Miracle-dz/UniFAR-FTUs huggingface dataset:
The Alteration Profiles of m6A-Tagged circRNAs in the Peri-Infarct Cortex After Cerebral Ischemia in Mice

The N6-methyladenosine (m6A) modification acts as a dynamic regulatory factor in diseases by regulating the metabolism and function of the transcriptome, especially mRNAs. However, little is known regarding the functional effects of m6A modifications on circRNAs. In this research, we established a distal middle cerebral artery occlusion (MCAO) model in adult C57BL/6J mice. The mice were divided into three groups: sham surgery, 3 days after MCAO (3d), and 7 days after MCAO (7d). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) demonstrated that the mRNA expression levels of m6A-related methyltransferases (METTL3, METTL14), demethylases (FTO, ALKBH5), and reading proteins (YTHDF1, YTHDF3) altered compared to the sham group. Furthermore, the translation level of ALKBH5 and YTHDF3 was significantly decreased in the 3d group while increased in 7d group. Methylated RNA immunoprecipitation (MeRIP) and circRNA microarray indicated 85 hypermethylated and 1621 hypomethylated circRNAs in the 3d group. In the 7d group, the methylation level increased in 57 and decreased in 66 circRNAs. Subsequently, our results were verified by MeRIP-qPCR. Bioinformatics analysis was performed to analyze the functions of differentially m6A-modified circRNAs. We found some m6A modified-circRNAs associated with cerebral infarction, providing a new direction for the molecular mechanism of stroke.
Pathogenesis and Treatment of T-Large Granular Lymphocytic Leukemia (T-LGLL) in the Setting of Rheumatic Disease

A complex relationship exists between rheumatic diseases and cancer. This delicate balance between chronic inflammation and malignant cell transformation in hematologic neoplasms has been observed, but is not well defined. Large Granular Lymphocyte (LGL) leukemia is at the intersection of a clonal lymphoproliferative disease, chronic inflammation, and autoimmunity. The association between rheumatoid arthritis (RA) and the spectrum of Felty’s Syndrome is well-known. Other rheumatic disorders have been reported including systemic lupus erythematosus (SLE), Sjogren’s Syndrome (SS), vasculitis, Behcet’s Disease (BD) and systemic sclerosis. The association between T-LGLL and rheumatic disease pathogenesis has been hypothesized, but has not yet been fully understood. Components of a shared pathogenesis includes chronic antigen stimulation, JAK-STAT pathway activation and overlap of various cytokines. We will summarize current knowledge on the molecular understanding between T-LGLL and rheumatic disease. There are many potential areas of research to help meet this need and lead to development of targeted therapeutic options.
Extracellular Adenosine Triphosphate Binding to P2Y1 Receptors Prevents Glutamate-Induced Excitotoxicity: Involvement of Erk1/2 Signaling Pathway to Suppress Autophagy

Glutamate-induced neuroexcitotoxicity could be related to the pathophysiology of some neurodegenerative diseases including Parkinson’s disease and Alzheimer’s disease. Extracellular ATP exerts a wide variety of functions, such as attenuating Aβ-mediated toxicity, inhibiting N-Methyl-D-Aspartate (NMDA) receptor subunit combinations, and aggravating ischemic brain injury. However, the effect of extracellular ATP on glutamate-induced neuroexcitotoxicity remains largely unknown. Herein, we showed that extracellular ATP prevented the glutamate-induced excitotoxicity via binding to its P2Y1 receptors. We found that excessive glutamate triggered cellular reactive oxygen species (ROS) overproduction and mitochondrial membrane potential damage, which were significantly attenuated by extracellular ATP. Besides, glutamate activated autophagy, as illustrated by the increased protein level of autophagic marker LC3II and decreased level of p62, and glutamate-induced neuroexcitotoxicity could be completely abolished by autophagy inhibitor chloroquine. In addition, we revealed that extracellular ATP activated Erk1/2 signaling to suppress autophagy and to exert its neuroprotective effects, which was further reduced by autophagy agonist rapamycin and the selective Erk1/2 inhibitor PD0325901. Taken together, our findings suggest that extracellular ATP binding to P2Y1 receptors protected against glutamate-induced excitotoxicity via Erk1/2-mediated autophagy inhibition, implying the potential of ATP for the treatment of neurodegenerative disorders.
Epigenetic Regulation in Gastroenteropancreatic Neuroendocrine Tumors

