Deep convolutional-neural-network-based metal artifact reduction for CT-guided interventional oncology procedures (MARIO).

BACKGROUND: Computed tomography (CT) is routinely used to guide cryoablation procedures. Notably, CT-guidance provides 3D localization of cryoprobes and can be used to delineate frozen tissue during ablation. However, metal-induced artifacts from ablation probes can make accurate probe placement challenging and degrade the ice ball conspicuity, which in combination could lead to undertreatment of potentially curable lesions. PURPOSE: In this work, we propose an image-based neural network (CNN) model for metal artifact reduction for CT-guided interventional procedures. METHODS: An image domain metal artifact simulation framework was developed and validated for deep-learning-based metal artifact reduction for interventional oncology (MARIO). CT scans were acquired for 19 different cryoablation probe configurations. The probe configurations varied in the number of probes and the relative orientations. A combination of intensity thresholding and masking based on maximum intensity projections (MIPs) was used to segment both the probes only and probes + artifact in each phantom image. Each of the probe and probe + artifact images were then inserted into 19 unique patient exams, in the image domain, to simulate metal artifact appearance for CT-guided interventional oncology procedures. The resulting 361 pairs of simulated image volumes were partitioned into disjoint training and test datasets of 304 and 57 volumes, respectively. From the training partition, 116 600 image patches with a shape of 128 × 128 × 5 pixels were randomly extracted to be used for training data. The input images consisted of a superposition of the patient and probe + artifact images. The target images consisted of a superposition of the patient and probe only images. This dataset was used to optimize a U-Net type model. The trained model was then applied to 50 independent, previously unseen CT images obtained during renal cryoablations. Three board-certified radiologists with experience in CT-guided ablations performed a blinded review of the MARIO images. A total of 100 images (50 original, 50 MARIO processed) were assessed across different aspects of image quality on a 4-point likert-type item. Statistical analyses were performed using Wilcoxon signed-rank test for paired samples. RESULTS: Reader scores were significantly higher for MARIO processed images compared to the original images across all metrics (all p < 0.001). The average scores of the overall image quality, iceball conspicuity, overall metal artifact, needle tip visualization, target region confidence, and worst metal artifact, needle tip visualization, iceball conspicuity, and target region confidence improved by 34.91%, 36.29%, 39.94%, 34.17%, 35.13%, and 45.70%, respectively. CONCLUSIONS: The proposed method of image-based metal artifact simulation can be used to train a MARIO algorithm to effectively reduce probe-related metal artifacts in CT-guided cryoablation procedures.

New recessive compound heterozygous variants of RP1L1 in RP1L1 maculopathy.

AIM: To identify a maculopathy patient caused by new recessive compound heterozygous variants in RP1L1. METHODS: Comprehensive retinal morphological and functional examinations were evaluated for the patient with RP1L1 maculopathy. Targeted sequence capture array technique was used to screen potential pathologic variants. Polymerase chain reaction and Sanger sequencing were used to confirm the screening results. RESULTS: Fundus examination showed round macular lesions appeared in both eyes. Optical coherence tomography showed that the inner segment/outer segment continuity was disorganized and disruptive in the left eye, but it was uneven and slightly elevated in the right eye. Fundus autofluorescence showed patchy hyper-autofluorescence in the macula. Visual field examination indicates central defects in both eyes. Electroretinogram (ERG) and multifocal ERG showed no obvious abnormalities. Fundus fluorescein angiography in the macula showed obviously irregular hyper-fluorescence in the right eye and slightly hyper-fluorescence in the left eye. We found that the proband carried a missense variant (c.1972C>T) and a deletion variant (c.4717_4718del) of RP1L1, which were originated from the parents and formed compound heterozygous variants. Both variants are likely pathogenic according to the ACMG criteria. Multimodal imaging, ERG and detailed medical history are important diagnostic tools for differentiating between acquired and inherited retinal disorders. CONCLUSION: A maculopathy case with detailed retinal phenotype and new recessive compound heterozygous variants of RP1L1 is identified in a Chinese family, which expands the understanding of phenotype and genotype in RP1L1 maculopathy.

