Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-scale attention-based convolutional neural network for classification of breast masses in mammograms.

PURPOSE Breast cancer is the cancer with the highest incidence in women, and early detection can effectively improve the survival rate of patients. Mammography is an important method for physicians to screening breast cancer, but the diagnosis of mammograms by physicians depends largely on clinical practice experience. Studies have shown that using computer aided diagnosis techniques can help doctors diagnose breast cancer. METHODS In this paper, the method of convolutional neural network is mainly used to classify benign and malignant breast masses in the mammograms. Firstly, we use multi-scale residual networks and densely connected networks as backbone networks to extract the features of global image patches and local image patches. Secondly, we use the attention module named Convolutional Block Attention Module (CBAM) to improve the two feature extraction networks to enhance the network's feature expression ability. Finally, we fuse the features of multi-scale image patches to achieve the classification of benign and malignant breast masses. RESULTS In the DDSM database, the accuracy, sensitivity, AUC value and corresponding standard deviation of our method are 0.9626±0.0110, 0.9719±0.0126, and 0.9576±0.0064, respectively. Compared with the commonly used ResNet (AUC=0.8823±0.0112) and DenseNet (AUC=0.9141±0.0085), the performance of our method has improved. In addition, we also used the INbreast database to train and validate the proposed method. The accuracy, sensitivity, AUC and corresponding standard deviations are 0.9554±0.0296, 0.9605±0.0228 and 0.9468±0.0085, respectively. CONCLUSIONS Compared with the previous work, our proposed method uses multi-scale image features, has better classification performance in breast mass patches classification tasks, and can effectively assist physicians in breast cancer diagnosis.
Iturin: cyclic lipopeptide with multifunction biological potential

Abstract Iturin, a metabolite produced by Bacillus subtilis, has a broad-spectrum antibacterial effect, and because they are secreted in the rhizosphere of plants, iturins are often mixed with many organic molecules. In recent years, people have improved their separation and purification methods but still cannot achieve simple and effective procedures, making Iturins an ideal biological control agent for insects and bacteria; commercial value still cannot be realized. With the in-depth studies of Iturins, its anti-cancer, hemolysis and other biological activities have gradually been discovered. This article reviews the branches of the Iturin family, structural features of these metabolite, separation and purification methods used for producing it, culture optimization, and various biological activities of the Iturin family, such as insecticidal, antibacterial, hemolytic and anticarcinogenic properties, among others have been summarized. Furthermore, this review revealed some commercial applications of Iturins and their relevance in research works. For example, in food packaging, clean water has good development potential.This can promote the commercial application of Iturins instead of other chemical and biological control agents that are environmentally friendly, pollution-free and have no side effects on humans. Furthermore, work documented anticancer, hemolytic and other biological activities of Iturin.
A critical review of filter transmittance measurements for aerosol light absorption, and de novo calibration for a decade of monitoring on PTFE membranes

ABSTRACT The IMPROVE (Interagency Monitoring of PROtected Visual Environments) network monitors the attenuation of light by PM2.5 samples (fine particulate matter, Daero = 2.5 μm) routinely collected on polytetrafluoroethylene (PTFE) filters throughout the United States. The results of this measurement have long been reported as an indicator of absorption, with no rigorous calibration as such. Filter-based absorption measurements more conventionally employ optically thick quartz- or glass-fiber collection media, for which a substantial calibration literature offers algorithms to correct for particle scattering and filter loading effects. PTFE membranes are optically thinner and less homogeneous than the fiber media, but they avoid interference from adsorbed organic gases that is associated with quartz and glass fiber media. IMPROVE's measurement system is a hybrid of integrating sphere and integrating plate that records the light backscattered as well as transmitted by each filter. This article introduces and validates a theory-based model for calibration and data reduction that accounts for particle scattering effects as well as variations in filter optics. Tests based on historical analyses of field blanks and recent reanalyses of archived samples establish that the current system has operated with a stable calibration since 2003. The newly calibrated IMPROVE absorption values correlate strongly with the refractory carbon fraction reported by thermal-optical analysis as “elemental” (EC). EC is sometimes treated as the only significant light absorber in PM2.5, but the general decline observed between 2005 and 2014 in IMPROVE EC was not accompanied by a comparable decline in IMPROVE absorption. Absorption also exhibits a distinct association with Fe concentrations, which at IMPROVE sites are attributable mainly to mineral dusts and have generally held steady or risen since 2003. An increased relative contribution by mineral dusts can explain some, but not all, of the observed difference between recent absorption and EC trends.
Affective communication: a mixed method investigation into COVID-19 outbreak communication using the Taiwanese government Facebook page

