Fast and exact fixed-radius neighbor search based on sorting.

Fixed-radius near neighbor search is a fundamental data operation that retrieves all data points within a user-specified distance to a query point. There are efficient algorithms that can provide fast approximate query responses, but they often have a very compute-intensive indexing phase and require careful parameter tuning. Therefore, exact brute force and tree-based search methods are still widely used. Here we propose a new fixed-radius near neighbor search method, called SNN, that significantly improves over brute force and tree-based methods in terms of index and query time, provably returns exact results, and requires no parameter tuning. SNN exploits a sorting of the data points by their first principal component to prune the query search space. Further speedup is gained from an efficient implementation using high-level basic linear algebra subprograms (BLAS). We provide theoretical analysis of our method and demonstrate its practical performance when used stand-alone and when applied within the DBSCAN clustering algorithm.

Palliative Approach Remains Lacking in Terminal Hospital Admissions for Chronic Disease Across Rural Settings: Multisite Retrospective Medical Record Audit.

INTRODUCTION/AIM: Despite clear benefit from palliative care in end-stage chronic diseases, access is often limited, and rural access largely undescribed. This study sought to determine if a palliative approach is provided to people with chronic disease in their terminal hospital admission. METHODS: Multisite, retrospective medical record audit, of decedents with a primary diagnosis of chronic lung, heart, or renal failure, or multimorbidity of these conditions over 2019. RESULTS: Of 241 decedents, across five clinical sites, 143 (59.3%) were men, with mean age 80.47 years (SD 11.509), and diagnoses of chronic lung (n = 56, 23.2%), heart (n = 56, 23.2%), renal (n = 24, 10.0%) or multimorbidity disease (n = 105, 43.6%), and had 2.88 (3.04SD) admissions within 12 months. Outpatient chronic disease care was evident (n = 171, 73.7%), however, contact with a private physician (n = 91, 37.8%), chronic disease program (n = 61, 25.3%), or specialist nurse (n = 17, 7.1%) were less apparent. "Not-for-resuscitation" orders were common (n = 139, 57.7%), however, advance care planning (n = 71, 29.5%), preferred place of death (n = 18, 7.9%), and spiritual support (n = 18, 7.5%) were rarely documented. Referral to and input from palliative services were low (n = 74, 30.7% and n = 49, 20.3%), as was review of nonessential medications or blood tests (n = 86, 35.7%, and n = 78, 32.4%). Opioids were prescribed in 45.2% (n = 109). Hospital site and diagnosis were significantly associated with outpatient care and palliative approach (P<0.001). CONCLUSIONS: End-of-life planning and specialist palliative care involvement occurred infrequently for people with chronic disease who died in rural hospitals. Targeted strategies are necessary to improve care for these prevalent and high needs rural populations.

Comprehensive insights into the differences of fungal communities at taxonomic and functional levels in stony coral Acropora intermedia under a natural bleaching event.

Previous studies have reported the correlations between bacterial communities and coral bleaching, but the knowledge of fungal roles in coral bleaching is still limited. In this study, the taxonomic and functional diversities of fungi in unbleached, partly bleached and bleached stony coral Acropora intermedia were investigated through the ITS-rRNA gene next-generation sequencing. An unexpected diversity of successfully classified fungi (a total of 167 fungal genera) was revealed in this study, and the partly bleached coral samples gained the highest fungal diversity, followed by bleached and unbleached coral samples. Among these fungi, 122 genera (nearly 73.2%) were rarely found in corals in previous studies, such as Calostoma and Morchella, which gave us a more comprehensive understanding of coral-associated fungi. Positively correlated fungal genera (Calostoma, Corticium, Derxomyces, Fusicolla, Penicillium and Vishniacozyma) and negative correlated fungal genera (Blastobotrys, Exophiala and Dacryopinax) with the coral bleaching were both detected. It was found that a series of fungal genera, dominant by Apiotrichum, a source of opportunistic infections, was significantly enriched; while another fungal group majoring in Fusicolla, a probiotic fungus, was distinctly depressed in the bleached coral. It was also noteworthy that the abundance of pathogenic fungi, including Fusarium, Didymella and Trichosporon showed a rising trend; while the saprotrophic fungi, including Tricladium, Botryotrichum and Scleropezicula demostrated a declining trend as the bleaching deteriorating. The rising of pathogenic fungi and the declining of saprotrophic fungi revealed the basic rules of fungal community transitions in the coral bleaching, but the mechanism of coral-associated fungal interactions still lacks further investigation. Overall, this is an investigation focused on the differences of fungal communities at taxonomic and functional levels in stony coral A. intermedia under different bleaching statuses, which provides a better comprehension of the correlations between fungal communities and the coral bleaching.

