SVhawkeye: an ultra-fast software for user-friendly visualization of targeted structural fragments from BAM files.

SVhawkeye is a novel visualization software created to rapidly extract essential structural information from third-generation sequencing data, such as data generated by PacBio or Oxford Nanopore Technologies. Its primary focus is on visualizing various structural variations commonly encountered in whole-genome sequencing (WGS) experiments, including deletions, insertions, duplications, inversions, and translocations. Additionally, SVhawkeye has the capability to display isoform structures obtained from iso-seq data and provides interval depth visualization for deducing local copy number variation (CNV). One noteworthy feature of SVhawkeye is its capacity to genotype structural variations, a critical function that enhances the accuracy of structural variant genotyping. SVhawkeye is an open-source software developed using Python and R languages, and it is freely accessible on GitHub (https://github.com/yywan0913/SVhawkeye).

Longitudinal ultrasound-based AI model predicts axillary lymph node response to neoadjuvant chemotherapy in breast cancer: a multicenter study.

OBJECTIVES: Developing a deep learning radiomics model from longitudinal breast ultrasound and sonographer's axillary ultrasound diagnosis for predicting axillary lymph node (ALN) response to neoadjuvant chemotherapy (NAC) in breast cancer. METHODS: Breast cancer patients undergoing NAC followed by surgery were recruited from three centers between November 2016 and December 2022. We collected ultrasound images for extracting tumor-derived radiomics and deep learning features, selecting quantitative features through various methods. Two machine learning models based on random forest were developed using pre-NAC and post-NAC features. A support vector machine integrated these data into a fusion model, evaluated via the area under the curve (AUC), decision curve analysis, and calibration curves. We compared the fusion model's performance against sonographer's diagnosis from pre-NAC and post-NAC axillary ultrasonography, referencing histological outcomes from sentinel lymph node biopsy or axillary lymph node dissection. RESULTS: In the validation cohort, the fusion model outperformed both pre-NAC (AUC: 0.899 vs. 0.786, p < 0.001) and post-NAC models (AUC: 0.899 vs. 0.853, p = 0.014), as well as the sonographer's diagnosis of ALN status on pre-NAC and post-NAC axillary ultrasonography (AUC: 0.899 vs. 0.719, p < 0.001). Decision curve analysis revealed patient benefits from the fusion model across threshold probabilities from 0.02 to 0.98. The model also enhanced sonographer's diagnostic ability, increasing accuracy from 71.9% to 79.2%. CONCLUSION: The deep learning radiomics model accurately predicted the ALN response to NAC in breast cancer. Furthermore, the model will assist sonographers to improve their diagnostic ability on ALN status before surgery. CLINICAL RELEVANCE STATEMENT: Our AI model based on pre- and post-neoadjuvant chemotherapy ultrasound can accurately predict axillary lymph node metastasis and assist sonographer's axillary diagnosis. KEY POINTS: Axillary lymph node metastasis status affects the choice of surgical treatment, and currently relies on subjective ultrasound. Our AI model outperformed sonographer's visual diagnosis on axillary ultrasound. Our deep learning radiomics model can improve sonographers' diagnosis and might assist in surgical decision-making.

Cortistatin protects against septic cardiomyopathy by inhibiting cardiomyocyte pyroptosis through the SSTR2-AMPK-NLRP3 pathway.

