Miracle-dz/UniFAR-FTUs huggingface dataset:
Chronic IL-1 Exposed AR+ PCa Cell Lines Show Conserved Loss of IL-1 Sensitivity and Evolve Both Conserved and Unique Differential Gene Expression Profiles

Introduction: Inflammation drives prostate cancer (PCa) progression. While inflammation is a cancer hallmark, the underlying mechanisms mediating inflammation-induced PCa are still under investigation. Interleukin-1 (IL-1) is an inflammatory cytokine that promotes cancer progression, including PCa metastasis and castration resistance. We previously found that acute IL-1 exposure represses PCa androgen receptor (AR) expression concomitant with the upregulation of pro-survival proteins, causing de novo accumulation of castration-resistant PCa cells. However, acute inflammation is primarily anti-tumorigenic, while chronic inflammation is pro-tumorigenic. Thus, using the LNCaP PCa cell line as model, we found that PCa cells can evolve insensitivity to chronic IL-1 exposure, restoring AR and AR activity and acquiring castration resistance. In this paper we expanded our chronic IL-1 model to include the MDA-PCa-2b PCa cell line to investigate the response to acute versus chronic IL-1 exposure and to compare the gene expression patterns that evolve in the LNCaP and MDA-PCa-2b cells chronically exposed to IL-1. Methods: We chronically exposed MDA-PCa-2b cells to IL-1α or IL-1β for several months to establish sublines. Once established, we determined subline sensitivity to exogenous IL-1 using cell viability assay, RT-qPCR and western blot. RNA sequencing was performed for parental and subline cells and over representation analysis (ORA) for geneset enrichment of biological process/pathway was performed. Results: MDA-PCa-2b cells repress AR and AR activity in response to acute IL-1 exposure and evolve insensitivity to chronic IL-1 exposure. While cell biological and molecular response to acute IL-1 signaling is primarily conserved in LNCaP and MDA-PCa-2b cells, including upregulation of NF-κB signaling and downregulation of cell proliferation, the LNCaP and MDA-PCa-2b cells evolve conserved and unique molecular responses to chronic IL-1 signaling that may promote or support tumor progression. Conclusions: Our chronic IL-1 subline models can be used to identify underlying molecular mechanisms that mediate IL-1-induced PCa progression.
The complete mitochondrial genome of the forest crested lizard, Calotes emma (Squamata, Agamidae) in China by the next generation sequencing

Abstract The whole mitogenome can prove useful tools for phylogenetic reconstruction and efficiently recover with reasonable taxon sampling. Calotes emma is widely distributed and arboreal in habits. However, studies of C. emma are still very limited, including population genetics and evolutionary biology. In this study, we reported the complete mitochondrial genome of the C. emma by next-generation sequencing for future more researches on systematics and evolution of C. emma from the perspective of mitochondrial DNA. The length of mitogenome was 17,688 bp, including 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 tRNA genes and a control region. The phylogenetic tree recovered the monophyly of the Calotes and revealed that newly sequenced C. emma well supported as the sister taxon to C. mystaceus by very high posterior probabilities (1.0). The complete mitochondrial genome of C.emma in this study will be helpful for understanding the phylogenetic systematics and relationships, and molecular evolution of Calotes in Agamidae.
Intraoperative transfusion practices and perioperative outcome in the European elderly: A secondary analysis of the observational ETPOS study

