Chromosomal-level genome assembly and annotation of the tropical sea cucumber Holothuria scabra.

Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra.

Orexin-A alleviates ferroptosis by activating the Nrf2/HO-1 signaling pathway in traumatic brain injury.

BACKGROUND: Traumatic Brain Injury (TBI) has high disability and mortality rate. Oxidative stress and ferroptosis are important pathophysiological characteristics after TBI. Orexin-A (OXA) can alleviate neuronal damage in diverse neurological disorders. Nevertheless, the role and mechanism of OXA in TBI stay unknown. OBJECTIVES: The research investigated protection influence of OXA on TBI and its potential mechanisms. METHODS: Male Sprague-Dawley rats were randomly grouped into: sham, TBI, TBI + normal saline (NS) and TBI+OXA groups. TBI model was constructed in rat via modified Feeney's approach, and OXA treatment was administered following construction of TBI model. RESULTS: Relative to TBI+NS group, TBI+OXA group displayed greatly recovered tissue damage and neurological deficits. Additionally, OXA eased oxidative stress as well as ferroptosis in cerebral cortex of rats following TBI. Furthermore, OXA increased Nrf2 expression and regulating factors HO-1 and NQO1 in cerebral cortex of TBI rats. CONCLUSIONS: Our research found OXA may restrain ferroptosis via Nrf2/HO-1 signaling pathway activation, thereby reducing brain injury after TBI.

MicroRNA sequencing analysis reveals immune responses in hepatopancreas of Fenneropenaeus penicillatus under white spot syndrome virus infection.

White Spot Disease is one of the most harmful diseases of the red tail shrimp, which can cause devastating economic losses due to the highest mortality up to 100% within a few days. MicroRNAs (miRNAs) are large class of small noncoding RNAs with the ability to post-transcriptionally repress the translation of target mRNAs. MiRNAs are considered to have a significant role in the innate immune response of crustaceans, particularly in relation to antiviral defense mechanisms. Numerous crustacean miRNAs have been verified to be required in host immune defense against viral infection, however, till present, the miRNAs functions of F. penicillatus defense WSSV infection have not been studied yet. Here in this study, for the first time, miRNAs involved in the F. penicillatus immune defense against WSSV infection were identified using high-throughput sequencing platform. A total of 432 miRNAs were obtained including 402 conserved miRNAs and 30 novel predicted miRNAs. Comparative analysis between the WSSV-challenged group and the control group revealed differential expression of 159 microRNAs in response to WSSV infection. Among these, 48 were up-regulated and 111 were down-regulated. Ten candidate MicroRNAs associated with immune activities were randomly selected for qRT-PCR analysis, which confirming the expression profiling observed in the MicroRNA sequencing data. As a result, most differentially expressed miRNAs were down-regulated lead to increase the expression of various target genes that mediated immune reaction defense WSSV infection, including genes related to signal transduction, Complement and coagulation cascade, Phagocytosis, and Apoptosis. Furthermore, the genes expression of the key members in Toll and Imd signaling pathways and apoptotic signaling were mediated by microRNAs to activate host immune responses including apoptosis against WSSV infection. These results will help to understand molecular defense mechanism against WSSV infection in F. penicillatus and to develop an effective WSSV defensive strategy in shrimp farming.

A predictive model for awakening in patients with prolonged disorders of consciousness after craniocerebral injury.

This study aimed to develop and validate a nomogram to predict awakening at 1 year in patients with prolonged disorders of consciousness (pDOC). We retrospectively analyzed the data of 381 patients with pDOC at 2 centers. The data were randomly divided into training and validation sets using a ratio of 6:4. For the training set, univariate and multivariate logical regression analyses were used to identify the predictive variables. Receiver operating characteristic curves, calibration curves, and a decision curve analysis were utilized to assess the predictive accuracy, discriminative ability, and clinical utility of the model, respectively. The final model included age, Glasgow Coma Scale score, serum albumin level, and computed tomography midline shift, all of which had a significant effect on awakening after pDOC. For the 1-year awakening in the training set, the model had good discriminative power, with an area under the curve of 0.733 (95% confidence interval: 0.667-0.789). For the validation set, the area under the curve for 1-year awakening was 0.721 (95% confidence interval: 0.617-0.826). Model performance was good for both the training and validation sets according to calibration plots and decision curve analysis. We developed a precise, effective nomogram to assist clinicians in better assessing patients' outcomes, guiding clinical judgment, and personalizing the therapeutic process.