BACKGROUND: Although the pathophysiological mechanism of septic cardiomyopathy has been continuously discovered, it is still a lack of effective treatment method. Cortistatin (CST), a neuroendocrine polypeptide of the somatostatin family, has emerged as a novel cardiovascular-protective peptide, but the specific mechanism has not been elucidated. PURPOSE: The aim of our study is to explore the role of CST in cardiomyocytes pyroptosis and myocardial injury in sepsis and whether CST inhibits cardiomyocytes pyroptosis through specific binding with somastatin receptor 2 (SSTR2) and activating AMPK/Drp1 signaling pathway. METHODS AND RESULTS: In this study, plasma CST levels were significantly high and were negatively correlated with N-terminal pro-B type natriuretic peptide (NT-proBNP), a biomarker for cardiac dysfunction, in patients with sepsis. Exogenous administration of CST significantly improved survival rate and cardiac function in mouse models of sepsis by inhibiting the activation of the NLRP3 inflammasome and pyroptosis of cardiomyocytes (decreased cleavage of caspase-1, IL-1ß and gasdermin D). Pharmacological inhibition and genetic ablation revealed that CST exerted anti-pyroptosis effects by specifically binding to somatostatin receptor subtype 2 (SSTR2), thus activating AMPK and inactivating Drp1 to inhibit mitochondrial fission in cardiomyocytes. CONCLUSIONS: This study is the first to report that CST attenuates septic cardiomyopathy by inhibiting cardiomyocyte pyroptosis through the SSTR2-AMPK-Drp1-NLRP3 pathway. Importantly, CST specifically binds to SSTR2, which promotes AMPK phosphorylation, inhibits Drp1-mediated mitochondrial fission, and reduces ROS levels, thereby inhibiting NLRP3 inflammasome activation-mediated pyroptosis and alleviating sepsis-induced myocardial injury.

A portable transistor immunosensor for fast identification of porcine epidemic diarrhea virus.

Widespread distribution of porcine epidemic diarrhea virus (PEDV) has led to catastrophic losses to the global pig farming industry. As a result, there is an urgent need for rapid, sensitive and accurate tests for PEDV to enable timely and effective interventions. In the present study, we develop and validate a floating gate carbon nanotubes field-effect transistor (FG CNT-FET)-based portable immunosensor for rapid identification of PEDV in a sensitive and accurate manner. To improve the affinity, a unique PEDV spike protein-specific monoclonal antibody is prepared by purification, and subsequently modified on FG CNT-FET sensor to recognize PEDV. The developed FET biosensor enables highly sensitive detection (LoD: 8.1 fg/mL and 100.14 TCID50/mL for recombinant spike proteins and PEDV, respectively), as well as satisfactory specificity. Notably, an integrated portable platform consisting of a pluggable FG CNT-FET chip and a portable device can discriminate PEDV positive from negative samples and even identify PEDV and porcine deltacoronavirus within 1 min with 100% accuracy. The portable sensing platform offers the capability to quickly, sensitively and accurately identify PEDV, which further points to a possibility of point of care (POC) applications of large-scale surveillance in pig breeding facilities.

Synthesis and structural optimization of oncolytic peptide LTX-315.

Oncolytic peptides represented potential novel candidates for anticancer treatments especially drug-resistant cancer cell lines. One of the most promising and extensively studied is LTX-315, which is considered as the first in class oncolytic peptide and has entered phase I/II clinical trials. Nevertheless, the shortcomings including poor proteolytic stability, moderate anticancer durability and high synthesis costs may hinder the widespread clinical applications of LTX-315. In order to reduce the synthesis costs, as well as develop derivatives possessing both high protease-stability and durable anticancer efficiency, twenty LTX-315-based derived-peptides were designed and efficiently synthesized. Especially, through solid-phase S-alkylation, as well as the optimized peptide cleavage condition, the derived peptides could be prepared with drastically reduced synthesis cost. The in vitro anticancer efficiency, serum stability, anticancer durability, anti-migration activity, and hemolysis effect were systematically investigated. It was found that derived peptide MS-13 exhibited comparable anticancer efficiency and durability to those of LTX-315. Strikingly, the D-type peptide MS-20, which is the enantiomer of MS-13, was demonstrated to possess significantly high proteolytic stability and sustained anticancer durability. In general, the cost-effective synthesis and stability-guided structural optimizations were conducted on LTX-315, affording the highly hydrolysis resistant MS-20 which possessed durable anticancer activity. Meanwhile, this study also provided a reliable reference for the future optimization of anticancer peptides through the solid-phase S-alkylation and L-type to D-type amino acid substitutions.

Design of High-Precision Driving Control System for Charge Management.