The demographic development suggests a dramatic growth in the number of elderly patients undergoing surgery in Europe. Most red blood cell transfusions (RBCT) are administered to older people, but little is known about perioperative transfusion practices in this population. In this secondary analysis of the prospective observational multicentre European Transfusion Practice and Outcome Study (ETPOS), we specifically evaluated intraoperative transfusion practices and the related outcomes of 3149 patients aged 65 years and older. Enrolled patients underwent elective surgery in 123 European hospitals, received at least one RBCT intraoperatively and were followed up for 30 days maximum. The mean haemoglobin value at the beginning of surgery was 108 (21) g/l, 84 (15) g/l before transfusion and 101 (16) g/l at the end of surgery. A median of 2 [1–2] units of RBCT were administered. Mostly, more than one transfusion trigger was present, with physiological triggers being preeminent. We revealed a descriptive association between each intraoperatively administered RBCT and mortality and discharge respectively, within the first 10 postoperative days but not thereafter. In our unadjusted model the hazard ratio (HR) for mortality was 1.11 (95% CI: 1.08–1.15) and the HR for discharge was 0.78 (95% CI: 0.74–0.83). After adjustment for several variables, such as age, preoperative haemoglobin and blood loss, the HR for mortality was 1.10 (95% CI: 1.05–1.15) and HR for discharge was 0.82 (95% CI: 0.78–0.87). Pre-operative anaemia in European elderly surgical patients is undertreated. Various triggers seem to support the decision for RBCT. A closer monitoring of elderly patients receiving intraoperative RBCT for the first 10 postoperative days might be justifiable. Further research on the causal relationship between RBCT and outcomes and on optimal transfusion strategies in the elderly population is warranted. A thorough analysis of different time periods within the first 30 postoperative days is recommended.
Forecasting of Electricity Load Based on Improved Particle Swarm Optimization and Support Vector Regression Machine

Support vector regression machine is suitable for small sample decision and it is good to data forecasting capabilities. Its nature of learning method is under the condition of limited information to obtain a good ability in data mining. Accurate electricity load forecasting is an important practical value to our lives. This paper presents a new algorithm that is an improved particle swarm optimization algorithm and support vector regression machine that is proposed to predict electricity load. It is of great significance to forecasting electricity load. The algorithm can optimize training parameters of support vector regression machine by improved particle swarm optimization algorithm. The simulation experimental results indicate that the new algorithm made a meaningful exploration on forecasting electricity load.
Optimization Model of Organizational Structure for Equipment Training Management System Based on Entropy Theory

Based on entropy theory, the organizational structure has been described by introducing time-effect and accuracy concepts. Then, evaluation model based on the information entropy theory has been established to analyze the order degree of equipment training management system. After the using of this evaluation model, we can comparatively analyze and optimize to several alternative projects. The results can provide a theoretical basis of the innovation of equipment training units’ establishment.
CACONET: a novel classification framework for microbial correlation networks

Abstract Motivation Existing microbiome-based disease prediction relies on the ability of machine learning methods to differentiate disease from healthy subjects based on the observed taxa abundance across samples. Despite numerous microbes have been implicated as potential biomarkers, challenges remain due to not only the statistical nature of microbiome data but also the lack of understanding of microbial interactions which can be indicative of the disease. Results We propose CACONET (classification of Compositional-Aware COrrelation NETworks), a computational framework that learns to classify microbial correlation networks and extracts potential signature interactions, taking as input taxa relative abundance across samples and their health status. By using Bayesian compositional-aware correlation inference, a collection of posterior correlation networks can be drawn and used for graph-level classification, thus incorporating uncertainty in the estimates. CACONET then employs a deep learning approach for graph classification, achieving excellent performance metrics by exploiting the correlation structure. We test the framework on both simulated data and a large real-world dataset pertaining to microbiome samples of colorectal cancer (CRC) and healthy subjects, and identify potential network substructure characteristic of CRC microbiota. CACONET is customizable and can be adapted to further improve its utility. Availability and implementation CACONET is available at https://github.com/yuanwxu/corr-net-classify. Supplementary information Supplementary data are available at Bioinformatics online.
Waterhammer Simulation of Oil Pipeline

To simulate the waterhammer process of oil pipeline, Allievi fundamental differential equations of waterhammer and several usual boundary conditions were described,and the model was solved by characteristic method.For a batchpipelining pipeline,batching interface location was computed with its transient flow velocity within each system's time-step,then the grids were divided again and interpolation calculation was executed.
Tactical vests worn by law enforcement: is this improving stability for optimal job performance?