Sulfated oligosaccharide activates endothelial Notch for inducing macrophage-associated arteriogenesis to treat ischemic diseases.

Ischemic diseases lead to considerable morbidity and mortality, yet conventional clinical treatment strategies for therapeutic angiogenesis fall short of being impactful. Despite the potential of biomaterials to deliver pro-angiogenic molecules at the infarct site to induce angiogenesis, their efficacy has been impeded by aberrant vascular activation and off-target circulation. Here, we present a semisynthetic low-molecular sulfated chitosan oligosaccharide (SCOS) that efficiently induces therapeutic arteriogenesis with a spontaneous generation of collateral circulation and blood reperfusion in rodent models of hind limb ischemia and myocardial infarction. SCOS elicits anti-inflammatory macrophages' (Mφs') differentiation into perivascular Mφs, which in turn directs artery formation via a cell-to-cell communication rather than secretory factor regulation. SCOS-mediated arteriogenesis requires a canonical Notch signaling pathway in Mφs via the glycosylation of protein O-glucosyltransferases 2, which results in promoting arterial differentiation and tissue repair in ischemia. Thus, this highly bioactive oligosaccharide can be harnessed to direct efficiently therapeutic arteriogenesis and perfusion for the treatment of ischemic diseases.

Pneumatic nano-sieve for CRISPR-based detection of drug-resistant bacteria.

The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieved an on-chip concentration factor of ∼15-fold for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU mL-1. This developed approach provides a rapid, precise, and centrifuge-free solution suitable for point-of-care diagnostics, with the potential to significantly improve patient outcomes in resource-limited medical conditions.

Indirubin derivatives as bifunctional molecules inducing DNA damage and targeting PARP for the treatment of cancer.

Based on the facts that significant synergistic effect existed between PARP inhibitors and DNA damage agents and the DNA damage caused by indirubin's derivatives, we herein adopted the strategy to combine the pharmacophores of PARP inhibitors and the unique scaffold of indirubin to design a series of bifunctional molecules inducing DNA damage and targeting PARP. After SAR studies, the most potent compound 12a, encoded as KWWS-12a, exhibited improved inhibitory effect against PARP1 compared with PARP1 inhibitor Olaparib (IC50 = 1.89 nM vs 7.48 nM) and enhanced antiproliferative activities than the combination of Olaparib and indirubin-3'-monoxime towards HCT-116 cells (IC50 = 0.31 µM vs 1.37 µM). In the normal NCM-460 cells, 12a showed low toxicity (IC50 > 60 µM). The mechanism research indicated that 12a could increase the levels of γH2AX concentration dependently, arrest the cell cycle in S phase and induce apoptosis in HCT-116 cells. In vivo experiments showed that 12a displayed more significant antitumor potential than that of the positive controls. Our studies demonstrated that 12a could be a promising candidate for cancer therapy.

Pneumatic Nano-Sieve for CRISPR-based Detection of Drug-resistant Bacteria.