Due to the interaction of accumulated charges on the surface of a test mass with the surrounding electric and magnetic fields, the performance of inertial sensors is affected, necessitating charge management for the test mass. Discharge technology based on Ultraviolet LEDs is internationally recognized as the optimal solution for charge management. Precision driving of Ultraviolet LEDs is considered a key technology in charge management. This paper presents the driving control system used for Ultraviolet LEDs, achieving precision pulse-width-modulation-type current output with controllable pulse width and amplitude. The system generates the pulse-width-controllable pulse voltage signal via analog pulse-width modulation, and subsequently regulates the amplitude of the PWM signal through range switching. To convert the voltage into the pulse-width-modulation-type driving current, the improved Howland current source is employed. The test results demonstrate that the driving control system can output controllable current in the range of 0.01 mA to 10 mA, with a minimum step of 0.01 mA. The accuracy of the current reaches 1%, the stability within 1 h is better than 1%, and the load regulation is better than 2%. The driving control system provides an important reference for the integration of charge management system and the precision drive control method for LEDs.

CCT6A facilitates lung adenocarcinoma progression and glycolysis via STAT1/HK2 axis.

BACKGROUND: Chaperonin Containing TCP1 Subunit 6 A (CCT6A) is a prominent protein involved in the folding and stabilization of newly synthesized proteins. However, its roles and underlying mechanisms in lung adenocarcinoma (LUAD), one of the most aggressive cancers, remain elusive. METHODS: Our study utilized in vitro cell phenotype experiments to assess CCT6A's impact on the proliferation and invasion capabilities of LUAD cell lines. To delve into CCT6A's intrinsic mechanisms affecting glycolysis and proliferation in lung adenocarcinoma, we employed transcriptomic sequencing and liquid chromatography-mass spectrometry analysis. Co-immunoprecipitation (Co-IP) and chromatin immunoprecipitation (CHIP) assays were also conducted to substantiate the mechanism. RESULTS: CCT6A was found to be significantly overexpressed in LUAD and associated with a poorer prognosis. The silencing of CCT6A inhibited the proliferation and migration of LUAD cells and elevated apoptosis rates. Mechanistically, CCT6A interacted with STAT1 protein, forming a complex that enhances the stability of STAT1 by protecting it from ubiquitin-mediated degradation. This, in turn, facilitated the transcription of hexokinase 2 (HK2), a critical enzyme in aerobic glycolysis, thereby stimulating LUAD's aerobic glycolysis and progression. CONCLUSION: Our findings reveal that the CCT6A/STAT1/HK2 axis orchestrated a reprogramming of glucose metabolism and thus promoted LUAD progression. These insights position CCT6A as a promising candidate for therapeutic intervention in LUAD treatment.

Oncogenic functions and therapeutic potentials of targeted inhibition of SMARCAL1 in small cell lung cancer.

Small cell lung cancer (SCLC) is a recalcitrant cancer characterized by high frequency loss-of-function mutations in tumor suppressors with a lack of targeted therapy due to absence of high frequency gain-of-function abnormalities in oncogenes. SMARCAL1 is a member of the ATP-dependent chromatin remodeling protein SNF2 family that plays critical roles in DNA damage repair and genome stability maintenance. Here, we showed that SMARCAL1 was overexpressed in SCLC patient samples and was inversely associated with overall survival of the patients. SMARCAL1 was required for SCLC cell proliferation and genome integrity. Mass spectrometry revealed that PAR6B was a downstream SMARCAL1 signal molecule which rescued inhibitory effects caused by silencing of SMARCAL1. By screening of 36 FDA-approved clinically available agents related to DNA damage repair, we found that an aza-anthracenedione, pixantrone, was a potent SMARCAL1 inhibitor which suppressed the expression of SMARCAL1 and PAR6B at protein level. Pixantrone caused DNA damage and exhibited inhibitory effects on SCLC cells in vitro and in a patient-derived xenograft mouse model. These results indicated that SMARCAL1 functions as an oncogene in SCLC, and pixantrone as a SMARCAL1 inhibitor bears therapeutic potentials in this deadly disease.

Achieving a Deeply Desodiated Stabilized Cathode Material by the High Entropy Strategy for Sodium-ion Batteries.