Gastroenteropancreatic neuroendocrine neoplasms are a rare, diverse group of neuroendocrine tumors that form in the pancreatic and gastrointestinal tract, and often present with side effects due to hormone hypersecretion. The pathogenesis of these tumors is known to be linked to several genetic disorders, but sporadic tumors occur due to dysregulation of additional genes that regulate proliferation and metastasis, but also the epigenome. Epigenetic regulation in these tumors includes DNA methylation, chromatin remodeling and regulation by noncoding RNAs. Several large studies demonstrate the identification of epigenetic signatures that may serve as biomarkers, and others identify innovative, epigenetics-based targets that utilize both pharmacological and theranostic approaches towards the development of new treatment approaches.
Differentiation of Bone Mesenchymal Stem Cells Into Vascular Endothelial Cell-Like Cells Using Functionalized Single-Walled Carbon Nanotubes

Carbon nanotubes (CNTs) are a promising bioactive scaffold for bone regeneration because of their superior mechanical and biological properties. Vascularization is crucial in bone tissue engineering, and insufficient vascularization is a long-standing problem in tissue-engineered scaffolds. However, the effect of CNTs on vascularization is still minimal. In the current study, pristine single-walled carbon nanotubes (SWNTs) were purified to prepare different ratios of SWNTs/EDC composites, and their surface morphology and physicochemical properties of SWNTs/EDC were studied. Furthermore, the effect of SWNTs/EDC on vascularization was investigated by inducing the differentiation of bone mesenchymal stem cells (BMSCs) into vascular endothelial cell-like cells (VEC-like cells). Results showed that SWNTs/EDC composite was successfully prepared, and EDC was embedded in the SWNTs matrix and uniformly distributed throughout the composites. The AFM, FTIR spectra, and Raman results confirmed the formation of SWNTs/EDC composites. Besides, the surface topography of the SWNTs/EDC composites presents a rough surface, which may positively affect cell function. In vitro cell culture revealed that SWNTs and SWNTs/EDC composites exhibited excellent biocompatibility and bioactivity. The SWNTs/EDC composite at mass/volume ratios 1:10 had the best enhancement of proliferation and differentiation of BMSCs. Moreover, after culture with SWNTs/EDC composite, approximately 78.3% ± 4.2% of cultured cells are double-positive for FITC-UEA-1 and DiI-Ac-LDL double staining. Additionally, the RNA expression of representative endothelial cell markers VEGF, VEGF-R2, CD31, and vWF in the SWNTs/EDC composite group was significantly higher than those in the control and SWNTs group. With the limitation of our study, the results suggested that SWNTs/EDC composite can promote BMSCs differentiation into VEC-like cells and positively affect angiogenesis and bone regeneration.
FetalGAN: Automated Segmentation of Fetal Functional Brain MRI Using Deep Generative Adversarial Learning and Multi-Scale 3D U-Net

An important step in the preprocessing of resting state functional magnetic resonance images (rs-fMRI) is the separation of brain from non-brain voxels. Widely used imaging tools such as FSL’s BET2 and AFNI’s 3dSkullStrip accomplish this task effectively in children and adults. In fetal functional brain imaging, however, the presence of maternal tissue around the brain coupled with the non-standard position of the fetal head limit the usefulness of these tools. Accurate brain masks are thus generated manually, a time-consuming and tedious process that slows down preprocessing of fetal rs-fMRI. Recently, deep learning-based segmentation models such as convolutional neural networks (CNNs) have been increasingly used for automated segmentation of medical images, including the fetal brain. Here, we propose a computationally efficient end-to-end generative adversarial neural network (GAN) for segmenting the fetal brain. This method, which we call FetalGAN, yielded whole brain masks that closely approximated the manually labeled ground truth. FetalGAN performed better than 3D U-Net model and BET2: FetalGAN, Dice score = 0.973 ± 0.013, precision = 0.977 ± 0.015; 3D U-Net, Dice score = 0.954 ± 0.054, precision = 0.967 ± 0.037; BET2, Dice score = 0.856 ± 0.084, precision = 0.758 ± 0.113. FetalGAN was also faster than 3D U-Net and the manual method (7.35 s vs. 10.25 s vs. ∼5 min/volume). To the best of our knowledge, this is the first successful implementation of 3D CNN with GAN on fetal fMRI brain images and represents a significant advance in fully automating processing of rs-MRI images.
Pilot Study of Effects of Intermittent Pneumatic Compression in the Immediate Peri-Operative Period on Hemodynamic Parameters in Patients After Laparoscopic Gynecologic Surgery