Objectives. The purpose of this study was to determine whether equipped tactical vests would improve postural stability of law enforcement officers (LEOs) versus a duty belt or without either condition. Methods. Volunteers were police officers (n = 25, 22 males, three females; age 42.4 ± 3.2 years; weight 101.65 ± 19.4 kg; height 178.92 ± 8.2 cm). The Institutional Review Board approved the investigation. A Bertec posturography plate (Bertec Inc., USA) determined four center of pressure (CoP) scores – eyes open stable surface (EOSS), eyes closed stable surface (ECSS), eyes open perturbed surface (EOPS), eyes closed perturbed surface (ECPS) – and four limit of stability (LoS) scores – frontal plane (LoSF), posterior plane (LoSP), left sagittal plane (LoSL), right sagittal plane (LoSR). Results. A repeated-measures multivariate analysis of variance (MANOVA) demonstrated no statistical difference within subject group CoP scores EOSS (p = 0.723), ECSS (p = 0.252), EOPS (p = 0.079) and ECPS (p = 0.137). Comparing between groups, the tactical vest demonstrated significance over the other CoP group conditions with ECPS (p = 0.001). The duty belt group showed significance with ECSS (p = 0.001). LoS variables indicated no significant results between groups. Conclusion. Tactical vests demonstrated improvements in ECPS scores (p = 0.001) compared to either group.
DNA-PK promotes activation of the survival kinase AKT in response to DNA damage through an mTORC2-ECT2 pathway

Description How the DNA damage response promotes cell survival through the kinase DNA-PK is revealed. DNA-PK’s double duty The kinase DNA-PK is a coordinator of the DNA damage response (DDR). DNA-PK also promotes cell survival and resistance to chemotherapy through activation of the kinase AKT. Liu et al. found that DNA-PK mediated a phosphorylation event that activated AKT in a manner dependent on mTOR complex 2 and the guanine nucleotide exchange factor ECT2. Disrupting this mechanism increased the toxicity of DNA-damaging agents in cultured cells. The findings elucidate a pathway linking the DDR to cell survival and may lead to new ways to overcome tumor resistance to DNA damage–associated therapies (see also the Focus by Shin et al.). The kinase AKT (also known as protein kinase B) is a key regulator of cell proliferation, survival, and metabolism. In addition to being activated by growth factors, AKT is activated in response to DNA damage. Here, we found that the DNA damage response kinase DNA-PK sustains cell survival through a phosphorylation event that leads to increased AKT activity. In various cancer and noncancer cells in culture, DNA damage caused by ionizing radiation or topoisomerase inhibitors triggered DNA-PK–dependent phosphorylation of the mTOR complex 2 (mTORC2) subunit Sin1, which enabled its interaction with the guanine nucleotide exchange factor ECT2. Depleting Sin1 or ECT2 or disrupting the protein interaction or catalytic function of ECT2 attenuated DNA damage–induced AKT activation, thereby enhancing cellular sensitivity to DNA-damaging agents. Our findings elucidate a mechanism mediating DNA damage–induced AKT activation and cell survival.
Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS

The tumor microenvironment (TME) is a complex mixture of cell types whose interactions affect tumor growth and clinical outcome. To discover such interactions, we developed CODEFACS (COnfident DEconvolution For All Cell Subsets), a tool deconvolving cell-type-specific gene expression in each sample from bulk expression, and LIRICS (LIgand Receptor Interactions between Cell Subsets), a statistical framework prioritizing clinically relevant ligand-receptor interactions between cell types from the deconvolved data. We first demonstrate the superiority of CODEFACS versus the state-of-the-art deconvolution method, CIBERSORTx. Second, analyzing the TCGA, we uncover cell-type-specific interactions of mismatch-repair-deficient tumors that are associated with their higher anti-PD1 response rates, including specific T-cell co-stimulating interactions that enhance immunotherapy response independently of the tumors mutation burden levels. Finally, we identify a subset of ligand-receptor interactions in the melanoma TME that predict patient response to anti-PD1 therapy better than recently published transcriptomics-based methods.
Quantitative Monitoring of Mycelial Growth of Aspergillus fumigatus in Liquid Culture by Optical Density