Global integrative meta-analysis of the responses in soil organic carbon stock to biochar amendment.

Applying biochar to soil has been recognized as a promising practice of climate-smart agriculture, with considerable potential in enhancing soil organic carbon (SOC) sequestration. Previous studies showed that biochar-induced increases in SOC stock varied substantially among experiments, while the explanatory factors responsible for such variability are still not well assessed. Here, we conducted an integrative meta-analysis of the magnitude and efficiency of biochar-induced change in SOC stock, using a database including 476 field measurements at 101 sites across the globe. Biochar amendment increased SOC stock by 6.13 ± 1.62 (95% confidence interval, CI) and 7.01 ± 1.11 (95% CI) Mg C ha-1, respectively, compared to their unfertilized (R0) and mineral nitrogen (N) fertilized (Rn) references. Of which approx. 52% (R0) and 50% (Rn) were contributed directly by biochar-C input. Corresponding biochar carbon efficiencies in R0 and Rn datasets were estimated as 58.20 ± 10.37% and 65.58 ± 9.26% (95% CI), respectively. The change magnitude of SOC stock increased significantly (p < 0.01) with the increasing amount of biochar-C input, while carbon efficiency of biochar showed an opposite trend. Biochar amendment sequestered larger amounts of SOC with higher efficiency in acidic and loamy soils than in alkaline and sandy soils. Biochar amendments with higher C/N ratio caused higher SOC increase than those with lower C/N ratio. Random forest (RF) algorithm showed that accumulative biochar-C input, soil pH, and biochar C/N ratio were the three most-important factors regulating the SOC stock responses. Overall, these results suggest that applying high C/N ratio biochar in acidic soils is a recommendable agricultural practice from the perspective of enhancing organic carbon.

The molecular genetics of anterior segment dysgenesis.

Anterior segment dysgenesis is a severe developmental eye disorder that leads to blindness in children. The exact mechanisms underlying this condition remain elusive. Recently, an increasing amount of studies have focused on genes and signal transduction pathways that affect anterior segment dysgenesis;these factors include transcription factors, developmental regulators, extracellular matrix genes, membrane-related proteins, cytoskeleton proteins and other associated genes. To date, dozens of gene variants have been found to cause anterior segment dysgenesis. However, there is still a lack of effective treatments. With a broader and deeper understanding of the molecular mechanisms underlying anterior segment development in the future, gene editing technology and stem cell technology may be new treatments for anterior segment dysgenesis. Further studies on the mechanisms of how different genes influence the onset and progression of anterior segment dysgenesis are still needed.

Acupuncture combined with ondansetron for prevention of postoperative nausea and vomiting in high-risk patients undergoing laparoscopic gynaecological surgery: A randomised controlled trial.

BACKGROUND: Consensus guidelines recommend the use of multiple antiemetics as prophylaxis in patients at high risk of postoperative nausea and vomiting (PONV), but the evidence regarding combining acupuncture and antiemetics as a multimodal approach was of very low quality. OBJECTIVE: This study aimed to assess the effect of combinations of acupuncture with ondansetron versus ondansetron alone for PONV prophylaxis in women at a high risk. METHODS: This parallel, randomised controlled trial was conducted in a tertiary hospital in China. Patients who had three or four PONV risk factors on the Apfel simplified risk score, undergoing elective laparoscopic gynaecological surgery for benign pathology, were recruited. Patients in the combination group received two sessions of acupuncture treatment and 8 mg intravenous ondansetron, whereas those in the ondansetron group received ondansetron alone. The primary outcome was the incidence of PONV within 24 h postoperatively. Secondary outcomes included the incidence of postoperative nausea, postoperative vomiting, adverse events etc. RESULTS: Between January and July 2021, a total of 212 women were recruited, 91 patients in the combination group and 93 patients in the ondansetron group were included in the modified intention-to-treat analysis. In the first 24 h postoperatively, 44.0% of the patients in the combination group and 60.2% of the patients in the ondansetron group experienced nausea, vomiting, or both (difference, -16.3% [95% CI, -30.5 to -2.0]; risk ratio, 0.73 [95% CI, 0.55-0.97]; p = 0.03). However, the results of the secondary outcomes showed that compared to ondansetron alone, acupuncture together with ondansetron was only effective in reducing nausea but did not have a significant impact on vomiting. The incidence of adverse events was similar between the groups. CONCLUSION: Acupuncture combined with ondansetron as a multimodal prophylaxis approach is more effective than ondansetron alone in preventing postoperative nausea in high-risk patients.