The randomized controlled study investigated the impacts of immediate peri-operative Intermittent pneumatic compression (IPC) on hemodynamic indicators in patients undergoing laparoscopic gynecologic surgery. Patients scheduled for elective laparoscopic gynecologic surgery were randomized to control (IPC not used), pre-operative IPC, post-operative IPC, and peri-operative IPC (performed both before and after surgery) groups. Systolic blood pressure (SBP), mean blood pressure (MBP) cardiac output (CO), heart rate (HR) and systemic vascular resistance (SVR) were measured at different time points. The results showed that SBP changes not obviously over time in the control and peri-operative IPC group. Compared with values before surgery, the pre-operative IPC group had a lower SBP (P < 0.01) at the end of PACU stay, whereas the post-operative IPC group had a higher SBP (P < 0.01) after surgery. All groups exhibited little or no variation in HR, CO and SVR. Conclusion is peri-operative IPC has no major adverse effects on hemodynamic parameters.
Continuous Vaginal Bleeding Induced By EGFR-TKI in Premenopausal Female Patients With EGFR Mutant NSCLC

EGFR-TKI is widely used for EGFR-mutant NSCLC patients. Bleeding is reported as a neglected adverse effect induced by EGFR-TKI. Female patients with lung adenocarcinoma have a high frequency of EGFR mutations. This study investigated the effect of EGFR-TKI on the menstrual cycle, especially on bleeding, in women of childbearing age. The underlying mechanism was further investigated in a patient with severe bleeding. We retrospectively investigated the effects on menstrual cycle in premenopausal female NSCLC patients who underwent EGFR-TKI treatment during 2013 to 2019. Menstrual changes including cycle disorders and prolonged bleeding were investigated via questionnaire survey. EGFR signaling, ER, PR and tissue factor expression were analyzed in endometrium tissue obtained from a 43-year-old patient who suffered from continuous vaginal bleeding during treatment with erlotinib and osimertinib. Among 42 premenopausal female patients taking EGFR tyrosine kinase inhibitor, 69.05% patients experienced abnormal menstruation. In women with abnormal menstruation, 41.37% had profuse menstruation and 20.69% had irregular menstruation. In most cases, the abnormal vaginal bleeding stopped when suspending EGFR-TKI. The EGFR-TKI induced abnormal vaginal bleeding might be associated with low progesterone level, decreased EGFR activation and tissue factor (TF) expression in endometrial tissues. EGFR-TKI unusually induce abnormal vaginal bleeding in premenopausal female NSCLC patients, which may be attributed to progesterone/EGFR/TF signaling. Megestrol acetate may be an available and effective drug for the uncommon adverse effect.
First extension groups of Verma modules and $R$-polynomials

We study the first extension groups between Verma modules. There was a conjecture which claims that the dimensions of the higher extension groups between Verma modules are the coefficients of $R$-polynomials defined by Kazhdan-Lusztig. This conjecture was known as the Gabber-Joseph conjecture (although Gebber and Joseph did not state.) However, Boe gives a counterexample to this conjecture. In this paper, we study how far are the dimensions of extension groups from the coefficients of $R$-polynomials.
Extrinsic control of the early postnatal CA1 hippocampal circuits

The adult CA1 region of the hippocampus produces coordinated neuronal dynamics with minimal reliance on its extrinsic inputs. In contrast, the neonatal CA1 is tightly linked to externally-generated sensorimotor activity but the circuit mechanisms underlying early synchronous activity in CA1 remain unclear. Here, using a combination of in vivo and ex vivo circuit mapping, calcium imaging and electrophysiological recordings in mouse pups, we show that early dynamics in the ventro-intermediate CA1 are under the mixed influence of entorhinal (EC) and thalamic (VMT) inputs. Both VMT and EC can drive internally-generated synchronous events ex vivo. However, movement-related population bursts detected in vivo are exclusively driven by the EC. These differential effects on synchrony reflect the different intrahippocampal targets of these inputs. Hence, cortical and subcortical pathways act differently on the neonatal CA1, implying distinct contributions to the development of the hippocampal microcircuit and related cognitive maps.
Evaluating the breadth of neutralizing antibody responses elicited by infectious bursal disease virus (IBDV) genogroup A1 strains using a novel chicken B-cell rescue system and neutralization assay

