PHE-SICH-CT-IDS: A benchmark CT image dataset for evaluation semantic segmentation, object detection and radiomic feature extraction of perihematomal edema in spontaneous intracerebral hemorrhage.

BACKGROUND AND OBJECTIVE: Intracerebral hemorrhage is one of the diseases with the highest mortality and poorest prognosis worldwide. Spontaneous intracerebral hemorrhage (SICH) typically presents acutely, prompt and expedited radiological examination is crucial for diagnosis, localization, and quantification of the hemorrhage. Early detection and accurate segmentation of perihematomal edema (PHE) play a critical role in guiding appropriate clinical intervention and enhancing patient prognosis. However, the progress and assessment of computer-aided diagnostic methods for PHE segmentation and detection face challenges due to the scarcity of publicly accessible brain CT image datasets. METHODS: This study establishes a publicly available CT dataset named PHE-SICH-CT-IDS for perihematomal edema in spontaneous intracerebral hemorrhage. The dataset comprises 120 brain CT scans and 7,022 CT images, along with corresponding medical information of the patients. To demonstrate its effectiveness, classical algorithms for semantic segmentation, object detection, and radiomic feature extraction are evaluated. The experimental results confirm the suitability of PHE-SICH-CT-IDS for assessing the performance of segmentation, detection and radiomic feature extraction methods. RESULTS: This study conducts numerous experiments using classical machine learning and deep learning methods, demonstrating the differences in various segmentation and detection methods on the PHE-SICH-CT-IDS. The highest precision achieved in semantic segmentation is 76.31%, while object detection attains a maximum precision of 97.62%. The experimental results on radiomic feature extraction and analysis prove the suitability of PHE-SICH-CT-IDS for evaluating image features and highlight the predictive value of these features for the prognosis of SICH patients. CONCLUSION: To the best of our knowledge, this is the first publicly available dataset for PHE in SICH, comprising various data formats suitable for applications across diverse medical scenarios. We believe that PHE-SICH-CT-IDS will allure researchers to explore novel algorithms, providing valuable support for clinicians and patients in the clinical setting. PHE-SICH-CT-IDS is freely published for non-commercial purpose at https://figshare.com/articles/dataset/PHE-SICH-CT-IDS/23957937.

Melatonin delayed senescence by modulating the contents of plant signalling molecules in postharvest okras.

Okra has been widely cultivated worldwide. Consumers appreciate its nutritional value and delicious taste. However, okra is very perishable after harvest because of rapid senescence and high susceptibility to mechanical injuries, which limits its storage life and reduces consumer acceptance. This study examined the influence of melatonin treatment on senescence process and endogenous plant signalling molecules in postharvest okras. The results indicated that melatonin treatment delayed senescence by increasing the endogenous melatonin content through upregulation of its biosynthetic genes. In addition, the treatment increased the contents of indole-3-acetic acid (IAA) and gibberellin (GA) due to the positive modulation of their metabolic and signalling genes. Furthermore, treated okras exhibited higher levels of γ-aminobutyric acid (GABA) but lower abscisic acid (ABA) content, contributing to the delayed senescence process compared to control. Overall, the findings suggested that melatonin postponed senescence in okras fruit by positively regulating endogenous signalling molecules such as melatonin, IAA, GABA, GA, and ABA.

Dynamical interplay between superconductivity and pseudogap in cuprates as revealed by terahertz third-harmonic generation spectroscopy.

We report on nonlinear terahertz third-harmonic generation (THG) measurements on YBa2Cu3O6+x thin films. Different from conventional superconductors, the THG signal starts to appear in the normal state, which is consistent with the crossover temperature T* of pseudogap over broad doping levels. Upon lowering the temperature, the THG signal shows an anomaly just below Tc in the optimally doped sample. Notably, we observe a beat pattern directly in the measured real-time waveform of the THG signal. We elaborate that the Higgs mode, which develops below Tc, couples to the mode already developed below T*, resulting in an energy level splitting. However, this coupling effect is not evident in underdoped samples. We explore different potential explanations for the observed phenomena. Our research offers valuable insight into the interplay between superconductivity and pseudogap.

Ultrasound synergistic slightly acidic electrolyzed water treatment of grapes: Impacts on microbial loads, wettability, and postharvest storage quality.

