Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 462
Filter
Add more filters

Publication year range
1.
Anal Chem ; 96(22): 9192-9199, 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38758357

ABSTRACT

Singlet oxygen (1O2) plays imperative roles in a variety of biotic or abiotic stresses in crops. The change of its concentration within a crop is closely related to the crop growth and development. Accordingly, there is an urgent need to develop an efficient analytical method for on-site quantitative detection of 1O2 in crops. Here, we judiciously constructed a novel ratiometric fluorescent probe, SX-2, for the detection of 1O2 in crops. Upon treating with 1O2, probe SX-2 displayed highly selective ratiometric fluorescence response, which is favorable for the quantitative detection of 1O2. Concurrently, the fluorescence solution color of probe SX-2 was varied, obviously from blue to yellow, indicating that the probe is beneficial for on-site detection by the naked eye. Sensing reaction mechanism studies showed that the 2,3-diphenyl imidazole group in SX-2 could function as a new selective recognition group for 1O2. Probe SX-2 was utilized for the detection of photoirradiation-induced 1O2 and endogenous 1O2 in living cells. The changes in the 1O2 level in zebrafish were also tracked by fluorescence imaging. In addition, the production of 1O2 in crop leaves under a light source of different wavelengths was studied. The results demonstrated more 1O2 were produced under a light source of 365 nm. Furthermore, to achieve on-site quantitative detection, a mobile fluorescence analysis device has been made. Probe SX-2 and mobile fluorescence analysis device were capable of on-site quantitative detecting of 1O2 in crops. The method developed herein will be convenient for the on-site quantitative measurement of 1O2 in distinct crops.


Subject(s)
Crops, Agricultural , Fluorescent Dyes , Singlet Oxygen , Zebrafish , Fluorescent Dyes/chemistry , Singlet Oxygen/metabolism , Singlet Oxygen/chemistry , Crops, Agricultural/chemistry , Crops, Agricultural/metabolism , Animals , Optical Imaging , Humans
2.
Bioinformatics ; 39(11)2023 11 01.
Article in English | MEDLINE | ID: mdl-37971961

ABSTRACT

SUMMARY: We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.7× to 19.8× over Kssd for the time-consuming sketch generation and distance computation on commonly used workstations. In addition, it significantly outperforms Mash, BinDash, and Dashing2. Moreover, RabbitKSSD can efficiently perform all-vs-all distance computation for all RefSeq complete bacterial genomes (455 GB in FASTA format) in just 2 min on a 64-core workstation. AVAILABILITY AND IMPLEMENTATION: RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD.


Subject(s)
Genome, Bacterial , Software , Biological Evolution
3.
Plant Physiol ; 191(1): 265-279, 2023 01 02.
Article in English | MEDLINE | ID: mdl-36047837

ABSTRACT

Cell cycle progression and the phytohormones auxin and abscisic acid (ABA) play key roles in primary root growth, but how ABA mediates the transcription of cell cycle-related genes and the mechanism of crosstalk between ABA and auxin requires further research. Here, we report that ABA inhibits primary root growth by regulating the ABA INSENSITIVE4 (ABI4)-CYCLIN-DEPENDENT KINASE B2;2 (CDKB2;2)/CYCLIN B1;1 (CYCB1;1) module-mediated cell cycle as well as auxin biosynthesis in Arabidopsis (Arabidopsis thaliana). ABA induced ABI4 transcription in the primary root tip, and the abi4 mutant showed an ABA-insensitive phenotype in primary root growth. Compared with the wild type (WT), the meristem size and cell number of the primary root in abi4 increased in response to ABA. Further, the transcription levels of several cell-cycle positive regulator genes, including CDKB2;2 and CYCB1;1, were upregulated in abi4 primary root tips. Subsequent chromatin immunoprecipitation (ChIP)-seq, ChIP-qPCR, and biochemical analysis revealed that ABI4 repressed the expression of CDKB2;2 and CYCB1;1 by physically interacting with their promoters. Genetic analysis demonstrated that overexpression of CDKB2;2 or CYCB1;1 fully rescued the shorter primary root phenotype of ABI4-overexpression lines, and consistently, abi4/cdkb2;2-cr or abi4/cycb1;1-cr double mutations largely rescued the ABA-insensitive phenotype of abi4 with regard to primary root growth. The expression levels of DR5promoter-GFP and PIN1promoter::PIN1-GFP in abi4 primary root tips were significantly higher than those in WT after ABA treatment, with these changes being consistent with changes in auxin concentration and expression patterns of auxin biosynthesis genes. Taken together, these findings indicated that ABA inhibits primary root growth through ABI4-mediated cell cycle and auxin-related regulatory pathways.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Abscisic Acid/pharmacology , Abscisic Acid/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Arabidopsis/metabolism , Cell Division , Indoleacetic Acids/metabolism , Gene Expression Regulation, Plant
4.
Opt Express ; 32(8): 13128-13139, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38859291

