Effect of Clonal Hematopoiesis Mutations and Canakinumab Treatment on Incidence of Solid Tumors in the CANTOS Randomized Clinical Trial

Clonal hematopoiesis (CH) is more common in older persons and has been associated with an increased risk of hematological cancers and cardiovascular diseases. The most common CH mutations occur in the DNMT3A and TET2 genes and result in increased pro-inflammatory signaling. The Canakinumab Anti-inflammatory Thrombosis Outcome Study (CANTOS, NCT01327846) evaluated the neutralizing anti-IL-1β antibody canakinumab in 10,061 randomized patients with a history of myocardial infarction and persistent inflammation; DNA samples were available from 3,923 patients for targeted genomic sequencing. We examined the incidence of non-hematological malignancy by treatment assignment and CH mutations and estimated the cumulative incidence of malignancy events during trial follow-up. Patients with TET2 mutations treated with canakinumab had the lowest incidence of non-hematological malignancy across cancer types. The cumulative incidence of at least one reported malignancy was lower for patients with TET2 mutations treated with canakinumab vs those treated with placebo. These findings support a potential role for canakinumab in cancer prevention and provide evidence of IL-1β blockade cooperating with CH mutations to modify the disease course.

Impact of stent retriever size on clinical outcomes in the RECO registry

Objective

In the RECO study, we investigated the impact of the operator's choice of stent retriever size on patients with internal carotid artery (ICA) occlusion.

Methods

Data from the RECO Registry, a prospective multicentre study, were utilized. Patients who underwent mechanical thrombectomy (MT) were divided according to the size of the stent into the RECO 4 × 20 group, the RECO 5 × 30 group and the RECO 6 × 30 group. The outcome measures assessed in the study were the 3-month modified Rankin Scale (mRS) score, occurrence of any intracranial haemorrhage (aICH), workflow timing, recanalization success rate, number of attempts, and all-cause mortality within a 3-month period.

Results

Analysis was conducted on a total of 89 patients with ICA occlusion. RECO 4 × 20, 5 × 30, and 6 × 30 stent retrievers were used in 19 (21.3%), 52 (58.4%), and 18 (20.2%) patients, respectively. The demographic and baseline characteristics showed considerable similarity across the three groups. The puncture-to-recanalization time of the RECO 6 × 30 group [56.5 min (IQR, 41.5-80.8)] was significantly shorter than that of the RECO 4 × 20 group [110 min (IQR, 47-135)]. In 10 out of 18 patients (55.6%), the RECO 6 × 30 stent retriever achieved reperfusion (modified Thrombolysis in Cerebral Infarction [mTICI] score 2b-3) after the initial attempt, surpassing the rates of 31.6% in the RECO 4 × 20 group and 32.7% in the RECO 5 × 30 group. In the RECO 4 × 20 group, the median number of passes was 2 (IQR, 1-3); in the RECO 5 × 30 group, it was 2 (IQR, 1-3); and in the RECO 6 × 30 groups, it was 1 (IQR, 1-2.5). There were no statistically significant differences observed among the three groups concerning aICH or good outcomes (mRS score 0-2).

Conclusion

Our study demonstrated the practical implications of stent-retriever size selection in the context of the MT for ICA occlusion. The routine use of a RECO 6 × 30 stent retriever holds the potential for early revascularization in clinical practice. The significant reduction in the puncture-to-reperfusion time and the greater first-pass effect associated with this stent size underscore its efficiency in treating ICA occlusion.

Factors influencing postoperative visual improvement in 208 patients with tuberculum sellae meningiomas

OBJECTIVE

Tuberculum sellae meningiomas (TSMs) usually compress the optic nerve and optic chiasma, thus affecting vision. Surgery is an effective means to remove tumors and improve visual outcomes. On a larger scale, this study attempted to further explore and confirm the factors related to postoperative visual outcomes to guide the treatment of TSMs.

METHODS

Data were obtained from 208 patients with TSMs who underwent surgery at our institution between January 2010 and August 2022. Demographics, ophthalmologic examination results, imaging data, extent of resection, radiotherapy status, and surgical approaches were included in the analysis. Univariate and multivariate logistic regressions were used to assess the factors that could lead to favorable visual outcomes.

RESULTS

The median follow-up duration was 63 months, and gross total resection (GTR) was achieved in 174 (83.7%) patients. According to our multivariate logistic regression analysis, age < 60 years (odds ratio [OR] = 0.310; P = 0.007), duration of preoperative visual symptoms (DPVS) < 10 months (OR = 0.495; P = 0.039), tumor size ≤ 27 mm (OR = 0.337; P = 0.002), GTR (OR = 3.834; P = 0.006), and a tumor vertical-to-horizontal dimensional ratio < 1 (OR = 2.593; P = 0.006) were found to be significant independent predictors of favorable visual outcomes.

CONCLUSION

Age, DPVS, tumor size, GTR, and the tumor vertical-to-horizontal dimensional ratio were found to be powerful predictors of favorable visual outcomes. This study may help guide decisions regarding the treatment of TSMs.