The increasing prevalence of antibiotic-resistant bacterial infections, particularly methicillin-resistant Staphylococcus aureus (MRSA), presents a significant public health concern. Timely detection of MRSA is crucial to enable prompt medical intervention, limit its spread, and reduce antimicrobial resistance. Here, we introduce a miniaturized nano-sieve device featuring a pneumatically-regulated chamber for highly efficient MRSA purification from human plasma samples. By using packed magnetic beads as a filter and leveraging the deformability of the nano-sieve channel, we achieve an on-chip concentration factor of 15 for MRSA. We integrated this device with recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas detection system, resulting in an on-chip limit of detection (LOD) of approximately 100 CFU/mL. This developed approach provides a rapid, precise, and centrifuge-free solution suitable for point-of-care diagnostics, with the potential to significantly improve patient outcomes in resource-limited medical conditions.

Design, synthesis and mechanism studies of dual EZH2/BRD4 inhibitors for cancer therapy.

Aberrant expression of EZH2 is frequently observed in cancers, and the EZH2 inhibitors are only effective in hematological malignancies and almost noneffective against solid tumors. It has been reported that the combination of EZH2 and BRD4 inhibitors may be a promising strategy to treat solid tumors being insensitive to EZH2 inhibitors. Thus, a series of EZH2/BRD4 dual inhibitors were designed and synthesized. The optimized compound 28, encoded as KWCX-28, was the most potential compound by the SAR studies. Further mechanism studies showed that KWCX-28 inhibited HCT-116 cells proliferation (IC50 = 1.86 µM), induced HCT-116 cells apoptosis, arrested cell cycle arrest at G0/G1 phase and resisted the histone 3 lysine 27 acetylation (H3K27ac) upregulation. Therefore, KWCX-28 was a potential dual EZH2/BRD4 inhibitors for treating solid tumors.

Discovery of dual PARP and CDK6 inhibitors for triple-negative breast cancer with wild-type BRCA.

Inhibition of PARP is synthetic lethal with defects in BRCA, which provide effective targeted therapy strategy for BRCA mutation type of TNBC patients. However, approximately 80% of TNBC patients do not have BRCA mutations. Recent studies have shown that CDK4/6 inhibitors can increase the sensitivity of wild-type BRCA cells to PARP inhibitors. We designed a series of dual PARP and CDK6 inhibitors, and the most promising compound, P4i, showed good inhibitory activity against PARP1 and CDK6 and good inhibitory effects on MDA-MB-231 (IC50 = 1.96 µM), MDA-MB-468 (IC50 = 2.81 µM) and BT-549 (IC50 = 2.37 µM) cells with wild-type BRCA. Compared with Olaparib, the inhibition capacity of the three BRCA wild-type (MDA-MB-231, MDA-MB-468 and BT-549) cells was about 10-20 times higher, and even better than the combination of Olaparib and Palbociclib. As a novel PARP multifunctional molecule, it is a potential compound for the treatment of BRCA wild-type TNBC.

Oxazole-4-carboxamide/butylated hydroxytoluene hybrids with GSK-3ß inhibitory and neuroprotective activities against Alzheimer's disease.

Neuronal cells overexpressing phosphorylated Tau proteins can increase the susceptibility to oxidative stress. Regulation of glycogen synthase-3ß (GSK-3ß) and reduction of Tau protein hyperphosphorylation, along with alleviation of oxidative stress, may be an effective way to prevent or treat Alzheimer's disease (AD). For this purpose, a series of Oxazole-4-carboxamide/butylated hydroxytoluene hybrids were designed and synthesized to achieve multifunctional effects on AD. The biological evaluation showed that the optimized compound KWLZ-9e displayed potential GSK-3ß (IC50 = 0.25 µM) inhibitory activity and neuroprotective capacity. Tau protein inhibition assays showed that KWLZ-9e reduced the expression of GSK-3ß and downstream p-Tau in HEK GSK-3ß 293T cells. Meanwhile, KWLZ-9e could alleviate H2O2-induced ROS damage, mitochondrial membrane potential imbalance, Ca2+ influx and apoptosis. Mechanistic studies suggest that KWLZ-9e activates the Keap1-Nrf2-ARE signaling pathway and enhances the expression of downstream oxidative stress proteins including TrxR1, HO-1, NQO1, GCLM to exert cytoprotective effects. We also confirmed that KWLZ-9e could ameliorate learning and memory impairments in vivo model of AD. The multifunctional properties of KWLZ-9e suggest that it is a promising lead for the treatment of AD.