Filamentous fungi generally form hyphal pellets in liquid culture. This property prevents filamentous fungi to apply the methods used for unicellular organisms such as yeast and bacteria. ABSTRACT Filamentous fungi form multicellular hyphae, which generally form pellets in liquid shake cultures, during the vegetative growth stage. Because of these characteristics, growth-monitoring methods commonly used in bacteria and yeast have not been applied to filamentous fungi. We have recently revealed that the cell wall polysaccharide α-1,3-glucan and extracellular polysaccharide galactosaminogalactan (GAG) contribute to hyphal aggregation in Aspergillus oryzae. Here, we tested whether Aspergillus fumigatus shows dispersed growth in liquid media that can be quantitatively monitored, similar to that of yeasts. We constructed a double disruptant mutant of both the primary α-1,3-glucan synthase gene ags1 and the putative GAG synthase gene gtb3 in A. fumigatus AfS35 and found that the hyphae of this mutant were fully dispersed. Although the mutant lost α-1,3-glucan and GAG, its growth and susceptibility to antifungal agents were not different from those of the parental strain. Mycelial weight of the mutant in shake-flask cultures was proportional to optical density for at least 18 h. We were also able to quantify the dose response of hyphal growth to antifungal agents by measuring optical density. Overall, we established a convenient strategy to monitor A. fumigatus hyphal growth. Our method can be directly used for screening for novel antifungals against Aspergillus species. IMPORTANCE Filamentous fungi generally form hyphal pellets in liquid culture. This property prevents filamentous fungi so that we may apply the methods used for unicellular organisms such as yeast and bacteria. In the present study, by using the fungal pathogen Aspergillus fumigatus strain with modified hyphal surface polysaccharides, we succeeded in monitoring the hyphal growth quantitatively by optical density. The principle of this easy measurement by optical density could lead to a novel standard of hyphal quantification such as those that have been used for yeasts and bacteria. Dose response of hyphal growth by antifungal agents could also be monitored. This method could be useful for screening for novel antifungal reagents against Aspergillus species.
Ocular ischaemia: signs, symptoms, and clinical considerations for primary eye care practitioners

ABSTRACT Ischaemic stroke is a major disease burden as well as a leading cause of death. Early signs of ischaemic stroke can manifest in the eye, placing primary eyecare practitioners in an important position to identify patients at risk of ischaemic stroke and initiate suitable referral pathways. The vascular supply to the brain is reviewed with reference to vision including the various retinal signs and ocular symptoms associated with transient ischaemic attacks and ischaemic stroke. Using a range of clinical cases, the diverse clinical presentations of retinal embolic events, as well as other forms of vascular occlusion, are highlighted and the underlying pathophysiology is discussed. A succinct scheme for the assessment and management of ischaemic events for primary eye care practitioners is provided.
Chronotype and time of day effects on verbal and facial emotional Stroop task performance in adolescents

ABSTRACT This study investigated chronotype and time of day effects on lexical and facial emotion processing tasks and explored relationships with sleep quality and mental health outcomes. Participants were 351 Taiwanese adolescents (204 males) aged 13 to 16 years of age who completed both a Facial-Emotional Stroop and a Lexical-Emotional Stroop task at 08:00–10:00 am or at 14:00–16:00 pm. Chronotype was measured using the Morningness-Eveningness Questionnaire (MEQ) and grouped into Morning (n = 46), Intermediate (n = 248) or Evening types (n = 57). Participants completed validated measures of sleep quality (PSQI) and mental health difficulties (DASS-21). The study observed independent effects of time of day and chronotype on the Facial-Emotional Stroop task. Independent of chronotype group, delayed reaction times to anger stimuli were observed in adolescents tested in the morning. Younger adolescents with an Evening chronotype showed delayed responses to anger faces independent of the time of testing. Facial-Emotional Stroop task performance correlated with reported sleep quality and mental health only in Evening chronotypes, with attenuated responses to anger versus neutral stimuli associated with poorer sleep quality and worse mental health outcomes. An exploratory simple mediation analysis indicated that the relationship between attenuated responses to anger and greater mental health difficulties was fully mediated by poorer sleep quality. This study provides evidence of diurnal and chronotype-related variation in facial threat-related processing in typical adolescent development. It also indicates how social emotional processing is vulnerable to sleep disruptions and is linked to the greater mental health problems observed in adolescents with an eveningness profile.
Validation of the Psychological Insight Scale: A new scale to assess psychological insight following a psychedelic experience