ABSTRACT

Silicon nanowire is a potential candidate to be used as polarization-sensitive material, but the relative mechanism of polarization response must be carried out. Herein, a sub-micron metal-single silicon nanowire-metal photodetector exhibits polarization-sensitive characteristics with an anisotropic photocurrent ratio of 1.59 at 780 nm, an excellent responsivity of 24.58 mA/W, and a high detectivity of 8.88 × 109 Jones at 980 nm. The underlying principle of optical anisotropy in silicon nanowire is attributed to resonance enhancement verified by polarizing light microscopy and simulation. Furthermore, Stokes parameter measurements and imaging are all demonstrated by detecting the characteristics of linearly polarized light and imaging the polarizer array, respectively. Given the maturity of silicon processing, the sub-micron linearly polarized light detection proposed in this study lays the groundwork for achieving highly integrated, simplified processes, and cost-effective on-chip polarization-sensitive optical chips in the future.

5.
J Exp Bot ; 75(1): 258-273, 2024 Jan 01.
Article in English | MEDLINE | ID: mdl-37721809

ABSTRACT

Intercropping improves resource utilization. Under wide-narrow-row maize (Zea mays) intercropping, maize plants are subjected to weak unilateral illumination and exhibit high photosynthetic performance. However, the mechanism regulating photosynthesis under unilateral weak light remains unknown. We investigated the relationship between photosynthesis and sugar metabolism in maize under unilateral weak light. Our results showed that the net photosynthetic rate (Pn) of unshaded leaves increased as the level of shade on the other side increased. On the contrary, the concentration of sucrose and starch and the number of starch granules in the unshaded leaves decreased with increased shading due to the transfer of abundant C into the grains. However, sink loss with ear removal reduced the Pn of unshaded leaves. Intense unilateral shade (40% to 20% normal light), but not mild unilateral shade (60% normal light), reduced grain yield (37.6% to 54.4%, respectively). We further found that in unshaded leaves, Agpsl, Bmy, and Mexl-like expression significantly influenced sucrose and starch metabolism, while Sweet13a and Sut1 expression was crucial for sugar export. In shaded leaves, expression of Sps1, Agpsl, and Sweet13c was crucial for sugar metabolism and export. This study confirmed that unshaded leaves transported photosynthates to the ear, leading to a decrease in sugar concentration. The improvement of photosynthetic performance was associated with altered sugar transport. We propose a narrow-row spacing of 40 cm, which provides appropriate unilateral shade and limits yield reduction.


Subject(s)
Photosynthesis , Zea mays , Photosynthesis/physiology , Zea mays/physiology , Plant Leaves/physiology , Starch , Sucrose
6.
BMC Cancer ; 24(1): 420, 2024 Apr 05.
Article in English | MEDLINE | ID: mdl-38580922