Discovery of Sibiriline derivatives as novel receptor-interacting protein kinase 1 inhibitors.

Receptor-interacting protein kinase 1 (RIPK1), a vital protein of the necroptosis pathway, plays a pivotal role in various inflammatory diseases. Sibiriline has been reported to be a potent ATP-competitive RIPK1 inhibitor, but its anti-necroptotic effects are limited. A series of structural analogues of Sibiriline were synthesized and evaluated for their anti-necroptotic activity. Comprehensive structure-activity relationship (SAR) was performed to left azaindole and right substituents of benzene of Sibiriline, respectively. The optimal compound KWCN-41, specifically inhibiting cell necroptosis but not apoptosis, protects cell survival by blocking the necroptotic pathway, which inhibits the phosphorylation of essential proteins of the necroptosis. It also prevented the development of inflammation and reduced the level of inflammatory factors in mice. KWCN-41 is expected to be a lead compound for further studies in inflammatory diseases.

Three-dimensional visualization of dentine occlusion based on FIB-SEM tomography.

The occlusion of dentinal tubules has become a rapid and effective method for treating dentin hypersensitivity. Accurate evaluation of dentin occlusion is critical to illustrate the efficacy of oral care products and to optimize dental therapy in the clinics, which is limited by the conventional two-dimensional (2-D) characterization methods. Here, we demonstrate the visualization of the dentin occlusion via three-dimensional (3-D) characterization using a focused ion beam-scanning electron microscopy (FIB-SEM) tomography. Using the "Slice and View" approach, the material used for occluding dentin tubules is imaged with a very high-resolution voxel (10 nm × 10 nm × 20 nm) from 2-D SEM images and then reconstructed into a 3-D volume, which presents the mode of action of toothpaste for treating dentin hypersensitivity. Meanwhile, quantitative analysis of the depth of occlusion is successfully obtained. This work validates the feasibility of FIB-SEM tomography in the analysis of dentin occlusion within the complicated networks of dentine tubules at the nanoscale, and provides a novel approach to facilitate the research and development of oral care products.

Digital-twin-based Online Parameter Personalization for Implantable Cardiac Defibrillators.

Implantable cardioverter defibrillators (ICDs) are developed to provide timely therapies when adverse patient conditions are detected. Device therapies need to be adjusted for individual patients and evolving patient conditions, which can be achieved by adjusting device parameter settings. However, there are no validated clinical guidelines for parameter personalization, especially for patients with complex and rare conditions. In this paper, we propose a reinforcement learning framework for online parameter personalization of ICDs. Heart states can be inferred from ECG signals from ECG patches, which can be used to create a digital twin of the patient. Reinforcement learning then use the digital twin as environment to explore parameter settings with less misdiagnosis. Experiments were performed on three virtual patients with specific and evolving heart conditions, and the result shows that our proposed approach can identify ICD parameter settings that can achieve better performance compared to default parameter settings. Clinical relevance-Patients with ICD and ECG patch can receive periodic ICD parameter adjustments that are appropriate for their current heart conditions.

Histone Deacetylase and Enhancer of Zeste Homologue 2 Dual Inhibitors Presenting a Synergistic Effect for the Treatment of Hematological Malignancies.

Aberrance of epigenetic modification is one of the important factors leading to hematological malignancies. Histone deacetylase (HDAC) inhibitors and enhancers of zeste homologue 2 (EZH2) inhibitors are demonstrated to be significant epigenic modulators. Cocktail therapy of HDAC inhibitors and EZH2 inhibitors was demonstrated to be a promising strategy in hematological malignancies. We designed HDAC and EZH2 dual inhibitors based on the strong synergistic effect of SAHA and GSK126. Compound 20 exhibited excellent inhibitory activity against HDAC1 (IC50 = 0.12 µM) and EZH2 (IC50 = 0.059 µM), it also showed good antiproliferation activity against MV4-11 (IC50 = 0.17 µM), which has more potential than the cocktail therapy of SAHA and GSK126 (IC50 = 0.40 µM). 20 suppressed tumor growth in vivo, which was as good as the combination therapy. These results suggested that 20 may be a promising drug candidate for treating hematological malignancies.

