Miracle-dz/UniFAR-FTUs huggingface dataset:
Third Generation Genome Sequencing Reveals That Endobacteria in Nematophagous Fungi Esteya vermicola Contain Multiple Genes Encoding for Nematicidal Proteins

Esteya vermicola is the first recorded endoparasitic nematophagous fungus with high infectivity capacity, attacking the pinewood nematode Bursaphelenchus xylophilus which causes pine wilt disease. Endosymbionts are found in the cytoplasm of E. vermicola from various geographical areas. We sequenced the genome of endobacteria residing in E. vermicola to discover possible biological functions of these widespread endobacteria. Multilocus phylogenetic analyses showed that the endobacteria form a previously unidentified lineage sister to Phyllobacterium myrsinacearum species. The number of genes in the endobacterium was 4542, with 87.8% of the proteins having a known function. It contained a high proportion of repetitive sequences, as well as more Acyl-CoA synthetase genes and genes encoding the electron transport chain, compared with compared with plant-associated P. zundukense Tri 48 and P. myrsinacearum DSM 5893. Thus, this symbiotic bacterium is likely to be more efficient in regulating gene expression and energy release. Furthermore, the endobacteria in nematophagous fungi Esteya vermicola contained multiple nematicidal subtilase/subtilisin encoding genes, so it is likely that endobacteria cooperate with the host to kill nematodes.
Apple Disease Recognition Based on Convolutional Neural Networks With Modified Softmax

Accurate and rapid identification of apple diseases is the basis for preventing and treating the apple diseases, and is very significant for assessing disease disaster. Apple disease recognition from its diseased leaf images is one of the interesting research areas in computer and agriculture field. An apple disease recognition method is proposed based on modified convolutional neural networks (MCNN). In MCNN, Inception is introduced into MCNN, global average pooling (GAP) operator is employed instead of several fully connected layers to speedup training model, and modified Softmax classifier is used in the output layer to improve the recognition performance. The modified Softmax classifier uses the modified linear element as the activation function in the hidden layer and adds the local response normalization in MCNN to avoid the gradient disappearance problem effectively. A series of experiments are conducted on two kinds of apple disease image datasets. The results show the feasibility of the algorithm.
Prevalence of Helicobacter pylori in Non-Cardia Gastric Cancer in China: A Systematic Review and Meta-Analysis

Non-cardia gastric cancer was significantly associated with Helicobacter pylori (H. pylori) infection. Reducing H. pylori prevalence was an important prevention strategy for non-cardia gastric cancer. However, national-level data on the H. pylori prevalence in non-cardia gastric cancer were limited in China. Therefore, we conducted this study to estimate the pooled prevalence of H. pylori in non-cardia gastric cancer in China. We searched PubMed, Embase, the Cochrane Library, China National Knowledge Infrastructure (CNKI), Wan Fang, and VIP Database for Chinese Technical Periodicals for studies reporting H. pylori prevalence in non-cardia gastric cancer in China which were published before September 1, 2021. Pooled prevalence was calculated using a random-effect model. Subgroup analysis and meta-regression were used to explore the potential sources of heterogeneity. Egger’s test and funnel plot were used to assess publication bias. A total number of 55 studies with 5324 cases of non-cardia gastric cancer were included in this study. The pooled prevalence of H. pylori in non-cardia gastric cancer in China was 66.5% (95%CI: 62%-71%, I2=93.8%, P<0.0001). In subgroup analysis, a significant difference in the prevalence of H. pylori in non-cardia gastric cancer was noted when stratified by geographic region of China (P=0.0112). The highest H. pylori prevalence (78.9%, 95%CI: 69.9%-87.8%) was noted in Northwest China and the lowest (53.1%, 95%CI: 38.9%-67.3%) was in North China. In meta-regression, a significant association between H. pylori prevalence and geographic region was found, while type of sample, H. pylori testing method, diagnosis period, detection timing, type of study design, quality grade, publication year, and sample size were not associated with the prevalence of H. pylori in non-cardia gastric cancer (P>0.05). A large proportion of non-cardia gastric cancers were associated with H. pylori infection in China, emphasizing the possible benefits of H. pylori eradication for the prevention and control of non-cardia gastric cancer.
Workplace Mental Health Interventions in India: A Rapid Systematic Scoping Review