Manganese-based layered oxides are currently of significant interest as cathode materials for sodium-ion batteries due to their low toxicity and high specific capacity. However, the practical applications are impeded by sluggish intrinsic Na+ migration and poor structure stability as a result of Jahn-Teller distortion and complicated phase transition. In this study, a high-entropy strategy is proposed to enhance the high-voltage capacity and cycling stability. The designed P2-Na0.67Mn0.6Cu0.08Ni0.09Fe0.18Ti0.05O2 achieves a deeply desodiation and delivers charging capacity of 158.1 mA h g-1 corresponding to 0.61 Na with a high initial Coulombic efficiency of 98.2%. The charge compensation is attributed to the cationic and anionic redox reactions conjunctively. Moreover, the crystal structure is effectively stabilized, leading to a slight variation of lattice parameters. This research carries implications for the expedited development of low-cost, high-energy-density cathode materials for sodium-ion batteries.

RETFound-enhanced community-based fundus disease screening: real-world evidence and decision curve analysis.

Visual impairments and blindness are major public health concerns globally. Effective eye disease screening aided by artificial intelligence (AI) is a promising countermeasure, although it is challenged by practical constraints such as poor image quality in community screening. The recently developed ophthalmic foundation model RETFound has shown higher accuracy in retinal image recognition tasks. This study developed an RETFound-enhanced deep learning (DL) model for multiple-eye disease screening using real-world images from community screenings. Our results revealed that our DL model improved the sensitivity and specificity by over 15% compared with commercial models. Our model also shows better generalisation ability than AI models developed using traditional processes. Additionally, decision curve analysis underscores the higher net benefit of employing our model in both urban and rural settings in China. These findings indicate that the RETFound-enhanced DL model can achieve a higher net benefit in community-based screening, advocating its adoption in low- and middle-income countries to address global eye health challenges.

Detection of monkeypox virus based on a convenient and sensitive single-step RPA-CRISPR/Cas12a strategy.

The global outbreak of monkeypox virus (MPXV) has highlighted the need for rapid molecular diagnostics techniques. In this study, a single-step recombinase polymerase amplification (RPA)-CRISPR/Cas12a system was developed for rapid and sensitive detection of MPXV. The limit of detection of this assay was 1 copy per µL of extracted nucleic acids. A heating lysis method was integrated to further simplify the sample processing workflow and shorten the assay time to 40 min from sample to result. The reaction mixture can be lyophilized to improve its accessibility in resource-limited settings. The analysis results of the proposed single-step RPA-CRISPR/Cas12a assay for clinical MPXV positive and negative samples were 100% consistent with standard PCR assay. These results demonstrate the feasibility and efficiency of this method for rapid and accurate MPXV detection in real-world settings, showcasing its potential utility in urgent and practical settings.

Paroxysmal sympathetic hyperexcitability after brain injury: A clinical analysis of case series.

BACKGROUND: Paroxysmal sympathetic hyperexcitability (PSH) is a group of complex syndromes with various etiologies. Previous studies were limited to the description of traumatic brain injury (TBI), and the description of PSH after other types of brain injury was rare. We explored the clinical features, treatment, and prognosis of PSH after various types of brain injuries. METHODS: Patients admitted to the neurosurgery intensive care unit with PSH after brain injury from July 2019 to December 2022 were included. Demographic data, clinical manifestations, drug therapy, and disease prognosis were retrospectively collected and analyzed. RESULTS: Fifteen male and 9 female patients with PSH after brain injury were selected. TBI was most likely to cause PSH (66.7%), followed by spontaneous intracerebral hemorrhage (25%). Glasgow coma scale scores of 19 patients (79.2%) were lower than 8 and 14 patients (58.3%) underwent tracheotomy. Electroencephalogram monitoring was performed in 12 individuals, none of which showed epileptic waves. Clinical symptom scale showed mild symptoms in 17 cases (70.8%). Almost all patients were administered a combination of drugs. After follow-up, most patients had a poor prognosis and 2 (8.3%) died after discharge. CONCLUSION: The etiology of PSH is complex. TBI may be the most common cause of PSH. Non-TBI may also be an important cause of PSH. Therefore, early identification, prevention and diagnosis are helpful for determining the prognosis and outcome of the disease.

Zinc Oxide Nanoclusters Encapsulated in MFI Zeolite as a Highly Stable Adsorbent for the Ultradeep Removal of Hydrogen Sulfide.

