Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient complement-mediated clearance of immunosuppressed T cells by macrophages

Cancer is one of the leading causes of death worldwide. Treatment outcome is largely dictated by the tumor type, disease stage, and treatment success rates, but also by the variation among patients in endogenous anti-tumor responses. Studies indicate that the presence of neutrophils in the tumor microenvironment is associated with a worse patient outcome due to their ability to suppress local anti-tumor T cell activity. Our previous studies investigated the mechanisms by which neutrophils suppress and damage T cells to become smaller in size (small T cells), debilitating their effector activities. Several studies indicate a role for tumor-associated macrophages in scavenging damaged or dead cells. We hypothesized that the observed lack of small T cells in the TME by confocal microscopy is due to immediate uptake by macrophages. In this study, we confirmed that indeed only the smaller, damaged T cells are taken up by macrophages, once serum-opsonized. Damaged T cells opsonized with complement factor C3 fragments were phagocytosed by macrophages, resulting in almost instantaneous and highly efficient uptake of these small T cells. Inhibition of the complement receptors CR1, CR3 and CR4 expressed by macrophages completely blocked phagocytosis. By contrast, actively proliferating T cells (large T cells) were neither impaired in neutrophil-MDSC activity nor opsonized for phagocytosis by macrophages. Rapid removal of damaged T cells suggests a role of complement and macrophages within the tumor microenvironment to clear suppressed T cells in cancer patients.
Examining indicators of psychosocial risk and resilience in parents of autistic children

Background Parents of autistic children experience increased levels of caregiver strain and adverse mental health outcomes, even in comparison to parents of children with other neurodevelopmental disabilities. Previous studies have largely attributed these increased levels of mental health concerns to their child behavioral concerns and autism symptomatology, but less attention has been given to other potential child factors, such as child adaptive functioning. Additionally, little is known about potential protective factors, such as parents’ emotion regulation (ER) abilities, that may ameliorate the experience of caregiver strain, anxiety, and depression. Objective The current study examined the impact of child characteristics (restricted and repetitive behaviors, adaptive functioning and behavioral concerns) on parent mental health outcomes (caregiver strain, anxiety, depression and wellbeing). Additionally, we explore parents’ ER abilities as a moderator of the impact of child characteristic on parents’ mental health outcomes. Results Results of linear mixed effect models indicated a significant relationship between parents’ ER abilities and all four parent outcomes. Additionally, children’s adaptive functioning abilities and repetitive behaviors (RRBs) were significant predictors of caregiving strain. Parents’ ER abilities were a significant moderator of the effect of children’s repetitive behaviors and adaptive functioning challenges on caregiver strain, such that better ER abilities mitigated the impact of child clinical factors on caregiver strain. Finally, a significant difference was detected for mothers’ and fathers’ mental health, with mothers reporting higher caregiver strain, and more symptoms of anxiety and depression than did fathers. Conclusion This study leveraged a large sample of autistic children and their biological parents to examine the relationship between children’s clinical characteristics and parents’ psychological wellbeing. Results indicate that, although parents of autistic children do experience high rates of internalizing mental health concerns that relate to child adaptive functioning and RRBs, parent ER abilities act as a protective factor against parents’ adverse mental health outcomes. Further, mothers in our sample reported significantly higher rates of depression, anxiety, and caregiver strain, as compared with fathers.
PLC regulates spontaneous glutamate release triggered by extracellular calcium and readily releasable pool size in neocortical neurons

Introduction Dynamic physiological changes in brain extracellular calcium ([Ca2+]o) occur when high levels of neuronal activity lead to substantial Ca2+ entry via ion channels reducing local [Ca2+]o. Perturbations of the extracellular microenvironment that increase [Ca2+]o are commonly used to study how [Ca2+] regulates neuronal activity. At excitatory synapses, the Ca2+-sensing receptor (CaSR) and other G-protein coupled receptors link [Ca2+]o and spontaneous glutamate release. Phospholipase C (PLC) is activated by G-proteins and is hypothesized to mediate this process. Methods Patch-clamping cultured neocortical neurons, we tested how spontaneous glutamate release was affected by [Ca2+]o and inhibition of PLC activity. We used hypertonic sucrose (HS) to evaluate the readily releasable pool (RRP) and test if it was affected by inhibition of PLC activity. Results Spontaneous glutamate release substantially increased with [Ca2+]o, and inhibition of PLC activity, with U73122, abolished this effect. PLC-β1 is an abundant isoform in the neocortex, however, [Ca2+]o-dependent spontaneous release was unchanged in PLC-β1 null mutants (PLC-β1–/–). U73122 completely suppressed this response in PLC-β1–/– neurons, indicating that this residual [Ca2+]o–sensitivity may be mediated by other PLC isoforms. The RRP size was substantially reduced after incubation in U73122, but not U73343. Phorbol esters increased RRP size after PLC inhibition. Discussion Together these data point to a strong role for PLC in mediating changes in spontaneous release elicited by [Ca2+]o and other extracellular cues, possibly by modifying the size of the RRP.
Middle School Mathematics Teachers’ Perceptions of the Common Core State Standards for Mathematics and Related Assessment and Teacher Evaluation Systems