Microbial contamination is the principal factor in the deterioration of postharvest storage quality in grapes. To mitigate this issue, we explored a synergistic treatment which combines ultrasound (US) and slightly acidic electrolyzed water (SAEW), and rigorously compared with conventional water cleaning (CW), exclusive US treatment, and standalone SAEW treatment. The US + SAEW treatment proved to be markedly superior in reducing total bacterial, mold & yeast counts on grapes. Specifically, it achieved reductions of 2.23 log CFU/g and 2.76 log CFU/g, respectively, exceeding the efficiencies of SAEW (0.78, 0.75), US (0.58, 0.65), and CW (0.24, 0.46). The efficacy of this synergistic treatment is attributed to the ultrasound removal of the wax layer on grape skins, which transitions the skin from hydrophobic to hydrophilic. This alteration increases the contact area between the grape surface and SAEW, thereby enhancing the antimicrobial efficacy of SAEW. From a physicochemical quality standpoint, the US + SAEW treatment exhibited multiple advantages. It not only minimized weight loss, color deviations, polyphenol oxidase activity and malondialdehyde synthesis in comparison to CW-treated samples but also preserved firmness, sugar-acid ratio and the activities of key enzymes including phenylalanine ammonia-lyase, superoxide dismutase and catalase, and thus maintaining high levels of total phenolics, total ascorbic acid, total anthocyanins, and antioxidants. Consequently, US + SAEW treatment put off the times of decay onset in grapes by 12 days, outperforming both SAEW (8) and US (4) in comparison to CW. These results highlight the potential of US + SAEW as an effective strategy for maintaining grape quality during their postharvest storage period.

Abscisic acid biosynthesis, metabolism and signaling in ripening fruit.

Fruits are highly recommended nowadays in human diets because they are rich in vitamins, minerals, fibers and other necessary nutrients. The final stage of fruit production, known as ripening, plays a crucial role in determining the fruit's quality and commercial value. This is a complex physiological process, which involves many phytohormones and regulatory factors. Among the phytohormones involved in fruit ripening, abscisic acid (ABA) holds significant importance. ABA levels generally increase during the ripening process in most fruits, and applying ABA externally can enhance fruit flavor, hasten softening, and promote color development through complex signal regulation. Therefore, gaining a deeper understanding of ABA's mechanisms in fruit ripening is valuable for regulating various fruit characteristics, making them more suitable for consumption or storage. This, in turn, can generate greater economic benefits and reduce postharvest losses. This article provides an overview of the relationship between ABA and fruit ripening. It summarizes the effects of ABA on ripening related traits, covering the biochemical aspects and the underlying molecular mechanisms. Additionally, the article discusses the interactions of ABA with other phytohormones during fruit ripening, especially ethylene, and provides perspectives for future exploration in this field.

Possible Eliashberg-Type Superconductivity Enhancement Effects in a Two-Band Superconductor MgB_{2} Driven by Narrow-Band THz Pulses.

We study THz-driven condensate dynamics in epitaxial thin films of MgB_{2}, a prototype two-band superconductor (SC) with weak interband coupling. The temperature and excitation density dependent dynamics follow the behavior predicted by the phenomenological bottleneck model for the single-gap SC, implying adiabatic coupling between the two condensates on the ps timescale. The amplitude of the THz-driven suppression of condensate density reveals an unexpected decrease in pair-breaking efficiency with increasing temperature-unlike in the case of optical excitation. The reduced pair-breaking efficiency of narrow-band THz pulses, displaying minimum near ≈0.7 T_{c}, is attributed to THz-driven, long-lived, nonthermal quasiparticle distribution, resulting in Eliashberg-type enhancement of superconductivity, competing with pair breaking.

A comprehensive survey of intestine histopathological image analysis using machine vision approaches.