The mental health initiatives at the workplace are growing in numbers over the past few years. Public and private sectors continue to explore avenues to navigate and adapt initiatives to promote employee's mental wellbeing. However, such initiatives in the Indian context are not thoroughly studied. We attempted to review existing literature on workplace mental health interventions in the Indian context. The scoping review was conducted following the standard process as recommended by the Joanna Briggs Institute and the Preferred Reporting Items for Systematic Review and Meta-Analysis extension for scoping reviews. We searched in the databases such as PubMed, Google Scholar and Scopus. Scientific literature including gray literature of the past decade was searched to synthesize evidence on types of mental health interventions and their unique features. Of the 1,311 records, 30 records that met the inclusion criteria were included for the final review. The review highlights evidence on stress and mental health problems faced by the working population and various strategies adopted by organizations to address mental health problems. However, very few interventions were accompanied by comprehensive needs assessment, impact evaluation and workplace policy initiatives. Most interventions were curative–provisioning counseling services, limiting the scope of mental health promotion activities. Addressing mental health wellbeing comprehensively and aligning an organization's policies are crucial. Research on employee mental health, its risk factors, and cost-effectiveness analysis of workplace mental health interventions in the Indian context need to be prioritized.
Comparative Genomics of Prunus-Associated Members of the Pseudomonas syringae Species Complex Reveals Traits Supporting Co-evolution and Host Adaptation

Members of the Pseudomonas syringae species complex cause symptoms that are ranging from leaf spots to cankers on a multitude of plant species, including some of the genus Prunus. To date, a total of two species of the P. syringae species complex and six different pathovars have been associated with diseases on Prunus spp. , which were shown to belong to different phylogenetic units (phylogroups, PG) based on sequence similarity of housekeeping genes or whole genomes, suggesting that virulence to Prunus spp. may be the result of convergent pathoadaptation. In this study, a comparative genomics approach was used to determine genes significantly associated with strains isolated from Prunus spp. across a phylogeny of 97 strains belonging to the P. syringae species complex. Our study revealed the presence of a set of orthologous proteins which were significantly associated with strains isolated from Prunus spp. than in strains isolated from other hosts or from non-agricultural environments. Among them, the type III effector HopAY predicted to encode for a C58 cysteine protease was found to be highly associated with strains isolated from Prunus spp. and revealed patterns supporting co-evolution and host adaptation.
3D Imaging Segmentation and 3D Rendering Process for a Precise Puncture Strategy During PCNL – a Pilot Study

Percutaneous nephrolithotomy (PCNL) is frequently used as the first-line treatment of large and complex stones. The key point for successful complex stone removal with minimal risk of complications is to establish the most appropriate access route. Understanding the three-dimensional (3D) relationship of kidney stones and renal collecting systems is crucial for planning and creating an optimal access route. By using a 3D volume segmentation tool a more accurate approach to the renal collecting system and stone treatment could be planned. The objective of this study was assessing the impact of 3D software in getting the desired access.
The Levels of Oxidized Phospholipids in High-Density Lipoprotein During the Course of Sepsis and Their Prognostic Value