Discovery of precision targeting EZH2 degraders for triple-negative breast cancer.

EZH2 is usually overexpressed in TNBC and other tumors, which has a great influence on the occurrence, development and prognosis of tumors. However, current EZH2 inhibitors, including Tazemetostat and GSK126, affect the methyl catalytic capacity of EZH2 and have little effect on the tumorigenic activity of EZH2 itself, resulting in poor efficacy against most solid tumors. Herein, we designed and optimized proteolytic targeting chimeras (PROTACs) precision targeting EZH2. The most active PROTAC molecule U3i has a high affinity for PRC2 complex (KD = 16.19 nM) and show good inhibitory effects on MDA-MB-231 (IC50 = 0.57 µM) and MDA-MB-468 (IC50 = 0.38 µM) cells. Compared with that of the GSK126, the growth inhibitory activities of U3i against these two TNBC cells increased by approximately 20- and 30-fold. Further studies showed that U3i can degrade PRC2 complex in TNBC cells, induce apoptosis, and cause little damage to normal cells. Therefore, U3i is a potential anticancer molecule for TNBC treatment.

Real-world opioid prescription to patients with serious, non-malignant, respiratory illnesses and chronic breathlessness.

BACKGROUND: Chronic breathlessness is a disabling symptom that is often under-recognised and challenging to treat despite optimal disease-directed therapy. Low-dose, oral opioids are recommended to relieve breathlessness, but little is known regarding long-term opioid prescription in this setting. AIM: To investigate the long-term efficacy of, and side-effects from, opioids prescribed for chronic breathlessness to patients with advanced, non-malignant, respiratory diseases. METHODS: A prospective cohort study of all patients managed by the advanced lung disease service, an integrated respiratory and palliative care service, at the Royal Melbourne Hospital from 1 April 2013 to 3 March 2020. RESULTS: One hundred and nine patients were prescribed opioids for chronic breathlessness. The median length of opioid use was 9.8 (interquartile range (IQR) = 2.8-19.8) months. The most commonly prescribed initial regimen was an immediate-release preparation (i.e. Ordine) used as required (37; 33.9%). For long-term treatment, the most frequently prescribed regimen included an extended-release preparation with an as needed immediate-release (37; 33.9%). The median dose prescribed was 12 (IQR = 8-28) mg oral morphine equivalents/day. Seventy-one (65.1%) patients reported a subjective improvement in breathlessness. There was no significant change in the mean modified Medical Research Council dyspnoea score (P = 0.807) or lung function measurements (P = 0.086-0.727). There was no association between mortality and the median duration of opioid use (P = 0.201) or dose consumed (P = 0.130). No major adverse events were reported. CONCLUSION: Within this integrated respiratory and palliative care service, patients with severe, non-malignant respiratory diseases safely used long-term, low-dose opioids for breathlessness with subjective benefits reported and no serious adverse events.

Harmine-based dual inhibitors targeting histone deacetylase (HDAC) and DNA as a promising strategy for cancer therapy.

Overexpression of histone deacetylases (HDACs) are observed in different types of cancers, but histone deacetylase inhibitors (HDACIs) have not shown significant efficacy as monotherapy against solid tumors. Recently, studies demonstrated that it is promising to combine HDACIs with DNA damage agents to improve DNA damage level to gain better effect on treating solid tumor. Harmine has been demonstrated to cause DNA damage by intercalating DNA. Therefore, we designed a series of harmine-based inhibitors targeting HDAC and DNA with multi-target strategy, the most potential compound 27 could bind to DNA and cause DNA damage. Furthermore 27 caused cells apoptosis through p53 signaling pathway, and exhibited significant anti-proliferation effects against HCT-116 cells (IC50 = 1.41 µM). As a DNA damage agent, 27 displayed low toxicity in normal cells. Compound 27 was demonstrated as a dual inhibitor targeting HDAC (HDAC1 IC50 = 0.022 µM and HDAC6 IC50 = 0.45 µM) and DNA, and had the potential in the treatment of solid tumor.