The COVID-19 outbreak has created an unprecedented challenge for governments to convey information to the public, and social media has become a critical method of COVID-19 communication in Taiwan. Objectives: This study examines a total of 1128 Facebook posts published by Taiwan’s principal health authority from December 1, 2019 to May 31, 2020. Methods: Using both qualitative and quantitative approaches, this study investigates strategies used by the Taiwan government to communicate the COVID-19 outbreak and public responses toward these strategies. Result: Novel uses of Facebook posts on outbreak communication were identified, including solidarity, reviews of actions, press conferences, and the use of animal and cartoon images. Quantitative results showed that the public responded significantly more frequently to messages generating positive affects, such as posts that reviewed government actions and public efforts; posts that expressed thanks, approval, or comradeship; and posts that paired text with photographs of frontline workers or cute animals. Conclusion: These results suggest that, amid a disease outbreak, the public not only look for updated situations and guidelines but also for affective affirmation from government agencies.
Prokaryotic reverse transcriptases: from retroelements to specialized defense systems

ABSTRACT Reverse transcriptases (RTs) catalyze the polymerization of DNA from an RNA template. These enzymes were first discovered in RNA tumor viruses in 1970, but it was not until 1989 that they were found in prokaryotes as a key component of retrons. Apart from RTs encoded by the ‘selfish’ mobile retroelements known as group II introns, prokaryotic RTs are extraordinarily diverse, but their function has remained elusive. However, recent studies have revealed that different lineages of prokaryotic RTs, including retrons, those associated with CRISPR-Cas systems, Abi-like RTs and other yet uncharacterized RTs, are key components of different lines of defense against phages and other mobile genetic elements. Prokaryotic RTs participate in various antiviral strategies, including abortive infection (Abi), in which the infected cell is induced to commit suicide to protect the host population, adaptive immunity, in which a memory of previous infection is used to build an efficient defense, and other as yet unidentified mechanisms. These prokaryotic enzymes are attracting considerable attention, both for use in cutting-edge technologies, such as genome editing, and as an emerging research topic. In this review, we discuss what is known about prokaryotic RTs, and the exciting evidence for their domestication from retroelements to create specialized defense systems.
The 5-HT3 Receptor Affects Rotavirus-Induced Motility

The mechanisms underlying rotavirus-induced diarrhea and vomiting are not yet fully understood. To better understand rotavirus pathophysiology, characterization of nerve signaling within the ENS and through vagal efferent nerves to the brain, which have been shown to be of great importance to the disease, is necessary. ABSTRACT Rotavirus infection is highly prevalent in children, and the most severe effects are diarrhea and vomiting. It is well accepted that the enteric nervous system (ENS) is activated and plays an important role, but knowledge of how rotavirus activates nerves within ENS and to the vomiting center is lacking. Serotonin is released during rotavirus infection, and antagonists to the serotonin receptor subtype 3 (5-HT3 receptor) can attenuate rotavirus-induced diarrhea. In this study, we used a 5-HT3 receptor knockout (KO) mouse model to investigate the role of this receptor in rotavirus-induced diarrhea, motility, electrolyte secretion, inflammatory response, and vomiting reflex. The number of diarrhea days (P = 0.03) and the number of mice with diarrhea were lower in infected 5-HT3 receptor KO than wild-type pups. In vivo investigation of fluorescein isothiocyanate (FITC)-dextran transit time showed that intestinal motility was lower in the infected 5-HT3 receptor KO compared to wild-type mice (P = 0.0023). Ex vivo Ussing chamber measurements of potential difference across the intestinal epithelia showed no significant difference in electrolyte secretion between the two groups. Immediate early gene cFos expression level showed no difference in activation of the vomiting center in the brain. Cytokine analysis of the intestine indicated a low effect of inflammatory response in rotavirus-infected mice lacking the 5-HT3 receptor. Our findings indicate that the 5-HT3 receptor is involved in rotavirus-induced diarrhea via its effect on intestinal motility and that the vagus nerve signaling to the vomiting center occurs also in the absence of the 5-HT3 receptor. IMPORTANCE The mechanisms underlying rotavirus-induced diarrhea and vomiting are not yet fully understood. To better understand rotavirus pathophysiology, characterization of nerve signaling within the ENS and through vagal efferent nerves to the brain, which have been shown to be of great importance to the disease, is necessary. Serotonin (5-HT), a mediator of both diarrhea and vomiting, has been shown to be released from enterochromaffin cells in response to rotavirus infection and the rotavirus enterotoxin NSP4. Here, we investigated the role of the serotonin receptor 5-HT3, which is known to be involved in the nerve signals that regulate gut motility, intestinal secretion, and signal transduction through the vagus nerve to the brain. We show that the 5-HT3 receptor is involved in rotavirus-induced diarrhea by promoting intestinal motility. The findings shed light on new treatment possibilities for rotavirus diarrhea.
Log reduction of leukemic cells and minimal residual disease by flow cytometry represent effective predictors of clinical outcome in elderly patients with acute myeloid leukemia

