Comprehensive benchmarking and guidelines of mosaic variant calling strategies.

Rapid advances in sequencing and analysis technologies have enabled the accurate detection of diverse forms of genomic variants represented as heterozygous, homozygous and mosaic mutations. However, the best practices for mosaic variant calling remain disorganized owing to the technical and conceptual difficulties faced in evaluation. Here we present our benchmark of 11 feasible mosaic variant detection approaches based on a systematically designed whole-exome-level reference standard that mimics mosaic samples, supported by 354,258 control positive mosaic single-nucleotide variants and insertion-deletion mutations and 33,111,725 control negatives. We identified not only the best practice for mosaic variant detection but also the condition-dependent strengths and weaknesses of the current methods. Furthermore, feature-level evaluation and their combinatorial usage across multiple algorithms direct the way for immediate to prolonged improvements in mosaic variant detection. Our results will guide researchers in selecting suitable calling algorithms and suggest future strategies for developers.

CLEMENT: genomic decomposition and reconstruction of non-tumor subclones.

Genome-level clonal decomposition of a single specimen has been widely studied; however, it is mostly limited to cancer research. In this study, we developed a new algorithm CLEMENT, which conducts accurate decomposition and reconstruction of multiple subclones in genome sequencing of non-tumor (normal) samples. CLEMENT employs the Expectation-Maximization (EM) algorithm with optimization strategies specific to non-tumor subclones, including false variant call identification, non-disparate clone fuzzy clustering, and clonal allele fraction confinement. In the simulation and in vitro cell line mixture data, CLEMENT outperformed current cancer decomposition algorithms in estimating the number of clones (root-mean-square-error = 0.58-0.78 versus 1.43-3.34) and in the variant-clone membership agreement (∼85.5% versus 70.1-76.7%). Additional testing on human multi-clonal normal tissue sequencing confirmed the accurate identification of subclones that originated from different cell types. Clone-level analysis, including mutational burden and signatures, provided a new understanding of normal-tissue composition. We expect that CLEMENT will serve as a crucial tool in the currently emerging field of non-tumor genome analysis.

Advances in Bioresorbable Triboelectric Nanogenerators.

With the growing demand for next-generation health care, the integration of electronic components into implantable medical devices (IMDs) has become a vital factor in achieving sophisticated healthcare functionalities such as electrophysiological monitoring and electroceuticals worldwide. However, these devices confront technological challenges concerning a noninvasive power supply and biosafe device removal. Addressing these challenges is crucial to ensure continuous operation and patient comfort and minimize the physical and economic burden on the patient and the healthcare system. This Review highlights the promising capabilities of bioresorbable triboelectric nanogenerators (B-TENGs) as temporary self-clearing power sources and self-powered IMDs. First, we present an overview of and progress in bioresorbable triboelectric energy harvesting devices, focusing on their working principles, materials development, and biodegradation mechanisms. Next, we examine the current state of on-demand transient implants and their biomedical applications. Finally, we address the current challenges and future perspectives of B-TENGs, aimed at expanding their technological scope and developing innovative solutions. This Review discusses advancements in materials science, chemistry, and microfabrication that can advance the scope of energy solutions available for IMDs. These innovations can potentially change the current health paradigm, contribute to enhanced longevity, and reshape the healthcare landscape soon.

Analysis of low-level somatic mosaicism reveals stage and tissue-specific mutational features in human development.

