A multisite observational real-world study on the effectiveness of repetitive transcranial magnetic stimulation therapy for patients with treatment-resistant depression in Japan.

The objective of this study was to reveal the effectiveness of repetitive transcranial magnetic stimulation (rTMS) for Japanese patients with treatment-resistant depression (TRD) in clinical practice, based on real-world data from a nationwide multicenter observational study in Japan. Clinical data of patients with TRD treated with rTMS (NeuroStar TMS treatment system) under public insurance coverage were retrospectively collected from 21 institutes nationwide between June 2019 and December 2023. Depression severity was assessed by the 17-item Hamilton Depression Rating Scale (HAMD-17).

A functional connection between the Microprocessor and a variant NEXT complex.

In mammalian cells, primary miRNAs are cleaved at their hairpin structures by the Microprocessor complex, whose core is composed of DROSHA and DGCR8. Here, we show that 5' flanking regions, resulting from Microprocessor cleavage, are targeted by the RNA exosome in mouse embryonic stem cells (mESCs). This is facilitated by a physical link between DGCR8 and the nuclear exosome targeting (NEXT) component ZCCHC8.

Anorexia nervosa in a postoperative patient with Ebstein's anomaly.

Background: Along with the improved prognosis of patients with congenital heart disease, the associated diverse complications are under scrutiny. Due to various medical restrictions on their upbringing, patients with congenital heart disease often have coexisting mental disorders. However, reports on patients with congenital heart disease and coexisting eating disorders are rare.

Long-term outcomes of neuroendoscopic cyst partial resection combined with stereotactic radiotherapy for craniopharyngioma.

Purpose: The aim of this study was to evaluate the treatment outcomes of neuroendoscopic cyst partial resection (ECPR) combined with stereotactic radiotherapy (SRT) for cystic craniopharyngiomas.

Methods: In this retrospective study, 22 craniopharyngioma patients undergoing ECPR combined with SRT were included. This combination therapy was indicated for suprasellar cystic craniopharyngiomas in patients whose pituitary function was preserved but would be difficult to preserve in direct surgery.

Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery.

Computational analysis of RNA sequences constitutes a crucial step in the field of RNA biology. As in other domains of the life sciences, the incorporation of artificial intelligence and machine learning techniques into RNA sequence analysis has gained significant traction in recent years. Historically, thermodynamics-based methods were widely employed for the prediction of RNA secondary structures; however, machine learning-based approaches have demonstrated remarkable advancements in recent years, enabling more accurate predictions.

CyberKnife Radiosurgery for Spinal Intramedullary Arteriovenous Malformations: A Single-Center Experience.

Background: Intramedullary spinal arteriovenous malformation (ISAVM, glomus type) is a type of spinal cord arteriovenous malformation, which is a rare disease known often to have a complex vascular supply interfering with that of the spinal cord, and is in complex anatomical relations with cord structures and nerve roots. Though microsurgical and endovascular treatment has mainly been the standard options, in high-risk cases with these treatments, stereotactic radiotherapy (SRT) might be the option of choice.

Methods: We retrospectively reviewed 10 consecutive patients with ISAVM who received SRT using CyberKnife at the Japanese Red Cross Medical Center (Tokyo, Japan) from January 2011 to March 2022.

RNA Secondary Structure Prediction Based on Energy Models.

This chapter introduces the RNA secondary structure prediction based on the nearest neighbor energy model, which is one of the most popular architectures of modeling RNA secondary structure without pseudoknots. We discuss the parameterization and the parameter determination by experimental and machine learning-based approaches as well as an integrated approach that compensates each other's shortcomings. Then, folding algorithms for the minimum free energy and the maximum expected accuracy using the dynamic programming technique are introduced.

Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots.

Existing approaches to predicting RNA secondary structures depend on how the secondary structure is decomposed into substructures, that is, the , to define their parameter space. However, architecture dependency has not been sufficiently investigated, especially for pseudoknotted secondary structures. In this study, we propose a novel algorithm for directly inferring base-pairing probabilities with neural networks that do not depend on the architecture of RNA secondary structures, and then implement this approach using two maximum expected accuracy (MEA)-based decoding algorithms: Nussinov-style decoding for pseudoknot-free structures and IPknot-style decoding for pseudoknotted structures.

Hypofractionated Stereotactic Radiotherapy with CyberKnife for Large Arteriovenous Malformations and Arteriovenous Malformations Located in Eloquent Areas.

Literature has yet to establish an appropriate treatment strategy for large arteriovenous malformations (AVMs) and AVMs located in eloquent areas. In this study, the treatment outcomes of hypofractionated stereotactic radiotherapy (HSRT) with CyberKnife (CK) for large AVMs and AVMs in eloquent areas were evaluated. This study retrospectively evaluated 38 consecutive patients with AVMs treated with HSRT in the Japanese Red Cross Medical Center between August 2010 and July 2015.

Integer programming for selecting set of informative markers in paternity inference.

Background: Parentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to accurately infer parentage even in non-model species. The optimization of sets of genome-wide markers is valuable for cost-effective applications but requires extremely large amounts of computation, which presses for the development of new efficient algorithms.

Transgenically expressed Helicobacter pylori CagA in vascular endothelial cells accelerates arteriosclerosis in mice.

Arteriosclerosis is intimately associated with cardiovascular diseases. Recently, evidence accumulated that infection with Helicobacter pylori cagA-positive strains, which causes gastritis, peptic ulceration, and gastric cancer, is also involved in the development of arteriosclerosis. The cagA-encoded CagA protein is injected into the attached gastric epithelial cells via the type IV secretion system.

