Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunization strategies for simplicial irreversible epidemic on simplicial complex

Higher-order networks can be used to describe the interaction of multiple entities in real-world collective behaviors such as dining, conference attendance, and public transportation use. Collective behavior is often one of the main reasons for “super-spreading events” during epidemics. How to propose effective immunization strategies is a Frontier research topic in network science and public health. To the best of our knowledge, there is a lack of systematic research on immunization strategies for epidemics on higher-order networks. We use synthetic networks and real-world networks as underlying structures to construct simplicial complexes to describe higher-order interaction networks, including pairwise and group interactions, and then propose a simplicial irreversible epidemic spreading model (i.e., simplicial Susceptible-Infected-Removed model). The temporal evolution process of nodes in different states in the system is described by extending the Microscopic Markov Chain Approach. Based on the node degree index and betweenness index, immunization strategies are proposed on the higher-order networks. Through theoretical analysis and numerical simulations, we discuss the effects of different higher-order infection rates, immunization ratios, and immunization strategies on the simplicial irreversible epidemic spread. Under some specific parameter configurations, we observe continuous growth, discontinuous growth, reduction of outbreak threshold, etc.
(Not) Home alone: Antigen presenting cell – T Cell communication in barrier tissues

Priming of T cells by antigen presenting cells (APCs) is essential for T cell fate decisions, enabling T cells to migrate to specific tissues to exert their effector functions. Previously, these interactions were mainly explored using blood-derived cells or animal models. With great advances in single cell RNA-sequencing techniques enabling analysis of tissue-derived cells, it has become clear that subsets of APCs are responsible for priming and modulating heterogeneous T cell effector responses in different tissues. This composition of APCs and T cells in tissues is essential for maintaining homeostasis and is known to be skewed in infection and inflammation, leading to pathological T cell responses. This review highlights the commonalities and differences of T cell priming and subsequent effector function in multiple barrier tissues such as the skin, intestine and female reproductive tract. Further, we provide an overview of how this process is altered during tissue-specific infections which are known to cause chronic inflammation and how this knowledge could be harnessed to modify T cell responses in barrier tissue.
The role and therapeutic significance of the anoikis pathway in renal clear cell carcinoma

Anoikis is a specialized mode of programmed cell death. Specifically, once cells detach from the original extracellular matrix, an apoptotic program is initiated, preventing colonization of the cells in distant parts of the organ. Therefore, both distant metastasis and colonization of cancer cells rely on the anoikis resistance of cancer cells. Bioinformatics analysis was performed to confirm the relation of anoikis to kidney renal cell carcinoma (KIRC). To construct a prognostic model for patients with KIRC, we investigated several genes of the anoikis pathway most closely related to KIRC and also contrasted the effects of common anticancer drugs on the KIRC pathway. Besides KIRC, we explored the expression of anoikis-related genes in various other cancers. We classified patients with KIRC into three clusters based on the coefficients and mRNA expression levels of anoikis-related genes selected using the GSVA algorithm. We used the GDSC database to predict the response of the anoikis pathway to common anticancer drugs and explored the potential targets of the anoikis pathway in KIRC. We then analyzed the response of common immunotherapies to the anoikis pathway to analyze the correlation between anoikis and immune checkpoint inhibitor therapy. Finally, eleven cancer-related genes were screened and a prognostic model was constructed using LASSO regression.
Detection of myocardial fibrosis: Where we stand

Myocardial fibrosis, resulting from the disturbance of extracellular matrix homeostasis in response to different insults, is a common and important pathological remodeling process that is associated with adverse clinical outcomes, including arrhythmia, heart failure, or even sudden cardiac death. Over the past decades, multiple non-invasive detection methods have been developed. Laboratory biomarkers can aid in both detection and risk stratification by reflecting cellular and even molecular changes in fibrotic processes, yet more evidence that validates their detection accuracy is still warranted. Different non-invasive imaging techniques have been demonstrated to not only detect myocardial fibrosis but also provide information on prognosis and management. Cardiovascular magnetic resonance (CMR) is considered as the gold standard imaging technique to non-invasively identify and quantify myocardial fibrosis with its natural ability for tissue characterization. This review summarizes the current understanding of the non-invasive detection methods of myocardial fibrosis, with the focus on different techniques and clinical applications of CMR.
Earth model-space exploration in Southern California: Influence of topography, geotechnical layer, and attenuation on wavefield accuracy