Most somatic mutations that arise during normal development are present at low levels in single or multiple tissues depending on the developmental stage and affected organs. However, the effect of human developmental stages or mutations of different organs on the features of somatic mutations is still unclear. Here, we performed a systemic and comprehensive analysis of low-level somatic mutations using deep whole-exome sequencing (average read depth ~500×) of 498 multiple organ tissues with matched controls from 190 individuals. Our results showed that early clone-forming mutations shared between multiple organs were lower in number but showed higher allele frequencies than late clone-forming mutations [0.54 vs. 5.83 variants per individual; 6.17% vs. 1.5% variant allele frequency (VAF)] along with less nonsynonymous mutations and lower functional impacts. Additionally, early and late clone-forming mutations had unique mutational signatures that were distinct from mutations that originated from tumors. Compared with early clone-forming mutations that showed a clock-like signature across all organs or tissues studied, late clone-forming mutations showed organ, tissue, and cell-type specificity in the mutation counts, VAFs, and mutational signatures. In particular, analysis of brain somatic mutations showed a bimodal occurrence and temporal-lobe-specific signature. These findings provide new insights into the features of somatic mosaicism that are dependent on developmental stage and brain regions.

Ajania pacifica (Nakai) K. Bremer and Humphries Extract Limits MYC Expression to Induce Apoptosis in Diffuse Large B Cell Lymphoma.

The proto-oncogene MYC is frequently dysregulated in patients with diffuse large B-cell lymphoma (DLBCL) and plays a critical role in disease progression. To improve the clinical outcomes of patients with DLBCL, the development of strategies to target MYC is crucial. The use of medicinal plants for developing anticancer drugs has garnered considerable attention owing to their diverse mechanisms of action. In this study, 100 plant extracts of flora from the Republic of Korea were screened to search for novel agents with anti-DLBCL effects. Among them, Ajania pacifica (Nakai) K. Bremer and Humphries extract (APKH) efficiently suppressed the survival of DLBCL cells, while showing minimal toxicity toward normal murine bone marrow cells. APKH suppressed the expression of anti-apoptotic BCL2 family members, causing an imbalance between the pro-apoptotic and anti-apoptotic BCL2 members. This disrupted mitochondrial membrane potential, cytochrome c release, and pro-caspase-3 activation and eventually led to DLBCL cell death. Importantly, MYC expression was markedly downregulated by APKH and ectopic expression of MYC in DLBCL cells abolished the pro-apoptotic effects of APKH. These results demonstrate that APKH exerts anti-DLBCL effects by inhibiting MYC expression. Moreover, when combined with doxorubicin, an essential component of the CHOP regimen (cyclophosphamide, doxorubicin, vincristine, and prednisone), APKH synergistically enhanced the therapeutic effect of doxorubicin. This indicates that APKH may overcome drug resistance, which is common in patients with refractory/relapsed DLBCL. To identify compounds with anti-DLBCL activities in APKH, the chemical profile analysis of APKH was performed using UPLC-QTOF/MSe analysis and assessed for its anticancer activity. Based on the UPLC-QTOF/MSe chemical profiling, it is conceivable that APKH may serve as a novel agent targeting MYC and sensitizing drug-resistant DLBCL cells to CHOP chemotherapy. Further studies to elucidate how the compounds in APKH exert tumor-suppressive role in DLBCL are warranted.

Self-Powered Water Splitting of Ni3FeN@Fe24N10 Bifunctional Catalyst Improved Catalytic Activity and Durability by Forming Fe24N10 on Catalyst Surface via the Kirkendall Effect.

Highly efficient water splitting electrocatalyst for producing hydrogen as a renewable energy source offers potential to achieve net-zero. However, it has significant challenges in using transition metal electrocatalysts as alternatives to noble metals due to their low efficiency and durability, furthermore, the reliance on electricity generation for electrocatalysts from fossil fuels leads to unavoidable carbon emissions. Here, a highly efficient self-powered water splitting system integrated is designed with triboelectric nanogenerator (TENG) and Ni3FeN@Fe24N10 catalyst with improved catalytic activity and durability. First, the durability of the Ni3FeN catalyst is improved by forming N, P carbon shell using melamine, polyetherimide, and phytic acid. The catalyst activity is improved by generating Fe24N10 in the carbon shell through the Kirkendall effect. The synthesized Ni3FeN@Fe24N10 catalyst exhibited excellent bifunctional catalytic activity (ηOER = 261.8 mV and ηHER = 151.8 mV) and remarkable stability (91.7% in OER and 90.5% in HER) in 1 m KOH. Furthermore, to achieve ecofriendly electricity generation, a rotation-mode TENG that sustainably generate high-performance is realized using butylated melamine formaldehyde. As a result, H2 is successfully generated using the integrated system composed of the designed TENG and catalyst. The finding provides a promising approach for energy generation to achieve net-zero.