The C2H2 family protein ZAT17 engages in the cadmium stress response by interacting with PRL1 in Arabidopsis

Cadmium (Cd) is a heavy metal and a toxic substance. Soil Cd pollution has emerged as a significant environmental issue that jeopardizes both the safety of agricultural products and human health. PLEIOTROPIC REGULATORY LOCUS 1 (PRL1) has been identified as a crucial factor in Cd stress and a series of defence mechanisms. However, the mechanism through which PRL1 mediates its downstream signalling has remained poorly understood. Here, we discovered a prl1-2 suppressor (sup8) for prl1-2 that complemented the defective development phenotype of prl1-2 under Cd stress. Gene cloning revealed a mutation in the C2H2 transcription factor ZAT17 as the basis for the sup8 phenotype. Genetic and biochemical studies indicated that ZAT17 acts as a negative regulator of Cd tolerance. Transcriptome analysis revealed that ZAT17 influences the alternative splicing (AS) process of multiple Cd-responsive genes by interacting with members of the MAC splicing complex, including PRL1 and CDC5. In conclusion, the identification of the novel gene ZAT17 enriches the understanding of the Cd stress response pathway and provides a valuable candidate locus for breeding Cd-resistant plant varieties.

A prospective, multicentre, registry study of RECO in the endovascular treatment of acute ischaemic stroke

The RECO is a novel endovascular treatment (EVT) device that adjusts the distance between two mesh segments to axially hold the thrombus. We organized this postmarket study to assess the safety and performance of RECO in acute ischaemic stroke (AIS) patients with large vessel occlusion (LVO). This was a single-arm prospective multicentre study that enrolled patients as first-line patients treated with RECO at 9 stroke centres. The primary outcome measures included functional independence at 90 days (mRS 0-2), symptomatic intracranial haemorrhage (sICH), time from puncture to recanalization and time from symptom onset to recanalization. The secondary outcome measures were a modified thrombolysis in cerebral infarction (mTICI) score of 2b or 3 after the first attempt and at the end of the procedure and the all-cause mortality rate within 90 days. From May 22, 2020, to July 30, 2022, a total of 268 consecutive patients were enrolled in the registry. The median puncture-to-recanalization time was 64 (IQR, 45-92), and the symptom onset-to-recanalization time was 328 min (IQR, 228-469). RECO achieved successful reperfusion (mTICI 2b-3) after the first pass in 133 of 268 patients (49.6%). At the end of the operation, 96.6% of the patients reached mTICI 2b-3, and 97.4% of the patients ultimately achieved successful reperfusion. Sixteen (7.2%) patients had sICH. A total of 132 (49.3%) patients achieved functional independence at 90 days, and the all-cause mortality rate within 90 days was 17.5%. In this clinical experience, the RECO device achieved a high rate of complete recanalization with a good safety profile and favourable 90-day clinical outcomes.Clinical trial registration: URL: https://www.clinicaltrials.gov/ ; Unique identifier: NCT04840719.

Online Passive-Aggressive Multilabel Classification Algorithms

Most existing multilabel classification methods are batch learning methods, which may suffer from expensive retraining costs when dealing with new incoming data. In order to overcome the drawbacks of batch learning, we develop a family of online multilabel classification algorithms, which can update the model instantly and efficiently, and make a timely online prediction when new data arrive. Our algorithms all take a closed-form update, which is obtained by solving a constrained optimization problem in each round of online learning. Label correlation is explicitly modeled in our optimization problem. The label thresholding function, an important component of our online classifier, can also be learned online. Our algorithms can be easily generalized to the nonlinear prediction cases using Mercer kernels. The worst case loss bounds for our algorithms are provided. The bounds are relative to the cumulative loss suffered by the best fixed predictive model that can be attained in hindsight. Finally, we corroborate the merits of our algorithms in both linear and nonlinear predictions on nine open multilabel benchmark datasets.

A Membrane Tension-Responsive Mechanosensitive DNA Nanomachine

Membrane curvature reflects physical forces operating on the lipid membrane, which plays important roles in cellular processes. Here, we design a mechanosensitive DNA (MSD) nanomachine that mimics natural mechanosensitive PIEZO channels to convert the membrane tension changes of lipid vesicles with different sizes into fluorescence signals in real time. The MSD nanomachine consists of an archetypical six-helix-bundle DNA nanopore, cholesterol-based membrane anchors, and a solvatochromic fluorophore, spiropyran (SP). We find that the DNA nanopore effectively amplifies subtle variations of the membrane tension, which effectively induces the isomerization of weakly emissive SP into highly emissive merocyanine isomers for visualizing membrane tension changes. By measuring the membrane tension via the fluorescence of MSD nanomachine, we establish the correlation between the membrane tension and the curvature that follows the Young-Laplace equation. This DNA nanotechnology-enabled strategy opens new routes to studying membrane mechanics in physiological and pathological settings.

Nitrile-Specific Protein NSP2 and Its Interacting Protein MPK3 Synergistically Regulate Plant Disease Resistance in Arabidopsis

Glucosinolates and their degradation products have a wide range of actions and are important components of plant defense. NSP2 (nitrile-specific protein 2) is a key regulator in the breakdown process of glucosinolates. However, the precise function of NSP2 in plant disease resistance beyond its role in glucosinolate degradation is still unclear. In this study, we discovered that NSP2 which was induced by Pst DC3000, influenced PR genes expression and reactive oxygen burst. Additionally, omics analysis revealed that NSP2 was engaged in plant-pathogen interaction and several hormone signal transduction pathways. Furthermore, immunoprecipitation-tandem mass spectrometry analysis (IP-MS), bimolecular fluorescence complementation (BiFC), and co-immunoprecipitation demonstrated that NSP2 interacts with MPK3. Genetic analysis shows that NSP2 may be a function downstream of MPK3. Upon pathogen inoculation, NSP2 protein levels increase while MPK3 protein levels decrease. Moreover, the level of phosphorylated NSP2 decreases. Taken together, this study sheds light on a new mode of synergistic action between NSP2 and MPK3 in the disease resistance process.