Colorectal Cancer (CRC) is currently one of the most common and deadly cancers. CRC is the third most common malignancy and the fourth leading cause of cancer death worldwide. It ranks as the second most frequent cause of cancer-related deaths in the United States and other developed countries. Histopathological images contain sufficient phenotypic information, they play an indispensable role in the diagnosis and treatment of CRC. In order to improve the objectivity and diagnostic efficiency for image analysis of intestinal histopathology, Computer-aided Diagnosis (CAD) methods based on machine learning (ML) are widely applied in image analysis of intestinal histopathology. In this investigation, we conduct a comprehensive study on recent ML-based methods for image analysis of intestinal histopathology. First, we discuss commonly used datasets from basic research studies with knowledge of intestinal histopathology relevant to medicine. Second, we introduce traditional ML methods commonly used in intestinal histopathology, as well as deep learning (DL) methods. Then, we provide a comprehensive review of the recent developments in ML methods for segmentation, classification, detection, and recognition, among others, for histopathological images of the intestine. Finally, the existing methods have been studied, and the application prospects of these methods in this field are given.

miR397-LACs mediated cadmium stress tolerance in Arabidopsis thaliana.

Cadmium (Cd) is a non-essential heavy metal, assimilated in plant tissue with other nutrients, disturbing the ions' homeostasis in plants. The plant develops different mechanisms to tolerate the hazardous environmental effects of Cd. Recently studies found different miRNAs that are involved in Cd stress. In the current study, miR397 mutant lines were constructed to explore the molecular mechanisms of miR397 underlying Cd tolerance. Compared with the genetically modified line of overexpressed miR397 (artificial miR397, amiR397), the lines of downregulated miR397 (Short Tandem Target Mimic miR397, STTM miR397) showed more substantial Cd tolerance with higher chlorophyll a & b, carotenoid and lignin content. ICP-OES revealed higher cell wall Cd and low total Cd levels in STTM miR397 than in the wild-type and amiR397 plants.Further, the STTM plants produced fewer reactive oxygen species (ROS) and lower activity of antioxidants enzymes (e.g., catalase [CAT], malondialdehyde [MDA]) compared with amiR397 and wild-type plants after stress, indicating that silencing the expression of miR397 can reduce oxidative damage. In addition, the different family transporters' gene expression was much higher in the amiR397 plants than in the wild type and STTM miRNA397. Our results suggest that miR397 plays a role in Cd tolerance in Arabidopsis thaliana. Overexpression of miR397 could decrease Cd tolerance in plants by regulating the expression of LAC 2/4/17, changing the lignin content, which may play an important role in inducing different stress-tolerant mechanisms and protecting the cell from a hazardous condition. This study provides a basis to elucidate the functions of miR397 and the Cd stress tolerance mechanism in Arabidopsis thaliana.

Involvement of a MYB Transcription Factor in Anthocyanin Biosynthesis during Chinese Bayberry (Morella rubra) Fruit Ripening.

Anthocyanin is a class of water-soluble flavonoids found in Chinese bayberry (Morella rubra) that is not only responsible for the variety of colors visible in nature but also has numerous health-promoting benefits in humans. Through comparative transcriptomics, we isolated and identified a transcription factor (TF) of the R2R3-MYB type, MrMYB9, in order to explore the anthocyanin biosynthesis pathway in red and white Chinese bayberries. MrMYB9 transcript was positively correlated with anthocyanin level and anthocyanin biosynthetic gene expression during Chinese bayberry fruit maturation (R-values in the range 0.54-0.84, p < 0.05). Sequence analysis revealed that MrMYB9 shared a similar R2R3 domain with MYB activators of anthocyanin biosynthesis in other plants. MrMYB9 substantially transactivated promoters of anthocyanin biosynthesis-related EBGs (MrCHI, MrF3'H, and MrANS) and LBGs (MrUFGT) upon co-expression of the AtEGL3 gene. Our findings indicated that MrMYB9 may positively modulate anthocyanin accumulation in Chinese bayberry.

Exogenous gibberellin delays maturation in persimmon fruit through transcriptional activators and repressors.

