Finding easy regions for short-read variant calling from pangenome data.

Background: While benchmarks on short-read variant calling suggest a low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher.

A fusion ORF3a-E subgenomic RNA involved in SARS-CoV-2 infection efficacy by influencing cellular protein synthesis.

Subgenomic RNAs (sgRNAs) are discontinuous transcription products of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that are involved in viral gene expression and replication, but their exact functions are still being studied. Here, we report the identification of a nested ORF3a-sgRNA, the fusion ORF3a-E-sgRNA, which is involved in the infection process of SARS-CoV-2. This sgRNA encodes both ORF3a and E and can be detected throughout the viral life cycle in SARS-CoV-2-infected cells with high copy numbers.

Design and mechanical evaluation of a novel dynamic growth rod to improve the surgical treatment of early-onset scoliosis.

Aims: Growth rods are the gold standard for treating early-onset scoliosis (EOS), but current treatments often fail to optimally promote spinal growth and require frequent distraction surgeries, leading to complications and significant burdens on patients.

Methods: We designed a novel growth rod (NGR) with unidirectional sliding and external regulation capabilities. Using a 3D model, we simulated the implantation of traditional growth rod (TGR) and NGR, applying a 400 N compressive load and a 1 Nm moment to test stiffness.

Universal NIR-II-Emitting Unimolecular Micelles with Tailorable Pharmacokinetic and Optical Properties for Adaptive Imaging.

π-Conjugated fluorophores show great potential for NIR-II bio-imaging owing to their superior brightness and photostability, yet their clinical translation has been hindered by suboptimal pharmacokinetics. To address this issue, a strategy is developed to tailor the in vivo behavior of π-conjugate fluorophores by breaking π-π stacking in polymer brush-engineered unimolecular micelles. This approach marks a significant shift from traditional methods of tuning micelles, which rely on varying the hydrophilic-to-hydrophobic ratios and are often ineffective for π-conjugated systems due to the dominance of π-π interactions.

Modular One-Pot Access to Boron-Carboxylated Dipyrromethene Dyes as Visible-Light and Two-Photon Activatable Photocages.

The photocage, an advanced platform for drug delivery and photoactivation imaging, has attracted wide attention in biomedicine. Despite recent advancements in shifting irradiation wavelengths to visible and near-infrared light, improving photolysis quantum yield and the corresponding uncaging cross section, key parameters for efficient photocages, remains highly challenging. Here, we address this challenge by introducing light-controlled COO-B bond cleavage from tetracoordinate boron linked to dipyrrin, aryl, and carboxylic acid groups.

Effects on muscular activity and usability of soft active versus rigid passive back exoskeleton during symmetric lifting tasks.

Low back injuries are globally prevalent among construction workers, leading to significant economic burdens. Despite various intervention strategies, their effectiveness remains uncertain. This study evaluates a lightweight active soft back exosuit (SV Exosuit) against a passive rigid exosuit (IX BACK) to assess muscle activity and usability.

The Expression Pattern of the Splice Variants of Coxsackievirus and Adenovirus Receptor Impacts CV-B3-Induced Encephalitis and Myocarditis in Neonatal Mice.

Coxsackievirus B3 (CV-B3) infection causes inflammatory conditions such as viral myocarditis and meningitis, and incidence rates are rising annually. While children are more likely to be affected by severe manifestations, the molecular basis of this age-dependent susceptibility is poorly understood. In this study, we used young Balb/c mice at three developmental stages (7-, 14-, and 30-day-old mice) to investigate CV-B3 pathogenesis.

Finding easy regions for short-read variant calling from pangenome data.

Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher.

Defining and cataloging variants in pangenome graphs.

Structural variation causes some human haplotypes to align poorly with the linear reference genome, leading to 'reference bias'. A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a 'genetic variant.

Detecting Foldback Artifacts in Long Reads.

Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of a foldback artifact in long-read data. Therefore, we developed the open-source Breakinator tool to flag putative foldback artifact reads, as well as previously known chimeric artifacts.

Supramalleolar osteotomy outcomes for post-traumatic fracture-related ankle arthritis: a retrospective analysis.

Background: This study aimed to investigate the early-to-mid-term efficacy of supramalleolar osteotomy (SMO) for the management of post-traumatic ankle arthritis resulting from previous fractures.

Methods: A retrospective analysis was conducted on the clinical data of 19 individuals with post-traumatic ankle arthritis secondary to old fractures treated with SMO between March 2018 and September 2022. The cohort included 6 males and 13 females, aged 15 to 59 years, with an average of 37.

Longitudinal relationships between changes in post-COVID mental fatigue and neuropsychiatric symptoms across distinct recovery trajectories.

Background: Persistent fatigue, often accompanied by neuropsychiatric symptoms (e.g., cognitive impairment, sleep disorders, depression, anxiety, and PTSD), commonly referred to as "long COVID".

Moving through time: The influence of body motion on temporal concepts of future in Chinese sighted and blind people.

According to Conceptual Metaphor Theory, individuals represent abstract concepts, such as time, through more concrete experiences, such as the sensorimotor system. For example, left and right spatial orientations can be projected onto temporal concepts of past and future in mental models, which is consistent with various writing systems across cultures. Although evidence indicates that manual and visual experiences can influence lateral mental timelines, it remains unclear whether passive whole-body motion can exert similar effects.

Emergence of carbapenem-resistant XDR Salmonella enterica in paediatric patients in South China: A genomic perspective study.

Background And Aim: Carbapenem-resistant Salmonella enterica (CRSE), mostly driven by plasmids, poses a growing public health threat, especially in paediatric populations. This study investigates a cluster of paediatric CRSE infections in paediatric populations, characterizes genomic features of CRSE isolates, assesses global CRSE prevalence, and explores plasmid-mediated horizontal gene transfer.