Diffusible signal factor primes plant immunity against Xanthomonas campestris pv. campestris (Xcc) via JA signaling in Arabidopsis and Brassica oleracea

Background

Many Gram-negative bacteria use quorum sensing (QS) signal molecules to monitor their local population density and to coordinate their collective behaviors. The diffusible signal factor (DSF) family represents an intriguing type of QS signal to mediate intraspecies and interspecies communication. Recently, accumulating evidence demonstrates the role of DSF in mediating inter-kingdom communication between DSF-producing bacteria and plants. However, the regulatory mechanism of DSF during the Xanthomonas-plant interactions remain unclear.

Methods

Plants were pretreated with different concentration of DSF and subsequent inoculated with pathogen Xanthomonas campestris pv. campestris (Xcc). Pathogenicity, phynotypic analysis, transcriptome combined with metabolome analysis, genetic analysis and gene expression analysis were used to evaluate the priming effects of DSF on plant disease resistance.

Results

We found that the low concentration of DSF could prime plant immunity against Xcc in both Brassica oleracea and Arabidopsis thaliana. Pretreatment with DSF and subsequent pathogen invasion triggered an augmented burst of ROS by DCFH-DA and DAB staining. CAT application could attenuate the level of ROS induced by DSF. The expression of RBOHD and RBOHF were up-regulated and the activities of antioxidases POD increased after DSF treatment followed by Xcc inoculation. Transcriptome combined with metabolome analysis showed that plant hormone jasmonic acid (JA) signaling involved in DSF-primed resistance to Xcc in Arabidopsis. The expression of JA synthesis genes (AOC2, AOS, LOX2, OPR3 and JAR1), transportor gene (JAT1), regulator genes (JAZ1 and MYC2) and responsive genes (VSP2, PDF1.2 and Thi2.1) were up-regulated significantly by DSF upon Xcc challenge. The primed effects were not observed in JA relevant mutant coi1-1 and jar1-1.

Conclusion

These results indicated that DSF-primed resistance against Xcc was dependent on the JA pathway. Our findings advanced the understanding of QS signal-mediated communication and provide a new strategy for the control of black rot in Brassica oleracea.

High-Valence Oxides for High Performance Oxygen Evolution Electrocatalysis

Valence tuning of transition metal oxides is an effective approach to design high-performance catalysts, particularly for the oxygen evolution reaction (OER) that underpins solar/electric water splitting and metal-air batteries. Recently, high-valence oxides (HVOs) are reported to show superior OER performance, in association with the fundamental dynamics of charge transfer and the evolution of the intermediates. Particularly considered are the adsorbate evolution mechanism (AEM) and the lattice oxygen-mediated mechanism (LOM). High-valence states enhance the OER performance mainly by optimizing the e_g -orbital filling, promoting the charge transfer between the metal d band and oxygen p band. Moreover, HVOs usually show an elevated O 2p band, which triggers the lattice oxygen as the redox center and enacts the efficient LOM pathway to break the "scaling" limitation of AEM. In addition, oxygen vacancies, induced by the overall charge-neutrality, also promote the direct oxygen coupling in LOM. However, the synthesis of HVOs suffers from relatively large thermodynamic barrier, which makes their preparation difficult. Hence, the synthesis strategies of the HVOs are discussed to guide further design of the HVO electrocatalysts. Finally, further challenges and perspectives are outlined for potential applications in energy conversion and storage.

Small DNAs That Specifically and Tightly Bind Transition Metal Ions

Specific DNA-binding to metal ions is a long-standing fundamental research topic with great potential to transform into nano/biotechnology and therapeutics applications. Herein, based on the mobility change of DNA in denaturing gels, we develop a selection strategy to discover a series of 40-45 nt small DNAs that can bind Zn²⁺ and Cd²⁺ specifically and tightly. The Zn²⁺- and Cd²⁺-bound DNA complexes can even tolerate harsh denaturing conditions of 8 M urea and 50 mM EDTA. The discovery not only exposes a new class of transition metal ion-binding DNAs but also provides potentially a new tool for targeting drug therapies based on metal ions.

Exclusively Posterior Circulation Stroke Caused by Internal Carotid Artery Thrombosis

A fetal posterior cerebral artery (FPCA) is an anatomic variant in which the posterior cerebral artery (PCA) is an embryological derivative of the internal carotid artery (ICA). Patients with FPCA may experience posterior circulation stroke (PCS) after a thrombotic event in the ICA system, while exclusively PCS caused by thrombosis of the ICA has rarely been reported. We report a patient with FPCA and summarize 3 types of exclusively PCS caused by FPCA due to thrombotic events in the ICA system. Type A: the thrombus involves the opening of the FPCA and obstructs the blood flow of the entire ICA. The contralateral ICA compensates the ipsilateral middle cerebral artery (MCA) and anterior cerebral artery (ACA) through the anterior communicating artery (ACOM). Type B: the thrombus involves the opening of the FPCA but does not block the blood flow of the entire ICA, which still perfuses the ipsilateral ACA and MCA. Type C: the thrombus only involves the FPCA and not the ipsilateral ICA. Patients with types A and B may obtain a good prognosis through endovascular treatment (EVT), while the benefits of this procedure in type C patients are unclear.