As the harvest season of most fruit is concentrated, fruit maturation manipulation is essential for the fresh fruit industry to prolong sales time. Gibberellin (GA), an important phytohormone necessary for plant growth and development, has also shown a substantial regulatory effect on fruit maturation; however, its regulatory mechanisms remain inconclusive. In this research, preharvest GA3 treatment effectively delayed fruit maturation in several persimmon (Diospyros kaki) cultivars. Among the proteins encoded by differentially expressed genes, 2 transcriptional activators (NAC TRANSCRIPTION FACTOR DkNAC24 and ETHYLENE RESPONSIVE FACTOR DkERF38) and a repressor (MYB-LIKE TRANSCRIPTION FACTOR DkMYB22) were direct regulators of GERANYLGERANYL DIPHOSPHATE SYNTHASE DkGGPS1, LYSINE HISTIDINE TRANSPORTER DkLHT1, and FRUCTOSE-BISPHOSPHATE ALDOLASE DkFBA1, respectively, resulting in the inhibition of carotenoid synthesis, outward transport of an ethylene precursor, and consumption of fructose and glucose. Thus, the present study not only provides a practical method to prolong the persimmon fruit maturation period in various cultivars but also provides insights into the regulatory mechanisms of GA on multiple aspects of fruit quality formation at the transcriptional regulation level.

Hydrogen-rich water treatment increased several phytohormones and prolonged the shelf life in postharvest okras.

Hydrogen-rich water (HRW) treatment has been reported to delay the softening and senescence of postharvest okras, but its regulatory mechanism remains unclear. In this paper, we investigated the effects of HRW treatment on the metabolism of several phytohormones in postharvest okras, which act as regulatory molecules in fruit ripening and senescence processes. The results showed that HRW treatment delayed okra senescence and maintained fruit quality during storage. The treatment upregulated all of the melatonin biosynthetic genes such as AeTDC, AeSNAT, AeCOMT and AeT5H, contributing to the higher melatonin content in the treated okras. Meanwhile, increased transcripts of anabolic genes but lower expression of catabolic genes involved in indoleacetic acid (IAA) and gibberellin (GA) metabolism were observed in okras when treated with HRW, which was related to the enhanced levels of IAA and GA. However, the treated okras experienced lower abscisic acid (ABA) content as compared to the non-treated fruit due to the down-regulation of its biosynthetic genes and up-regulation of the degradative gene AeCYP707A. Additionally, there was no difference in γ-aminobutyric acid between the non-treated and HRW-treated okras. Collectively, our results indicated that HRW treatment increased levels of melatonin, GA and IAA, but decreased ABA content, which ultimately delayed fruit senescence and prolonged shelf life in postharvest okras.

EBHI-Seg: A novel enteroscope biopsy histopathological hematoxylin and eosin image dataset for image segmentation tasks.

Background and purpose: Colorectal cancer is a common fatal malignancy, the fourth most common cancer in men, and the third most common cancer in women worldwide. Timely detection of cancer in its early stages is essential for treating the disease. Currently, there is a lack of datasets for histopathological image segmentation of colorectal cancer, which often hampers the assessment accuracy when computer technology is used to aid in diagnosis. Methods: This present study provided a new publicly available Enteroscope Biopsy Histopathological Hematoxylin and Eosin Image Dataset for Image Segmentation Tasks (EBHI-Seg). To demonstrate the validity and extensiveness of EBHI-Seg, the experimental results for EBHI-Seg are evaluated using classical machine learning methods and deep learning methods. Results: The experimental results showed that deep learning methods had a better image segmentation performance when utilizing EBHI-Seg. The maximum accuracy of the Dice evaluation metric for the classical machine learning method is 0.948, while the Dice evaluation metric for the deep learning method is 0.965. Conclusion: This publicly available dataset contained 4,456 images of six types of tumor differentiation stages and the corresponding ground truth images. The dataset can provide researchers with new segmentation algorithms for medical diagnosis of colorectal cancer, which can be used in the clinical setting to help doctors and patients. EBHI-Seg is publicly available at: https://figshare.com/articles/dataset/EBHI-SEG/21540159/1.

γ-Aminobutyric acid treatment induced chilling tolerance in postharvest kiwifruit (Actinidia chinensis cv. Hongyang) via regulating ascorbic acid metabolism.

The effect of γ-Aminobutyric acid (GABA) treatment on ascorbic acid (AsA) metabolism and chilling injury in postharvest kiwifruit was studied. The results revealed that kiwifruit treated with GABA displayed higher chilling tolerance and better quality maintenance as compared to the controls. Higher AsA was observed in GABA-treated fruit which was beneficial to cell membrane protection and damage alleviation against chilling mediated oxidative stress. Gene expression analysis found the increased expression of AsA anabolic and regenerative genes and down-regulation of its catabolic genes together could contribute to the elevation of AsA levels in kiwifruit after GABA treatment. In addition, the transcripts of several candidate transcription factors such as bHLHs and HZ1 involved in AsA biosynthesis were also enhanced by GABA treatment. Collectively, our results indicated that GABA induced chilling tolerance in postharvest kiwifruit due to the higher AsA content by positively regulating ascorbate metabolic genes and candidate transcription factors.