Optimized management strategy increased grain yield, promoted nitrogen balance, and improved water productivity in winter wheat.

The increasing costs of agricultural production and environmental concerns reinforce the need to reduce resource inputs. Improvements in nitrogen (N) use efficiency (NUE) and water productivity (WP) are critical for sustainable agriculture. We aimed to optimize management strategy to increase wheat grain yield, promote N balance, and improve NUE and WP. A 3-year experiment was conducted with four integrated treatments: conventional practice treatment (CP); improvement of conventional practice treatment (ICP); high-yield management treatment (HY), which aimed for maximizing grain yield regardless of resource inputs cost; and integrated soil and crop system management treatment (ISM), which aimed for testing an optimal combination of sowing date, seeding rate, and fertilization and irrigation management. The average grain yield for ISM was 95.86% of that for HY and was 5.99% and 21.72% higher than that for ICP and CP, respectively. ISM promoted N balance as relatively higher aboveground N uptake, lower inorganic N residue, and lowest inorganic N loss. The average NUE for ISM was 4.15% lower than that for ICP and was remarkably higher than that for HY and CP by 26.36% and 52.37%, respectively. The increased soil water consumption under ISM was mainly due to its increased root length density. Along with a high level of grain yield, ISM obtained a relatively adequate water supply due to the effective use of soil water storage, thereby increasing the average WP by 3.63%-38.10% in comparison with other integrated management treatments. These results demonstrated that optimized management strategy (appropriately delaying sowing date, increasing seeding rate, and optimizing fertilization and irrigation management) used under ISM could promote N balance and improve WP while increasing grain yield and NUE in winter wheat. Therefore, ISM can be considered a recommendable management strategy in the target region.

Magnitude and efficiency of straw return in building up soil organic carbon: A global synthesis integrating the impacts of agricultural managements and environmental conditions.

Enhancing soil organic carbon (SOC) through straw return (SR) has been widely recommended as a promising practice of climate-smart agriculture. Many studies have investigated the relative effect of straw return on SOC content, while the magnitude and efficiency of straw return in building up SOC stock remain uncertain. Here, we present an integrative synthesis of the magnitude and efficiency of SR-induced SOC changes, using a database comprising 327 observations at 115 sites globally. Straw return increased SOC by 3.68 ± 0.69 (95 % Confidence Interval, CI) Mg C ha-1, with a corresponding C efficiency of 20.51 ± 9.58 % (95 % CI), of which <30 % was contributed directly by straw-C input. The magnitude of SR-induced SOC changes increased (P < 0.05) with increasing straw-C input and experiment duration. However, the C efficiency decreased significantly (P < 0.01) with these two explanatory factors. No-tillage and crop rotation were found to enhance the SR-induced SOC increase, in both magnitude and efficiency. Straw return sequestrated larger amount of C in acidic and organic-rich soils than in alkaline and organic-poor soils. A machine learning random forest (RF) algorithm showed that the amount of straw-C input was the most important single factor governing the magnitude and efficiency of straw return. However, local agricultural managements and environmental conditions were together the dominant explanatory factors determining the spatial differences in SR-induced SOC stock changes. This entails that by optimizing agricultural managements in regions with favorable environmental conditions the farmer can accumulate more C with minor negative impacts. By clarifying the significance and relative importance of multiple local factors, our findings may aid the development of tailored region-specific straw return policies integrating the SOC increment and its environmental side costs.