NURSING IN SPORTS ANKLE INJURY BASED ON THE FITNESS EXERCISE

ABSTRACT Introduction Ankle injury is an acute soft tissue pathology where the ankle ligaments are distended, lacerated, or ruptured due to violence during sport. This joint is also one of the most vulnerable in sports. After an injury, immediate and adequate care is significant in reducing pain and complication. Objective Statistically analyze the sports injuries of the ankle cases, determining the principal reasons for injury and outlining preventive measures. Methods A statistical investigation on the sports injuries of 275 Qiqihar higher education students was performed with questionnaires and teaching practice methods. The research was focused on the injured structures and the injury causes analysis. In parallel, corresponding proposals aimed at preventing these sports injuries were raised. Results Joint injuries and ankle sprains followed by hematomas represented the most significant proportion of ankle injuries. The reasons are lack of physical fitness, lack of awareness of self-protection, inadequate preparation in the sporting environment facilities, and performing tasks outside what the superior specified was specified. Conclusion Medical work needs to increase dissemination so that people realize the causes of sports injuries. At the same time, it helps people master the care measures before and after the injury. This reduces the incidence of sports injuries and reduces the occurrence of complications. Evidence level II; Therapeutic Studies - Investigating the results.

Advancing pathogen detection for airborne diseases

Airborne diseases including SARS, bird flu, and the ongoing Coronavirus Disease 2019 (COVID-19) have stimulated the demand for developing novel bioassay methods competent for early-stage diagnosis and large-scale screening. Here, we briefly summarize the state-of-the-art methods for the detection of infectious pathogens and discuss key challenges. We highlight the trend for next-generation technologies benefiting from multidisciplinary advances in microfabrication, nanotechnology and synthetic biology, which allow sensitive, rapid yet inexpensive pathogen assays with portable intelligent device.

Few-layered Bi4O5I2 nanosheets enclosed by {1 0-1} facets with oxygen vacancies for highly-efficient removal of water contaminants

Few-layered Bi₄O₅I₂ nanosheets (FL-Bi₄O₅I₂) were synthesized by intergrowth with Bi₂O₂CO₃ under room temperature. The photoactivity of FL-Bi₄O₅I₂ was 2.5 and 9.5 times higher than that of Bi₄O₅I₂ nanoflakes (NF-Bi₄O₅I₂, about 30 nm thickness) and standard visible-light-driven N-TiO₂, respectively. Moreover, FL-Bi₄O₅I₂ exhibited a wide pH application range (3.0 - 10.0) and excellent photostability. The characterization results showed FL-Bi₄O₅I₂ was consisted of 5 - 8 layers with thickness of 4 - 7 nm and enclosed by {1 0 - 1} facets. The ultrathin characteristics could accelerate the charge transfer to the surface due to the shortened transport distance. Compared to NF-Bi₄O₅I₂, surface oxygen vacancies and the more negative CB potential were formed on FL-Bi₄O₅I₂. The photogenerated electrons were confirmed to be captured by surface oxygen vacancies to effectively reduce surface adsorbed O₂ into HO₂^•/O₂^•-, leaving more h⁺ to oxidize organic pollutants. This process was further facilitated by the more negative CB potential of FL-Bi₄O₅I₂, resulting in the highly efficient removal of pollutants.

Programmable Assembly of Amphiphilic DNA through Controlled Cholesterol Stacking

The excellent programmability and modifiability of DNA has enabled chemists to reproduce a series of specific molecular interactions in self-assembled synthetic systems. Among diverse modifications, cholesterol conjugation can turn DNA into an amphiphilic molecule (cholesterol-DNA), driving the formation of DNA assemblies through the cholesterol-endowed hydrophobic interaction. However, precise control of such an assembly process remains difficult because of the unbiased accumulation of cholesterol. Here, we report the serendipitous discovery of the favored tetramerization of cholesterol in cholesterol-DNA copolymers that carry the cholesterol modification at the blunt end of DNA. The discovery expands the repertoire of controllable molecular interactions by DNA and provides an effective way to precisely control the hydrophobic stacking of cholesterol for programmed cholesterol-DNA assembly.

Impact of obstructive sleep apnea on aortic disease occurrence: a meta-analysis

Objective

Aortic diseases, mainly including aortic dilatation, aortic aneurysm (AA) and aortic dissection (AD), have high morbidity and mortality. Many studies have suggested that obstructive sleep apnea (OSA) acts as a candidate risk factor for aortic diseases. Thus, we performed a meta-analysis to explore comprehensively the effect of OSA on the risk of aortic disease occurrence.

Methods

We searched PubMed, Embase and Cochrane Library databases from inception to February 2022 to identify studies investigating the association between OSA and aortic diameter dilatation, the prevalence of OSA in individuals with or without AA/AD and the incidence of AA/AD in individuals with or without OSA. The Newcastle-Ottawa Scale (NOS) and the Agency for Healthcare Research and Quality (AHRQ) were respectively used to evaluate the quality of the included cohort and cross-sectional studies. A random or fixed effect model was used to generate pooled effects according to interstudy heterogeneity. Sensitivity analyses were performed to test the robustness of the results.

Results

We identified 10 observational publications with 214,127 participants in this meta-analysis. OSA was significantly associated with increased aortic diameter (WMD = 1.46, 95% CI, 1.10–1.83, p < 0.001). OSA prevalence was higher in patients with AA/AD compared to their counterparts without AA/AD (OR = 1.90, 95% CI, 1.30–2.76, p = 0.001). No significant difference in the incidence of AA/AD was observed in individuals with or without OSA (RR = 0.85, 95% CI, 0.62–1.16, p = 0.307). Sensitivity analyses did not modify these results.