There is a need to evaluate the ability of vaccines to neutralize diverse IBDV genogroups and to better understand the relationship between HVR sequence, structure, and antigenicity. Here, we used a chicken B-cell line to rescue a panel of chimeric IBDVs with the HVR from seven diverse IBDV field strains and to conduct neutralization assays and protein modeling. ABSTRACT Eight infectious bursal disease virus (IBDV) genogroups have been identified based on the sequence of the capsid hypervariable region (HVR) (A1 to A8). Given reported vaccine failures, there is a need to evaluate the ability of vaccines to neutralize the different genogroups. To address this, we used a reverse genetics system and the chicken B-cell line DT40 to rescue a panel of chimeric IBDVs and perform neutralization assays. Chimeric viruses had the backbone of a lab-adapted strain (PBG98) and the HVRs from diverse field strains as follows: classical F52-70 (A1), U.S. variant Del-E (A2), Chinese variant SHG19 (A2), very virulent UK661 (A3), M04/09 distinct (A4), Italian ITA-04 (A6), and Australian variant Vic-01/94 (A8). Rescued viruses showed no substitutions at amino acid positions 253, 284, or 330, previously found to be associated with cell-culture adaptation. Sera from chickens inoculated with wild-type (wt) (F52-70) or vaccine (228E) A1 strains had the highest mean virus neutralization (VN) titers against the A1 virus (log2 15.4 and 12.7) and the lowest against A2 viruses (log2 7.4 to 7.9; P = 0.0001 to 0.0274), consistent with A1 viruses being most antigenically distant from A2 strains, which correlated with the extent of differences in the predicted HVR structure. VN titers against the other genogroups ranged from log2 9.3 to 13.3, and A1 strains were likely more closely antigenically related to genogroups A3 and A4 than A6 and A8. Our data are consistent with field observations and validate the new method, which can be used to screen future vaccine candidates for breadth of neutralizing antibodies and evaluate the antigenic relatedness of different genogroups. IMPORTANCE There is a need to evaluate the ability of vaccines to neutralize diverse IBDV genogroups and to better understand the relationship between HVR sequence, structure, and antigenicity. Here, we used a chicken B-cell line to rescue a panel of chimeric IBDVs with the HVR from seven diverse IBDV field strains and to conduct neutralization assays and protein modeling. We evaluated the ability of sera from vaccinated or infected birds to neutralize the different genogroups. Our novel chicken B-cell rescue system and neutralization assay can be used to screen IBDV vaccine candidates, platforms, and regimens for the breadth of neutralizing antibody responses elicited, evaluate the antigenic relatedness of diverse IBDV strains, and when coupled with structural modeling, elucidate immunodominant and conserved epitopes to strategically design novel IBDV vaccines in the future.
Spatial learning overshadows learning novel odors and sounds in both predatory and frugivorous bats

To forage efficiently, animals should selectively attend to and remember the cues of food that best predict future meals. One hypothesis is that animals with different foraging strategies should vary in their reliance on spatial versus feature cues. Specifically, animals that store food in dispersed caches or that feed on spatially stable food, such as fruits or flowers, should be relatively biased towards learning a meal’s location, whereas predators that hunt mobile prey should instead be relatively biased towards learning feature cues such as odor or sound. Several authors have predicted that nectar-feeding and fruit-feeding bats would rely relatively more on spatial cues, whereas closely related predatory bats would rely more on feature cues, yet no experiment has compared these two foraging strategies under the same conditions. To test this hypothesis, we compared learning in the frugivorous bat, Artibeus jamaicensis, and the predatory bat, Lophostoma silvicolum, which hunts katydids using acoustic cues. We trained bats to find food paired with a unique and novel odor, sound, and location. To assess which cues each bat had learned, we then dissociated these cues to create conflicting information. Rather than finding that the frugivore and predator clearly differ in their relative reliance on spatial versus feature cues, we found that both species used spatial cues over sounds or odors in subsequent foraging decisions. We interpret these results alongside past findings on how foraging animals use spatial cues versus feature cues, and explore why spatial cues may be fundamentally more rich, salient, or memorable.
Heat stress does not induce wasting symptoms in the giant California sea cucumber (Apostichopus californicus)