The Treatment Outcome of CyberKnife-Based Stereotactic Radiotherapy for Intracranial and Extracranial Nonvestibular Schwannomas: A Single-Center Experience.

Background: Data on the outcomes of CyberKnife-based hypofractionated stereotactic radiosurgery (hSRS) for intracranial and extracranial nonvestibular schwannomas (nVSs) are not sufficient.

Methods: Patients who underwent hSRS for nVSs between 2010 and 2019 were retrospectively reviewed.

Results: A total of 39 patients with 39 nVSs were identified.

A Max-Margin Model for Predicting Residue-Base Contacts in Protein-RNA Interactions.

Protein-RNA interactions (PRIs) are essential for many biological processes, so understanding aspects of the sequences and structures involved in PRIs is important for unraveling such processes. Because of the expensive and time-consuming techniques required for experimental determination of complex protein-RNA structures, various computational methods have been developed to predict PRIs. However, most of these methods focus on predicting only RNA-binding regions in proteins or only protein-binding motifs in RNA.

Prediction of RNA secondary structure including pseudoknots for long sequences.

RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is infeasible to construct an efficiently computable secondary structure model including pseudoknots, secondary structure prediction methods considering pseudoknots are not yet widely available. We developed IPknot, which uses heuristics to speed up computations, but it has remained difficult to apply it to long sequences, such as messenger RNA and viral RNA, because it requires cubic computational time with respect to sequence length and has threshold parameters that need to be manually adjusted.

The Long-Term Outcome of CyberKnife-Based Stereotactic Radiotherapy for Head and Neck Paragangliomas: A Single-Center Experience.

Objective: To assess long-term outcomes of hypofractionated stereotactic radiotherapy (hSRT) for head and neck paragangliomas (HNPGs).

Methods: Patients who underwent hSRT with CyberKnife for HNPGs from 2010 to 2019 were retrospectively reviewed.

Results: A total of 34 HNPGs in 29 patients were identified.

The long-term outcome of CyberKnife-based stereotactic radiotherapy for central skull base meningiomas: a single-center experience.

Few reports exist demonstrating the effects of stereotactic radiotherapy (SRT) on the central skull base meningiomas (CSMs). A retrospective analysis of 113 patients was performed. The median age was 62 (IQR 50-72) years old, and 78 patients (69%) were female.

A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs.

The programmability of RNA-RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of RNA devices that artificially regulate gene expression. An in silico design for interacting structured RNA sequences that satisfies multiple design criteria becomes a complex multi-objective problem. Although multi-objective optimization is a powerful technique that explores a vast solution space without empirical weights between design objectives, to date, no web service for multi-objective design of RNA switches that utilizes RNA-RNA interaction has been proposed.

RNA secondary structure prediction using deep learning with thermodynamic integration.

Accurate predictions of RNA secondary structures can help uncover the roles of functional non-coding RNAs. Although machine learning-based models have achieved high performance in terms of prediction accuracy, overfitting is a common risk for such highly parameterized models. Here we show that overfitting can be minimized when RNA folding scores learnt using a deep neural network are integrated together with Turner's nearest-neighbor free energy parameters.

Neural correlates of head restraint: Unsolicited neuronal activation and dopamine release.

To minimize motion-related distortion of reconstructed images, conventional positron emission tomography (PET) measurements of the brain inevitably require a firm and tight head restraint. While such a restraint is now a routine procedure in brain imaging, the physiological and psychological consequences resulting from the restraint have not been elucidated. To address this problem, we developed a restraint-free brain PET system and conducted PET scans under both restrained and non-restrained conditions.

Roles of the kisspeptin/GPR54 system in pathomechanisms of atherosclerosis.

Aims: Kisspeptin-10 (KP-10), a potent vasoconstrictor and inhibitor of angiogenesis, and its receptor, GPR54, have currently received much attention with respect to atherosclerosis, since both KP-10 and GPR54 are expressed at high levels in atheromatous plaques and restenotic lesions after wire-injury. The present review introduces the emerging roles of the KP-10/GPR54 system in atherosclerosis.

Data Synthesis: KP-10 suppresses migration and proliferation of human umbilical vein endothelial cells (HUVECs), and induces senescence in HUVECs.

-Endorphin Mediates the Development and Instability of Atherosclerotic Plaques.

-Endorphin, an endogenous opioid peptide, and its -opioid receptor are expressed in brain, liver, and peripheral tissues. -Endorphin induces endothelial dysfunction and is related to insulin resistance. We clarified the effects of -endorphin on atherosclerosis.

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data.

Background: The common marmoset (Callithrix jacchus) is one of the most studied primate model organisms. However, the marmoset genomes available in the public databases are highly fragmented and filled with sequence gaps, hindering research advances related to marmoset genomics and transcriptomics.

Results: Here we utilize single-molecule, long-read sequence data to improve and update the existing genome assembly and report a near-complete genome of the common marmoset.

Lipocalin-2 exerts pro-atherosclerotic effects as evidenced by in vitro and in vivo experiments.

Lipocalin-2 (LCN2), a multiple bioactive hormone particularly expressed in adipose tissue, neutrophils, and macrophages, is known to exhibit anti-microbial effect, increase inflammatory cytokine levels, and maintain glucose homeostasis. Serum LCN2 level is positively correlated with the severity of coronary artery disease. However, it still remains unknown whether LCN2 affects atherogenesis.