Emerging Roles and Mechanisms of RNA Modifications in Neurodegenerative Diseases and Glioma.

Despite a long history of research, neurodegenerative diseases and malignant brain tumor gliomas are both considered incurable, facing challenges in the development of treatments. Recent evidence suggests that RNA modifications, previously considered as static components of intracellular RNAs, are in fact dynamically regulated across various RNA species in cells and play a critical role in major biological processes in the nervous system. Innovations in next-generation sequencing have enabled the accurate detection of modifications on bases and sugars within various RNA molecules. These RNA modifications influence the stability and transportation of RNA, and crucially affect its translation. This review delves into existing knowledge on RNA modifications to offer a comprehensive inventory of these modifications across different RNA species. The detailed regulatory functions and roles of RNA modifications within the nervous system are discussed with a focus on neurodegenerative diseases and gliomas. This article presents a comprehensive overview of the fundamental mechanisms and emerging roles of RNA modifications in these diseases, which can facilitate the creation of innovative diagnostics and therapeutics for these conditions.

Spin-State Control of Shallow Single NV Centers in Hydrogen-Terminated Diamond.

The ability to control the charge and spin states of nitrogen-vacancy (NV) centers near the diamond surface is of pivotal importance for quantum applications. Hydrogen-terminated diamond is promising for long spin coherence times and ease of controlling the charge states due to the low density of surface defects. However, it has so far been challenging to create negatively charged single NV centers with controllable spin states beneath a hydrogen-terminated surface because atmospheric adsorbates that act as acceptors induce surface holes. In this study, we optically detected the magnetic resonance of shallow single NV centers in hydrogen-terminated diamond through precise control of the nitrogen implantation fluence. Furthermore, we found that the probability of detecting the resonance was enhanced by reducing the surface acceptor density through passivation of the hydrogen-terminated surface with hexagonal boron nitride without air exposure. This control method opens up new opportunities for using NV centers in quantum applications.

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation.

Ependymomas encompass multiple clinically relevant tumor types based on localization and molecular profiles. Tumors of the methylation class "spinal ependymoma" (SP-EPN) represent the most common intramedullary neoplasms in children and adults. However, their developmental origin is ill-defined, molecular data are scarce, and the potential heterogeneity within SP-EPN remains unexplored. The only known recurrent genetic events in SP-EPN are loss of chromosome 22q and NF2 mutations, but neither types and frequency of these alterations nor their clinical relevance have been described in a large, epigenetically defined series. Transcriptomic (n = 72), epigenetic (n = 225), genetic (n = 134), and clinical data (n = 112) were integrated for a detailed molecular overview on SP-EPN. Additionally, we mapped SP-EPN transcriptomes to developmental atlases of the developing and adult spinal cord to uncover potential developmental origins of these tumors. The integration of transcriptomic ependymoma data with single-cell atlases of the spinal cord revealed that SP-EPN display the highest similarities to mature adult ependymal cells. Unsupervised hierarchical clustering of transcriptomic data together with integrated analysis of methylation profiles identified two molecular SP-EPN subtypes. Subtype A tumors primarily carried previously known germline or sporadic NF2 mutations together with 22q loss (bi-allelic NF2 loss), resulting in decreased NF2 expression. Furthermore, they more often presented as multilocular disease and demonstrated a significantly reduced progression-free survival as compared to SP-EP subtype B. In contrast, subtype B predominantly contained samples without NF2 mutation detected in sequencing together with 22q loss (monoallelic NF2 loss). These tumors showed regular NF2 expression but more extensive global copy number alterations. Based on integrated molecular profiling of a large multi-center cohort, we identified two distinct SP-EPN subtypes with important implications for genetic counseling, patient surveillance, and drug development priorities.

Oral 5-aminolevulinic acid administration before transurethral resection of bladder tumor induces perioperative nausea and vomiting.