Accurately predicting the seismic wavefield is important for physics-based earthquake hazard studies and is dependent on an accurate source model, a good model of the subsurface geology, and the full physics of wave propagation. Here, we conduct numerical experiments to investigate the effect of different representations of the Southern California Earthquake Center and Harvard community velocity models on seismic waveform predictions in the vicinity of the San Andreas fault in Salton Trough. We test general preconceptions about the importance of topography, near-surface geotechnical layering, and anelastic attenuation up to a maximum frequency of 0.5 Hz. For the Southern California Earthquake Center model developed without topography, we implement 1D and linear model extensions that preserve the geologic structure and a pull-up approach that adapts the original model to topographic variations and distorts the subsurface. The Harvard model includes an elevation model, so we test the squashed topography representation, which flattens it. For both community models, we modify the top 350 m by partially applying the Ely geotechnical layer using a minimum shear wave velocity of 600 m/s and incorporate an Olsen attenuation model using a ratio of 0.05. We evaluate the resulting 24 model representations using the classical waveform misfit and five moderate-magnitude earthquakes. Only the inclusion of attenuation consistently improves the wavefield predictions. It becomes more impactful at higher frequencies, where it significantly improves the performance levels of the crude 1D and linear extension models close to that of the original version. The pull-up topography representation also enhances the waveform prediction ability of the original model. Squashing the topography of the elevation-referenced Harvard model produces better seismogram fits, suggesting that seismic imagers construct community tomographic models without topography to avoid issues related to missing model parameters near the free surface or discrepancies with a different elevation model. Although full implementation of the Ely geotechnical layer that would permit shear wave velocities as low as 90 m/s proves computationally expensive, our partial implementation provides slightly better results in some cases. Our results can serve as recommendations for implementing these community models for future validation or optimization studies.
Novel inhibitors and activity-based probes targeting serine proteases

Serine proteases play varied and manifold roles in important biological, physiological, and pathological processes. These include viral, bacterial, and parasitic infection, allergic sensitization, tumor invasion, and metastasis. The use of activity-based profiling has been foundational in pinpointing the precise roles of serine proteases across this myriad of processes. A broad range of serine protease-targeted activity-based probe (ABP) chemotypes have been developed and we have recently introduced biotinylated and “clickable” peptides containing P1 N-alkyl glycine arginine N-hydroxy succinimidyl (NHS) carbamates as ABPs for detection/profiling of trypsin-like serine proteases. This present study provides synthetic details for the preparation of additional examples of this ABP chemotype, which function as potent irreversible inhibitors of their respective target serine protease. We describe their use for the activity-based profiling of a broad range of serine proteases including trypsin, the trypsin-like protease plasmin, chymotrypsin, cathepsin G, and neutrophil elastase (NE), including the profiling of the latter protease in clinical samples obtained from patients with cystic fibrosis.
The self-efficacy of private school teachers toward the implementation of inclusive education in Ghana: A mixed-methods study

Background Although efforts toward practicing inclusive education have stalled in countries such as Ghana, the available data have mainly centred on enacting inclusive education in public schools. With private schools being notable alternative service providers to public schools, understanding private school teachers’ perceived self-efficacy toward teaching students with disabilities in the classroom is essential. Method To develop insights into inclusive practices, a two-phase mixed-methods design was adopted for this study. In the first phase, 82 teachers from six private schools responded to the self-reported Teacher Efficacy for Inclusive Practice (TEIP) scale. In the second phase, there were 10 participants, including principals (n = 3), heads of department (n = 4) and teachers (n = 3). While the quantitative data were subjected to confirmatory factor analysis, t-tests, analysis of variance and linear regression, the qualitative data were analysed thematically using the components of the TEIP scale as a priori themes. Result The study confirmed the structural validity of the TEIP scale in measuring teachers’ self-efficacy and the correlations and covariances between efficacy in managing behaviour and performing instruction and collaboration. There was divergence between the quantitative and qualitative data and background variables, such as educational qualifications, pre-service training in inclusive education and participation in professional development, which provided additional insights into the teachers’ self-efficacy. Conclusion The findings show that some private school teachers teach students with disabilities despite having no confidence in their capabilities. The study findings underscore the need to create more training opportunities for private school teachers to enhance their confidence in practicing inclusive education in schools.
Incoherent quantum feedback control of collective light scattering by Bose-Einstein condensates