Methods: An epidemiological investigation of 18 paediatric CRSE cases was conducted.

Polymerase Chain Reaction-Based Diagnosis of Leishmaniasis Targeting Kinetoplast Minicircle DNA in Infants with Hemophagocytic Lymphohistiocytosis.

In this study, we aimed to assess the efficacy of polymerase chain reaction (PCR) targeting Leishmania kinetoplast minicircle DNA (kDNA) for diagnosing visceral leishmaniasis-associated hemophagocytic lymphohistiocytosis (VL-HLH). Three pediatric patients diagnosed with VL-HLH via the microscopic examination of bone marrow smears were selected to explore the diagnostic value of kDNA PCR in Leishmania species identification and parasite load quantification in three cases of visceral leishmaniasis. Total DNA was extracted from the bone marrow samples, and PCR testing targeting the Leishmania kDNA was conducted.

A Fractional Order Standard Linear Solid Model for Extracting the Elastic Moduli of Internal Cell Structures.

As the mechanomarker of cellular behavior, the elastic moduli of internal cell structures can be measured through complex experimental procedure operated on micro or nano scale. Herein, a fractional-order standard linear solid model consisting of nucleus, cytoskeleton, and cytoplasm as the load-bearing components, is proposed. By fitting this model to the cell creep curves obtained by atomic force microscope (AFM), the elastic moduli of nucleus, intermediate filaments, microtubules and membrane-cytoplasm-actin cortex composite element can be extracted.

Proton minibeam radiotherapy: a review.

Radiotherapy plays a crucial role in cancer treatment. Spatially fractionated radiotherapy (SFRT) has garnered significant interest as a therapeutic strategy that delivers alternating regions of high and low radiation doses, thereby optimizing the therapeutic ratio by minimizing damage to adjacent normal tissues while achieving tumoricidal effects. Proton minibeam radiotherapy (pMBRT), a cutting-edge iteration within the SFRT paradigm, has attracted considerable attention owing to its purported benefits in dose distribution optimization, enhanced tumor control, and superior preservation of normal tissue.

Advances in ORMDL Research in Malignant Tumors: A Review.

ORMDL proteins (ORMDL1, ORMDL2, ORMDL3) are transmembrane proteins in the endoplasmic reticulum (ER) that regulate sphingolipid metabolism, maintain ER homeostasis, and modulate cellular stress responses. They influence cell proliferation, apoptosis, and metabolic balance. Recent studies have highlighted the altered expression and function of ORMDL proteins in various tumors, including breast cancer, DLBCL, colorectal cancer, and lung cancer.

Diagnostic Performance of Imaging-Based Artificial Intelligence Models for Preoperative Detection of Cervical Lymph Node Metastasis in Clinically Node-Negative Papillary Thyroid Carcinoma: A Systematic Review and Meta-Analysis.

Purpose: This systematic review and meta-analysis evaluated the performance of imaging-based artificial intelligence (AI) models in diagnosing preoperative cervical lymph node metastasis (LNM) in clinically node-negative (cN0) papillary thyroid carcinoma (PTC).

Methods: We conducted a literature search in PubMed, Embase, and Web of Science until February 25, 2025. Studies were selected that focused on imaging-based AI models for predicting cervical LNM in cN0 PTC.

Switchable high-Q and high-sensitivity nanoscale MIM waveguide-based biaxial optical accelerometer.

Nanoscale biaxial accelerometers based on metal-insulator-metal (MIM) waveguides offer high sensitivity and strong immunity to electromagnetic interference, making them attractive for next-generation inertial sensing. However, achieving multi-axis detection, device miniaturization, and high performance simultaneously remains challenging. In this work, we propose, to the best of our knowledge, a novel dual-axis optical accelerometer that integrates a circular-shaped ring resonant cavity (CSRRC) and a square-shaped ring resonant cavity (SSRRC) within a compact MIM structure.

Burden of aortic aneurysm in China from 1990 to 2021: A comparative analysis with G20 countries based on the Global Burden of Disease Study 2021.

Objectives: Aortic aneurysm (AA) is a life-threatening disease with high mortality. Up-to-date, information on AA burden in China is limited, which is required for health-care planning, resource allocation, and disease prevention. This study investigated the burden of AA in China from 1990 to 2021, and then compared it with other G20 countries.

Single-cell analysis unravels the role of NK cells and monocytes in the control of SARS-CoV-2 breakthrough infections in vaccinated individuals.

Analyzing the antiviral response of natural killer (NK) cells and monocytes is essential to understanding vaccine protection in an immunized population facing SARS-CoV-2 variant breakthrough infections (BTIs). In this study, in peripheral blood mononuclear cells (PBMCs) from vaccinated individuals with SARS-CoV-2 infections, we observed an increase in adaptive CD57NKG2C NK cells and classical monocytes (CMs). Single-cell sequencing analysis showed that the transcriptomic profiles of IFN-induced IFIT3 and other IFN-stimulated genes exhibited marked upregulation in NK cells, defined as CD56CD57NKG2CIFIT3 NK cells.

How to achieve sodium salt reduction in bean-based fermented foods: strategies, application cases and future perspectives.

High sodium salt concentration is crucial for successful fermentation and flavor development in bean-based fermented foods (BBFFs), yet excessive sodium intake poses health risks. As healthy diet awareness grows, reducing sodium salt in BBFFs is increasingly demanded but highly challenging due to the critical role of sodium salt reduction in BBFFs production. To resolve this challenge, researchers and manufacturers have developed various methods, however they showed differentiated results due to the diversity of BBFFs.