MRM-BERT: a novel deep neural network predictor of multiple RNA modifications by fusing BERT representation and sequence features.

RNA modifications play crucial roles in various biological processes and diseases. Accurate prediction of RNA modification sites is essential for understanding their functions. In this study, we propose a hybrid approach that fuses a pre-trained sequence representation with various sequence features to predict multiple types of RNA modifications in one combined prediction framework. We developed MRM-BERT, a deep learning method that combined the pre-trained DNABERT deep sequence representation module and the convolutional neural network (CNN) exploiting four traditional sequence feature encodings to improve the prediction performance. MRM-BERT was evaluated on multiple datasets of 12 commonly occurring RNA modifications, including m6A, m5C, m1A and so on. The results demonstrate that our hybrid model outperforms other models in terms of area under receiver operating characteristic curve (AUC) for all 12 types of RNA modifications. MRM-BERT is available as an online tool (http://117.122.208.21:8501) or source code (https://github.com/abhhba999/MRM-BERT), which allows users to predict RNA modification sites and visualize the results. Overall, our study provides an effective and efficient approach to predict multiple RNA modifications, contributing to the understanding of RNA biology and the development of therapeutic strategies.

A mini case report: Klebsiella pneumoniae-induced metastatic neck abscess following laparoscopic appendectomy.

Common complications following laparoscopic appendectomy include wound infection, bleeding, intra-abdominal abscess, small bowel obstruction, stump leakage, and stump appendicitis. Here, we presented a case reporting detailing a rare complication following laparoscopic appendectomy: the development of a metastatic neck abscess induced by Klebsiella pneumoniae(K. pneumoniae). A 49-year-old male underwent emergency laparoscopic surgery with prophylactic antibiotic administration for acute appendicitis. Subsequently, he experienced persistent neck pain and fever postoperatively, prompting further investigation. Pus and blood cultures revealed K. pneumoniae, with magnetic resonance imaging confirming the presence of a neck abscess. Antibiotic therapy was adjusted, and surgical drainage of the abscess was performed after multidisciplinary consultation. The patient was discharged without complications. While rare, metastatic abscesses following appendectomy warrant consideration, particularly in K. pneumoniae infections. Comprehensive clinical assessment, imaging, and laboratory evaluation are crucial for timely diagnosis and management of such complications.

Experimental Ischemic Stroke Induces Secondary Bihemispheric White Matter Degeneration and Long-Term Cognitive Impairment.

Clinical studies have identified widespread white matter degeneration in ischemic stroke patients. However, contemporary research in stroke has predominately focused on the infarct and periinfarct penumbra regions. The involvement of white matter degeneration after ischemic stroke and its contribution to post-stroke cognitive impairment and dementia (PSCID) has remained less explored in experimental models. In this study, we examined the progression of locomotor and cognitive function up to 4 months after inducing ischemic stroke by middle cerebral artery occlusion in young adult rats. Despite evident ongoing locomotor recovery, long-term cognitive and affective impairments persisted after ischemic stroke, as indicated by Morris water maze, elevated plus maze, and open field performance. At 4 months after stroke, multimodal MRI was conducted to assess white matter degeneration. T2-weighted MRI (T2WI) unveiled bilateral cerebroventricular enlargement after ischemic stroke. Fluid Attenuated Inversion Recovery MRI (FLAIR) revealed white matter hyperintensities in the corpus callosum and fornix across bilateral hemispheres. A positive association between the volume of white matter hyperintensities and total cerebroventricular volume was noted in stroke rats. Further evidence of bilateral white matter degeneration was indicated by the reduction of fractional anisotropy and quantitative anisotropy at bilateral corpus callosum in diffusion-weighted MRI (DWI) analysis. Additionally, microglia and astrocyte activation were identified in the bilateral corpus callosum after stroke. Our study suggests that experimental ischemic stroke induced by MCAO in young rat replicate long-term cognitive impairment and bihemispheric white matter degeneration observed in ischemic stroke patients. This model provides an invaluable tool for unraveling the mechanisms underlying post-stroke secondary white matter degeneration and its contribution to PSCID.

Metabolic Heterogeneity of Cerebral Cortical and Cerebellar Astrocytes.

Astrocytes play critical roles in regulating neuronal synaptogenesis, maintaining blood-brain barrier integrity, and recycling neurotransmitters. Increasing numbers of studies have suggested astrocyte heterogeneity in morphology, gene profile, and function. However, metabolic phenotype of astrocytes in different brain regions have not been explored. In this paper, we investigated the metabolic signature of cortical and cerebellar astrocytes using primary astrocyte cultures. We observed that cortical astrocytes were larger than cerebellar astrocytes, whereas cerebellar astrocytes had more and longer processes than cortical astrocytes. Using a Seahorse extracellular flux analyzer, we demonstrated that cortical astrocytes had higher mitochondrial respiration and glycolysis than cerebellar astrocytes. Cerebellar astrocytes have lower spare capacity of mitochondrial respiration and glycolysis as compared with cortical astrocytes. Consistently, cortical astrocytes have higher mitochondrial oxidation and glycolysis-derived ATP content than cerebellar astrocytes. In addition, cerebellar astrocytes have a fuel preference for glutamine and fatty acid, whereas cortical astrocytes were more dependent on glucose to meet energy demands. Our study indicated that cortical and cerebellar astrocytes display distinct metabolic phenotypes. Future studies on astrocyte metabolic heterogeneity and brain function in aging and neurodegeneration may lead to better understanding of the role of astrocyte in brain aging and neurodegenerative disorders.