It is well known that in the presence of a ring cavity the light scattering from a uniform atomic ensemble can become unstable resulting in the collective atomic recoil lasing. This is the result of a positive feedback due to the cavity. We propose to add an additional electronic feedback loop based on the photodetection of the scattered light. The advantage is a great flexibility in choosing the feedback algorithm, since manipulations with electric signals are very well developed. In this paper we address the application of such a feedback to atoms in the Bose-Einstein condensed state and explore the quantum noise due to the incoherent feedback action. We show that although the feedback based on the photodetection does not change the local stability of the initial uniform distribution with respect to small disturbances, it reduces the region of attraction of the uniform equilibrium. The feedback-induced nonlinearity enables quantum fluctuations to bring the system out of the stability region and cause an exponential growth even if the uniform state is globally stable without the feedback. Using numerical solution of the feedback master equation we show that there is no feedback-induced noise in the quadratures of the excited atomic and light modes. The feedback loop, however, introduces additional noise into the number of quanta of these modes. Importantly, the feedback opens an opportunity to position the modulated BEC inside a cavity as well as tune the phase of scattered light. This can find applications in precision measurements and quantum simulations.
Evaluation of crack propagation in concrete bridges from vehicle-mounted camera images using deep learning and image processing

In Japan, all bridges should be inspected every 5 years. Usually, the inspection has been performed through the visual evaluation of experienced engineers. However, it requires a lot of load and expense. In order to reduce the inspection work, an attempt is made in this paper to develop a new inspection method using deep learning and image processing technologies. While using the photos obtained by vehicle-mounted camera, the damage states of bridges can be evaluated manually, it still requires a lot of time and load. To save the time and load, deep learning, which is a method of artificial intelligence is introduced. For image processing, it is necessary to utilize such pre-processing techniques as binarization of pictures and morphology treatment. To illustrate the applicability of the method developed here, some experiments are conducted by using the photos of running surface of concrete bridges of a monorail took by vehicle-mounted camera.
The effects of different stress on intestinal mucosal barrier and intestinal microecology were discussed based on three typical animal models

Recent studies have revealed that the effect of intestinal microecological disorders on organismal physiology is not limited to the digestive system, which provides new perspectives for microecological studies and new ideas for clinical diagnosis and prevention of microecology-related diseases. Stress triggers impairment of intestinal mucosal barrier function, which could be duplicated by animal models. In this paper, pathological animal models with high prevalence and typical stressors—corresponding to three major stressors of external environmental factors, internal environmental factors, and social psychological factors, respectively exemplified by burns, intestinal ischemia-reperfusion injury (IIRI), and depression models—were selected. We summarized the construction and evaluation of these typical animal models and the effects of stress on the organism and intestinal barrier, as well as systematically discussed the effects of different stresses on the intestinal mucosal barrier and intestinal microecology.
Influence of oxygen concentration on the neuroprotective effect of hydrogen inhalation in a rat model of cardiac arrest