Dynamic Prognostic Score to Predict Survival in East Asian Elderly Populations with Dysphagia.

INTRODUCTION: Dysphagia is a common disorder in older adults, leading to severe complications, including aspiration pneumonia, dehydration, malnutrition, weight loss, and even death. However, no prognostic model has been developed to predict the prognosis of older adults with dysphagia. METHODS: Data from patients with dysphagia at a single center were retrospectively reviewed between 2014 and 2017. All data were obtained from the Dryad Digital Repository. The least absolute shrinkage and selection operator regression model was used to select potentially relevant features. Multiple Cox proportional hazard analysis was used to develop a model based on the training set. RESULTS: The nomogram comprised age, sex, percutaneous endoscopic gastrostomy, chronic heart failure, total lymphocyte count, daily calorie intake, and severe pneumonia, which provided favorable calibration and discrimination in the training dataset, with AUCs for the 1-year, 2-year, and 3-year survival predictions of 0.833, 0.871, and 0.886, respectively. Furthermore, it showed acceptable discrimination in the validation cohort, with AUCs for the 1-year, 2-year, and 3-year survival predictions of 0.884, 0.834, and 0.782, respectively. Moreover, the decision curve analysis results revealed that the nomogram was clinically beneficial. CONCLUSION: A nomogram, combining seven demographic and clinical factors, provided an excellent preoperative prediction of survival probability in older individuals with dysphagia. This predictive model can be used as a reference to assist clinicians in making clinical decisions.

MicroRNA sequencing analysis reveals injury-induced immune responses of Scylla paramamosain against cheliped autotomy.

During pond culture or intensive culture system of crabs (mainly Eriocheir sinensis, Portunus trituberculatus and Scylla paramamosain), high-density farming has typically contributed to a higher limb autotomy level in juvenile animals, especially in S. paramamosain which has a high level of cannibalism. Due to the high limb autotomy level, the survival and growth rates in S. paramamosain farming are restricted, which limit the growth of the mud crab farming industry. MicroRNAs (miRNAs) are small noncoding RNAs that regulate a series of biological processes including innate immune responses by post-transcriptional suppression of their target genes. MiRNAs are believed to be crucial for innate immune process of host wound healing. Many miRNAs have been verified to be required in host immune responses to repair wound and to defense pathogen after tissue damage. However, to our best knowledge, the miRNAs functions of crustacean innate immune reactions against injury induced by limb autotomy have not been studied yet. Here in this study, for the first time, miRNAs involved in the S. paramamosain immune reactions against injury induced by cheliped autotomy were obtained by high-throughput sequencing. A total of 575 miRNAs (518 known miRNAs and 57 novel predicted miRNAs) were obtained, of which 141 differentially expressed microRNAs (93 up-regulated microRNAs and 48 down-regulated microRNAs) were revealed to be modified against cheliped autotomy, and the qPCR results of randomly selected miRNAs confirmed the expression patterns in the miRNAs sequencing data. Numerous immune-related target genes associated with innate immune system were mediated by miRNAs to induce host humoral immune and cellular immune defense to minimize acute physical damage. Furthermore, the genes expression in hemolymph coagulation and melanization pathways, as well as Toll and Imd signaling pathways were mediated by miRNAs to activate host immune responses including melanization and antimicrobial peptides for rapid wound healing and killing invaded pathogens. These results will help to understand injury-induced immune responses in crabs and to develop an effective control strategy of autotomy rate in crabs farming.

Global Instance Tracking: Locating Target More Like Humans.

Target tracking, the essential ability of the human visual system, has been simulated by computer vision tasks. However, existing trackers perform well in austere experimental environments but fail in challenges like occlusion and fast motion. The massive gap indicates that researches only measure tracking performance rather than intelligence. How to scientifically judge the intelligence level of trackers? Distinct from decision-making problems, lacking three requirements (a challenging task, a fair environment, and a scientific evaluation procedure) makes it strenuous to answer the question. In this article, we first propose the global instance tracking (GIT) task, which is supposed to search an arbitrary user-specified instance in a video without any assumptions about camera or motion consistency, to model the human visual tracking ability. Whereafter, we construct a high-quality and large-scale benchmark VideoCube to create a challenging environment. Finally, we design a scientific evaluation procedure using human capabilities as the baseline to judge tracking intelligence. Additionally, we provide an online platform with toolkit and an updated leaderboard. Although the experimental results indicate a definite gap between trackers and humans, we expect to take a step forward to generate authentic human-like trackers. The database, toolkit, evaluation server, and baseline results are available at http://videocube.aitestunion.com.