Often, trace impurities in a feed stream will cause failures in industrial applications. The efficient removal of such a trace impurity from industrial steams, however, is a daunting challenge due to the extremely small driving force for mass transfer. The issue lies in an activity-stability dilemma, that is, an ultrafine adsorbent that offers a high exposure of active sites is favorable for capturing species of a low concentration, but free-standing adsorptive species are susceptible to rapidly aggregating in working conditions, thus losing their intrinsic high activity. Confining ultrafine adsorbents in a porous matrix is a feasible solution to address this activity-stability dilemma. We herein demonstrate a proof of concept by encapsulating ZnO nanoclusters into a pure-silica MFI zeolite (ZnO@silicalite-1) for the ultradeep removal of H2S, a critical need in the purification of hydrogen for fuel cells. The Zn species and their interaction with silicalite-1 were thoroughly investigated by a collection of characterization techniques such as HADDF-STEM, UV-visible spectroscopy, DRIFTS, and 1H MAS NMR. The results show that the zeolite offers rich silanol defects, which enable the guest nanoclusters to be highly dispersed and anchored in the silicious matrix. The nanoclusters are present in two forms, Zn(OH)+ and ZnO, depending on the varying degrees of interaction with the silanol defects. The ultrafine nanoclusters exhibit an excellent desulfurization performance in terms of the adsorption rate and utilization. Furthermore, the ZnO@silicalite-1 adsorbents are remarkably stable against sintering at high temperatures, thus maintaining a high activity in multiple adsorption-regeneration cycles. The results demonstrate that the encapsulation of active metal oxide species into zeolite is a promising strategy to develop fast responsive and highly stable adsorbents for the ultradeep removal of trace impurities.

The 2024 Magnonics Roadmap.

Magnonicsis a research field that has gained an increasing interest in both the fundamental and applied sciences in recent years. This field aims to explore and functionalize collective spin excitations in magnetically ordered materials for modern information technologies, sensing applications, and advanced computational schemes. Spin waves, also known as magnons, carry spin angular momenta that allow for the transmission, storage, and processing of information without moving charges. In integrated circuits, magnons enable on-chip data processing at ultrahigh frequencies without the Joule heating, which currently limits clock frequencies in conventional data processors to a few GHz. Recent developments in the field indicate that functional magnonic building blocks for in-memory computation, neural networks, and Ising machines are within reach. At the same time, the miniaturization of magnonic circuits advances continuously as the synergy of materials science, electrical engineering, and nanotechnology allows for novel on-chip excitation and detection schemes. Such circuits can already enable magnon wavelengths of 50 nm at microwave frequencies in a 5G frequency band. Research into non-charge-based technologies is urgently needed in view of the rapid growth of machine learning and artificial intelligence applications, which consume substantial energy when implemented on conventional data processing units. In its first part, the 2024 Magnonics Roadmap provides an update on the recent developments and achievements in the field of nano-magnonics while defining its future avenues and challenges. In its second part, the Roadmap addresses the rapidly growing research endeavors on hybrid structures and magnonics-enabled quantum engineering. We anticipate that these directions will continue to attract researchers to the field and, in addition to showcasing intriguing science, will enable unprecedented functionalities that enhance the efficiency of alternative information technologies and computational schemes.

Deep Learning-Enhanced Hand Grip and Release Test for Degenerative Cervical Myelopathy: Shortening Assessment Duration to 6 Seconds.