ABSTRACT

BACKGROUND: Clear cell carcinoma of the kidney is a common urological malignancy characterized by poor patient prognosis and treatment outcomes. Modulation of vasculogenic mimicry in tumor cells alters the tumor microenvironment and the influx of tumor-infiltrating lymphocytes, and the combination of its inducers and immune checkpoint inhibitors plays a synergistic role in enhancing antitumor effects. METHODS: We downloaded the data from renal clear cell carcinoma samples and vasculogenic mimicry-related genes to establish a new vasculogenic mimicry-related index (VMRI) using a machine learning approach. Based on VMRI, patients with renal clear cell carcinoma were divided into high VMRI and low VMRI groups, and patients' prognosis, clinical features, tumor immune microenvironment, chemotherapeutic response, and immunotherapeutic response were systematically analyzed. Finally, the function of CDH5 was explored in renal clear cell carcinoma cells. RESULTS: VMRI can be used for prognostic and immunotherapy efficacy prediction in a variety of cancers, which consists of four vasculogenic mimicry-related genes (CDH5, MMP9, MAPK1, and MMP13), is a reliable predictor of survival and grade in patients with clear cell carcinoma of the kidney and has been validated in multiple external datasets. We found that the high VMRI group presented higher levels of immune cell infiltration, which was validated by pathological sections. We performed molecular docking prediction of vasculogenic mimicry core target proteins and identified natural small molecule drugs with the highest affinity for the target protein. Knockdown of CDH5 inhibited the proliferation and migration of renal clear cell carcinoma. CONCLUSIONS: The VMRI identified in this study allows for accurate prognosis assessment of patients with renal clear cell carcinoma and identification of patient populations that will benefit from immunotherapy, providing valuable insights for future precision treatment of patients with renal clear cell carcinoma.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Humans , Molecular Docking Simulation , Carcinoma, Renal Cell/drug therapy , Carcinoma, Renal Cell/genetics , Prognosis , Kidney Neoplasms/genetics , Kidney Neoplasms/therapy , Kidney Neoplasms/pathology , Immunotherapy , Tumor Microenvironment/genetics
7.
J Neural Transm (Vienna) ; 131(4): 315-322, 2024 04.
Article in English | MEDLINE | ID: mdl-38548920

ABSTRACT

Parkinson's disease (PD) is a highly heterogeneous neurodegenerative disorder with varying clinical subtypes. Recently, a novel classification called MNCD (Motor/Non-motor/Cognition/Dependency) has been proposed, which can also include staging based on disease severity. We aim to investigate which staging, the MNCD classification and staging or Hoehn and Yahr (H&Y) staging, exhibits a stronger correlation with the 39-item Parkinson's Disease Questionnaire (PDQ-39). In a cross-sectional study conducted at our single center, 357 PD patients were recruited. Data encompassed scores from various assessments such as the Movement Disorder Society of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS) Parts I, II, III and IV, Montreal Cognitive Assessment (MoCA), PDQ-39, and the H&Y scale. The mean age of these patients was 66.4 ± 9.1 years old, and the majority (54.6%) were male. MNCD stages: stage 1 (N = 3, 0.8%), stage 2 (N = 62, 17.4%), stage 3 (N = 187, 52.4%), stage 4 (N = 86, 24.1%), and stage 5 (N = 19, 5.3%). The top 5 most frequent PD-related clinical symptoms were sleep disturbances (89.6%), fatigue (69.7%), mild cognitive impairment (68.9%), constipation (65.8%), and postural instability (65.5%). The PDQ-39 demonstrated a positive correlation with both MNCD staging and H&Y staging. Moreover, the MNCD staging exhibited a stronger correlation with PDQ-39 compared to H&Y staging. The correlation between the MNCD classification and staging with the quality of life in PD patients is more statistically significant compared to the H&Y staging.


Subject(s)
Parkinson Disease , Humans , Male , Female , Middle Aged , Aged , Parkinson Disease/diagnosis , Quality of Life/psychology , Cross-Sectional Studies , Severity of Illness Index , Fatigue
8.
Methods ; 216: 39-50, 2023 08.
Article in English | MEDLINE | ID: mdl-37330158

ABSTRACT

Assessing the quality of sequencing data plays a crucial role in downstream data analysis. However, existing tools often achieve sub-optimal efficiency, especially when dealing with compressed files or performing complicated quality control operations such as over-representation analysis and error correction. We present RabbitQCPlus, an ultra-efficient quality control tool for modern multi-core systems. RabbitQCPlus uses vectorization, memory copy reduction, parallel (de)compression, and optimized data structures to achieve substantial performance gains. It is 1.1 to 5.4 times faster when performing basic quality control operations compared to state-of-the-art applications yet requires fewer compute resources. Moreover, RabbitQCPlus is at least 4 times faster than other applications when processing gzip-compressed FASTQ files and 1.3 times faster with the error correction module turned on. Furthermore, it takes less than 4 minutes to process 280 GB of plain FASTQ sequencing data, while other applications take at least 22 minutes on a 48-core server when enabling the per-read over-representation analysis. C++ sources are available at https://github.com/RabbitBio/RabbitQCPlus.