Conclusions

This meta-analysis suggests that OSA is associated with aortic diameter dilatation but does not affect AA/AD occurrence.

Workflow Intervals and Outcomes of Endovascular Treatment for Acute Large-Vessel Occlusion During On-Vs. Off-hours in China: The ANGEL-ACT Registry

Background: There may be a delay in or a poor outcome of endovascular treatment (EVT) among acute ischemic stroke (AIS) patients with large-vessel occlusion (LVO) during off-hours. By using a prospective, nationwide registry, we compared the workflow intervals and radiological/clinical outcomes between patients with acute LVO treated with EVT presenting during off- and on-hours.

Methods: We analyzed prospectively collected Endovascular Treatment Key Technique and Emergency Work Flow Improvement of Acute Ischemic Stroke (ANGEL-ACT) data. Patients presenting during off-hours were defined as those presenting to the emergency department from Monday to Friday between 17:30 and 08:00, on weekends (from 17:30 on Friday to 08:00 on Monday), and on national holidays. We used logistic regression models with adjustment for potential confounders to determine independent associations between the time of presentation and outcomes.

Results: Among 1,788 patients, 1,079 (60.3%) presented during off-hours. The median onset-to-door time and onset-to-reperfusion time were significantly longer during off-hours than during on-hours (165 vs. 125 min, P = 0.002 and 410 vs. 392 min, P = 0.027). The rates of successful reperfusion and symptomatic intracranial hemorrhage were similar in both groups. The adjusted odds ratio (OR) for the 90-day modified Rankin Scale score was 0.892 [95% confidence interval (CI), 0.748–1.064]. The adjusted OR for the occurrence of functional independence was 0.892 (95% CI, 0.724–1.098), and the adjusted OR for mortality was 1.214 (95% CI, 0.919–1.603).

Conclusions: Off-hours presentation in the nationwide real-world registry was associated with a delay in the visit and reperfusion time of EVT in patients with AIS. However, this delay was not associated with worse functional outcomes or higher mortality rates.

Clinical Trial Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT03370939.

Water-Dispersible Gold Nanoclusters: Synthesis Strategies, Optical Properties, and Biological Applications

Atomically precise gold nanoclusters (AuNCs) are an emerging class of quantum-sized nanomaterials. Intrinsic discrete electronic energy levels have endowed them with fascinating electronic and optical properties. They have been widely applied in the fields of optoelectronics, photovoltaics, catalysis, biochemical sensing, bio-imaging, and therapeutics. Nevertheless, most AuNCs are synthesized in organic solvents and do not disperse in aqueous solutions; this restricts their biological applications. In this review, we focus on the recent progress in the preparation of water-dispersible AuNCs and their biological applications. We first review different methods of synthesis, including direct synthesis from hydrophilic templates and indirect phase transfer of hydrophobic AuNCs. We then discuss their photophysical properties, such as emission enhancement and fluorescence lifetimes. Next, we summarize their latest applications in the fields of biosensing, biolabeling, and bioimaging. Finally, we outline the challenges and potential for the future development of these AuNCs.

MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations

MOTIVATION

Cancer somatic driver mutations associated with genes within a pathway often show a mutually exclusive pattern across a cohort of patients. This mutually exclusive mutational signal has been frequently used to distinguish driver from passenger mutations and to investigate relationships among driver mutations. Current methods for de novo discovery of mutually exclusive mutational patterns are limited because the heterogeneity in background mutation rate can confound mutational patterns, and the presence of highly mutated genes can lead to spurious patterns. In addition, most methods only focus on a limited number of pre-selected genes and are unable to perform genome-wide analysis due to computational inefficiency.

RESULTS

We introduce a statistical framework, MEScan, for accurate and efficient mutual exclusivity analysis at the genomic scale. Our framework contains a fast and powerful statistical test for mutual exclusivity with adjustment of the background mutation rate and impact of highly mutated genes, and a multi-step procedure for genome-wide screening with the control of false discovery rate. We demonstrate that MEScan more accurately identifies mutually exclusive gene sets than existing methods and is at least two orders of magnitude faster than most methods. By applying MEScan to data from four different cancer types and pan-cancer, we have identified several biologically meaningful mutually exclusive gene sets.

AVAILABILITY AND IMPLEMENTATION

MEScan is available as an R package at https://github.com/MarkeyBBSRF/MEScan.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Near-field probing of dielectric screening by hexagonal boron nitride in graphene integrated on silicon photonics

Hexagonal boron nitride (hBN) is one of the most suitable 2D materials for supporting graphene in electronic devices, and it plays a fundamental role in screening out the effect of charge impurities in graphene in contrast to inhomogeneous supports such as silicon dioxide (SiO₂). Although many interesting surface science techniques such as scanning tunneling microscopy (STM) revealed dielectric screening by hBN and emergent physical phenomena were observed, STM is only appropriate for graphene electronics. In this paper, we demonstrate the dielectric screening by hBN in graphene integrated on a silicon photonic waveguide from the perspective of a near-field scanning optical microscopy (NSOM) and Raman spectroscopy. We found shifts in the Raman spectra and about three times lower slope decrease in the measured electric near-field amplitude for graphene on hBN relative to that for graphene on SiO₂. Based on finite-difference time-domain simulations, we confirm lower electric field slope and scattering rate in graphene on hBN, which implies dielectric screening, in agreement with the NSOM signal. Graphene on hBN integrated on silicon photonics can pave the way for high-performance hybrid graphene photonics.