Hydrogen-rich water delays fruit softening and prolongs shelf life of postharvest okras.

The effect of hydrogen-rich water (HRW) treatment on softening, cell wall components and cell wall metabolic genes in okras after harvest was studied. The results showed that HRW treatment could maintain fruit firmness and delay softening, thereby prolonging shelf life in okras during storage. The treated okras displayed significantly lower levels water- and chelate-soluble pectins while higher contents of Na2CO3-soluble pectin, hemicellulose and cellulose. The cell wall biosynthesis was maintained by HRW treatment via up-regulating genes involved in biosynthesis of pectin, hemicellulose and cellulose at the beginning of storage. On the contrary, the treatment could inhibit the cell wall disassembly due to the down-regulation of numerous cell wall degradative genes including AePME, AeGAL and AeCX at the end of storage. Taken together, our results suggested that HRW treatment delayed softening and extended shelf life in postharvest okras through modifying cell wall biosynthesis and disassembly at different times of storage.

Comparative Evaluation of Quality Attributes of the Dried Cherry Blossom Subjected to Different Drying Techniques.

Choosing an appropriate drying method is crucial for producing dried cherry blossoms with desirable quality. This study is designed to assess the effects of seven different drying methods-hot-air drying (HAD), infrared hot-air drying (IHAD), catalytic infrared drying (CID), relative humidity drying (RHD), pulsed vacuum drying (PVD), microwave vacuum drying (MVD), and vacuum freeze drying (VFD)-on drying time and various attributes of cherry blossoms, such as appearance, bioactive compounds, antioxidant activity, α-glucosidase activity, and sensory properties. Our findings revealed that MVD recorded the shortest drying time, followed by PVD, CID, IHAD, RHD, HAD, and VFD. In qualities, VFD-dried petals exhibited superior appearance, bioactive compounds, antioxidant activity, and α-glucosidase inhibitory capability; MVD-dried petals were a close second. Furthermore, the quality of tea infusions prepared from the dried petals was found to be significantly correlated with the quality of the dried petals themselves. Regarding sensory attributes, VFD-dried petals produced tea infusions most similar in flavor and taste to those made with fresh petals and received the highest sensory evaluation scores, followed by MVD, PVD, RHD, CID, IHAD, and HAD. These results could offer a scientific foundation for the mass production of high-quality dried cherry blossoms in the future.

γ-Aminobutyric acid treatment induced chilling tolerance in postharvest peach fruit by upregulating ascorbic acid and glutathione contents at the molecular level.

Peach fruit was treated with 5 mM γ-aminobutyric acid (GABA) to further investigate the mechanism by which GABA induced chilling tolerance. Here, we found that GABA not only inhibited the occurrence of chilling injury in peach fruit during cold storage but also maintained fruit quality. Most of the ascorbic acid (AsA) and glutathione (GSH) biosynthetic genes were up-regulated by GABA treatment, and their levels were increased accordingly, thus reducing chilling damage in treated peaches. Meanwhile, the increased transcript of genes in the AsA-GSH cycle by GABA treatment was also related to the induced tolerance against chilling. GABA treatment also increased the expression levels of several candidate ERF transcription factors involved in AsA and GSH biosynthesis. In conclusion, our study found that GABA reduced chilling injury in peach fruit during cold storage due to the higher AsA and GSH contents by positively regulating their modifying genes and candidate transcription factors.

Membrane lipid metabolism influences chilling injury during cold storage of peach fruit.