A novel pupilloplasty in crescent-shaped suturing pattern for coloboma and traumatic iris defects.

OBJECTIVE: PURPOSE: To observe the safety and effect of the C-pupilloplasty for the treatment of iris coloboma and traumatic iris defects. METHODS: A total of 21 cases (21 eyes) with iris coloboma or traumatic iris defects who underwent C-pupilloplasty (a single-pass three-throw technique) from Feb. 2016 to Mar. 2020 were analyzed retrospectively. Uncorrected visual acuity, refraction, corneal topographic keratometry and endothelial cell density were examined. RESULTS: All the patients were successfully treated, and a central and round pupil was restored. The mean follow-up duration was 8.76 ± 3.58 months (ranging from 2 to 14 months). All patients had round or round-like pupils with a diameter less than or equal to 3 mm after the C-pupilloplasty. Very slightly endothelial loss, negligible symptoms such as glare, distortion, dizziness and photophobia were observed. CONCLUSION: We introduced a new technique of pupilloplasty (C-pupilloplasty) which could be a more straight forward and more effective treatment for iris coloboma and traumatic iris defect.

Hepatic dual-contrast CT imaging: slow triple kVp switching CT with CNN-based sinogram completion and material decomposition.

Purpose: Dual-contrast protocols are a promising clinical multienergy computed tomography (CT) application for focal liver lesion detection and characterization. One avenue to enable multienergy CT is the introduction of photon-counting detectors (PCD). Although clinical translation is highly desired because of the diagnostic benefits of PCDs, it will still be a decade or more before they are broadly available. In our work, we investigated an alternative solution that can be implemented on widely used conventional CT systems (single source and integrating detector) to perform multimaterial spectral decomposition for dual-contrast imaging. Approach: We propose to slowly alternate the x-ray tube voltage between 3 kVp levels so each kVp level covers a few degrees of gantry rotation. This leads to the challenge of sparsely sampled projection data in each energy level. Performing the material decomposition (MD) in the sinogram domain is not directly possible as the projection images of the three energy levels are not angularly aligned. In order to overcome this challenge, we developed a convolutional neural network (CNN) framework for sparse sinogram completion (SC) and MD. To evaluate the feasibility of the slow kVp switching scheme, simulation studies of an abdominal phantom, which included liver lesions, were conducted. Results: The line-integral SC network yielded sinograms with a pixel-wise RMSE < 0.05 of the line-integrals compared to the ground truth. This provided acceptable image quality up to a switching angle of 9 deg per kVp. The MD network we developed allowed us to differentiate iodine and gadolinium in the sinogram domain. The average relative quantification errors for iodine and gadolinium were below 10%. Conclusions: We developed a slow triple kVp switching data acquisition scheme and a CNN-based data processing pipeline. Results from a digital phantom validation illustrate the potential for future applications of dual-contrast agent protocols on practically available single-energy CT systems.

Responses of soil organic carbon stock to animal manure application: A new global synthesis integrating the impacts of agricultural managements and environmental conditions.

