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Displaying publications 21 - 26 of 26 in total

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Efficient detection of copy-number variations using exome data: Batch- and sex-based analyses

Uchiyama Y, Yamaguchi D, Iwama K, Miyatake S, Hamanaka K, Tsuchida N, et al.

Hum Mutat, 2021 01;42(1):50-65.
PMID: 33131168 DOI: 10.1002/humu.24129

Many algorithms to detect copy number variations (CNVs) using exome sequencing (ES) data have been reported and evaluated on their sensitivity and specificity, reproducibility, and precision. However, operational optimization of such algorithms for a better performance has not been fully addressed. ES of 1199 samples including 763 patients with different disease profiles was performed. ES data were analyzed to detect CNVs by both the eXome Hidden Markov Model (XHMM) and modified Nord's method. To efficiently detect rare CNVs, we aimed to decrease sequencing biases by analyzing, at the same time, the data of all unrelated samples sequenced in the same flow cell as a batch, and to eliminate sex effects of X-linked CNVs by analyzing female and male sequences separately. We also applied several filtering steps for more efficient CNV selection. The average number of CNVs detected in one sample was <5. This optimization together with targeted CNV analysis by Nord's method identified pathogenic/likely pathogenic CNVs in 34 patients (4.5%, 34/763). In particular, among 142 patients with epilepsy, the current protocol detected clinically relevant CNVs in 19 (13.4%) patients, whereas the previous protocol identified them in only 14 (9.9%) patients. Thus, this batch-based XHMM analysis efficiently selected rare pathogenic CNVs in genetic diseases.
Robotic Mounted Rail Arm System for implementing effective workplace safety for migrant workers

Wei H, Rahman MA, Hu X, Zhang L, Guo L, Tao H, et al.

Work, 2021;68(3):845-852.
PMID: 33612527 DOI: 10.3233/WOR-203418

BACKGROUND: The selection of orders is the method of gathering the parts needed to assemble the final products from storage sites. Kitting is the name of a ready-to-use package or a parts kit, flexible robotic systems will significantly help the industry to improve the performance of this activity. In reality, despite some other limitations on the complexity of components and component characteristics, the technological advances in recent years in robotics and artificial intelligence allows the treatment of a wide range of items.
OBJECTIVE: In this article, we study the robotic kitting system with a Robotic Mounted Rail Arm System (RMRAS), which travels narrowly to choose the elements.
RESULTS: The objective is to evaluate the efficiency of a robotic kitting system in cycle times through modeling of the elementary kitting operations that the robot performs (pick and room, move, change tools, etc.). The experimental results show that the proposed method enhances the performance and efficiency ratio when compared to other existing methods.
CONCLUSION: This study with the manufacturer can help him assess the robotic area performance in a given design (layout and picking a policy, etc.) as part of an ongoing project on automation of kitting operations.
Fulltext Genomic insights into the evolution of Echinochloa species as weed and orphan crop

Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, et al.

Nat Commun, 2022 02 03;13(1):689.
PMID: 35115514 DOI: 10.1038/s41467-022-28359-9

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
Contributions of climate change and human activities to grassland degradation and improvement from 2001 to 2020 in Zhaosu County, China

Zhang M, Zhang F, Guo L, Dong P, Cheng C, Kumar P, et al.

J Environ Manage, 2023 Dec 15;348:119465.
PMID: 37924697 DOI: 10.1016/j.jenvman.2023.119465

Grassland degradation poses a serious threat to biodiversity, ecosystem services, and human well-being. In this study, we investigated grassland degradation in Zhaosu County, China, between 2001 and 2020, and analyzed the impacts of climate change and human activities using the Miami model. The actual net primary productivity (ANPP) obtained with CASA (Carnegie-Ames-Stanford Approach) modeling, showed a decreasing trend, reflecting the significant degradation that the grasslands in Zhaosu County have experienced in the past 20 years. Grassland degradation was found to be highest in 2018, while the degraded area continuously decreased in the last 3 years (2018-2020). Climatic factors for found to be the dominant factor affecting grassland degradation, particularly the decrease in precipitation. On the other hand, human activities were found to be the main factor affecting improvement of grasslands, especially in recent years. This finding profoundly elucidates the underlying causes of grassland degradation and improvement and helps implement ecological conservation and restoration measures. From a practical perspective, the research results provide an important reference for the formulation of policies and management strategies for sustainable land use.
The incompatibility between industrial restructuring and low-carbon economy: a comprehensive analysis

Zhang X, Zhu H, Sang B, Guo L

Environ Sci Pollut Res Int, 2023 Aug;30(36):85611-85625.
PMID: 37389755 DOI: 10.1007/s11356-023-28316-z

Numerous studies have demonstrated that the development of low-carbon economy and industrial restructuring cannot occur in a coordinated manner. However, academic literature does not provide further explanations for this phenomenon. In this paper, we introduce a novel decomposition method to reassess the relationship between industrial restructuring and low-carbon economy, which yields similar findings. Next, we construct a straightforward theoretical model to investigate two fundamental reasons that interrelate with this issue: excessively high proportion of secondary sector and excessive carbon intensity of tertiary sector. Finally, we implement a rigorous causal identification using three-dimensional panel data at the provincial, industrial, and yearly levels by undergoing multiple robustness tests and mitigating endogeneity issues. Our heterogeneity tests suggest that the impact of industrial restructuring is greater in high-polluting industries, the Eastern region, and non-digital pilot regions. Overall, our theoretical and empirical analysis serves as a vital reference for other developing and developed countries to attain harmonious development between low-carbon economy and industrial restructuring.
Flotation separation of poly (ethylene terephthalate and vinyl chloride) mixtures based on clean corona modification: Optimization using response surface methodology

Zhao Y, Han F, Guo L, Zhang J, Zhang H, Abdelaziz IIM, et al.

Waste Manag, 2021 Dec;136:184-194.
PMID: 34689097 DOI: 10.1016/j.wasman.2021.10.018

Postconsumer polyethylene terephthalate (PET) has potential applications in many areas of manufacturing, but contamination by hazardous polyvinyl chloride (PVC) in common waste streams can reduce its recyclable value. Separating collected PET-PVC mixtures before recycling remains very challenging because of the similar physicochemical properties of PET and PVC. Herein, we describe a novel flotation process with corona modification pretreatment to facilitate the separation of PET-PVC mixtures. Through water contact angle, surface free energy, X-ray photoelectron and FT-IR characterization, we found that polar hydroxyl groups can be more easily introduced on the PVC surface than on the PET surface induced by corona modification. This selective wetting can suppress the floatability of PVC, leading to the separation of PET as floating product. A reliable mechanism including two different hydrogen-abstraction pathways was established. Response surface methodology consisting of Plackett-Burman and Box-Behnken designs was adopted for optimization of the combined process, and control parameters were solved based on high-quality prediction models, with fitting from significant variables and interactions. For physical or chemical circulation strategies with PET purity prioritization, the validated purity of the product reached 96.05% at a 626 W corona power, 5.42 m/min passing speed, 24.78 mg/L frother concentration and 286 L/h air flow rate. For the energy recuperation strategy with PET recovery prioritization, the factual recovery reached 98.08% under a 601 W corona power, 6.04 m/min passing speed, 27.55 mg/L frother concentration and 184 L/h air flow rate. The current work provides technological insights into the cleaner disposal of waste plastics.