Mechanics of the cellular microenvironment as probed by cells in vivo during zebrafish presomitic mesoderm differentiation.

Tissue morphogenesis, homoeostasis and repair require cells to constantly monitor their three-dimensional microenvironment and adapt their behaviours in response to local biochemical and mechanical cues. Yet the mechanical parameters of the cellular microenvironment probed by cells in vivo remain unclear. Here, we report the mechanics of the cellular microenvironment that cells probe in vivo and in situ during zebrafish presomitic mesoderm differentiation. By quantifying both endogenous cell-generated strains and tissue mechanics, we show that individual cells probe the stiffness associated with deformations of the supracellular, foam-like tissue architecture. Stress relaxation leads to a perceived microenvironment stiffness that decreases over time, with cells probing the softest regime. We find that most mechanical parameters, including those probed by cells, vary along the anteroposterior axis as mesodermal progenitors differentiate. These findings expand our understanding of in vivo mechanosensation and might aid the design of advanced scaffolds for tissue engineering applications.

Exceptionally dense and resilient critically jammed polydisperse disk packings.

Understanding the way disordered particle packings transition between jammed (rigid) and unjammed (fluid) states is of both great practical importance and strong fundamental interest. The values of critical packing fraction (and other state variables) at the jamming transition are protocol dependent. Here, we demonstrate that this variability can be systematically traced to structural measures of packing, as well as to energy measures inside the jammed regime. A novel generalized simultaneous particle swap algorithm constructs overjammed states of desired energy, which upon decompression lead to predictable critical packing fractions. Thus, for a given set of particle sizes, states with extraordinarily high critical packing fractions can be found efficiently, which sustain substantial shear strain and preserve their special structure over the entire jammed domain. The close relation revealed here between the energy landscape of overjammed soft-particle packings and the behavior near the jamming transition points towards new ways of understanding and constructing disordered materials with exceptional properties.

Self-Powered Disinfection Using Triboelectric, Conductive Wires of Metal-Organic Frameworks.

Efficient water disinfection is vitally needed in rural and disaster-stricken areas lacking power supplies. However, conventional water disinfection methods strongly rely on external chemical input and reliable electricity. Herein, we present a self-powered water disinfection system using synergistic hydrogen peroxide (H2O2) assisted electroporation mechanisms driven by triboelectric nanogenerators (TENGs) that harvest electricity from the flow of water. The flow-driven TENG, assisted by power management systems, generates a controlled output with aimed voltages to drive a conductive metal-organic framework nanowire array for effective H2O2 generation and electroporation. The injured bacteria caused by electroporation can be further damaged by facile diffused H2O2 molecules at high throughput. A self-powered disinfection prototype enables complete disinfection (>99.9999% removal) over a wide range of flows up to 3.0 × 104 L/(m2 h) with low water flow thresholds (200 mL/min; ∼20 rpm). This rapid, self-powered water disinfection method is promising for pathogen control.

Evaluation of Lipopolysaccharide and Interleukin-6 as Useful Screening Tool for Chronic Endometritis.