BACKGROUND: The efficacy of photodynamic diagnosis using 5-aminolevulinic acid during transurethral resection of bladder tumors has been demonstrated, albeit with limited information regarding its side effects. This study aimed to clarify the impact of oral 5-aminolevulinic acid on perioperative nausea and vomiting (NV) for the first time in a real-world clinical practice setting. METHODS: Patients who underwent transurethral surgery at Kagawa University between April 2017 and March 2020 were included. Perioperative NV and antiemetic use status were prospectively assessed and compared between the patients who received oral 5-aminolevulinic acid and those who did not. Additionally, univariate and multivariate analyses were performed for predicting postoperative nausea and vomiting. RESULTS: Of 214 patients, 74 (34.6%) received oral 5-aminolevulinic acid preoperatively. The proportions of preoperative NV and antiemetic use in the patients who received 5-aminolevulinic acid were 9.5% and 4.1%, respectively, and higher than in those who did not (0% and 0%; P < 0.01 and P = 0.04, respectively). Postoperative NV (25.7%) and antiemetics use (8.0%) ratios in the patients who received 5-aminolevulinic acid were significantly different from those in the non-users group (3.6% and 2.1%, P < 0.01 and P < 0.01, respectively). Although no differences in risk factors were found for postoperative NV between the two groups, multivariate analyses indicated 5-aminolevulinic acid use as an independent predictive factor for postoperative NV (odds ratio, 11.5; 95% confidence interval, 3.98-33.3; P < 0.01). CONCLUSIONS: Our study clearly showed that oral administration of 5-aminolevulinic acid was associated with perioperative NV even without risk factors, highlighting the need for addressing its application.

Recurrent glioblastoma metastatic to the lumbar vertebra: A case report and literature review: Surgical oncology.

Background: Glioblastoma is a malignant tumor, and its prognosis is as poor as 1.5 to 2 years. Most cases recur within one year even under the standard treatment. The majority of recurrences are local, and in rare cases, metastasize mostly within the centra nervous system. Extradural metastasis of glioma is exceedingly rare. Here, we present a case of vertebral metastasis of glioblastoma. Case presentation: We present a 21-year-old man post total resection of the right parietal glioblastoma, diagnosed with lumbar metastasis. He originally presented with impaired consciousness and left hemiplegia and underwent gross total resection of the tumor. Given the diagnosis of glioblastoma, he was treated with radiotherapy combined with concurrent and adjuvant temozolomide. Six months after tumor resection, the patient presented with severe back pain, and was diagnosed as metastatic glioblastoma on the first lumbar vertebrae. Posterior decompression with fixation and postoperative radiotherapy were conducted. He went on to receive temozolomide and bevacizumab. However, at 3 months after the diagnosis of lumbar metastasis, further disease progression was noted, and his care was transitioned to best supportive care. Comparison on copy number status between primary and metastatic lesions on methylation array analysis revealed more enhanced chromosomal instability including 7p loss, 7q gain and 8 gain in the metastatic lesion. Conclusion: Based upon the literature review and our case, younger age of initial presentation, multiple surgical interventions, and long overall survival seem to be the risk factors of vertebral metastasis. As the prognosis of glioblastoma improves over time, its vertebral metastasis is seemingly more common. Therefore, extradural metastasis should be kept in mind in the treatment of glioblastoma. Further, detailed genomic analysis on multiple paired specimens is mandated to elucidate the molecular mechanisms of vertebral metastasis.

Mobilizing Citizens' Ears: Aural Training as Civil Defense, 1941-45.

In the mid-twentieth century, the Japanese state trained its citizens to identify the sound of a falling bomb. This article explores the little-studied impact of audio-based military technology on wider society, beyond the military sector and beyond Western contexts. In 1941, Japan's elementary schools-renamed National People's Schools-provided new musical training in perfect pitch to strengthen Japan's national defense efforts in wartime. "Explosive sound training" taught children to identify recorded explosive sounds of enemy aircraft, though ultimately such training could not mitigate widespread destruction. This article argues that the recent discussion of "the story of acoustic defense" can benefit from a much broader historiographical framework, one focused not just on the military frame. In the Japanese case, the story was shaped through the active interactions between the military, society, and educational institutions. A multidisciplinary analytical perspective provides a more critical and nuanced understanding of how modern sound-politics overlapped with exercising wartime power.

Cover Essay: Visual Images in Sound Studies.