Neuronal injuries in cerebral infarction and ischemic stroke: From mechanisms to treatment (Review).

Stroke is the leading cause of disabilities and cognitive deficits, accounting for 5.2% of all mortalities worldwide. Transient or permanent occlusion of cerebral vessels leads to ischemic strokes, which constitutes the majority of strokes. Ischemic strokes induce brain infarcts, along with cerebral tissue death and focal neuronal damage. The infarct size and neurological severity after ischemic stroke episodes depends on the time period since occurrence, the severity of ischemia, systemic blood pressure, vein systems and location of infarcts, amongst others. Ischemic stroke is a complex disease, and neuronal injuries after ischemic strokes have been the focus of current studies. The present review will provide a basic pathological background of ischemic stroke and cerebral infarcts. Moreover, the major mechanisms underlying ischemic stroke and neuronal injuries are summarized. This review will also briefly summarize some representative clinical trials and up­to­date treatments that have been applied to stroke and brain infarcts.

Understanding microbeads stacking in deformable Nano-Sieve for Efficient plasma separation and blood cell retrieval.

Efficient separation of blood cells and plasma is key for numerous molecular diagnosis and therapeutics applications. Despite various microfluidics-based separation strategies having been developed, there is still a need for a simple, reliable, and multiplexing separation device that can process a large volume of blood. Here we show a microbead-packed deformable microfluidic system that can efficiently separate highly purified plasma from whole blood, as well as retrieve blocked blood cells from the device. To support and rationalize the experimental validation of the proposed device, a highly accurate model is constructed to help understand the link between the mechanical properties of the microfluidics, flow rate, and microbeads packing/leaking based on the microscope imaging and the optical coherence tomography (OCT) scanning. This deformable nano-sieve device is expected to offer a new solution for centrifuge-free diagnosis and treatment of bloodborne diseases and contribute to the design of next-generation deformable microfluidics for separation applications.

Semen Sojae Praeparatum alters depression-like behaviors in chronic unpredictable mild stress rats via intestinal microbiota.

A large number of Chinese medical books present that Semen Sojae Praeparatum, a fermented food, possesses antidepressant effect, but the mechanism of this antidepressant effect remains largely unknown. This study aimed to explore the effect of Semen Sojae Praeparatum on rats with chronic unpredictable mild stress (CUMS)-induced depression. The results showed that Semen Sojae Praeparatum improved depression-like behaviors (negative preference of sugar water and increased swimming immobility time and time spent in the dark zone) and effectively reduced cell morphological changes in the dentate gyrus of the hippocampus in CUMS rats. In addition, Semen Sojae Praeparatum significantly promoted the contents of norepinephrine (NE), 5-hydroxytryptamine (5-HT), brain-derived neurotrophic factor (BDNF), and gamma-aminobutyric acid (GABA) in the hippocampus and the content of BDNF in the serum (p < 0.05). 16S rRNA sequencing analysis results showed that Semen Sojae Praeparatum increased the abundance of genus Ruminococcaceae_UCG-008 and decreased those of genera Lactobacillus and Bacteroides. Genus Ruminococcaceae_UCG-008 was positively correlated with GABA and BDNF levels in the hippocampus; genus Lactobacillus had a positive correlation with 5-HT; and genus Bacteroides had negative correlations with 5-HT, BDNF, and NE. In addition, Semen Sojae Praeparatum considerably decreased the concentration of short-chain fatty acids (SCFAs). These results indicated that Semen Sojae Praeparatum fermented by Rhizopus chinensis 12 and Bacillus sp. DU-106 alleviated the neurotransmitter levels and structural changes in the neuronal morphology of the hippocampus associated with the modulation of gut microbiota and SCFAs. Therefore, this study confirmed that Semen Sojae Praeparatum could alter depression and provide a theoretical basis for the investigation of the relationship between the microbiota-gut-brain axis and antidepressant.