Subject(s)
Data Compression , Software , High-Throughput Nucleotide Sequencing , Quality Control , Algorithms , Sequence Analysis, DNA
9.
Appl Opt ; 63(9): 2241-2247, 2024 Mar 20.
Article in English | MEDLINE | ID: mdl-38568578

ABSTRACT

For conventional refractive lenses, chromatic aberration inevitably occurs due to the refractive index variation of the lens material with the incident wavelength, leading to axial aberrations and lower imaging system quality. Achromatic metalenses have demonstrated a great capability to solve this problem and been extensively investigated. However, the metalens achromatic method involves construction of a unit structure satisfying a phase distribution greater than 0-2π or phase compensation. Although this design method can obtain a good achromatic effect, finding a unit that satisfies a linear distribution during design is difficult. In this paper, we use subregion discrete wavelength modulation to achieve broadband achromatism. The total number of structural units in each region is optimized for different incident wavelengths, and the internal and external ring unit structures are also optimized. This achromatic metalens exhibits a large aperture and a high numerical aperture in the 4.2-4.7 µm mid-infrared band (NA = 0.83). Our research has strong potential and application prospects in ultracompact imaging and laser beam shaping.

10.
BMC Public Health ; 24(1): 107, 2024 01 06.
Article in English | MEDLINE | ID: mdl-38184557

ABSTRACT

OBJECTIVE: Tobacco has been identified as a significant contributory element to the development of breast cancer. Our objective was to evaluate the spatiotemporal trends of tobacco-related breast cancer at the global, regional, and national scales during 1990-2019. METHODS: We extracted data on mortality, disability adjusted of life years (DALYs), age-standardized mortality rate (ASMR), and age-standardized DALYs rate (ASDR) from the Global Burden of Disease (GBD) study 2019. Estimated annual percentage change (EAPC) was computed to assess the temporal change in ASDR and ASMR. RESULTS: In 2019, the deaths and DALYs attributed to tobacco-related breast cancer were estimated to be 35,439 (95% UI: 22,179-48,119) and 1,060,590 (95% UI: 622,550-1,462,580), respectively. These figures accounted for 5.1% and 5.2% of the total burden of breast cancer. ASMR and ASDR increased in low SDI regions, remained stable in low-middle and middle SDI regions and declined in high and high-middle SDI regions. The burden of breast cancer attributable to tobacco varied notably among regions and nations. Oceania, Southern Latin America, and Central Europe were the GBD regions with the highest number of ASMR and DALYs. There was a positive relationship between age-standardized rate and SDI value in 2019 across 204 nations or territories. A negative association was observed between the EAPC in ASMR or ASDR and the human development index (HDI) in 2019 (R = -0.55, p < 0.01 for ASMR; R = -0.56, p < 0.01 for ASDR). CONCLUSION: Tobacco is one important and modifiable risk factor for breast cancer. The heterogeneity in both the spatial and temporal distribution can be attributed to factors such as aging, population growth, and SDI. These findings substantiate the necessity of expediting the enforcement of tobacco-free legislation in order to safeguard populations from the detrimental effects of tobacco.


Subject(s)
Breast Neoplasms , Humans , Female , Breast Neoplasms/epidemiology , Breast Neoplasms/etiology , Global Burden of Disease , Cost of Illness , Breast , Tobacco Products
11.
J Integr Plant Biol ; 66(5): 909-927, 2024 May.
Article in English | MEDLINE | ID: mdl-38328870

ABSTRACT

Transcriptional regulation plays a key role in the control of seed dormancy, and many transcription factors (TFs) have been documented. However, the mechanisms underlying the interactions between different TFs within a transcriptional complex regulating seed dormancy remain largely unknown. Here, we showed that TF PHYTOCHROME-INTERACTING FACTOR4 (PIF4) physically interacted with the abscisic acid (ABA) signaling responsive TF ABSCISIC ACID INSENSITIVE4 (ABI4) to act as a transcriptional complex to promote ABA biosynthesis and signaling, finally deepening primary seed dormancy. Both pif4 and abi4 single mutants exhibited a decreased primary seed dormancy phenotype, with a synergistic effect in the pif4/abi4 double mutant. PIF4 binds to ABI4 to form a heterodimer, and ABI4 stabilizes PIF4 at the protein level, whereas PIF4 does not affect the protein stabilization of ABI4. Subsequently, both TFs independently and synergistically promoted the expression of ABI4 and NCED6, a key gene for ABA anabolism. The genetic evidence is also consistent with the phenotypic, physiological and biochemical analysis results. Altogether, this study revealed a transcriptional regulatory cascade in which the PIF4-ABI4 transcriptional activator complex synergistically enhanced seed dormancy by facilitating ABA biosynthesis and signaling.