This essay discusses the significance of visual images in sound studies. The field of sound studies allows us to focus on hearing and soundscapes in cultural experiences and has challenged the primacy of vision as a framework for social analysis. This issue's cover shows Japanese Emperor Hirohito examining Type 90 Air Sound Detectors (also known as "war tubas") in 1936. From the mid-1930s to the early 1940s, these acoustic locators featured not only in experts' books but also in air-defense and military textbooks and in popular Japanese magazines. Magazines for young people highlighted their visuality rather than their actual functioning, mechanisms, and technicality. This essay demonstrates that the acoustic locator's visuality was instrumental for public relations, while its auditory function served practical military purposes. The image suggests that visuals play a vital role in studying the complex ecologies of sound.

Incidental Sacral Meningocele in an Elderly Patient Diagnosed After Epidermal Inclusion Cyst Removal: A Case Report.

A meningocele is a congenital neural tube defect, and the majority of the meningocele cases are identified perinatally. We present the case of a 67-year-old patient with a sacral meningocele undiagnosed until the removal of a symptomatic epidermal inclusion cyst adjacent to it. Cerebrospinal fluid leakage occurred due to an incision in an undiagnosed meningocele adjacent to the epidermal inclusion cyst. Repair of the cerebrospinal fluid leakage was performed successfully without any deficit. The present case underscores the importance of considering a meningocele as a differential diagnosis for a mass occurring in the midline of the back at any age.

Ultra-wide-band millimeter-wave generator using spin torque oscillator with strong interlayer exchange couplings.

Recent increased development interest in millimeter-wave oscillator devices has necessitated realization of small oscillators with high frequency, wide frequency tunability, and room-temperature operation. Spin-torque oscillators (STOs) are fascinating candidates for such applications because of their nanometer size and suitability for room-temperature operation. However, their oscillation frequency and tunable range are limited to the order of 100 MHz-10 GHz. Here, we propose use of bilinear (J1) and biquadratic (J2) interlayer exchange couplings between ferromagnets in STOs to overcome these problems. The bilinear coupling contributes to oscillation frequency enhancement, whereas the biquadratic coupling facilitates frequency tunability via a current. Using micromagnetic simulation with parameters estimated from a material with small saturation magnetization, for J1 = 0 and J2 = - 1.0 mJ/m2, respectively, we find that the STO exhibits high frequency from 23 to 576 GHz and that its tunability reaches 61 GHz/(1011 A/m2) for current densities of - 0.5 to - 9.5 × 1011 A/m2. An analytical theory based on the macrospin model is also developed, which exhibits good quantitative agreement with the micromagnetic simulations. These results introduce new possibilities for spintronics applications in high-frequency devices such as next-generation mobile communications.

Magnetic polarization selective spectroscopy of magnetic thin films probed by wideband crossed microstrip circuit in GHz regime.

We have developed a method to obtain wideband magnetic polarization selective spectra of magnetic thin films by using circularly polarized microwaves. The combination of an over-coupled crossed microstrip resonator and a hybrid coupler enables broadband and accurate control of circularly polarized microwaves. The performance of the present method was demonstrated with an yttrium iron garnet thin film, and we detected the magnetic polarization dependence of a Kittel mode and a perpendicular standing spin wave mode in the range of 3-20 GHz. In addition, three types of crossed microstrip resonators were systematically studied with experiments and simulations. As a result, we achieved the polarization efficiency of 80% and found how to optimize the crossed microstrip resonator depending on the desired sensitivity, bandwidth, or sample size.

Designing Single-Component Optogenetic Membrane Recruitment Systems: The Rho-Family GTPase Signaling Toolbox.

We describe the efficient creation of single-component optogenetic tools for membrane recruitment-based signaling perturbation using BcLOV4 technology. The workflow requires two plasmids to create six different domain arrangements of the dynamic membrane binder BcLOV4, a fluorescent reporter, and the fused signaling protein of interest. Screening of this limited set of genetic constructs for expression characteristics and dynamic translocation in response to one pulse of light is sufficient to identify viable signaling control tools. The reliability of this streamlined approach is demonstrated by the creation of an optogenetic Cdc42 GTPase and Rac1-activating Tiam1 GEF protein, which together with our other recently reported technologies, completes a toolbox for spatiotemporally precise induction of Rho-family GTPase signaling at the GEF or GTPase level, for driving filopodial protrusions, lamellipodial protrusions, and cell contractility, respectively mediated by Cdc42, Rac1, and RhoA.