Relationship between consciousness level and perfusion computed tomography in patients with prolonged disorders of consciousness.

PURPOSE: We assessed the relationship between consciousness level and values of cerebral blood flow (CBF), cerebral blood volume (CBV), mean transit time (MTT), and time to peak (TTP) obtained by whole-brain perfusion computed tomography (pCT) in patients with prolonged disorders of consciousness (pDOC). METHODS: This study included 29 patients in vegetative state (VS), 34 with minimally consciousness state minus (MCS-), and 13 with minimally consciousness state plus (MCS+). All patients were evaluated using the Coma Recovery Scale-Revised (CRS-R), the Glasgow Coma Scale (GCS), and the Full Outline of UnResponsiveness (FOUR). The values of CBF, CBV, MTT, and TTP were obtained from patients who underwent pCT. Differences in CBF, CBV, MTT, and TTP were compared between the three types of pDOC. Correlations between the CRS-R, GCS, and FOUR scores and the pCT results were analyzed. RESULTS: Among the three groups, patients in VS showed a significantly decreased CBF in the bilateral frontal lobe, thalamus, temporal lobe, occipital lobe, brainstem, and damaged part. CBV was significantly reduced in patients with VS in the bilateral frontal lobe, thalamus, temporal lobe, brainstem, and damaged part. The total CRS-R, GCS, and FOUR scores were positively correlated with CBF, CBV, and TTP in almost all regions of interest. CONCLUSION: Reductions in CBF and CBV calculated with pCT are associated with impaired consciousness and perfusion CT could be a promising tool in evaluating the conscious level in patients with pDOC.

Deaminative-cleaved S. monotuberculatus fucosylated glycosaminoglycan: Structural elucidation and anticoagulant activity.

Stichopus monotuberculatus is a tropical sea cucumber species and used as a folk medicine and tonic food. In this study, a fucosylated glycosaminoglycan (SmFG), the depolymerized SmFG (dSmFG) and its oligosaccharide fractions were prepared. The SmFG and its depolymerized products were comprised of a chondroitin-sulfate-E backbone, and various sulfated fucose side chains, including an unusual disaccharide side chain connected to the C-3 position of D-glucuronic acid (GlcA) or GlcA-ol. A peeling reaction occurred during the deaminative depolymerization process. The dSmFG and its fractions showed strong anticoagulant activity by selectively inhibiting intrinsic tenase complex, and had no anti-factor IIa, Xa and VIIa activity. The anticoagulant activity reduced with the decrease of molecular weight, and the unusual branch and novel reducing end may enhance the anticoagulant activity. These findings can provide significant information for development and utilization of depolymerized products from SmFG in food and pharmaceutical industries.

Characterization and phylogenetic analysis of the complete mitogenome of sea cucumber Stichopus ocellatus (Massin, Zulfigar, Hwai & Boss, 2002) (Aspidochirotida: Stichopodidae).

Stichopus ocellatus, known as eye-spotted sea cucumber, is a commercially important Stichopodidae holothuroid in Indo-Pacific region for its valuable nutrition and medicinal ingredients. However, because the taxonomic analyses based on morphological characters and molecular data within Aspidochirotida are limited, the deep-level evolutionary relationships of Aspidochirotida are still poorly understood. Here, for providing better insight of future evolutionary and taxonomic classification of Stichopodidae, we report the first complete mitogenome of S. ocellatus along with 37 annotated and characterized mitochondrial genes, and the phylogenetic analysis based on mitogenome data reveals sister relationship between S. ocellatus and S. monotuberculatus.

Median Nerve Stimulation Attenuates Traumatic Brain Injury-Induced Comatose State by Regulating the Orexin-A/RasGRF1 Signaling Pathway.