Subject(s)
Abscisic Acid , Arabidopsis Proteins , Arabidopsis , Gene Expression Regulation, Plant , Plant Dormancy , Signal Transduction , Transcription Factors , Abscisic Acid/metabolism , Abscisic Acid/pharmacology , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Arabidopsis/metabolism , Arabidopsis/genetics , Plant Dormancy/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Protein Binding , Seeds/metabolism , Seeds/genetics , Mutation/genetics
12.
Neurobiol Dis ; 185: 106254, 2023 09.
Article in English | MEDLINE | ID: mdl-37558169

ABSTRACT

BACKGROUND: Presently, neurotransmitter deficits in GBA-related Parkinson's disease (GBA-PD) and relationships with cognitive impairment are poorly understood. A better understanding of neurotransmitter impairments in GBA-PD - particularly in the newly diagnosed drug-naïve phase - may support developing targeted intervention strategies. We aimed to investigate patterns of neurotransmitter deficits in GBA-PD and idiopathic PD (iPD) and cognitive performance correlations. METHODS: We recruited 189 newly diagnosed PD patients for GBA sequencing. Voxel-wise gray matter volume (GMV) was evaluated in a subgroup of 17 GBA-PD, 100 iPD, and 32 age- and sex-matched healthy controls (HCs). The JuSpace toolbox covering various neurotransmitter maps helped assess whether the spatial patterns of GMV alterations in GBA-PD or iPD patients (relative to HCs) were associated with specific neurotransmitter systems. RESULTS: GBA-PD patients indicated widespread GM atrophy in the fronto-temporal-occipital region compared with HCs. GMV atrophy was spatially correlated in GBA-PD and iPD with serotonergic, dopaminergic, and acetylcholinergic pathway distributions (p < 0.05, false discovery rate corrected). Executive function and language in cognitive domains were also associated with the strength of GMV colocalization of serotonergic, dopaminergic, and acetylcholinergic circuits. CONCLUSIONS: Regional GM atrophy related to specific neurotransmitter deficits in de novo GBA-PD and iPD patients could provide new insights into pathophysiological processes, facilitating potential therapeutic targets to support PD management.


Subject(s)
Cognitive Dysfunction , Parkinson Disease , Humans , Cognitive Dysfunction/pathology , Gray Matter/pathology , Temporal Lobe , Atrophy/pathology , Magnetic Resonance Imaging
13.
Eur J Neurosci ; 58(11): 4371-4383, 2023 12.
Article in English | MEDLINE | ID: mdl-37857484

ABSTRACT

Growing evidence supports that depression in Parkinson's disease (PD) depends on disruptions in specific neural networks rather than regional dysfunction. According to the resting-state functional magnetic resonance imaging data, the study attempted to decipher the alterations in the topological properties of brain networks in de novo depression in PD (DPD). The study also explored the neural network basis for depressive symptoms in PD. We recruited 20 DPD, 37 non-depressed PD and 41 healthy controls (HC). The Graph theory and network-based statistical methods helped analyse the topological properties of brain functional networks and anomalous subnetworks across these groups. The relationship between altered properties and depression severity was also investigated. DPD revealed significantly reduced nodal efficiency in the left superior temporal gyrus. Additionally, DPD decreased five hubs, primarily located in the temporal-occipital cortex, and increased seven hubs, mainly distributed in the limbic cortico-basal ganglia circuit. The betweenness centrality of the left Medio Ventral Occipital Cortex was positively associated with depressive scores in DPD. In contrast to HC, DPD had a multi-connected subnetwork with significantly lower connectivity, primarily distributed in the visual, somatomotor, dorsal attention and default networks. Regional topological disruptions in the temporal-occipital region are critical in the DPD neurological mechanism. It might suggest a potential network biomarker among newly diagnosed DPD patients.