Prediction of RNA-protein interactions using a nucleotide language model.

Motivation: The accumulation of sequencing data has enabled researchers to predict the interactions between RNA sequences and RNA-binding proteins (RBPs) using novel machine learning techniques. However, existing models are often difficult to interpret and require additional information to sequences. Bidirectional encoder representations from transformer (BERT) is a language-based deep learning model that is highly interpretable. Therefore, a model based on BERT architecture can potentially overcome such limitations. Results: Here, we propose BERT-RBP as a model to predict RNA-RBP interactions by adapting the BERT architecture pretrained on a human reference genome. Our model outperformed state-of-the-art prediction models using the eCLIP-seq data of 154 RBPs. The detailed analysis further revealed that BERT-RBP could recognize both the transcript region type and RNA secondary structure only based on sequence information. Overall, the results provide insights into the fine-tuning mechanism of BERT in biological contexts and provide evidence of the applicability of the model to other RNA-related problems. Availability and implementation: Python source codes are freely available at https://github.com/kkyamada/bert-rbp. The datasets underlying this article were derived from sources in the public domain: [RBPsuite (http://www.csbio.sjtu.edu.cn/bioinf/RBPsuite/), Ensembl Biomart (http://asia.ensembl.org/biomart/martview/)]. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Impact of subcallosal artery origin and A1 asymmetry on surgical outcomes of anterior communicating artery aneurysms.

BACKGROUND: Surgical clipping of anterior communicating artery (ACoA) aneurysms remains challenging due to their complex anatomy. Anatomical risk factors for ACoA aneurysm surgery require further elucidation. The aim of this study is to investigate whether proximity of the midline perforating artery, subcallosal artery (SubCA), and associated anomaly of the ACoA complex affect functional outcomes of ACoA aneurysm surgery. METHODS: A total of 92 patients with both unruptured and ruptured ACoA aneurysms, who underwent surgical clipping, were retrospectively analyzed from a multicenter, observational cohort database. Association of ACoA anatomy with SubCA origin at the aneurysmal neck under microsurgical observation was analyzed in the interhemispheric approach subgroup (n = 56). Then, we evaluated whether anatomical factors associated with SubCA neck origin affected surgical outcomes in the entire cohort (both interhemispheric and pterional approaches, n = 92). RESULTS: In the interhemispheric approach cohort, combination of A1 asymmetry and aneurysmal size ≥ 5.0 mm was stratified to have the highest probability of the SubCA neck origin by a decision tree analysis. Then, among the entire cohort using either interhemispheric or pterional approach, combination of A1 asymmetry and aneurysmal size ≥ 5.0 mm was significantly associated with poor functional outcomes by multivariable logistic regression analysis (OR 6.76; 95% CI 1.19-38.5; p = 0.03) as compared with A1 symmetry group in the acute subarachnoid hemorrhage settings. CONCLUSION: Combination of A1 asymmetry and larger aneurysmal size was significantly associated with SubCA aneurysmal neck origin and poor functional outcomes in ACoA aneurysm surgery. Interhemispheric approach may be proposed to provide a wider and unobstructed view of SubCA for ACoA aneurysms with this high-risk anatomical variant.

Single-Component Optogenetic Tools for Inducible RhoA GTPase Signaling.

Optogenetic tools are created to control RhoA GTPase, a central regulator of actin organization and actomyosin contractility. RhoA GTPase, or its upstream activator ARHGEF11, is fused to BcLOV4, a photoreceptor that can be dynamically recruited to the plasma membrane by a light-regulated protein-lipid electrostatic interaction with the inner leaflet. Direct membrane recruitment of these proteins induces potent contractile signaling sufficient to separate adherens junctions with as little as one pulse of blue light. Induced cytoskeletal morphology changes are dependent on the alignment of the spatially patterned stimulation with the underlying cell polarization. RhoA-mediated cytoskeletal activation drives yes-associated protein (YAP) nuclear localization within minutes and consequent mechanotransduction verified by YAP-transcriptional enhanced associate domain transcriptional activity. These single-transgene tools do not require protein binding partners for dynamic membrane localization and permit spatiotemporally precise control over RhoA signaling to advance the study of its diverse regulatory roles in cell migration, morphogenesis, and cell cycle maintenance.