Purpose To examine the levels of 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero phosphatidylcholine (POVPC) and 1-palmitoyl-2-glutaroyl-sn-glycero-phosphatidylcholine (PGPC) (the oxidized phosphatidylcholines) in HDL during the course of sepsis and to evaluate their prognostic value. Materials and Methods This prospective cohort pilot study enrolled 25 septic patients and 10 healthy subjects from 2020 to 2021. The HDLs were extracted from patient plasmas at day 1, 3 and 7 after sepsis onset and from healthy plasmas (total 81 plasma samples). These HDLs were then subjected to examining POVPC and PGPC by using an ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) system. We further measured the levels of 38 plasma cytokines by Luminex and evaluated the correlation of HDL-POVPC level with these cytokines. Patients were further stratified into survivors and non-survivors to analyze the association of HDL-POVPC level with 28-day mortality. Results Septic patients exhibited significant increase of HDL-POVPC at day 1, 3 and 7 after sepsis onset (POVPC-D1, p=0.0004; POVPC-D3, p=0.033; POVPC-D7, p=0.004, versus controls). HDL-PGPC was detected only in some septic patients (10 of 25) but not in healthy controls. Septic patients showed a significant change of the plasma cytokines profile. The correlation assay showed that IL-15 and IL-18 levels were positively correlated with HDL-POVPC level, while the macrophage-derived chemokine (MDC) level was negatively correlated with HDL-POVPC level. Furthermore, HDL-POVPC level in non-survivors was significantly increased versus survivors at day 1 and 3 (POVPC-D1, p=0.002; POVPC-D3, p=0.003). Area under ROC curves of POVPC-D1 and POVPC-D3 in predicting 28-day mortality were 0.828 and 0.851. POVPC-D1and POVPC-D3 were the independent risk factors for the death of septic patients (p=0.046 and 0.035). Conclusions HDL-POVPC was persistently increased in the course of sepsis. POVPC-D1 and POVPC-D3 were significantly correlated with 28-mortality and might be valuable to predict poor prognosis.
Coxiella Endosymbiont of Rhipicephalus microplus Modulates Tick Physiology With a Major Impact in Blood Feeding Capacity

In the past decade, metagenomics studies exploring tick microbiota have revealed widespread interactions between bacteria and arthropods, including symbiotic interactions. Functional studies showed that obligate endosymbionts contribute to tick biology, affecting reproductive fitness and molting. Understanding the molecular basis of the interaction between ticks and their mutualist endosymbionts may help to develop control methods based on microbiome manipulation. Previously, we showed that Rhipicephalus microplus larvae with reduced levels of Coxiella endosymbiont of R. microplus (CERM) were arrested at the metanymph life stage (partially engorged nymph) and did not molt into adults. In this study, we performed a transcriptomic differential analysis of the R. microplus metanymph in the presence and absence of its mutualist endosymbiont. The lack of CERM resulted in an altered expression profile of transcripts from several functional categories. Gene products such as DA-P36, protease inhibitors, metalloproteases, and evasins, which are involved in blood feeding capacity, were underexpressed in CERM-free metanymphs. Disregulation in genes related to extracellular matrix remodeling was also observed in the absence of the symbiont. Taken together, the observed alterations in gene expression may explain the blockage of development at the metanymph stage and reveal a novel physiological aspect of the symbiont-tick-vertebrate host interaction.
Acutely Inhibiting AQP4 With TGN-020 Improves Functional Outcome by Attenuating Edema and Peri-Infarct Astrogliosis After Cerebral Ischemia

Background Ischemic stroke is one of the leading causes of human death and disability. Brain edema and peri-infarct astrocyte reactivity are crucial pathological changes, both involving aquaporin-4 (AQP4). Studies revealed that acute inhibition of AQP4 after stroke diminishes brain edema, however, its effect on peri-infarct astrocyte reactivity and the subacute outcome is unclear. And if diffusion-weighted imaging (DWI) could reflect the AQP4 expression patterns is uncertain. Methods Rats were subjected to middle cerebral artery occlusion (MCAO) and allocated randomly to TGN 020-treated and control groups. One day after stroke, brain swelling and lesion volumes of the rats were checked using T2-weighted imaging (T2-WI). Fourteen days after stroke, the rats successively underwent neurological examination, T2-WI and DWI with standard b-values and ultra-high b-values, apparent diffusion coefficient (ADC) was calculated correspondingly. Finally, the rats’ brains were acquired and used for glial fibrillary acidic protein (GFAP) and AQP4 immunoreactive analysis. Results At 1 day after stroke, the TGN-020-treated animals exhibited reduced brain swelling and lesion volumes compared with those in the control group. At 14 days after stroke, the TGN-020-treated animals showed fewer neurological function deficits and smaller lesion volumes. In the peri-infarct region, the control group showed evident astrogliosis and AQP4 depolarization, which were reduced significantly in the TGN-020 group. In addition, the ultra-high b-values of ADC (ADCuh) in the peri-infarct region of the TGN-020 group was higher than that of the control group. Furthermore, correlation analysis revealed that peri-infarct AQP4 polarization correlated negatively with astrogliosis extent, and ADCuh correlated positively with AQP4 polarization. Conclusion We found that acutely inhibiting AQP4 using TGN-020 promoted neurological recovery by diminishing brain edema at the early stage and attenuating peri-infarct astrogliosis and AQP4 depolarization at the subacute stage after stroke. Moreover, ADCuh could reflect the AQP4 polarization.
Alterations of Oxidative Stress Indicators, Antioxidant Enzymes, Soluble Sugars, and Amino Acids in Mustard [Brassica juncea (L.) Czern and Coss.] in Response to Varying Sowing Time, and Field Temperature