Introduction: As their name suggests, ‘psychedelic’ (mind-revealing) compounds are thought to catalyse processes of psychological insight; however, few satisfactory scales exist to sample this. This study sought to develop a new scale to measure psychological insight after a psychedelic experience: the Psychological Insight Scale (PIS). Methods: The PIS is a six- to seven-item questionnaire that enquires about psychological insight after a psychedelic experience (PIS-6) and accompanied behavioural changes (PIS item 7). In total, 886 participants took part in a study in which the PIS and other questionnaires were completed in a prospective fashion in relation to a planned psychedelic experience. For validation purposes, data from 279 participants were analysed from a non-specific ‘global psychedelic survey’ study. Results: Principal components analysis of PIS scores revealed a principal component explaining 73.57% of the variance, which displayed high internal consistency at multiple timepoints throughout the study (average Cronbach’s α = 0.94). Criterion validity was confirmed using the global psychedelic survey study, and convergent validity was confirmed via the Therapeutic-Realizations Scale. Furthermore, PIS scores significantly mediated the relationship between emotional breakthrough and long-term well-being. Conclusion: The PIS is complementary to current subjective measures used in psychedelic studies, most of which are completed in relation to the acute experience. Insight – as measured by the PIS – was found to be a key mediator of long-term psychological outcomes following a psychedelic experience. Future research may investigate how insight varies throughout a psychedelic process, its underlying neurobiology and how it impacts behaviour and mental health.
Optimal Multiple-Layered Anterior Skull Base Reconstruction Using a 360° Suturing Technique

BACKGROUND: Advances in technique and instrumentation have improved outcomes after resection of anterior skull base tumors. However, cerebrospinal fluid (CSF) leak occurs in 4%-20% of patients. To reduce the risk of CSF leak, we have developed a novel reconstruction technique that consists of a 4-layered graft with patchwork suturing and hard material. OBJECTIVE: To evaluate the effectiveness of this reconstruction technique when used for resection of anterior skull base tumors. METHODS: This case series included 59 patients with anterior skull base tumors in whom the 4-layered closure technique was used. The main outcome measures were complications, including CSF leak, meningitis, postoperative bleeding, and infection. RESULTS: There were no CSF leak cases or serious complications after closure of the anterior skull base using the 4-layered technique. CONCLUSION: Closure of the anterior skull base in 4 layers prevented CSF leak and was not associated with any serious complications. However, further studies in larger numbers of patients are needed to confirm our outcomes using this closure method.
Amplification of anticancer efficacy by co-delivery of doxorubicin and lonidamine with extracellular vesicles

Abstract Chemotherapy is commonly used for the treatment of lung cancer, but strong side effects and low treatment efficacy limit its clinical application. Here, extracellular vesicles (EVs) as natural drug delivery carriers were used to load conventional anticancer drug doxorubicin (DOX) and a chemosensitizer lonidamine (LND). Two types of EVs with different sizes (16k EVs and 120k EVs) were prepared using different centrifugation forces. We found that co-delivery of DOX and LND with both EVs enhanced the cytotoxicity and reduced the dose of the anticancer drug significantly in vitro. Effective delivery of anti-cancer drugs to cancer cells was achieved by direct fusion of EVs with the plasma membrane of cancer cells. On the other hand, DOX and LND inhibited cancer cell proliferation by increasing DNA damage, suppressing ATP production, and accelerating ROS generation synergistically. DOX and LND loaded EVs were also applied to the mouse lung cancer model and exhibited significant anticancer activity. In vivo study showed that smaller EVs exhibited higher anticancer efficiency. In conclusion, the co-delivery of the anticancer drug and the chemosensitizer with EVs may have potential clinical applications for cancer therapy.