Universal diagnostic criteria for chronic endometritis (CE) have not been established due to differences in study design among researchers and a lack of typical clinical cases. Lipopolysaccharides (LPSs) have been reported to cause inflammation in the reproductive systems of several animals. This study aimed to elucidate the influence of LPS in the pathogenesis of CE in humans. We investigated whether LPS affected cytokine production and cell proliferation in the endometrium using in vivo and in vitro experiments. LPS concentrations were analyzed between control and CE patients using endometrial tissues. LPS administration stimulated the proliferation of EM-E6/E7 cells derived from human endometrial cells. High LPS concentrations were detected in CE patients. LPS concentration was found to correlate with IL-6 gene expression in the endometrium. Inflammation signaling evoked by LPS led to the onset of CE, since LPS stimulates inflammatory responses and cell cycles in the endometrium. We identified LPS and IL-6 as suitable candidate markers for the diagnosis of CE.

Failure after intramedullary nailing for geriatric trochanteric fracture: does quality of fracture reduction on the AP and lateral planes show the same results?

PURPOSE: This study aimed to investigate the failure of trochanteric fracture fixation according to the quality of fracture reduction on the anteroposterior (AP) and lateral views. METHODS: Data from 340 female and 152 male patients ≥ 60 years of age who underwent intramedullary nailing for a trochanteric fracture between 2016 and 2020 were analysed retrospectively. The quality of fracture reduction was classified as type A, type E, and type I on the AP view and type N, type A, and type P on the lateral view according to the relative position of the proximal and distal fragments. The failure rate was evaluated and compared according to the quality of fracture reduction. The risk factors of the fixation failure were investigated by comparison of variables between patients with and without failure and by regression analysis. RESULTS: Patients with poor reduction, type I and type P had higher failure rates. However, a statistically significant difference was found only for patients with poor reduction (type P) on the lateral view (p < 0.001). Patients with failure showed significantly higher rates of poor reduction on the lateral view and AO/OTA type A3 fractures. The regression analysis also showed that poor reduction on the lateral view (odds ratio [OR] 12.70; 95% confidence interval [CI] 4.0-40.6; p < 0.001) and AO/OTA type A3 fractures (OR 5.40; 95% CI 1.24-23.49, p = 0.025) were risk factors for failure. CONCLUSION: Poor reduction such as type P reduction was associated with failure after intramedullary nailing for trochanteric fractures. Surgeons should check the quality of fracture reduction carefully with the proper fluoroscopic view to prevent failure in geriatric patients with trochanteric fractures.

CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris).

BACKGROUND: The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. RESULTS: We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. CONCLUSIONS: CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .

Facet-Dependent Passivation for Efficient Perovskite Solar Cells.

Understanding the interplay between the surface structure and the passivation materials and their effects associated with surface structure modification is of fundamental importance; however, it remains an unsolved problem in the perovskite passivation field. Here, we report a surface passivation principle for efficient perovskite solar cells via a facet-dependent passivation phenomenon. The passivation process selectively occurs on facets, which is observed with various post-treatment materials with different functionality, and the atomic arrangements of the facets determine the alignments of the passivation layers. The profound understanding of facet-dependent passivation leads to the finding of 2-amidinopyridine hydroiodide as the material for a uniform and effective passivation on both (100) and (111) facets. Consequently, we achieved perovskite solar cells with an efficiency of 25.10% and enhanced stability. The concept of facet-dependent passivation can provide an important clue on unidentified passivation principles for perovskite materials and a novel means to enhance the performance and stability of perovskite-based devices.

Anti-Leukemic Effects of Idesia polycarpa Maxim Branch on Human B-Cell Acute Lymphoblastic Leukemia Cells.