Recurrent Transient Ischemic Attack Induces Neural Cytoskeleton Modification and Gliosis in an Experimental Model.

Transient ischemic attack (TIA) presents a high risk for subsequent stroke, Alzheimer's disease (AD), and related dementia (ADRD). However, the neuropathophysiology of TIA has been rarely studied. By evaluating recurrent TIA-induced neuropathological changes, our study aimed to explore the potential mechanisms underlying the contribution of TIA to ADRD. In the current study, we established a recurrent TIA model by three times 10-min middle cerebral artery occlusion within a week in rat. Neither permanent neurological deficit nor apoptosis was observed following recurrent TIA. No increase of AD-related biomarkers was indicated after TIA, including increase of tau hyperphosphorylation and ß-site APP cleaving enzyme 1 (BACE1). Neuronal cytoskeleton modification and neuroinflammation was found at 1, 3, and 7 days after recurrent TIA, evidenced by the reduction of microtubule-associated protein 2 (MAP2), elevation of neurofilament-light chain (NFL), and increase of glial fibrillary acidic protein (GFAP)-positive astrocytes and ionized calcium binding adaptor molecule 1 (Iba1)-positive microglia at the TIA-affected cerebral cortex and basal ganglion. Similar NFL, GFAP and Iba1 alteration was found in the white matter of corpus callosum. In summary, the current study demonstrated that recurrent TIA may trigger neuronal cytoskeleton change, astrogliosis, and microgliosis without induction of cell death at the acute and subacute stage. Our study indicates that TIA-induced neuronal cytoskeleton modification and neuroinflammation may be involved in the vascular contribution to cognitive impairment and dementia.

Characterizing region-specific glucose metabolic profile of the rodent brain using Seahorse XFe96 analyzer.

The brain is highly complex with diverse structural characteristics in accordance with specific functions. Accordingly, differences in regional function, cellular compositions, and active metabolic pathways may link to differences in glucose metabolism at different brain regions. In the current study, we optimized an acute biopsy punching method and characterized region-specific glucose metabolism of rat and mouse brain by a Seahorse XFe96 analyzer. We demonstrated that 0.5 mm diameter tissue punches from 180-µm thick brain sections allow metabolic measurements of anatomically defined brain structures using Seahorse XFe96 analyzer. Our result indicated that the cerebellum displays a more quiescent phenotype of glucose metabolism than cerebral cortex, basal ganglia, and hippocampus. In addition, the cerebellum has higher AMPK activation than other brain regions evidenced by the expression of pAMPK, upstream pLKB1, and downstream pACC. Furthermore, rodent brain has relatively low mitochondrial oxidative phosphorylation efficiency with up to 30% of respiration linked to proton leak. In summary, our study discovered region-specific glucose metabolic profile and relative high proton leak coupled respiration in the brain. Our study warrants future research on spatial mapping of the brain glucose metabolism in physiological and pathological conditions and exploring the mechanisms and significance of mitochondrial uncoupling in the brain.

A nociceptive neuronal ensemble in the dorsomedial prefrontal cortex underlies pain chronicity.

Pain chronicity involves unpleasant experience in both somatosensory and affective aspects, accompanied with the prefrontal cortex (PFC) neuroplastic alterations. However, whether specific PFC neuronal ensembles underlie pain chronicity remains elusive. Here we identify a nociceptive neuronal ensemble in the dorsomedial prefrontal cortex (dmPFC), which shows prominent reactivity to nociceptive stimuli. We observed that this ensemble shows distinct molecular characteristics and is densely connected to pain-related regions including basolateral amygdala (BLA) and lateral parabrachial nuclei (LPB). Prolonged chemogenetic activation of this nociceptive neuronal ensemble, but not a randomly transfected subset of dmPFC neurons, induces chronic pain-like behaviors in normal mice. By contrast, silencing the nociceptive dmPFC neurons relieves both pain hypersensitivity and anxiety in mice with chronic inflammatory pain. These results suggest the presence of specific dmPFC neuronal ensembles in processing nociceptive information and regulating pain chronicity.

Early loss of cerebellar Purkinje cells in human and a transgenic mouse model of Alzheimer's disease.