Enhancing soil organic carbon (SOC) through applying animal manure is of interest for both sustaining cereal production and mitigating greenhouse gas (GHG) emissions. Previous syntheses showed that manuring-induced SOC changes varied substantially with agricultural managements and environmental conditions, while their significance and relative importance to such variability are still largely uncertain. Here, we presented a new synthesis using an updated and balanced database integrating the manuring-induced SOC stock changes and their plausible explanatory factors in 250 observations at global 120 sites. Manure application increased SOC stock by 7.41 ± 1.14 (95% confidence interval, CI) and 8.96 ± 1.83 (95% CI) Mg C ha-1 , respectively, compared to their mineral fertilized (REF-min) and unfertilized (REF-zero) references. Of which approx. 72% and 34% were directly contributed by manure-C input, respectively. Following the IPCC (Intergovernmental Panel on Climate Change) approach, these changes corresponded to the manuring-induced SOC change factors of 1.27 ± 0.04 (95% CI) and 1.40 ± 0.08 (95% CI), respectively. Basing on a balanced database, we identified the amount of manure-C input as the most important factor to the global variations in the resultant SOC stock changes. More importantly, our integrative analysis distinguished the significance of soil properties (e.g., soil pH and initial SOC content) in regulating the efficiency of manure application in enhancing SOC stock. These results indicate that, at the similar rate, applying manure could sequestrate much more carbon in alkaline soils than in neutral and acidic soils. By integrating the impacts of agricultural managements and environmental conditions, our findings would help to develop region-specific tailor-made manure application measures in agriculture and to refine the SOC change factors for regional GHG inventories.

Exploration and validation of related hub gene expression during SARS-CoV-2 infection of human bronchial organoids.

BACKGROUND: In the novel coronavirus pandemic, the high infection rate and high mortality have seriously affected people's health and social order. To better explore the infection mechanism and treatment, the three-dimensional structure of human bronchus has been employed in a better in-depth study on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: We downloaded a separate microarray from the Integrated Gene Expression System (GEO) on a human bronchial organoids sample to identify differentially expressed genes (DEGS) and analyzed it with R software. After processing with R software, Gene Ontology (GO) and Kyoto PBMCs of Genes and Genomes (KEGG) were analyzed, while a protein-protein interaction (PPI) network was constructed to show the interactions and influence relationships between these differential genes. Finally, the selected highly connected genes, which are called hub genes, were verified in CytoHubba plug-in. RESULTS: In this study, a total of 966 differentially expressed genes, including 490 upregulated genes and 476 downregulated genes were used. Analysis of GO and KEGG revealed that these differentially expressed genes were significantly enriched in pathways related to immune response and cytokines. We construct protein-protein interaction network and identify 10 hub genes, including IL6, MMP9, IL1B, CXCL8, ICAM1, FGF2, EGF, CXCL10, CCL2, CCL5, CXCL1, and FN1. Finally, with the help of GSE150728, we verified that CXCl1, CXCL8, CXCL10, CCL5, EGF differently expressed before and after SARS-CoV-2 infection in clinical patients. CONCLUSIONS: In this study, we used mRNA expression data from GSE150819 to preliminarily confirm the feasibility of hBO as an in vitro model to further study the pathogenesis and potential treatment of COVID-19. Moreover, based on the mRNA differentiated expression of this model, we found that CXCL8, CXCL10, and EGF are hub genes in the process of SARS-COV-2 infection, and we emphasized their key roles in SARS-CoV-2 infection. And we also suggested that further study of these hub genes may be beneficial to treatment, prognostic prediction of COVID-19.

Effects of composting and carbon based materials on carbon and nitrogen loss in the arable land utilization of cow manure and corn stalks.

Recycling organic wastes to arable land as fertilizers has been recognized as a sustainable utilization to reduce environmental pollution. Techniques used for the treatment of organic wastes determine their nutrient contents and thus fertilizer efficiency for agricultural applications. The current study investigated the influences of composting and carbon based materials (biochar and woody peat), on carbon and nitrogen loss in the process of agricultural wastes utilization in the soil batch experiments. The results indicated composting process significantly strengthened the organic matter mineralization, increased the carbon loss rates from 33.46-38.96% to 60.54-86.15% and the nitrogen loss rates from 5.01-22.22% to 48.64-58.16%, dominant lost as carbon dioxide (CO2) and ammonia (NH3) emissions. Addition of carbon based materials could effectively reduce the carbon and nitrogen loss during both composting and soil incubation process. When the composted organic wastes were used in the soil batch experiments, woody peat was more effective to reduce nitrogen loss, while biochar was more effective to control carbon loss. When organic wastes were directly fertilized to soil, biochar could effectively reduce nitrogen loss. These results suggested that fertilizing raw agricultural wastes to with carbon based materials could reduce carbon and nitrogen losses, and increased the nutrient bioavailability in soil in comparison with their farmland application after composting.