The impact of elevated temperature at the reproductive stage of a crop is one of the critical limitations that influence crop growth and productivity globally. This study was aimed to reveal how sowing time and changing field temperature influence on the regulation of oxidative stress indicators, antioxidant enzymes activity, soluble sugars (SS), and amino acids (AA) in Indian Mustard. The current study was carried out during the rabi 2017–2018 and 2018–2019 where, five varieties of mustard viz. Pusa Mustard 25 (PM-25) (V1), PM-26 (V2), BPR-541-4 (V3), RH-406 (V4), and Urvashi (V5) were grown under the field conditions on October 30 (normal sowing; S1), November 18 (late sowing; S2) and November 30 (very late sowing; S3) situations. The S1 and S3 plants, at mid-flowering stage, showed a significant variation in accumulation of SS (8.5 and 17.3%), free AA (235.4 and 224.6%), and proline content (118.1 and 133%), respectively, and played a crucial role in the osmotic adjustment under stress. The results showed that S3 sowing, exhibited a significant induction of the hydrogen peroxide (H2O2) (110.2 and 86.6%) and malondialdehyde (23.5 and 47.5%) concentrations, respectively, which indicated the sign of oxidative stress in plants. Interestingly, the polyphenol oxidase, peroxidase, superoxide dismutase, and catalase enzyme activities were also significantly increased in S3 plants compared to S1 plants, indicating their significant roles in ameliorating the oxidative stress. Furthermore, the concentration of fatty acid levels such as palmitic, stearic, oleic, and linoleic acids level also significantly increased in S3 plants, which influenced the seed and oil quality. The study suggests that the late sowing significantly impaired the biochemical mechanisms in Indian mustard. Further, the mustard variety V4 (RH-406) was found to be effective for cultivation as well as environmental stress adoption in Indian soils, and it could be highly useful in breeding for developing heat-tolerant genotypes for ensuring the food security.
The Molecular Properties and Roles of Pannier in Harmonia axyridis’s Metamorphosis and Melanin Synthesis

The GATA transcription factor Pannier is identified as the major regulatory gene in color pattern formation in the Asian multi-colored ladybird beetle (Harmonia axyridis). however, the mechanisms of Pannier in regulating melanin synthesis and development in H. axyridis remain elusive. In this study, we identified and characterized Pannier in H. axyridis (HaPnr) and showed it to have two alternative spliced variants named HaPnr-α and HaPnr-β. Analyses of developmental stage expression patterns revealed that HaPnr, HaPnr-α and HaPnr-β were constitutively expressed throughout all developmental stages. To examine the role of HaPnr in H. axyridis development, RNA interference was performed in late larvae (the fourth instar) and early pupae (the first day of pupa stage). The transcript levels of HaPnr were effectively suppressed after the injection of double-stranded RNA of HaPnr (dsHaPnr). The fourth instar larvae injected with dsHaPnr reduced the pupation rates to only 61.50%, compared with 88.5% in the dsGFP-injected group. The un-pupated larvae gradually died after 1 week, and visually unaffected pupae emerged into abnormal adults with malformed hind wings and melanin absent from the cuticle. These abnormal adults gradually died 10 days after eclosion. However, when early pupae were injected with dsHaPnr, the normal eclosion rate was achieved at 88.41% on day 6 after the injection. In addition, these successful eclosion adults also showed an absence of melanin in the cuticle, but they could mate normally and have normal fecundity as compared with the control. We further demonstrated that the suppression of HaPnr-α or HaPnr-β individually did not affect the pupation and eclosion process. The suppression of HaPnr-α expression resulted in elytra melanin decreasing in both the conspicua and the succinea subgroup in H. axyridis. Even though the suppression of HaPnr-β expression only affected the melanin synthesis in the succinea subgroup, it significantly prolonged the time taken for melanin synthesis to occur in the conspicua subgroup in H. axyridis. These results indicate that HaPnr plays an essential role in insect development, especially during their metamorphosis, and also support our hypothesis that HaPnr could regulate melanin synthesis in H. axyridis under the combined action with its two splicing variants, HaPnr-α and HaPnr-β.
High Mass Resolution fs-LIMS Imaging and Manifold Learning Reveal Insight Into Chemical Diversity of the 1.88 Ga Gunflint Chert