Nowadays minimal residual disease (MRD) and log‐reduction of leukemic cells are poorly investigated in elderly patients with acute myeloid leukemia (AML) treated with hypometilating agents (HMAs). Studies focusing on MRD in elderly AML patients who received HMAs are scant and devoid of rigorous criteria for both enrollment and monitoring. Log‐reduction has never been investigated in these patients. Thus, the purpose of our study was to compare the prognostic impact of MRD and log‐reduction of leukemic cells at the optimal time of assessment in older AML patients.
Engineering the Growth of MoS2 via Atomic Layer Deposition of Molybdenum Oxide Film Precursor

Dr. C. Martella, P. Melloni, Dr. E. Cinquanta, Dr. E. Cianci, M. Alia, Dr. M. Longo, Dr. A. Lamperti, Dr. S. Vangelista, Prof. M. Fanciulli, Dr. A. Molle Laboratorio MDM IMM-CNR via C. Olivetti 2 , I-20864 Agrate Brianza (MB) , Italy E-mail: christian.martella@mdm.imm. cnr.it; alessandro.molle@mdm.imm. cnr.it P. Melloni, Prof. M. Fanciulli Dipartimento di Scienza dei Materiali Università degli Studi di Milano Bicocca via R. Cozzi 53 , I-20126 Milano (MI) , Italy
Soil sample pooling generates no consistent inference bias: a meta-analysis of 71 plant-soil feedback experiments.

There is current debate on how soil sample pooling affects the measurement of plant-soil feedbacks. Several studies have suggested that pooling soil samples among experimental units reduces variance and can bias estimates of plant-soil feedbacks. However, it is unclear whether pooling has resulted in systematic mismeasurement of plant-soil feedbacks in the literature. Using data from 71 experiments, we tested whether pairwise plant-soil feedback direction, magnitude, and variance differed among soil pooling treatments. We also tested whether pooling has altered our understanding of abiotic and biotic drivers that influence pairwise plant-soil feedbacks. Pooling of soil samples among experimental units was used in 42% of examined experiments. Contrary to predictions, pooling did not affect mean pairwise plant-soil feedback effect size or within-experiment variance. Accounting for soil sample pooling also did not significantly alter our understanding of the drivers of pairwise plant-soil feedbacks. We conclude that there is no evidence that soil sample pooling systematically biases estimates of plant-soil feedback direction, magnitude, variance, or drivers across many studies. Given the debate of whether to pool soil samples, researchers should be aware of potential criticisms and carefully consider how experimental design and soil pooling methods influence experiment interpretation.
Innate Antiviral Cytokine Response to Swine Influenza Virus by Swine Respiratory Epithelial Cells

Swine are considered intermediate hosts that have facilitated influenza virus reassortment events that have given rise pandemics or genetically related viruses have become established in swine. In this study, we examine the innate antiviral response to swine influenza virus in primary and immortalized swine nasal and tracheal epithelial cells, and show virus strain- and host cell type-dependent differential expression of key interferons and interferon-stimulated genes. ABSTRACT Swine influenza virus (SIV) can cause respiratory illness in swine. Swine contribute to influenza virus reassortment, as avian, human, and/or swine influenza viruses can infect swine and reassort, and new viruses can emerge. Thus, it is important to determine the host antiviral responses that affect SIV replication. In this study, we examined the innate antiviral cytokine response to SIV by swine respiratory epithelial cells, focusing on the expression of interferon (IFN) and interferon-stimulated genes (ISGs). Both primary and transformed swine nasal and tracheal respiratory epithelial cells were examined following infection with field isolates. The results show that IFN and ISG expression is maximal at 12 h postinfection (hpi) and is dependent on cell type and virus genotype. IMPORTANCE Swine are considered intermediate hosts that have facilitated influenza virus reassortment events that have given rise pandemics or genetically related viruses have become established in swine. In this study, we examine the innate antiviral response to swine influenza virus in primary and immortalized swine nasal and tracheal epithelial cells, and show virus strain- and host cell type-dependent differential expression of key interferons and interferon-stimulated genes.
Inhibition of exosome release augments neuroinflammation following intracerebral hemorrhage