BACKGROUND: Despite the arousal effect of median nerve stimulation (MNS) being well documented in the clinical treatment of coma patients with traumatic brain injury (TBI), the mechanisms underlying the observed effect are still not completely understood. This study aimed to evaluate the protective effects and potential mechanism of MNS in comatose rats with TBI. METHODS: A total of 60 rats were randomly divided into 5 groups: the control group, sham-stimulated group, MNS group, orexins receptor type 1 (OX1R) antagonist group, and antagonist control group. The free-fall drop method was used to establish a TBI model. After administrating MNS or OX1R antagonist, consciousness was evaluated. Protein levels in the prefrontal cortex were measured using an enzyme-linked immunosorbent assay, Western blotting, and immunofluorescence. RESULTS: In the MNS group, tissue damage and consciousness state was markedly improved compared with that in the sham-stimulated group. Administration of the OX1R antagonist attenuated the beneficial effects of MNS in TBI-induced comatose rats. Additionally, MNS also significantly enhanced the expression of orexin-A/OX1R and the activation of Ras guanine nucleotide-releasing factor 1 (RasGRF1). CONCLUSIONS: These data show that MNS exerts its wake-promoting effect by activating the OX1R-RasGRF1 pathway in TBI-induced comatose rats.

Low-intensity focused ultrasound attenuates early traumatic brain injury by OX-A/NF-κB/NLRP3 signaling pathway.

BACKGROUND: Traumatic brain injury (TBI) is a serious hazard to human health and is characterized by high rates of disability and mortality. It is necessary to explore new effective treatment methods to reduce the impact of TBI on individuals and society. As an emerging neuromodulation technique, ultrasound is used to treat some neurological diseases, but the neuroprotective mechanism of low-intensity focused ultrasound (LIFUS) in TBI remains unclear. We aimed to investigate the protective effects and potential mechanisms of LIFUS in TBI. METHODS: A rat model of TBI was established using the free-fall method. After establishing the TBI model, the hypothalamus region was covered with LIFUS radiation, and an orexin receptor 1 (OXR1) antagonist (SB334867) was injected intraperitoneally. Neurobehavioral examination, Nissl staining, hematoxylin and eosin staining of the brain tissue, and brain water content, were performed 3 days later. Western blotting, quantitative real-time polymerase chain reaction, immunofluorescence staining, and immunohistochemical staining, were used to evaluate the neuroprotective mechanisms of LIFUS. RESULTS: LIFUS improved tissue damage, neurological deficits, and brain edema. LIFUS can increase the expression of orexin-A (OX-A) and OXR1, significantly inhibit the activation of nuclear factor-κB (NF-κB) protein and nucleotide-binding domain-like receptor protein 3 (NLRP3) inflammasome after TBI, and reduce the release of pro-inflammatory factors after TBI; however, SB334867 can reverse this effect. CONCLUSIONS: This study suggests that LIFUS may play a neuroprotective role by promoting the release of OX-A from the hypothalamus and inhibiting the inflammatory response after TBI through the OX-A /NF-κB/NLRP3 pathway.

Development and Validation of a Website to Guide Decision-Making for Disorders of Consciousness.

Background: This study aimed to develop and validate a nomogram and present it on a website to be used to predict the overall survival at 16, 32, and 48 months in patients with prolonged disorder of consciousness (pDOC). Methods: We retrospectively analyzed the data of 381 patients with pDOC at two centers. The data were randomly divided into training and validation sets using a ratio of 6:4. On the training set, Cox proportional hazard analyses were used to identify the predictive variables. In the training set, two models were screened by COX regression analysis, and based on clinical evidence, model 2 was eventually selected in the nomogram after comparing the receiver operating characteristic (ROC) of the two models. In the training and validation sets, ROC curves, calibration curves, and decision curve analysis (DCA) curves were utilized to measure discrimination, calibration, and clinical efficacy, respectively. Results: The final model included age, Glasgow coma scale (GCS) score, serum albumin level, and computed tomography (CT) midline shift, all of which had a significant effect on survival after DOCs. For the 16-, 32-, and 48-month survival on the training set, the model had good discriminative power, with areas under the curve (AUCs) of 0.791, 0.760, and 0.886, respectively. For the validation set, the AUCs for the 16-, 32-, and 48-month survival predictions were 0.806, 0.789, and 0.867, respectively. Model performance was good for both the training and validation sets according to calibration plots and DCA. Conclusion: We developed an accurate, efficient nomogram, and a corresponding website based on four correlated factors to help clinicians improve their assessment of patient outcomes and help personalize the treatment process and clinical decisions.

A dynamic model to predict long-term outcomes in patients with prolonged disorders of consciousness.