Immunostimulatory AIE Dots for Live-Cell Imaging and Drug Delivery

The mechanical properties of nanoscale drug carriers play critical roles in regulating nano-bio interactions. For example, the superior deformability of the softer nanoparticles enables them to pass through the biofilters efficiently, facilitating their long blood circulation and better tumor penetration. However, as a novel nanocarrier system, the elimination efficiency of soft nanoparticles from cells is poorly investigated. Here, we report a facile strategy to prepare soft luminescent nanoparticles through self-assembly of amphiphilic aggregation-induced emission (AIE) fluorophores. The prepared soft AIE dots exhibit strong light emission (quantum yield, ∼27.1%) and can reveal the encapsulation and excretion process of NPs in real time. The cell results showed that soft NPs can greatly increase the transfer speed of nanomaterials into cells and accelerate their elimination from cells through the sacrifice of soft AIE dots. We also show that soft AIE dots loaded with cytosine-phosphate-guanine (CpG) oligodeoxynucleotides can induce strong immunostimulatory effects, producing a high level of various proinflammatory cytokines including tumor necrosis factor (TNF)-R, interleukin (IL)-6, and IL-12. This work demonstrates a new design strategy for synthesizing a soft nanocarrier system that can deliver drugs into cells efficiently and then be eliminated from cells quickly.

Genome-wide identification and characterization of microRNAs responding to ABA and GA in maize embryos during seed germination

MicroRNAs (miRNAs) are an important class of non-coding small RNAs that regulate the expression of target genes through mRNA cleavage or translational inhibition. Previous studies have revealed their roles in regulating seed dormancy and germination in model plants such as Arabidopsis thaliana, rice (Oryza sativa) and maize (Zea mays). However, the miRNA response to exogenous gibberellic acid (GA) and abscisic acid (ABA) during seed germination in maize has yet to be explored. In this study, small RNA libraries were generated and sequenced from maize embryos treated with GA, ABA or double-distilled water as control. A total of 247 miRNAs (104 known and 143 novel) were identified, of which 45 known and 53 novel miRNAs were differentially expressed in embryos in the different treatment groups. In total, 74 (37 up-regulated and 37 down-regulated) and 55 (23 up-regulated and 32 down-regulated) miRNAs were expressed in response to GA and to ABA, respectively, and a total of 18 known and 38 novel miRNAs displayed differential expression between the GA- and ABA-treated groups. Using bioinformatics tools, we predicted the target genes of the differentially expressed miRNAs. Using GO enrichment and KEGG pathway analysis of these targets, we showed that miRNAs differentially expressed in our samples affect genes encoding proteins involved in the peroxisome, ribosome and plant hormonal signalling pathways. Our results indicate that miRNA-mediated gene expression influences the GA and ABA signalling pathways during seed germination.

Effect of butylphthalide on new cerebral microbleeds in patients with acute ischemic stroke

BACKGROUND

To evaluate the effect of dl-3-N-butylphthalide (NBP) on new cerebral microbleeds (CMBs) in patients with acute ischemic stroke (AIS).

METHODS

We will prospectively enroll patients with AIS admitted to the stroke center of Jingjiang People's Hospital. Qualified participants will be randomly assigned to either the NBP group (NBP injection) or the control group (NBP injection placebo) in a ratio of 1:1. Patients will complete the brain magnetic resonance imaging within 48 hours and 14 days after stroke onset to observe the CMBs through susceptibility weighted imaging, and evaluate whether the use of NBP will affect the new CMBs in AIS patients. SPSS 20.0 will be used for statistical analyses.

RESULT

We will provide practical and targeted results assessing the safety of NBP for AIS patients, to provide reference for clinical use of NBP.

CONCLUSION

The stronger evidence about the effect of NBP on new CMBs in AIS patients will be provided for clinicians.

Determination of aminophylline based on fluorescence quenching of amino-functionalized graphene quantum dots induced by photoilluminated riboflavin-aminophylline system

A new method based on fluorescence spectroscopy for the sensitive determination of aminophylline (AP), an antiasthmatic drug, was developed in this work. Amino-functionalized graphene quantum dots (afGQDs) were synthesized based on a two-step method and they were characterized by transmission electron microscope, UV-vis absorption spectrum and infrared spectrum. The fluorescence of afGQDs was quenched by riboflavin (Rf) via both dynamic quenching and inner filter effect. Photoilluminated Rf-AP system in the presence of oxygen produced hydroxyl radicals (OH). The latter accepted electrons from afGQDs owing to a photo-induced electron transfer process and led to the further fluorescence decline. The changing extent of the fluorescence intensity was found to be proportional to the concentration of AP in the range of 0.10-10 μg mL^-1 and the limit of detection arrived at 40 ng mL^-1. The proposed method was successfully employed for the determination of AP in a pharmaceutical sample and the recovery rate varied in the range of 99%-106%.