BACKGROUND: The cerebellum's involvement in AD has been under-appreciated by historically labeling as a normal control in AD research. METHODS: We determined the involvement of the cerebellum in AD progression. Postmortem human and APPswe/PSEN1dE9 mice cerebellums were used to assess the cerebellar Purkinje cells (PC) by immunohistochemistry. The locomotor and spatial cognitive functions were assessed in 4- to 5-month-old APPswe/PSEN1dE9 mice. Aß plaque and APP processing were determined in APPswe/PSEN1dE9 mice at different age groups by immunohistochemistry and Western blot. RESULTS: We observed loss of cerebellar PC in mild cognitive impairment and AD patients compared with cognitively normal controls. A strong trend towards PC loss was found in AD mice as early as 5 months. Impairment of balance beam and rotorod performance, but no spatial learning and memory dysfunction was observed in AD mice at 4-5 months. Aß plaque in the cerebral cortex was evidenced in AD mice at 2 months and dramatically increased at 6 months. Less and smaller Aß plaques were observed in the cerebellum than in the cerebrum of AD mice. Similar intracellular APP staining was observed in the cerebellum and cerebrum of AD mice at 2 to 10 months. Similar expression of full-length APP and C-terminal fragments were indicated in the cerebrum and cerebellum of AD mice during aging. DISCUSSION: Our study in post-mortem human brains and transgenic AD mice provided neuropathological and functional evidence that cerebellar dysfunction may occur at the early stage of AD and likely independent of Aß plaque.

Magnetism-induced topological transition in EuAs3.

The nature of the interaction between magnetism and topology in magnetic topological semimetals remains mysterious, but may be expected to lead to a variety of novel physics. We systematically studied the magnetic semimetal EuAs3, demonstrating a magnetism-induced topological transition from a topological nodal-line semimetal in the paramagnetic or the spin-polarized state to a topological massive Dirac metal in the antiferromagnetic ground state at low temperature. The topological nature in the antiferromagnetic state and the spin-polarized state has been verified by electrical transport measurements. An unsaturated and extremely large magnetoresistance of ~2 × 105% at 1.8 K and 28.3 T is observed. In the paramagnetic states, the topological nodal-line structure at the Y point is proven by angle-resolved photoemission spectroscopy. Moreover, a temperature-induced Lifshitz transition accompanied by the emergence of a new band below 3 K is revealed. These results indicate that magnetic EuAs3 provides a rich platform to explore exotic physics arising from the interaction of magnetism with topology.

Determination of metformin bio-distribution by LC-MS/MS in mice treated with a clinically relevant paradigm.

Metformin, an anti-diabetes drug, has been recently emerging as a potential "anti-aging" intervention based on its reported beneficial actions against aging in preclinical studies. Nonetheless, very few metformin studies using mice have determined metformin concentrations and many effects of metformin have been observed in preclinical studies using doses/concentrations that were not relevant to therapeutic levels in human. We developed a liquid chromatography-tandem mass spectrometry protocol for metformin measurement in plasma, liver, brain, kidney, and muscle of mice. Young adult male and female C57BL/6 mice were voluntarily treated with metformin of 4 mg/ml in drinking water which translated to the maximum dose of 2.5 g/day in humans. A clinically relevant steady-state plasma metformin concentrations were achieved at 7 and 30 days after treatment in male and female mice. Metformin concentrations were slightly higher in muscle than in plasma, while, ~3 and 6-fold higher in the liver and kidney than in plasma, respectively. Low metformin concentration was found in the brain at ~20% of the plasma level. Furthermore, gender difference in steady-state metformin bio-distribution was observed. Our study established steady-state metformin levels in plasma, liver, muscle, kidney, and brain of normoglycemic mice treated with a clinically relevant dose, providing insight into future metformin preclinical studies for potential clinical translation.

Radiotherapy with temozolomide provides better survival in the newly diagnosed glioblastoma multiforme: A meta-analysis.

BACKGROUND: The optimal treatment for patients with newly diagnosed glioblastoma multiforme (GBM) remains controversial. The purpose of this meta-analysis was to systematically evaluate radiotherapy/temozolomide (TMZ) versus radiotherapy for treating newly diagnosed GBM. MATERIALS AND METHODS: Six electronic databases (PubMed, EMBASE, MEDLINE, Web of Science, Cochrane Library, and CNKI) were searched for relevant publications up to November 05, 2014. RevMan version 5.2 software was used for statistical analysis. RESULTS: A total of 9 studies were identified in this analyses, which included 986 patients. The summary risk ratio (RR) for overall survival and the progression-free survival (PFS) was the measure of interest. Results revealed that the addition of TMZ to radiotherapy resulted in a statistically significant survival benefit in poor prognosis patients with newly diagnosed glioblastoma (RR = 2.93 [95% confidence interval (CI) 2.29, 3.75], P < 0.00001). Moreover, radiotherapy plus TMZ was more beneficial than radiotherapy alone in improving PFS (RR = 3.52, [95% CI 2.53, 4.89], P < 0.00001). However, certain grade 3-4 hematological toxicities were significantly more common with TMZ. CONCLUSIONS: This meta-analysis suggests that radiotherapy/TMZ provides better survival than radiotherapy alone in treating GBM.