OBJECTIVE: Hand clumsiness and reduced hand dexterity can signal early signs of degenerative cervical myelopathy (DCM). While the 10-second grip and release (10-s G&R) test is a common clinical tool for evaluating hand function, a more accessible method is warranted. This study explores the use of deep learning-enhanced hand grip and release test (DL-HGRT) for predicting DCM and evaluates its capability to reduce the duration of the 10-s G&R test. METHODS: The retrospective study included 508 DCM patients and 1,194 control subjects. Propensity score matching (PSM) was utilized to minimize the confounding effects related to age and sex. Videos of the 10-s G&R test were captured using a smartphone application. The 3D-MobileNetV2 was utilized for analysis, generating a series of parameters. Additionally, receiver operating characteristic curves were employed to assess the performance of the 10-s G&R test in predicting DCM and to evaluate the effectiveness of a shortened testing duration. RESULTS: Patients with DCM exhibited impairments in most 10-s G&R test parameters. Before PSM, the number of cycles achieved the best diagnostic performance (area under the curve [AUC], 0.85; sensitivity, 80.12%; specificity, 74.29% at 20 cycles), followed by average grip time. Following PSM for age and gender, the AUC remained above 0.80. The average grip time achieved the highest AUC of 0.83 after 6 seconds, plateauing with no significant improvement in extending the duration to 10 seconds, indicating that 6 seconds is an adequate timeframe to efficiently evaluate hand motor dysfunction in DCM based on DL-HGRT. CONCLUSION: DL-HGRT demonstrates potential as a promising supplementary tool for predicting DCM. Notably, a testing duration of 6 seconds appears to be sufficient for accurate assessment, enhancing the test more feasible and practical without compromising diagnostic performance.

Comparison of indocyanine green and blue-stained glue for preoperative localization for pulmonary nodules.

Background: In patients with pulmonary nodules undergoing computed tomography (CT)-guided localization procedures, a range of liquid-based materials have been employed to date in an effort to guide video-assisted thoracoscopic surgery (VATS) procedures to resect target nodules. However, the relative performance of these different liquid-based localization strategies has yet to be systematically evaluated. Accordingly, this study was developed with the aim of examining the relative safety and efficacy of CT-guided indocyanine green (IG) and blue-stained glue (BSG) PN localization. Methods: Consecutive patients with PNs undergoing CT-guided localization prior to VATS from November 2021 - April 2022 were enrolled in this study. Safety and efficacy outcomes were compared between patients in which different localization materials were used. Results: In total, localization procedures were performed with IG for 121 patients (140 PNs), while BSG was used for localization procedures for 113 patients (153 PNs). Both of these materials achieved 100% technical success rates for localization, with no significant differences between groups with respect to the duration of localization (P = 0.074) or visual analog scale scores (P = 0.787). Pneumothorax affected 8 (6.6%) and 8 (7.1%) patients in the respective IG and BSG groups (P = 0.887), while 12 (9.9%) and 10 (8.8%) patients of these patients experienced pulmonary hemorrhage. IG was less expensive than BSG ($17.2 vs. $165). VATS sublobar resection procedure technical success rates were also 100% in both groups, with no instances of conversion to thoracotomy. Conclusions: IG and BSG both offer similarly high levels of clinical safety and efficacy when applied for preoperative CT-guided PN localization, with IG being less expensive than BSG.

Case Report: Can preoperative implantation of veno-arterial extracorporeal membrane oxygenation lead to embolic events in infective endocarditis?

Early-stage infective endocarditis (IE) can lead to severe complications, including infarctions and metastatic infections caused by inflammatory embolus shedding. Common embolism sites include the brain, spleen, kidneys, lungs, and intestines. Additionally, acute heart failure (AHF) can occur in up to 40% of cases, and its presence can impact the clinical outcomes of patients with IE. Cardiogenic shock (CGS) is often more likely to occur after AHF has taken place. If bacteria invade the blood, infectious shock can occur. Patients with IE can experience simple CGS, septic shock, or a combination of the two. Extracorporeal membrane oxygenation (ECMO) typically serves as a Bridge for Heart failure and Cardiogenic shock. Previous research indicates that there are limited reports of ECMO support for patients with IE after CGS has occurred. Because CGS may occur at any time during IE treatment, it is important to understand the timing of ECMO auxiliary support and how to carry out comprehensive treatment after support. Timely treatment can help to reduce or avoid the occurrence of serious complications and improve the prognosis of patients with IE. Our work combines a case study to review the ECMO support of IE patients after CGS through a literature review. Overall, we suggest that when patients with IE have large bacterial thrombosis and a greater risk of shedding, it is recommended to carefully evaluate the indications and contraindications for ECMO after discussion by a multidisciplinary team (MDT). Still, active surgical treatment at an early stage is recommended.