Encapsulation and release of living tumor cells using hydrogels with the hybridization chain reaction

Circulating tumor cells (CTCs) enable noninvasive liquid biopsy and identification of cancer. Various approaches exist for the capture and release of CTCs, including microfluidic methods and those involving magnetic beads or nanostructured solid interfaces. However, the concomitant cell damage and fragmentation that often occur during capture make it difficult to extensively characterize and analyze living CTCs. Here, we describe an aptamer-trigger-clamped hybridization chain reaction (atcHCR) method for the capture of CTCs by porous 3D DNA hydrogels. The 3D environment of the DNA networks minimizes cell damage, and the CTCs can subsequently be released for live-cell analysis. In this protocol, initiator DNAs with aptamer-toehold biblocks specifically bind to the epithelial cell adhesion molecule (EpCAM) on the surface of CTCs, which triggers the atcHCR and the formation of a DNA hydrogel. The DNA hydrogel cloaks the CTCs, facilitating quantification with minimal cell damage. This method can be used to quantitively identify as few as 10 MCF-7 cells in a 2-µL blood sample. Decloaking of tumor cells via gentle chemical stimulus (ATP) is used to release living tumor cells for subsequent cell culture and live-cell analysis. We also describe how to use the protocol to encapsulate and release cells of cancer cell lines, which can be used in preliminary experiments to model CTCs. The whole protocol takes ~2.5 d to complete, including downstream cell culture and analysis.

Cathelicidin aggravates myocardial ischemia/reperfusion injury via activating TLR4 signaling and P2X7R/NLRP3 inflammasome

AIMS

The antimicrobial peptide cathelicidin (Camp) has multifunctional immunomodulatory activities. However, its roles in inflammation-related myocardial ischemia/reperfusion (MI/R) injury remain unclear.

METHODS AND RESULTS

In this study, adult male C57BL/6 wild-type (WT) mice were subjected to MI/R injury by left anterior descending coronary artery ligation for 45 min followed by 3 or 24 h of reperfusion. An abundant cardiac expression of cathelicidin was observed during ischemia and reperfusion, which was mainly derived from heart-infiltrating neutrophils. Knockout of Camp in mice reduced MI/R-induced myocardial inflammation, infarct size, and circulating cTnI levels (an indicator of heart damage). CRAMP (the mature form of murine cathelicidin) administration of WT mice immediately before MI/R exerted detrimental effects on the reperfused heart. CRAMP exacerbates MI/R injury via a TLR4 and P2X₇R/NLRP3 inflammasome-dependent mechanism, since I/R-induced myocardial infarction was reserved by inhibition of TLR4, P2X₇R, or NLRP3 inflammasome in CRAMP-treated WT mice. Depletion of neutrophils before MI/R abrogated the amplification of infarct size in CRAMP-treated WT mice. Heart-infiltrating neutrophils were found to be one of major cellular sources of myocardial IL-1β (a "first line" pro-inflammatory cytokine) at the early stage of MI/R. At this stage, CRAMP administration just before MI/R induced pro-IL-1β protein expression in heart-infiltrating neutrophils, but not in non-neutrophils. In vitro experiments showed that LL-37 (the mature form of human cathelicidin) treatment promotes the processing and secretion of IL-1β from human neutrophils via stimulating TLR4 signaling and P2X₇R/NLRP3 inflammasome.

CONCLUSIONS

Our findings reveal that, at the early stage of MI/R, neutrophil-derived cathelicidin plays an injurious role in the heart. Cathelicidin aggravates MI/R injury by over-activating TLR4 signaling and P2X₇R/NLRP3 inflammasome in heart-infiltrating neutrophils, which leads to the excessive secretion of IL-1β and subsequent inflammatory injury.

Cathelicidin deficiency exacerbates cardiac dysfunction in lipopolysaccharide-induced endotoxaemic mice

The therapeutic potential of the antimicrobial peptide cathelicidin (Camp) administration in sepsis has been widely investigated. However, little is known about the pathophysiological roles of cathelicidin in septic cardiomyopathy. In a lipopolysaccharide (LPS)-induced endotoxaemic model, we found that the mRNA and protein expression of cardiac cathelicidin were induced in C57BL/6J wild-type (WT) mice upon LPS challenge, accompanied by increased circulating cathelicidin levels. We showed that this peptide was mainly derived from neutrophils and monocytes/macrophages. Camp deficiency exacerbated LPS-induced myocardial depression, while the administration of CRAMP (the mature form of mouse cathelicidin) decreased the LPS-induced mortality in a D-galactosamine hydrochloride (D-GalN)-sensitized endotoxin shock model. In vivo, LPS-treated Camp knockout mice had a significant higher protein level of myocardial and circulating tumour necrosis factor-alpha (TNF-α), a major contributing factor to septic cardiomyopathy, compared to LPS-treated WT mice, while CRAMP administration inhibited LPS-induced TNF-α production in the heart and plasma in D-GalN-sensitized endotoxaemic mice. In vitro, CRAMP treatment suppressed LPS-induced Tnf-α mRNA expression in cultured neonatal mouse cardiomyocytes and reduced TNF-α secretion in the culture supernatant. The inhibitory effects of CRAMP on TNF-α production may be related to its neutralizing ability of LPS, since CRAMP application had no effects on another toll-like receptor 4 ligand paclitaxel-induced Tnf-α mRNA expression in cardiomyocytes. These findings suggest that LPS-induced cathelicidin protects the heart against myocardial depression partly through the inhibition of TNF-α production via neutralizing LPS.