Patients with pediatric B-cell acute lymphoblastic leukemia (B-ALL) have a high survival rate, yet the prognosis of adults and patients with relapsed/refractory disease is relatively poor. Therefore, it is imperative to develop new therapeutic strategies. Here, we screened 100 plant extracts from South Korean Flora and investigated their anti-leukemic effect using CCRF-SB cells as a B-ALL model. The top cytotoxic extract identified in this screening was the Idesia polycarpa Maxim. branch (IMB), which efficiently inhibited the survival and proliferation of CCRF-SB cells, while having minimal to no impact on normal murine bone marrow cells. Mechanistically, the IMB-induced proapoptotic effect involves the increase of caspase 3/7 activity, which was shown to be associated with the disruption of the mitochondrial membrane potential (MMP) through the reduction in antiapoptotic Bcl-2 family expression. IMB also promoted the differentiation of CCRF-SB cells via the upregulation of the expression of differentiation-related genes, PAX5 and IKZF1. Given that resistance to glucocorticoid (GC) is often found in patients with relapsed/refractory ALL, we investigated whether IMB could restore GC sensitivity. IMB synergized GC to enhance apoptotic rate by increasing GC receptor expression and downmodulating mTOR and MAPK signals in CCRF-SB B-ALL cells. These results suggest that IMB has the potential to be a novel candidate for the treatment of B-ALL.

Assessing the manufacturable 32-channel cochlear electrode array: evaluation results for clinical trials.

Reliability evaluation results of a manufacturable 32-channel cochlear electrode array are reported in this paper. Applying automated laser micro-machining process and a layer-by-layer silicone deposition scheme, authors developed the manufacturing methods of the electrode array for fine patterning and mass production. The developed electrode array has been verified through the requirements specified by the ISO Standard 14708-7. And the insertion trauma of the electrode array has been evaluated based on human temporal bone studies. According to the specified requirements, the electrode array was assessed through elongation & insulation, flexural, and fatigue tests. In addition, Temporal bone study was performed using eight fresh-frozen cadaver temporal bones with the electrode arrays inserted via the round window. Following soaking in saline condition, the impedances between conducting wires of the electrode array were measured over 100 kΩ (the pass/fail criterion). After each required test, it was shown that the electrode array maintained the electrical continuity and insulation condition. The average insertion angle of the electrode array inside the scala tympani was 399.7°. The human temporal bone studies exhibited atraumatic insertion rate of 60.3% (grade 0 or 1). The reliability of the manufacturable electrode array is successfully verified in mechanical, electrical, and histological aspects. Following the completion of a 32-channel cochlear implant system, the performance and stability of the 32-channel electrode array will be evaluated in clinical trials.

Treatment Considerations for Patients with Locoregionally Advanced Head and Neck Cancer with a Contraindication to Cisplatin.

OPINION STATEMENT: Significant advancements have been made in the treatment of locally advanced head and neck cancer, predominantly driven by the integration of concurrent chemotherapy with radiation therapy as a standard of care for many patients. The most heavily investigated chemotherapeutic is cisplatin, yet many patients are ineligible for cisplatin due to the presence of pre-existing medical comorbidities. Moreover, given the toxicity profile of cisplatin, identifying which patients stand to benefit from cisplatin is challenging, which is particularly evident in older patients. Efforts to better risk-stratify patients based on age, performance status, and the degree of pre-existing comorbidities are ongoing and have been increasingly utilized in national clinical trials. In parallel, exploration into alternative systemic agents, including novel targeted therapies and immunotherapies, in cisplatin-ineligible patients are rapidly expanding. Cumulatively, identifying appropriate treatment paradigms in patients who harbor contraindications to cisplatin can not only improve clinical outcomes but also critically mitigate detrimental adverse effects.

Genome-Wide Identification and Comprehensive Analysis of the GASA Gene Family in Peanuts (Arachis hypogaea L.) under Abiotic Stress.