Extraction of useful information from unstructured, large and complex mass spectrometric signals is a challenge in many application fields of mass spectrometry. Therefore, new data analysis approaches are required to help uncover the complexity of such signals. In this contribution, we examined the chemical composition of the 1.88 Ga Gunflint chert using the newly developed high mass resolution laser ionization mass spectrometer (fs-LIMS-GT). We report results on the following: 1) mass-spectrometric multi-element imaging of the Gunflint chert sample; and 2) identification of multiple chemical entities from spatial mass spectrometric data utilizing nonlinear dimensionality reduction and spectral similarity networks. The analysis of 40′000 mass spectra reveals the presence of chemical heterogeneity (seven minor compounds) and two large clusters of spectra registered from the organic material and inorganic host mineral. Our results show the utility of fs-LIMS imaging in combination with manifold learning methods in studying chemically diverse samples.
Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides

Medicinal plants are inhabited by diverse microbes in every compartment, and which play an essential role in host growth and development, nutrient absorption, synthesis of secondary metabolites, and resistance to biological and abiotic stress. However, the ecological processes that manage microbiota assembly and the phenotypic and metabolic characteristics of the core microbiota of Eucommia ulmoides remain poorly explored. Here, we systematically evaluated the effects of genotypes, compartment niches, and environmental conditions (climate, soil nutrition, and secondary metabolites) on the assembly of rhizosphere soil and bark associated bacterial communities. In addition, phenotypic and metabolic characteristics of E. ulmoides core microbiota, and their relationship with dominant taxa, rare taxa, and pharmacologically active compounds were deciphered. Results suggested that microbiota assembly along the two compartments were predominantly shaped by the environment (especially pH, relative humidity, and geniposide acid) and not by host genotype or compartment niche. There were 690 shared genera in the rhizosphere soil and bark, and the bark microbiota was mainly derived from rhizosphere soil. Core microbiota of E. ulmoides was a highly interactive “hub” microbes connecting dominant and rare taxa, and its phenotypic characteristics had a selective effect on compartment niches. Metabolic functions of the core microbiota included ammonia oxidation, nitrogen fixation, and polyhydroxybutyrate storage, which are closely related to plant growth or metabolism. Moreover, some core taxa were also significantly correlated with three active compounds. These findings provide an important scientific basis for sustainable agricultural management based on the precise regulation of the rhizosphere soil and bark microbiota of E. ulmoides.
Memristive Izhikevich Spiking Neuron Model and Its Application in Oscillatory Associative Memory

The Izhikevich (IZH) spiking neuron model can display spiking and bursting behaviors of neurons. Based on the switching property and bio-plausibility of the memristor, the memristive Izhikevich (MIZH) spiking neuron model is built. Firstly, the MIZH spiking model is introduced and used to generate 23 spiking patterns. We compare the 23 spiking patterns produced by the IZH and MIZH spiking models. Secondly, the MIZH spiking model actively reproduces various neuronal behaviors, including the excitatory cortical neurons, the inhibitory cortical neurons, and other cortical neurons. Finally, the collective dynamic activities of the MIZH neuronal network are performed, and the MIZH oscillatory network is constructed. Experimental results illustrate that the constructed MIZH spiking neuron model performs high firing frequency and good frequency adaptation. The model can easily simulate various spiking and bursting patterns of distinct neurons in the brain. The MIZH neuronal network realizes the synchronous and asynchronous collective behaviors. The MIZH oscillatory network can memorize and retrieve the information patterns correctly and efficiently with high retrieval accuracy.