Tracking Sparse Linear Classifiers

In this paper, we investigate the problem of sparse online linear classification in changing environments. We first analyze the tracking performance of standard online linear classifiers, which use gradient descent for minimizing the regularized hinge loss. The derived shifting bounds highlight the importance of choosing appropriate step sizes in the presence of concept drifts. Notably, we show that a better adaptability to concept drifts can be achieved using constant step sizes rather than the state-of-the-art decreasing step sizes. Based on these observations, we then propose a novel sparse approximated linear classifier, called sparse approximated linear classification (SALC), which uses a constant step size. In essence, SALC simply rounds small weights to zero for achieving sparsity and controls the truncation error in a principled way for achieving a low tracking regret. The degree of sparsity obtained by SALC is continuous and can be controlled by a parameter which captures the tradeoff between the sparsity of the model and the regret performance of the algorithm. Experiments on nine stationary data sets show that SALC is superior to the state-of-the-art sparse online learning algorithms, especially when the solution is required to be sparse; on seven groups of nonstationary data sets with various total shifting amounts, SALC also presents a good ability to track drifts. When wrapped with a drift detector, SALC achieves a remarkable tracking performance regardless of the total shifting amount.

The MAGI2 gene polymorphism rs2160322 is associated with Graves' disease but not with Hashimoto's thyroiditis

PURPOSE

Autoimmune thyroid diseases (AITDs) are chronic organ-specific autoimmune disorders, predominantly including Graves' disease (GD), and Hashimoto's thyroiditis (HT). This study aimed to investigate whether single-nucleotide polymorphisms (SNPs) in MAGI2 and MAGI3 gene contributed to the etiology of AITDs.

METHODS

We conducted a case-control study including 1001 patients with AITDs (625 GD, 376 HT) and 846 healthy controls. Subgroup analyses in GD and HT were also performed.

RESULTS

The genotypes of rs2160322 in MAGI2 showed a borderline association with AITDs (P = 0.048), and they had a strong correlation with GD (P = 0.012). The frequency of the minor allele G of rs2160322 was significantly higher in the GD patients than in the controls (P = 0.027; OR 1.91; 95% CI 1.020-1.391), especially for GD females (P = 0.008; OR 1.304; 95% CI 1.072-1.587), and those who had positive family history (P = 0.011; OR 1.412; 95% CI 1.083-1.843). For genetic model analysis, the recessive model and homozygous model of rs2160322 showed significant associations with AITDs (P = 0.009; P = 0.019) and GD (P = 0.004; P = 0.005). Nevertheless, our study could not identify any relationship between these SNPs and HT. Due to the low mutation rate of rs1343126 in MAGI3, we were unable to obtain a credible conclusion on its association with AITDs.

CONCLUSIONS

Our study identified that MAGI2 rs2160322 was strongly associated with GD susceptibility. The potential dysfunction of tight junction proteins and aberrant epithelial barrier caused by abnormal MAGI2 expression may be a novel mechanism of GD.

The efficacy and safety of tirofiban for patients with acute ischemic stroke: A protocol for systematic review and a meta-analysis

BACKGROUND

The clinical use of tirofiban remains controversial for patients with acute ischemic stroke (AIS), we aimed to conduct a meta- analysis of cohort studies to assess the efficacy and safety of tirofiban for AIS patients.

METHODS

All apparently unconfounded randomized controlled trials (RCTs) and case-controlled studies, with or without blinding, of tirofiban in individuals with AIS will be included in this review. We will conduct a literature search in 2 databases Pubmed and Embase, using indexing terms related to cerebral infarctions and tirofiban to include articles indexed as of Jan 31, 2019 in the English language only. Two reviewers will independently select trials for inclusion and assess trial quality. Two pairs of review authors will independently extract information for each included trials. Primary outcomes are any intracerebral hemorrhage (aICH), symptomatic intracranial hemorrhage (sICH), fatal ICH, recanalization rate and long-term outcome. The risk of bias of the included studies will be evaluated based on Cochrane assessment tool. Revman 5.3 will be used for heterogeneity assessment, generating funnel-plots, data synthesis, subgroup analysis, and sensitivity analysis.

RESULT

We will provide practical and targeted results assessing the efficacy and safety of tirofiban for AIS patients, to provide reference for clinical use of tirofiban.

CONCLUSION

The stronger evidence about the efficacy and safety of tirofiban for AIS patients will be provided for clinicians.

The urate-lowering efficacy and safety of febuxostat versus allopurinol in Chinese patients with asymptomatic hyperuricemia and with chronic kidney disease stages 3-5

BACKGROUND

While the dose of allopurinol is limited in patients with chronic kidney disease (CKD), information is lacking concerning the efficacy, safety, and maintenance dose of febuxostat in Chinese patients with hyperuricemia and with CKD stages 3-5.

METHODS

A single center, prospective cohort study was conducted in patients with CKD stages 3-5 and with hyperuricemia who had not yet begun to undergo renal replacement therapy. We enrolled 208 patients who were newly treated with febuxostat (n = 112) or allopurinol (n = 96) in this study. The efficacy of febuxostat was determined by the proportion of patients with serum uric acid (sUA) < 360 µmol/L at the end of the study and changes of renal function.

RESULTS

The target of sUA < 360 µmol/L was reached by 96.4% of participants in the febuxostat group and 37.5% in the allopurinol group at 6 months. The eGFR in the febuxostat group showed an increase from 28.45 to 30.65 mL/min/1.73 m² at 6 months, while in the allopurinol group, the eGFR decreased from 28.06 to 24.39 mL/min/1.73 m². Linear regression analysis showed that the reduction in sUA was significantly associated with an increase in eGFR and decrease in proteinuria. We found that 83.0% of the patients could remain with sUA < 360 µmol/L at a maintenance dose of febuxostat 20 mg/day.

CONCLUSION

Febuxostat had superior urate-lowering efficacy to that of allopurinol in Chinese Han patients with hyperuricemia with CKD stages 3-5, and the reduction in sUA levels was associated with a slower progression of renal function.