In this study, U.S. middle school teachers’ perceptions of Common Core State Standards for Mathematics (CCSSM), CCSSM-related assessments, teacher evaluation processes, and resources for implementing CCSSM were investigated. Using a mixed methods design, a national sample of 366 teachers was surveyed, and 24 teachers were interviewed. Findings indicated that teachers viewed CCSSM as including new content for their grade level. Teachers also reported using multiple curriculum resources to align with CCSSM and indicated that new assessments would serve as a proxy for CCSSM. Implications for rapidly changing policy, curriculum, assessment, instruction, and professional development related to CCSSM are discussed.
Probiotic characteristics and whole-genome sequence analysis of Pediococcus acidilactici isolated from the feces of adult beagles

The beneficial effects of lactic acid bacteria are well known and recognized as functional foods that are health benefits for companion animals. This study, for the first time, reports the probiotic properties, safety, and whole-genome sequence of Pediococcus acidilactici GLP06 isolated from feces of beagles. In this study, candidate probiotic bacteria P. acidilactici GLP02 and GLP06 were morphologically characterized and tested for their antimicrobial capacity, tolerance to different conditions (low pH, bile salts, an artificial gastrointestinal model, and high temperature), antibiotic sensitivity, hemolytic activity, cell surface hydrophobicity, autoaggregation activity, and adhesion to Caco-2 cells. P. acidilactici GLP06 showed better probiotic potential. Therefore, P. acidilactici GLP06 was evaluated for in vivo safety in mice and whole-genome sequencing. The results showed, that the supplemented MG06 group (1010 cfu/mL), GLP06 was not only nontoxic to mice, but also promoted the development of the immune system, improved resistance to oxidative stress, and increased the diversity of intestinal microorganisms and the abundance of Lactobacillus. Whole-genome sequencing showed that P. acidilactici GLP06 was 2,014,515 bp and contained 1,976 coding sequences, accounting for 86.12% of the genome, with no drug resistance genes and eight CRISPR sequences. In conclusion, the newly isolated canine-derived P. acidilactici GLP06 had good probiotic potential, was nontoxic to mice and promoted the development of immune organs, improved the biodiversity of the intestinal flora, and had no risk of drug-resistant gene transfer, indicating that P. acidilactici GLP06 can be used as a potential probiotic for the prevention and treatment of gastrointestinal diseases in companion animals.
Editorial: Stability across spatial and temporal scales

COPYRIGHT © 2023 Zelnik, Clark, Radchuk, Hodapp and Dominguez-Garcia. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Stability across spatial and temporal scales
Multidrug-resistant non-typhoidal Salmonella of public health significance recovered from migratory birds in Bangladesh

Non-typhoidal Salmonella provides an exemplar for the One Health approach as it encompasses public and animal health, food safety, and environmental considerations. The contribution of environmental aspects is currently less well-defined. The purpose of this study was to determine the carriage occurrence of non-typhoidal Salmonella in migratory birds in Bangladesh and assess the potential significance to public and animal health. Cloacal swabs (N = 453) were collected in the years 2018–2020 from Tanguar and Hakaluki Haors, important wetland ecosystems in Northeastern Bangladesh. The prevalence of Salmonella was 13.5% (61 positive swabs). Classical serotyping identified six serovars: Salmonella enterica subsp. enterica serovars Perth, Kentucky, Albany, Infantis, Weltevreden, and Brancaster. Resistance towards 14 antimicrobials was assessed by broth microdilution minimum inhibitory concentration determination and the antimicrobial resistance (AMR) genotype established by whole-genome sequencing. S. Perth and S. Weltevreden isolates were susceptible and harbored no acquired AMR genes. Isolates from the remaining serovars were multidrug resistant, commonly possessing resistance to tetracycline, ampicillin, chloramphenicol, sulfamethoxazole, trimethoprim, and ciprofloxacin. Salmonella resistant to ciprofloxacin meets WHO criteria for priority pathogens. There was excellent concordance between resistance phenotype and the presence of corresponding AMR genes, many of which reside on Salmonella Genomic Islands. High-level ciprofloxacin resistance correlated with the presence of mutations in the chromosomal gyrB and/or parC genes. The S. Kentucky isolates were ST198, a widely distributed multidrug-resistant lineage reported in humans and animals, and constituting an ongoing risk to public health worldwide. We have demonstrated that multidrug-resistant non-typhoidal Salmonella of public health significance can be recovered from migratory birds. A potential for risk can manifest through direct interaction, transmission to food-producing livestock on farms, and dissemination via the long range migratory movements of birds. Risks can be mitigated by measures including continued surveillance and implementation of good farm biosecurity practices.
The persistence of stress-induced physical inactivity in rats: an investigation of central monoamine neurotransmitters and skeletal muscle oxidative stress