Subject(s)
Connectome , Parkinson Disease , Humans , Parkinson Disease/diagnostic imaging , Depression/diagnostic imaging , Brain/diagnostic imaging , Basal Ganglia , Magnetic Resonance Imaging
14.
BMC Plant Biol ; 23(1): 438, 2023 Sep 19.
Article in English | MEDLINE | ID: mdl-37726682

ABSTRACT

Intercropping can obtain yield advantages, but the mechanism of yield advantages of maize-legume intercropping is still unclear. Then, we explored the effects of cropping systems and N input on yield advantages in a two-year experiment. Cropping systems included monoculture maize (Zea mays L.) (MM), monoculture soybean (Glycine max L. Merr.) (MS), monoculture peanut (Arachis hypogaea L.) (MP), maize-soybean substitutive relay intercropping (IMS), and maize-peanut substitutive strip intercropping (IMP). N input included without N (N0) and N addition (N1). Results showed that maize's leaf area index was 31.0% and 34.6% higher in IMS and IMP than in MM. The specific leaf weight and chlorophyll a (chl a) of maize were notably higher by 8.0% and 18.8% in IMS, 3.1%, and 18.6% in IMP compared with MM. Finally, N addition resulted in a higher thousand kernels weight of maize in IMS and IMP than that in MM. More dry matter accumulated and partitioned to the grain, maize's averaged partial land equivalent ratio and the net effect were 0.76 and 2.75 t ha-1 in IMS, 0.78 and 2.83 t ha-1 in IMP. The leaf area index and specific leaf weight of intercropped soybean were 16.8% and 26% higher than MS. Although soybean suffers from shade during coexistence, recovered growth strengthens leaf functional traits and increases dry matter accumulation. The averaged partial land equivalent ratio and the net effect of intercropped soybean were 0.76 and 0.47 t ha-1. The leaf area index and specific leaf weight of peanuts in IMP were 69.1% and 14.4% lower than in the MP. The chlorophyll a and chlorophyll b of peanut in MP were 17.0% and 24.4% higher than in IMP. A less dry matter was partitioned to the grain for intercropped peanut. The averaged pLER and NE of intercropped peanuts were 0.26 and -0.55 t ha-1. In conclusion, the strengthened leaf functional traits promote dry matter accumulation, maize-soybean relay intercropping obtained a win-win yield advantage, and maize-peanut strip intercropping achieved a trade-off yield advantage.


Subject(s)
Fabaceae , Zea mays , Chlorophyll A , Vegetables , Glycine max , Arachis , Plant Leaves , Edible Grain
15.
Bioinformatics ; 38(10): 2932-2933, 2022 05 13.
Article in English | MEDLINE | ID: mdl-35561184

ABSTRACT

MOTIVATION: Detection and identification of viruses and microorganisms in sequencing data plays an important role in pathogen diagnosis and research. However, existing tools for this problem often suffer from high runtimes and memory consumption. RESULTS: We present RabbitV, a tool for rapid detection of viruses and microorganisms in Illumina sequencing datasets based on fast identification of unique k-mers. It can exploit the power of modern multi-core CPUs by using multi-threading, vectorization and fast data parsing. Experiments show that RabbitV outperforms fastv by a factor of at least 42.5 and 14.4 in unique k-mer generation (RabbitUniq) and pathogen identification (RabbitV), respectively. Furthermore, RabbitV is able to detect COVID-19 from 40 samples of sequencing data (255 GB in FASTQ format) in only 320 s. AVAILABILITY AND IMPLEMENTATION: RabbitUniq and RabbitV are available at https://github.com/RabbitBio/RabbitUniq and https://github.com/RabbitBio/RabbitV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
COVID-19 , Viruses , Algorithms , High-Throughput Nucleotide Sequencing , Humans , Sequence Analysis, DNA , Software , Viruses/genetics
16.
Mov Disord ; 38(5): 774-782, 2023 05.
Article in English | MEDLINE | ID: mdl-36947674