Representation learning applications in biological sequence analysis.

Although remarkable advances have been reported in high-throughput sequencing, the ability to aptly analyze a substantial amount of rapidly generated biological (DNA/RNA/protein) sequencing data remains a critical hurdle. To tackle this issue, the application of natural language processing (NLP) to biological sequence analysis has received increased attention. In this method, biological sequences are regarded as sentences while the single nucleic acids/amino acids or k-mers in these sequences represent the words. Embedding is an essential step in NLP, which performs the conversion of these words into vectors. Specifically, representation learning is an approach used for this transformation process, which can be applied to biological sequences. Vectorized biological sequences can then be applied for function and structure estimation, or as input for other probabilistic models. Considering the importance and growing trend for the application of representation learning to biological research, in the present study, we have reviewed the existing knowledge in representation learning for biological sequence analysis.

X-ray Photoemission Spectroscopy Study of Uniaxial Magnetic Anisotropy Induced in a Ni Layer Deposited on a LiNbO3 Substrate.

The competition between magnetic shape anisotropy and the induced uniaxial magnetic anisotropy in the heterojunction between a ferromagnetic layer and a ferroelectric substrate serves to control magnetic domain structures as well as magnetization reversal characteristics. The uniaxial magnetic anisotropy, originating from the symmetry breaking effect in the heterojunction, plays a significant role in modifying the characteristics of magnetization dynamics. Magnetoelastic phenomena are known to generate uniaxial magnetic anisotropy; however, the interfacial electronic states that may contribute to the uniaxial magnetic anisotropy have not yet been adequately investigated. Here, we report experimental evidence concerning the binding energy change in the ferromagnetic layer/ferroelectric substrate heterojunction using X-ray photoemission spectroscopy. The binding energy shifts, corresponding to the chemical shifts, reveal the binding states near the interface. Our results shed light on the origin of the uniaxial magnetic anisotropy induced from the heterojunction. This knowledge can provide a means for the simultaneous control of magnetism, mechanics, and electronics in a nano/microsystem consisting of ferromagnetic/ferroelectric materials.

Discrimination of skyrmion chirality via spin-orbit and -transfer torques for logic operation.

Recently many works on magnetic memories and logic circuits, which use a magnetic skyrmion have been reported. Previously we micromagnetically simulated a method to switch a chirality of a magnetic skyrmion formed in a magnetic thin film by introducing a pulsed heat spot. In this paper, we propose a method to discriminate the chirality of a skyrmion in a branched nanowire by using spin-orbit torque (SOT) and spin-transfer torque (STT), and confirm the validity of the method by using simulation. The simulated results show that the motion changes depending on the chirality when additional SOT is applied on a skyrmion moving in a branch by STT. This method can be used as a fundamental building block for electrical detection in memory and logic devices using the chirality of skyrmions as a data bit in addition to the presence (and polarity) of the skyrmions as conventionally used, which can be lead to multiple-valued operation.

Novel LCAT (Lecithin:Cholesterol Acyltransferase) Activator DS-8190a Prevents the Progression of Plaque Accumulation in Atherosclerosis Models.