Peach fruit is prone to chilling injury (CI) during long-term low temperature (LT) storage, and develops protective mechanisms against LT stress. This study revealed that 4 °C storage induced the occurrence of CI in peach fruit by promoting the expression of membrane lipid metabolism genes and phosphatidic acid (PA) accumulation, and stimulated a protective mechanism for peach fruit against LT by increasing diacylglycerol (DAG), triacylglycerol (TAG) and several phosphatidylcholine (PC) components in the later storage stage. In contrast, 0 °C delayed the occurrence of CI in peach fruit by delaying the degradation of phospholipids, upregulation of fatty acid desaturase (FAD) and the process of fatty acid unsaturation, and maintaining higher levels of PC and PE. Results from this study provide new information on the mechanism of CI in peach fruit, and lay the foundation for the transcriptional regulation mechanism of CI and cold tolerance in peach fruit mediated by membrane lipid metabolism.

BrpNAC895 and BrpABI449 coregulate the transcription of the afflux-type Cd transporter BrpHMA2 in Brassica parachinensis.

Brassica parachinensis is a popular leafy vegetable. It is able to accumulate high concentration of Cd, however, the molecular mechanism of Cd accumulation is unknown. This study investigated the function and regulatory mechanism of the Cd-responsive metal ion transporter gene BrpHMA2. BrpHMA2 was induced by Cd stress and specifically expressed in vascular tissues, and the protein was localized in the plasma membrane. Heterologous expression of BrpHMA2 enhanced Cd accumulation and Cd sensitivity in transgenic Arabidopsis and yeast. After Cd stress, the transcriptional factors BrpNAC895 and BrpABI449, which may recognize the ABREs in the BrpHMA2 promoter, were also differentially expressed. The transcriptional regulation of BrpHMA2 was further investigated using ChIP-qPCR, EMSA and LUC reporter activity analysis employing the transient expression system of Brassica parachinensis protoplasts and tobacco leaves and the E. coli expression system. By binding to the promoter, BrpNAC895 induced the transcription of BrpHMA2. BrpABI449 might bind to the BrpHMA2 promoter or interact with BrpNAC895 to interfere with the action of BrpNAC895. The findings suggest that BrpHMA2 is a membrane-based afflux-type Cd transporter involved in the Cd2+ uptake and long-distance transport in plants. BrpNAC895 and BrpABI449, which function as the transcription activator and repressor respectively, coregulate BrpHMA2 expression.

[Identification of laccase gene family members in peach and its relationship with chilling induced browning].

The laccase (PpLAC) gene family members in peach fruit were identified and the relationship between their expression pattern and chilling induced browning were investigated. The study was performed using two varieties of peaches with different chilling tolerance, treated with or without exogenous γ-aminobutyric acid (GABA) during cold storage. Twenty-six genes were screened from the peach fruit genome. These genes were distributed on 6 chromosomes and each contained 5-7 exons. The PpLAC gene family members shared relatively similar gene structure and conserved motifs, and they were classified into 7 subgroups based on the cluster analysis. Transcriptome sequencing revealed that the expression levels of PpLAC7 and PpLAC9 exhibited an increasing pattern under low temperature storage, and displayed a similar trend with the browning index of peach fruit. Notably, GABA treatment reduced the degree of browning and inhibited the expression of PpLAC7 and PpLAC9. These results suggested that PpLAC7 and PpLAC9 might be involved in the browning of peach fruit during cold storage.

Small RNAs encoded by human endogenous retrovirus K overexpressed in PBMCs may contribute to the diagnosis and evaluation of systemic lupus erythematosus as novel biomarkers.

This study aimed to identify the genes and small RNAs (sRNAs) expressed by the human endogenous retrovirus K (HERV-K) HML2 and their associations with the immune process of systemic lupus erythematosus (SLE). RNA-Seq data including 99 SLE patients and 18 controls (GSE72420) was obtained from the Gene Expression Omnibus. Differentially expressed genes (DEGs) as well as HML2-DEGs between SLE patients and normal controls were identified. Five HML2-DEGs involved in immune-regulating function were identified using weighted gene co-expression network analysis. The associations between these genes and the proportions of immune cells were determined by CIBERSORT. Ten candidate HML2-encoded sRNAs were identified based on specific criteria, and three of them were further validated in SLE patients by qRT-PCR. The diagnostic values of these three sRNAs were evaluated in SLE and lupus nephritis (LN). This study suggested that HML2 genes and their encoded sRNAs might be involved in the immune regulation and progress of SLE. These potential sRNAs might function as regulatory molecules and diagnostic biomarkers of SLE and LN.