Background Post-cardiac arrest (CA) brain injury is the main cause of death in patients resuscitated from CA. Previous studies demonstrated that hydrogen inhalation mitigates post-CA brain injury. However, factors affecting the efficacy of hydrogen remain unknown. In the present study, we investigated the influence of oxygen concentration and targeted temperature on neuroprotective effect in a CA rat model of ventricular fibrillation (VF). Methods Cardiopulmonary resuscitation (CPR) was initiated after 7 min of untreated VF in adult male Sprague–Dawley rats. Immediately following successful resuscitation, animals were randomized to be ventilated with 21% oxygen and 79% nitrogen (21%O2); 2% hydrogen, 21% oxygen, and 77% nitrogen (2%H2 + 21%O2); 2% hydrogen, 50% oxygen, and 48% nitrogen (2%H2 + 50%O2); or 2% hydrogen and 98% oxygen (2%H2 + 98%O2) for 3 h. For each group, the target temperature was 37.5°C for half of the animals and 35.0°C for the other half. Results No statistical differences in baseline measurements and CPR characteristics were observed among groups. For animals with normothermia, 2%H2 + 50%O2 (123 [369] vs. 500 [393], p = 0.041) and 2%H2 + 98%O2 (73 [66] vs. 500 [393], p = 0.002) groups had significantly lower neurological deficit scores (NDSs) at 96 h and significantly higher survival (75.0 vs. 37.5%, p = 0.033 and 81.3 vs. 37.5%, p = 0.012) than 21%O2 group. For animals with hypothermia, no statistical difference in NDS among groups but 2%H2 + 98%O2 has significantly higher survival than the 21%O2 group (93.8 vs. 56.3%, p = 0.014). Conclusion In this CA rat model, inhaling 2% hydrogen combined with a high concentration of oxygen improved 96-h survival, either under normothermia or under hypothermia.
Foot-and-mouth disease virus non-structural protein 2B downregulates the RLR signaling pathway via degradation of RIG-I and MDA5

Foot-and-mouth disease virus (FMDV) is a single-stranded, positive-sense RNA virus containing at least 13 proteins. Many of these proteins show immune modulation capabilities. As a non-structural protein of the FMDV, 2B is involved in the rearrangement of the host cell membranes and the disruption of the host secretory pathway as a viroporin. Previous studies have also shown that FMDV 2B plays a role in the modulation of host type-I interferon (IFN) responses through the inhibition of expression of RIG-I and MDA5, key cytosolic sensors of the type-I IFN signaling. However, the exact molecular mechanism is poorly understood. Here, we demonstrated that FMDV 2B modulates host IFN signal pathway by the degradation of RIG-I and MDA5. FMDV 2B targeted the RIG-I for ubiquitination and proteasomal degradation by recruiting E3 ubiquitin ligase ring finger protein 125 (RNF125) and also targeted MDA5 for apoptosis-induced caspase-3- and caspase-8-dependent degradation. Ultimately, FMDV 2B significantly inhibited RNA virus-induced IFN-β production. Importantly, we identified that the C-terminal amino acids 126-154 of FMDV 2B are essential for 2B-mediated degradation of the RIG-I and MDA5. Collectively, these results provide a clearer understanding of the specific molecular mechanisms used by FMDV 2B to inhibit the IFN responses and a rational approach to virus attenuation for future vaccine development.
The association between outdoor air pollution and lung cancer risk in seven eastern metropolises of China: Trends in 2006-2014 and sex differences

There is a positive association between air pollution and lung cancer burden. This study aims to identify and examine lung cancer risks and mortality burdens associated with air pollutants, including PM10, NO2 and SO2, in seven eastern metropolises of China. The study population comprised a population from seven eastern metropolises of China. The yearly average values (YAV, μg/m3) of the PM10, NO2 and SO2 levels were extracted from China Statistical Yearbook (CSYB) for each selected city from 2006 to 2014. Data collected in the China Cancer Registry Annual Report (CCRAR) provide lung cancer incidence and mortality information. A two-level normal random intercept regression model was adopted to analyze the association between the lung cancer rates and individual air pollutant concentration within a five-year moving window of past exposure. The yearly average values of PM10, SO2 and NO2 significantly decreased from 2006 to 2014. Consistently, the male age-adjusted incidence rate (MAIR) and male age-adjusted mortality rate (MAMR) decreased significantly from 2006 to 2014.Air pollutants have a lag effect on lung cancer incidence and mortality for 2-3 years. NO2 has the significant association with MAIR (RR=1.57, 95% CI: 1.19-2.05, p=0.002), MAMR (RR=1.70, 95% CI: 1.32-2.18, p=0.0002) and female age-adjusted mortality rate (FAMR) (RR=1.27, 95% CI: 1.08-1.49, p=0.003). Our findings suggested that air pollutants may be related to the occurrence and mortality of lung cancer. NO2 was significantly associated with the risk of lung cancer, followed by SO2. Air pollutants have the strongest lag effect on the incidence and mortality of lung cancer within 2-3 years.
Characterization of lncRNA/circRNA-miRNA-mRNA network to reveal potential functional ceRNAs in the skeletal muscle of chicken