[Nitrous Oxide Production in Response to Oxygen in a Solar Greenhouse Vegetable Soil].

To explore the sources of peak nitrous oxide (N2O) flushes in solar greenhouse vegetable field, an experiment was conducted with two conventional vegetable soils under different initial volume fractions of oxygen (O2) (0%, 1%, 3%, 5%, and 10%). A robotized incubation system was employed to analyze the gas kinetics[O2, N2O, nitric oxide (NO), nitrogen (N2), and carbon dioxide (CO2)] every 6 or 8 h and calculate the N2O/(NO+N2O+N2) index. Sodium chlorate (NaClO3) was used to inhibit the oxidation of NO2- to further explore the relationship between N2O and nitrite (NO2-). A parallel off-line incubation in triplicates was conducted under similar conditions to measure the dynamic changes in inorganic nitrogen content[ammonia (NH4+), nitrate (NO3-), and NO2-]. The results showed that N2O production under anaerobic condition was significantly higher than that under aerobic condition. The peak value of N2O in the soil collected from a straw-added plot (DIS) was significantly higher than that in the soil from non-straw added plot (DI) (P<0.01) when the volume fraction of oxygen was ≤ 1%. Oxygen can directly affect N2O production by delaying or inhibiting N2O reduction, with significant increase in N2O production rate under oxygen-depleted condition. However, the N2production rate decreased significantly with increase in initial oxygen volume fraction (P<0.01). When the initial volume fraction of oxygen was between 1% and 5%, a continuous accumulation of NO2- was observed during the incubation period, resulting in the significantly higher N2O/(NO+N2O+N2) index than that in either anaerobic or 10% of oxygen treatments. Furthermore, a linear correlation was observed between NO2- and N2O at 5% and 10% of oxygen with the addition of NaClO3 (R2 ≥ 0.85). Incomplete denitrification and nitrifier denitrification from NO2- induction co-occurred in the range of 1% and 5% volume fractions of oxygen, significantly increasing the soil N2O production and N2O/(NO+N2O+N2) index. In addition, N2O production under anaerobic condition was significantly higher than that under aerobic condition (P<0.01).

Abiotic nitrate loss and nitrogenous trace gas emission from Chinese acidic forest soils.

There are an increasing number of studies, which have shown the potential importance of abiotic denitrification in nitrogen biogeochemistry through pure chemical coupling between nitrate/nitrite reduction and Fe(II) oxidation. However, there is little direct evidence showing the environmental significance of abiotic nitrate (NO3-) reduction in acidic soils. We assessed the magnitude and gaseous product stoichiometry of abiotic nitrate reduction in acidic forest soils based on sterilized anoxic soil incubations at different soil pHs and nitrate loadings. The results showed that 24.9, 53.4, and 88.7% of added nitrate (70 mg N kg-1) were lost during 15 days incubation at pHs 3.9, 4.8, and 5.6, respectively. Nitrous oxide (N2O) was found as the dominant gaseous product of abiotic nitrate reduction, accounting for 5.0, 28.9, and 47.9% of nitrate losses at three pH levels, respectively. Minor but clear NO accumulations were observed for all nitrate-amended treatments, with the maxima at intermediate pH 4.8. The percentage of NO increased significantly with soil pH decline, leading to a negative correlation between NO/N2O ratio and soil pH. Though saturations were found under excessive nitrogen loading (i.e., 140 mg N kg-1), we still pose that abiotic nitrate reduction may represent a potentially important pathway for nitrate loss from acidic forest soils receiving nitrogen deposition. Our results here highlight the importance of abiotic nitrate reduction in the soil nitrogen cycle, with special relevance to nitrate removal and nitrogenous trace gas (NO and N2O) emissions from acidic soils.

Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.

Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.