PURPOSE: It is important to predict the prognosis of patients with prolonged disorders of consciousness (DOC). This study established and validated a nomogram and corresponding web-based calculator to predict outcomes for patients with prolonged DOC. METHODS: All data were obtained from the First Affiliated Hospital of Nanchang University and the Shangrao Hospital of Traditional Chinese Medicine. Predictive variables were identified by univariate and multiple logistic regression analyses. Receiver operating characteristic curves, calibration curves, and a decision curve analysis (DCA) were utilized to assess the predictive accuracy, discriminative ability, and clinical utility of the model, respectively. RESULTS: Independent prognostic factors, such as age, Glasgow coma scale score, state of consciousness, and brainstem auditory-evoked potential grade were integrated into a nomogram. The model demonstrated good discrimination in the training and validation cohorts, with area-under-the-curve values of 0.815 (95% confidence interval [CI]: 0.748-0.882) and 0.805 (95% CI: 0.727-0.883), respectively. The calibration plots and DCA demonstrated good model performance and clear clinical benefits in both cohorts. CONCLUSIONS: Based on our nomogram, we developed an effective, simple, and accurate model of a web-based calculator that may help individualize healthcare decision-making. Further research is warranted to optimize the system and update the predictors.

The first complete mitochondrial genome of Phyrella fragilis (Mitsukuri & Ohshima in Ohshima, 1912) (Dendrochirotida: Phyllophoridae).

Echinoderms (Echinodermata) are morphologically diverse and ecologically important groups of marine invertebrate, many of which are key components of local benthic ecosystem. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in echinoderms have not been completely resolved. The phylogenetic relationships of Phyllophoridae genera and species remain controversial and many species are incorrectly assigned within genus Phyrella. In this study, we report the first complete mitochondrial genome of Phyrella from Phyrella fragilis. The mitogenome has 15,910 base pairs (64.32% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study will provide useful genetic data for future phylogenetic and taxonomic classification of Phyllophoridae.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Actinopyga lecanora (Jaeger, 1833) (Holothuriida: Holothuriidae).

The white-bottomed sea cucumber, Actinopyga lecanora, is a valuable inshore fisheries resource which is famous for its high nutrition and pharmacological compounds. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in the genus Actinopyga have not been completely resolved yet. Moreover, there remains a complex of cryptic species within Actinopyga, many of which are incorrectly assigned within the family Holothuriidae. In this study, we report the complete mitochondrial genome of A. lecanora. The mitogenome has 15,568 base pairs (63.40% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study offers useful mitogenome data for future phylogenetic and taxonomic classification of Holothuriidae.

The first complete mitochondrial genome of Stomopneustes variolaris (Lamarck, 1816) from the Stomechinidae (Echinoidea: Stomopneustoida).

Sea urchins (Echinoidea) are key components of marine benthic communities and many are commercially important fishery resources as luxury and healthy seafood. However, despite their high ecological and economic value, the mitochondrial genomes of all sea urchins have yet to be analyzed. In this study, we report the first complete mitochondrial genome of Stomopneustidae from Stomopneustes variolaris. The mitogenome has 15,767 base pairs (59.77% A + T content) and contains 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study provides useful molecular resources for clarifying evolutionary and phylogenetic histories of sea urchins.

Orexin-A Attenuates Inflammatory Responses in Lipopolysaccharide-Induced Neural Stem Cells by Regulating NF-KB and Phosphorylation of MAPK/P38/Erk Pathways.

BACKGROUND: Neuronal damage is the main cause of neurological diseases. Neural stem cells (NSCs) have the functions of cell repair and replacement of neurons, secretion of neurotrophic factors, and immune regulation of the neural microenvironment. OBJECTIVE: Previous study found that Orexin-A had a protective effect on neurons in the central nervous system, but it is lacking in making great efforts on the function of Orexin-A on NSCs. This study aimed to investigate the anti-inflammatory responses and signaling mechanisms of Orexin-A on lipopolysaccharide (LPS)-induced NSCs. METHODS: Quantitative real-time polymerase chain reaction was used to detect the mRNA level. Signaling pathway-related protein expression was detected by Western blot. The proliferation and migration of NSCs were investigated by Cell Counting Kit-8 (CCK-8) detection kit and transwell assay. Besides, the staining of hematoxylin and eosin (HE) was performed to study the morphology of cell. RESULTS: Orexin-A decreased the pro-inflammatory cytokines of IL-1ß, TNF-α, and IL-6 induced by LPS by regulating nuclear factor-k-gene binding (NF-kB) and phosphorylation of P38/Erk-mitogen-activated protein kinases (MAPKs) pathways, but not p-JNK signaling. CONCLUSION: Our findings indicate that Orexin-A can alleviate the inflammatory response of NSC. It can provide beneficial help in neural stem cell therapy applications.