Oceanic heat waves have significant impacts on disease dynamics in marine ecosystems. A severe sea cucumber wasting event occurred in Nanoose Bay, British Columbia, Canada, following an extreme heat wave, resulting in mass mortality of Apostichopus californicus. Here, we sought to determine if heat stress in isolation could trigger wasting symptoms in A. californicus. We exposed sea cucumbers to i) a simulated marine heat wave (22ºC), ii) an elevated temperature treatment (17ºC), or iii) control conditions (12ºC). We measured the presence of skin ulcers, mortality, posture maintenance, antipredator defences, spawning, and organ evisceration during the 79-hour thermal exposure, as well as 7-days post-exposure. Both the 22°C and 17°C treatments elicited stress responses where individuals exhibited a reduced ability to maintain posture and an increase in stress spawning. The 22ºC heat wave was particularly stressful, as it was the only treatment where mortality was observed. However, none of the treatments induced wasting symptoms as observed in the Nanoose Bay event. This study provides evidence that sea cucumber wasting is not triggered by heat stress in isolation, leaving the cause of the mass mortality event observed in Nanoose unknown.
A probabilistic successor representation for context-dependent prediction

The different strategies that animals use for predicting reward are often classified as model-based or model-free reinforcement learning (RL) algorithms. Model-based RL involves explicit simulation the future to make decisions while model-free strategies rely on learning associations between stimuli and predicted reward by trial and error. An alternative, intermediate strategy for RL is based on the “successor representation” (SR), an encoding of environmental states in terms of predicted future states. A recent theoretical proposal suggests that the hippocampus encodes the SR in order to facilitate prediction of future reward. However, this proposal does not take into account how learning should adapt under uncertainty and switches of context. Here, we introduce a theory of learning SRs using prediction errors which includes optimally balancing uncertainty in new observations versus existing knowledge. We then generalise that approach to a multi-context setting, allowing the model to learn and maintain multiple task-specific SRs and infer which one to use at any moment based on the accuracy of its predictions. Thus, the context used for predictions can be determined by both the contents of the states themselves and the distribution of transitions between them. This probabilistic SR model captures animal behaviour in tasks which require contextual memory and generalisation, and unifies previous SR theory with hippocampal-dependent contextual decision making.
Biology of Asaccharolytic Black-Pigmented Bacteroides Species

B. asaccharolyticus . 136 B. endodontalis.136 Experimental Infections Involving Asaccharolytic BPBs . 136 ULTRASRUCTURAL STUDIES . 137 NUTRITION, PHYSIOLOGY, AND CELL COMPONENTS . 138 ANTIGENIC AND SEROLOGIC CHARACTERIZATION . 140 PATHOGENICITY OF ASACCHAROLYTIC BPBs . 141 FACTORS AFFECTING VIRULENCE . 142
ACCUMULATING BACTERIA IN CRUSTACEAN LARVICULTURE

Bacillus species are used in animal production directly as microbial feed additives or as the source of other feed additives, notably enzymes. The principal safety concern for consumers and, to a lesser extent livestock, associated with Bacillus is a capacity for toxin production. However, the capacity for toxin production and the nature of the toxins produced is unevenly distributed over the genus, occurring frequently in some species and more rarely in others. In principle, the selection of strains belonging to the B. cereus taxonomic group for direct use in animal production is considered inadvisable. If, however, they are proposed then the full genome should be sequenced and a bioinformatic analysis made to search for genes coding for enterotoxins and cereulide synthase. If there is evidence of homology, the nonfunctionality of the genes (e.g. mutation, deletion) must be demonstrated. For other species, concerns appear to be associated to the production of surfactin like-lipopeptides, although the relation between the presence of these compounds and/or other toxic factors and the risk of illness in human has not yet been established. In the absence of animal models shown to be able to distinguish hazardous from non hazardous strains, the FEEDAP Panel relies on the use of in vitro cell-based methods to detect evidence of a cytotoxic effect. Such tests should be made with culture supernatants since the concentration of cells obtained in a broth culture would always exceed that found in animal food products. If the strain proves to be cytotoxic it is not recommended for use.