Skeletal muscle, comprising approximately 40% of body mass, is a highly complex and heterogeneous tissue serving a multitude of functions in the organism. Non-coding RNAs (ncRNAs) are known to participate in skeletal muscle development as critical regulators. However, the regulatory mechanisms of ncRNAs on chicken muscle traits are not well understood. In the present study, we collected the leg muscle from male embryos of Tibetan chicken at embryonic (E) 10 and E18 for RNA sequencing. A total of 6,583 differentially expressed mRNAs (DEMs) including 3,055 down-regulated and 3,528 up-regulated were identified in E18. We identified 695 differentially expressed lncRNAs (DELs) (187 down-regulated and 508 up-regulated) and 1,906 differentially expressed circRNAs (DECs) (1,224 down-regulated and 682 up-regulated) in E18. Among the 130 differentially expressed miRNAs (DEMIs), 59 were up-regulated and 71 were down-regulated in E18. Numerous DEMs and target genes for miRNAs/lncRNAs were significantly enriched in the muscle system process and cell cycle. We constructed a miRNA-gene-pathway network by considering target relationships between genes related to skeletal muscle development and miRNAs. A competing endogenous RNA (ceRNA) network was also constructed by integrating competing relationships between DEMs, DELs, and DECs. Several DELs and DECs were predicted to regulate the ADRA1B, ATP2A2, ATP2B1, CACNA1S, CACNB4, MYLK2, and ROCK2 genes. We discovered the crosstalk between the ncRNAs and their competing mRNAs, which provides insights into ceRNA function and mechanisms in the skeletal muscle development of chicken.
Cannabidiol modulates expression of type I IFN response genes and HIV infection in macrophages

Cannabis (Cannabis sativa) is a widely used drug in the United States and the frequency of cannabis use is particularly high among people living with HIV (PLWH). One key component of cannabis, the non-psychotropic (−)-cannabidiol (CBD) exerts a wide variety of biological actions, including anticonvulsive, analgesic, and anti-inflammatory effects. However, the exact mechanism of action through which CBD affects the immune cell signaling remains poorly understood. Here we report that CBD modulates type I interferon responses in human macrophages. Transcriptomics analysis shows that CBD treatment significantly attenuates cGAS-STING-mediated activation of type I Interferon response genes (ISGs) in monocytic THP-1 cells. We further showed that CBD treatment effectively attenuates 2’3-cGAMP stimulation of ISGs in both THP-1 cells and primary human macrophages. Interestingly, CBD significantly upregulates expression of autophagy receptor p62/SQSTM1. p62 is critical for autophagy-mediated degradation of stimulated STING. We observed that CBD treated THP-1 cells have elevated autophagy activity. Upon 2’3’-cGAMP stimulation, CBD treated cells have rapid downregulation of phosphorylated-STING, leading to attenuated expression of ISGs. The CBD attenuation of ISGs is reduced in autophagy deficient THP-1 cells, suggesting that the effects of CBD on ISGs is partially mediated by autophagy induction. Lastly, CBD decreases ISGs expression upon HIV infection in THP-1 cells and human primary macrophages, leading to increased HIV RNA expression 24 hours after infection. However, long term culture with CBD in infected primary macrophages reduced HIV viral spread, suggesting potential dichotomous roles of CBD in HIV replication. Our study highlights the immune modulatory effects of CBD and the needs for additional studies on its effect on viral infection and inflammation.