Intracerebral hemorrhage (ICH) is a severe stroke subtype without effective pharmacological treatment. Following ICH, peripheral leukocytes infiltrate into the brain and contribute to neuroinflammation and brain edema. However, the intercellular machinery controlling the initiation and propagation of leukocyte infiltration remains elusive. Exosomes are small extracellular vesicles released from donor cells and bridge intercellular communication. In this study, we investigated the effects of inhibition of exosome release on neuroinflammation and ICH injury. Using a mouse model of ICH induced by collagenase injection, we found that ICH induced an increase of exosome level in the brain. Inhibition of exosome release using GW4869 augmented neurological deficits and brain edema after ICH. The exacerbation of ICH injury was accompanied by increased barrier disruption and brain infiltration of leukocytes. The detrimental effects of GW4869 were ablated in ICH mice receiving antibody depletion of Gr‐1+ myeloid cells. Extracted exosomes from the ICH brains suppressed the production of inflammatory factors by splenocytes. Additionally, exosomes extracted from brain tissues of donor ICH mice reduced ICH injury in recipient mice. These results demonstrate that inhibition of exosome release augments neuroinflammation and ICH injury. The impact of exosomes released from the ICH brain on the immune system deserves further investigation.
Subsystem macroarchitecture of the intrinsic midbrain neural network and its tectal and tegmental subnetworks

Significance The midbrain is one of the vertebrate brain’s three basic divisions, and it plays an especially important role in sensory–motor mechanisms, motivation and reward, reproductive and agonistic behaviors, and behavioral state. Network science methods were applied here to reveal organizing principles of intramidbrain circuitry, which include a hierarchy of subsystems that was used to construct a structure–function model of the circuitry. The results show fundamental differences between intramidbrain and previously determined intraforebrain network organization and provide a theoretical framework for experimental analysis of intramidbrain circuit involvement in specific behaviors. The midbrain is the smallest of three primary vertebrate brain divisions. Here we use network science tools to reveal the global organizing principles of intramidbrain axonal circuitry before adding extrinsic connections with the remaining nervous system. Curating the experimental neuroanatomical literature yielded 17,248 connection reports for 8,742 possible connections between the 94 gray matter regions forming the right and left midbrain. Evidence for the existence of 1,676 connections suggests a 19.2% connection density for this network, similar to that for the intraforebrain network [L. W. Swanson et al., Proc. Natl. Acad. Sci. U.S.A. 117, 31470–31481 (2020)]. Multiresolution consensus cluster analysis parceled this network into a hierarchy with 6 top-level and 30 bottom-level subsystems. A structure–function model of the hierarchy identifies midbrain subsystems that play specific functional roles in sensory–motor mechanisms, motivation and reward, regulating complex reproductive and agonistic behaviors, and behavioral state control. The intramidbrain network also contains four bilateral region pairs designated putative hubs. One pair contains the superior colliculi of the tectum, well known for participation in visual sensory–motor mechanisms, and the other three pairs form spatially compact right and left units (the ventral tegmental area, retrorubral area, and midbrain reticular nucleus) in the tegmentum that are implicated in motivation and reward mechanisms. Based on the core hypothesis that subsystems form functionally cohesive units, the results provide a theoretical framework for hypothesis-driven experimental analysis of neural circuit mechanisms underlying behavioral responses mediated in part by the midbrain.
Endoplasmic Reticulum-Associated Degradation Controls Virus Protein Homeostasis, Which Is Required for Flavivirus Propagation

The results of this study reveal the cellular ERAD system controls the amount of each viral protein in virus-infected cells and that this “viral protein homeostasis” is critical for viral propagation. Furthermore, we clarified that the “convoluted membrane (CM),” which was previously considered a structure with unknown function, serves as a kind of waste dump where viral protein degradation occurs. ABSTRACT Many positive-stranded RNA viruses encode polyproteins from which viral proteins are generated by processing the polyproteins. This system produces an equal amount of each viral protein, though the required amounts for each protein are not the same. In this study, we found the extra membrane-anchored nonstructural (NS) proteins of Japanese encephalitis virus and dengue virus are rapidly and selectively degraded by the endoplasmic reticulum-associated degradation (ERAD) pathway. Our gene targeting study revealed that ERAD involving Derlin2 and SEL1L, but not Derlin1, is required for the viral genome replication. Derlin2 is predominantly localized in the convoluted membrane (CM) of the viral replication organelle, and viral NS proteins are degraded in the CM. Hence, these results suggest that viral protein homeostasis is regulated by Derlin2-mediated ERAD in the CM, and this process is critical for the propagation of these viruses. IMPORTANCE The results of this study reveal the cellular ERAD system controls the amount of each viral protein in virus-infected cells and that this “viral protein homeostasis” is critical for viral propagation. Furthermore, we clarified that the “convoluted membrane (CM),” which was previously considered a structure with unknown function, serves as a kind of waste dump where viral protein degradation occurs. We also found that the Derlin2/SEL1L/HRD1-specific pathway is involved in this process, whereas the Derlin1-mediated pathway is not. This novel ERAD-mediated fine-tuning system for the stoichiometries of polyprotein-derived viral proteins may represent a common feature among polyprotein-encoding viruses.