ABSTRACT

BACKGROUND: Substantia nigra (SN) free water has been suggested as a good surrogate marker in Parkinson's disease (PD). However, its usefulness for diagnosing prodromal PD (pPD) and monitoring disease progression warrants further validation. OBJECTIVE: The aim was to investigate SN free water values across prodromal and clinical stages of PD. METHODS: Four groups were enrolled in this study: 48 healthy controls (HC), 43 pPD patients, 50 de novo PD (dnPD) patients, and 49 medicated PD (mPD) patients. Based on diffusion tensor images, free water maps were calculated, and SN free water values were extracted from the anterior SN (ASN) and posterior SN (PSN). The SN free water values were compared among the four groups, and associations between free water and clinical symptoms were explored. The distinguishing power of PSN free water was evaluated using the receiver operating characteristic curve analysis. Follow-up was performed for 14 pPD patients. RESULTS: PSN free water in the pPD group was significantly higher than that in the HC group and significantly lower than that in the dnPD group. Surprisingly, the mPD group showed decreased PSN free water compared to the dnPD group. There was a positive correlation between motor symptoms and PSN free water in the pPD and dnPD groups. Longitudinal analysis showed a significant increase in PSN free water in pPD patients over time. CONCLUSIONS: The PSN free water increased from prodromal to early clinical stages, but the trend might be reversed in late disease stages. This biphasic trend should be considered when applying this marker in future studies. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.


Subject(s)
Parkinson Disease , Prodromal Symptoms , Substantia Nigra , Female , Humans , Male , Middle Aged , Diffusion Tensor Imaging , Monitoring, Physiologic/methods , Parkinson Disease/diagnostic imaging , Substantia Nigra/diagnostic imaging , Water
17.
Rapid Commun Mass Spectrom ; 37(4): e9450, 2023 Feb 28.
Article in English | MEDLINE | ID: mdl-36478616

ABSTRACT

RATIONALE: Gas chromatography-combustion-isotope ratio mass spectrometry (GC/C/IRMS) is widely used for compound-specific carbon isotopic analysis. However, current isotopic analysis systems utilize the GC IsoLink combustion reactor, and independent reduction furnaces are not implemented. Therefore, whether this limitation in furnace use affects the precision of compound-specific carbon isotopic analysis needs to be evaluated. METHODS: We attempted to add a separate reduction furnace to the GC IsoLink interface and compared the δ13 C values of n-alkanes (including C and H elements), fatty acid methyl ester (including C, H, and O elements), caffeine (USGS61 and USGS62, including C, H, O, and N elements), and 9-ethylcarbazole (including C, H, and N elements) before and after the addition of the reduction furnace using the GC IsoLink combustion reactor. RESULTS: For n-alkanes and fatty acid methyl esters, the δ13 C differences between the measured values and their standard values were basically falling within 0.5‰ whether or not an independent reduction furnace was added. However, for the nitrogen-containing compounds (caffeine and 9-ethylcarbazole), the δ13 C differences between the measured values and their standard values were much larger without an independent reduction furnace (1.0-3.71‰ for USGS61, 1.78-2.19‰ for USGS62, and 0.39-1.13‰ for 9-ethylcarbazole) than with a reduction furnace (-0.31-0.68‰ for USGS61, -0.44-0.06‰ for USGS62, and -0.04-0.25‰ for 9-ethylcarbazole). CONCLUSIONS: The addition of an independent reduction furnace had no significant effect on the δ13 C of n-alkanes and fatty acid methyl esters, but it had a significant effect on the δ13 C of nitrogen-containing compounds. It is suggested that GC IsoLink needs an independent reduction furnace to effectively eliminate the interference of NOx on CO2 isotopic determination to improve the accuracy of δ13 C for nitrogen-containing compounds.


Subject(s)
Caffeine , Nitrogen , Carbon Isotopes/analysis , Reproducibility of Results , Gas Chromatography-Mass Spectrometry/methods , Alkanes/analysis
18.
Proc Natl Acad Sci U S A ; 117(52): 33005-33010, 2020 Dec 29.
Article in English | MEDLINE | ID: mdl-33323486