Peanut (Arachis hypogaea L.) is a globally cultivated crop of significant economic and nutritional importance. The role of gibberellic-acid-stimulated Arabidopsis (GASA) family genes is well established in plant growth, development, and biotic and abiotic stress responses. However, there is a gap in understanding the function of GASA proteins in cultivated peanuts, particularly in response to abiotic stresses such as drought and salinity. Thus, we conducted comprehensive in silico analyses to identify and verify the existence of 40 GASA genes (termed AhGASA) in cultivated peanuts. Subsequently, we conducted biological experiments and performed expression analyses of selected AhGASA genes to elucidate their potential regulatory roles in response to drought and salinity. Phylogenetic analysis revealed that AhGASA genes could be categorized into four distinct subfamilies. Under normal growth conditions, selected AhGASA genes exhibited varying expressions in young peanut seedling leaves, stems, and roots tissues. Notably, our findings indicate that certain AhGASA genes were downregulated under drought stress but upregulated under salt stress. These results suggest that specific AhGASA genes are involved in the regulation of salt or drought stress. Further functional characterization of the upregulated genes under both drought and salt stress will be essential to confirm their regulatory roles in this context. Overall, our findings provide compelling evidence of the involvement of AhGASA genes in the mechanisms of stress tolerance in cultivated peanuts. This study enhances our understanding of the functions of AhGASA genes in response to abiotic stress and lays the groundwork for future investigations into the molecular characterization of AhGASA genes.

Subclavian Artery Pseudoaneurysm Following Bedside Temporary Hemodialysis Catheter Insertion: A Case Report.

A pseudoaneurysm of the subclavian artery following central venous catheter placement is a rare but potentially fatal complication that often requires surgical intervention. However, surgical repair of the subclavian artery remains challenging. Herein, we report the case of a male patient undergoing hemodialysis who developed a pseudoaneurysm of the subclavian artery after a bedside central vein catheter placement. Hemostasis was successfully achieved by selecting the pseudoaneurysm using a microcatheter. At the 10-month follow-up, the pseudoaneurysm was completely excluded, and the patient was in a stable condition. The patient underwent native arteriovenous fistula creation and hemodialysis. Endovascular treatment could be an effective nonsurgical treatment for subclavian artery pseudoaneurysms and has been attempted as a first-line treatment option.

Ambient Humidity-Induced Phase Separation for Fiber Morphology Engineering toward Piezoelectric Self-Powered Sensing.

Electrospun polymeric piezoelectric fibers have a considerable potential for shape-adaptive mechanical energy harvesting and self-powered sensing in biomedical, wearable, and industrial applications. However, their unsatisfactory piezoelectric performance remains an issue to be overcome. While strategies for increasing the crystallinity of electroactive ß phases have thus far been the major focus in realizing enhanced piezoelectric performance, tailoring the fiber morphology can also be a promising alternative. Herein, a design strategy that combines the nonsolvent-induced phase separation of a polymer/solvent/water ternary system and electrospinning for fabricating piezoelectric poly(vinylidene fluoride-trifluoroethylene) (P(VDF-TrFE) fibers with surface porosity under ambient humidity is presented. Notably, electrospun P(VDF-TrFE) fibers with higher surface porosity outperform their smooth-surfaced counterparts with a higher ß phase content in terms of output voltage and power generation. Theoretical and numerical studies also underpin the contribution of the structural porosity to the harvesting performance, which is attributable to local stress concentration and reduced dielectric constant due to the air in the pores. This porous fiber design can broaden the application prospects of shape-adaptive energy harvesting and self-powered sensing based on piezoelectric polymer fibers with enhanced voltage and power performance, as successfully demonstrated in this work by developing a communication system based on self-powered motion sensing.

Structural Measures as Guides to Ultrastable States in Overjammed Packings.

Jammed, disordered packings of given sets of particles possess a multitude of equilibrium states with different mechanical properties. Identifying and constructing desired states, e.g., of superior stability, is a complex task. Here, we show that in two-dimensional particle packings the energy of all metastable states (inherent structures) is reliably classified by simple scalar measures of local steric packing. These structural measures are insensitive to the particle interaction potential and so robust that they can be used to guide a modified swap algorithm that anneals polydisperse packings toward low-energy metastable states exceptionally fast. The low-energy states are extraordinarily stable against applied shear, so that the approach also efficiently identifies ultrastable packings.