-Zip class IV transcription factor family in wheat (Triticum aestivum L.). Sequence polymorphism analysis showed that TaHDZ-A34, TaHDZ-B34, and TaHDZ-D34 formed five, six, and six haplotypes, respectively, and the genes were divided into two main haplotype groups. We also developed functional molecular markers. The TaHDZ34 genes were divided into eight main haplotype combinations. Association analysis and distinct population validation preliminarily indicated that TaHDZ34 genes modulate grain number per spike, effective spikelet number per spike, thousand kernel weight, and flag leaf area per plant in wheat. Hap-ABD was the most effective haplotype combination of TaHDZ34. Subcellular localization showed that TaHDZ-A34 was localized to the nucleus. The interacting proteins of TaHDZ-A34 were involved in protein synthesis/degradation, energy production and transportation, and photosynthesis. Geographic distribution and frequencies of TaHDZ34 haplotype combinations suggested that Hap-Abd and Hap-AbD were preferentially selected in Chinese wheat breeding programs. The high-yield-related haplotype combination Hap-ABD provided beneficial genetic resources for the marker-assisted selection of new wheat cultivars. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01298-5.

Responses of microbial community and antibiotic resistance genes to co-existence of chloramphenicol and salinity.

In recent years, the risk from environmental pollution caused by chloramphenicol (CAP) has emerged as a serious concern worldwide, especially for the co-selection of antibiotic resistance microorganisms simultaneously exposed to CAP and salts. In this study, the multistage contact oxidation reactor (MCOR) was employed for the first time to treat the CAP wastewater under the co-existence of CAP (10-80 mg/L) and salinity (0-30 g/L NaCl). The CAP removal efficiency reached 91.7% under the co-existence of 30 mg/L CAP and 10 g/L NaCl in the influent, but it fluctuated around 60% with the increase of CAP concentration and salinity. Trichococcus and Lactococcus were the major contributors to the CAP and salinity shock loads. Furthermore, the elevated CAP and salinity selection pressures inhibited the spread of CAP efflux pump genes, including cmlA, tetC, and floR, and significantly affected the composition and abundance of antibiotic resistance genes (ARGs). As the potential hosts of CAP resistance genes, Acinetobacter, Enterococcus, and unclassified_d_Bacteria developed resistance against high osmotic pressure and antibiotic environment using the efflux pump mechanism. The results also revealed that shifting of potential host bacteria significantly contributed to the change in ARGs. Overall, the co-existence of CAP and salinity promoted the enrichment of core genera Trichococcus and Lactococcus; however, they inhibited the proliferation of ARGs. KEY POINTS: • Trichococcus and Lactococcus were the core bacteria related to CAP biodegradation • Co-existence of CAP and salinity inhibited proliferation of cmlA, tetC, and floR • The microorganism resisted the CAP using the efflux pump mechanism.

Accurate estimation of camera response function for high dynamic range measurement.

A high dynamic range surface has large reflectivity variations and measuring it with a structured light technique could cause pixel saturation that will seriously degrade the measurement accuracy. Accurate identification of saturated pixels will significantly improve the measurement accuracy. This paper introduces an accurate estimation approach to the camera response function (CRF) for high dynamic range measurement and proposes a method that uses the estimated CRF to identify the saturated pixels in captured images. We perform experiments using the proposed saturation identification method and the other existing methods to compare both the saturation identification accuracy and measurement accuracy. The experiment results verify both the accuracy and suitability of the proposed method.

High-frequency ultrasound features in vulvar lichen sclerosus and correlation with histopathology.

BACKGROUND: Vulvar lichen sclerosus (VLS) is a chronic inflammatory disease initially involving anogenital areas. Noninvasive assessment is essential for precise management in VLS. We aim to analyze high-frequency ultrasound (HFUS) features and correlate HFUS with histopathological changes. MATERIALS AND METHODS: Forty patients with histopathologically confirmed VLS lesions were retrospectively identified from August 2020 to September 2021. The clinical manifestations, dermoscopic images as well as both 20 and 50 MHz HFUS images were assessed. HFUS assessment included epidermal morphology, hypoechoic dermal band thickness, and hypoechoic dermal band internal echo. We compared HFUS images with histopathology, and Pearson's correlation coefficient was used to assess the relationship between hypoechoic dermal band thickness and histopathological depth. RESULTS: Hypoechoic dermal band was present in 100% (40/40) VLS lesions. There was a significant linear positive correlation between the histopathological depth and corresponding hypoechoic dermal band thickness, with a Pearson correlation coefficient of 0.685 (p < 0.001). Besides, 95% (38/40) lesions revealed smooth epidermis, and the internal echo of hypoechoic dermal band was assessed as homogeneous in 60% (24/40) and inhomogeneous in 40% (16/40) lesions. CONCLUSION: HFUS characteristics, as well as measurable hypoechoic dermal band thickness, may provide valuable information in the precise diagnosis and the treatment monitoring of VLS.