ABSTRACT

Anthropogenic combustion-derived water (CDW) may accumulate in an airshed due to stagnant air, which may further enhance the formation of secondary aerosols and worsen air quality. Here we collected three-winter-season, hourly resolution, water-vapor stable H and O isotope compositions together with atmospheric physical and chemical data from the city of Xi'an, located in the Guanzhong Basin (GZB) in northwestern China, to elucidate the role of CDW in particulate pollution. Based on our experimentally determined water vapor isotope composition of the CDW for individual and weighted fuels in the basin, we found that CDW constitutes 6.2% of the atmospheric moisture on average and its fraction is positively correlated with [PM2.5] (concentration of particulate matter with an aerodynamic diameter less than 2.5 µm) as well as relative humidity during the periods of rising [PM2.5]. Our modeling results showed that CDW added additional average 4.6 µg m-3 PM2.5 during severely polluted conditions in the GZB, which corresponded to an average 5.1% of local anthropogenic [PM2.5] (average at ∼91.0 µg m-3). Our result is consistent with the proposed positive feedback between the relative humidity and a moisture sensitive air-pollution condition, alerting to the nontrivial role of CDW when considering change of energy structure such as a massive coal-to-gas switch in household heating in winter.

19.
Sensors (Basel) ; 23(16)2023 Aug 08.
Article in English | MEDLINE | ID: mdl-37631557

ABSTRACT

The autonomous driving technology based on deep reinforcement learning (DRL) has been confirmed as one of the most cutting-edge research fields worldwide. The agent is enabled to achieve the goal of making independent decisions by interacting with the environment and learning driving strategies based on the feedback from the environment. This technology has been widely used in end-to-end driving tasks. However, this field faces several challenges. First, developing real vehicles is expensive, time-consuming, and risky. To further expedite the testing, verification, and iteration of end-to-end deep reinforcement learning algorithms, a joint simulation development and validation platform was designed and implemented in this study based on VTD-CarSim and the Tensorflow deep learning framework, and research work was conducted based on this platform. Second, sparse reward signals can cause problems (e.g., a low-sample learning rate). It is imperative for the agent to be capable of navigating in an unfamiliar environment and driving safely under a wide variety of weather or lighting conditions. To address the problem of poor generalization ability of the agent to unknown scenarios, a deep deterministic policy gradient (DDPG) decision-making and planning method was proposed in this study in accordance with a multi-task fusion strategy. The main task based on DRL decision-making planning and the auxiliary task based on image semantic segmentation were cross-fused, and part of the network was shared with the main task to reduce the possibility of model overfitting and improve the generalization ability. As indicated by the experimental results, first, the joint simulation development and validation platform built in this study exhibited prominent versatility. Users were enabled to easily substitute any default module with customized algorithms and verify the effectiveness of new functions in enhancing overall performance using other default modules of the platform. Second, the deep reinforcement learning strategy based on multi-task fusion proposed in this study was competitive. Its performance was better than other DRL algorithms in certain tasks, which improved the generalization ability of the vehicle decision-making planning algorithm.

20.
Fa Yi Xue Za Zhi ; 39(6): 564-570, 2023 Dec 25.
Article in English, Zh | MEDLINE | ID: mdl-38228475

ABSTRACT

OBJECTIVES: To establish a method for the simultaneous quantitative analysis of etomidate and its metabolite etomidate acid in blood, and to discuss its application value in actual cases. METHODS: Acetonitrile precipitate protein method was used, and C18 column was selected. Gradient elution was performed with acetonitrile and 5 mmol/L ammonium acetate within 6 min. Electrospray ionization source in positive ion mode was used. The internal standard etomidate acid-d5 was obtained by etomidate-d5 alkaline hydrolysis reaction. Ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used for quantitative analysis. The methodological verification was conducted. RESULTS: Etomidate and etomidate acid in blood showed good linear relationship in the quantitative linear range (r>0.999), with the lower limit of quantification was 2.5 ng/mL and 7.5 ng/mL, respectively. The accuracy, precision, recovery rate, and matrix effect of the method met the professional verification standards. The practical application results showed that etomidate and etomidate acid could be detected in the blood of the abusers, and their mass concentrations ranged from 17.24 to 379.93 ng/mL. CONCLUSIONS: The method established in this study can simultaneously quantify etomidate and etomidate acid in blood, which is simple and convenient to operate with accuracy. It can meet the detection needs of actual cases and provide technical support for law enforcement to crack down on etomidate abuse.


Subject(s)
Etomidate , Chromatography, High Pressure Liquid/methods , Chromatography, Liquid , Tandem Mass Spectrometry/methods , Liquid Chromatography-Mass Spectrometry , Acetonitriles
SELECTION OF CITATIONS
SEARCH DETAIL