OBJECTIVE: Enhancement of LCAT (lecithin:cholesterol acyltransferase) activity has possibility to be beneficial for atherosclerosis. To evaluate this concept, we characterized our novel, orally administered, small-molecule LCAT activator DS-8190a, which was created from high-throughput screening and subsequent derivatization. We also focused on its mechanism of LCAT activation and the therapeutic activity with improvement of HDL (high-density lipoprotein) functionality. Approach and Results: DS-8190a activated human and cynomolgus monkey but not mouse LCAT enzymes in vitro. DS-8190a was orally administered to cynomolgus monkeys and dose dependently increased LCAT activity (2.0-fold in 3 mg/kg group on day 7), resulting in HDL cholesterol elevation without drastic changes of non-HDL cholesterol. Atheroprotective effects were then evaluated using Ldl-r KO×hLcat Tg mice fed a Western diet for 8 weeks. DS-8190a treatment achieved significant reduction of atherosclerotic lesion area (48.3% reduction in 10 mg/kg treatment group). Furthermore, we conducted reverse cholesterol transport study using Ldl-r KO×hLcat Tg mice intraperitoneally injected with J774A.1 cells loaded with [3H]-cholesterol and confirmed significant increases of [3H] count in plasma (1.4-fold) and feces (1.4-fold on day 2 and 1.5-fold on day3) in the DS-8190a-treated group. With regard to the molecular mechanism involved, direct binding of DS-8190a to human LCAT protein was confirmed by 2 different approaches: affinity purification by DS-8190a-immobilized beads and thermal shift assay. In addition, the candidate binding site of DS-8190a in human LCAT protein was identified by photoaffinity labeling. CONCLUSIONS: This study demonstrates the potential of DS-8190a as a novel therapeutic for atherosclerosis. In addition, this compound proves that a small-molecule direct LCAT activator can achieve HDL-C elevation in monkey and reduction of atherosclerotic lesion area with enhanced HDL function in rodent.

Activation of Naturally Occurring Lecithin:Cholesterol Acyltransferase Mutants by a Novel Activator Compound.

Lecithin:cholesterol acyltransferase (LCAT) is a unique plasma enzyme able to esterify cholesterol, and it plays an important role in HDL maturation and promotion of reverse cholesterol transport. Familial LCAT deficiency (FLD; OMIM number 245900) is a rare recessive disease that results from loss-of-function mutations in the LCAT gene and has no cure. In this study, we assessed the in vitro efficacy of a novel small-molecule LCAT activator. Cholesterol esterification rate (CER) and LCAT activity were tested in plasma from six controls and five FLD homozygous carriers of various LCAT mutations at different doses of the compound (0.1, 1, and 10 µg/ml). In control plasma, the compound significantly increased both CER (P < 0.001) and LCAT activity (P = 0.007) in a dose-dependent manner. Both CER and LCAT activity increased by 4- to 5-fold, reaching maximum activation at the dose of 1 µg/ml. Interestingly, Daiichi Sankyo compound produced an increase in CER in two of the five tested LCAT mutants (Leu372--Arg and Val309--Met), while LCAT activity increased in three LCAT mutants (Arg147--Trp, Thr274--Ile and Leu372--Arg); mutant Pro254--Ser was not activated at any of the tested doses. The present findings form the basis for personalized therapeutic interventions in FLD carriers and support the potential LCAT activation in secondary LCAT defects. SIGNIFICANCE STATEMENT: We characterized the pharmacology of a novel small-molecule LCAT activator in vitro on a subset of naturally occurring LCAT mutants. Our findings form the basis for personalized therapeutic interventions for familial LCAT deficiency carriers, who can face severe complications and for whom no cure exists.

Retro-odontoid Pseudotumor: Two Cases of Intradural Ganglion Cysts Arising From the Odontoid Process with Syringobulbia.

BACKGROUND: Ganglion cysts mostly occur in the knuckles and wrists, but they rarely present in the odontoid process and can cause neurological symptoms by compressing the spinal cord. They are mostly localized in the epidural space, but may very rarely appear in the intradural space. There are no reports of cases of intradural ganglion cyst involving syringobulbia. CASE DESCRIPTION: We report the presentation and management of 2 cases of an intradural ganglion cyst of the odontoid process. Several treatment options for ganglion cysts of the odontoid process have been reported, such as rest and use of a neck collar, posterior decompression and fusion, and transoral anterior decompression. Because our 2 cases progressed rapidly and had severe neurological symptoms, surgical treatment was performed for rapid decompression and definitive pathological diagnosis. The mass was resected as much as possible using the lateral occipital fossa approach, and the operation was completed without dissection of the brain stem or manipulation of the syringobulbia. Postoperatively, neurological symptoms promptly improved, and the syringobulbia reduced. CONCLUSIONS: For intradural ganglion cysts with syringobulbia, we suggest relief of the compression by resection of the mass and treatment of the syringobulbia in 2 stages, if necessary, to avoid the risk of damage to the brainstem.