Introduction Sedentary lifestyles have reached epidemic proportions world-wide. A growing body of literature suggests that exposures to adverse experiences (e.g., psychological traumas) are a significant risk factor for the development of physically inactive lifestyles. However, the biological mechanisms linking prior stress exposure and persistent deficits in physical activity engagement remains poorly understood. Methods The purpose of this study was twofold. First, to identify acute stress intensity thresholds that elicit long-term wheel running deficits in rats. To that end, young adult male rats were exposed to a single episode of 0, 50, or 100 uncontrollable tail shocks and then given free access to running wheels for 9 weeks. Second, to identify stress-induced changes to central monoamine neurotransmitters and peripheral muscle physiology that may be maladaptive to exercise output. For this study, rats were either exposed to a single episode of uncontrollable tail shocks (stress) or left undisturbed in home cages (unstressed). Eight days later, monoamine-related neurochemicals were quantified by ultra-high performance liquid chromatography (UHPLC) across brain reward, motor, and emotion structures immediately following a bout of graded treadmill exercise controlled for duration and intensity. Additionally, protein markers of oxidative stress, inflammation, and metabolic activity were assessed in the gastrocnemius muscle by Western blot. Results For experiment 1, stress exposure caused a shock number-dependent two to fourfold decrease in wheel running distance across the entire duration of the study. For experiment 2, stress exposure curbed an exercise-induced increase of dopamine (DA) turnover measures in the prefrontal cortex and hippocampus, and augmented serotonin (5HT) turnover in the hypothalamus and remaining cortical area. However, stress exposure also caused several monoaminergic changes independent of exercise that could underlie impaired motivation for physical activity, including a mild dopamine deficiency in the striatal area. Finally, stress potently increased HSP70 and lowered SOD2 protein concentrations in the gastrocnemius muscle, which may indicate prolonged oxidative stress. Discussion These data support some of the possible central and peripheral mechanisms by which exposure to adverse experiences may chronically impair physical activity engagement.
Dysregulated early transcriptional signatures linked to mast cell and interferon responses are implicated in COVID-19 severity

Background Dysregulated immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are thought to underlie the progression of coronavirus disease 2019 (COVID-19) to severe disease. We sought to determine whether early host immune-related gene expression could predict clinical progression to severe disease. Methods We analysed the expression of 579 immunological genes in peripheral blood mononuclear cells taken early after symptom onset using the NanoString nCounter and compared SARS-CoV-2 negative controls with SARS-CoV-2 positive subjects with mild (SARS+ Mild) and Moderate/Severe disease to evaluate disease outcomes. Biobanked plasma samples were also assessed for type I (IFN-α2a and IFN-β), type II (IFN-γ) and type III (IFN-λ1) interferons (IFNs) as well as 10 additional cytokines using multiplex immunoassays. Results We identified 19 significantly deregulated genes in 62 SARS-CoV-2 positive subject samples within 5 days of symptom onset and 58 SARS-CoV-2 negative controls and found that type I interferon (IFN) signalling (MX1, IRF7, IFITM1, IFI35, STAT2, IRF4, PML, BST2, STAT1) and genes encoding proinflammatory cytokines (TNF, TNFSF4, PTGS2 and IL1B) were upregulated in both SARS+ groups. Moreover, we found that FCER1, involved in mast cell activation, was upregulated in the SARS+ Mild group but significantly downregulated in the SARS+ Moderate/Severe group. In both SARS+ groups we discovered elevated interferon type I IFN-α2a, type II IFN and type III IFN λ1 plasma levels together with higher IL-10 and IL-6. These results indicate that those with moderate or severe disease are characterised by deficiencies in a mast cell response together with IFN hyper-responsiveness, suggesting that early host antiviral immune responses could be a cause and not a consequence of severe COVID-19. Conclusions This study suggests that early host immune responses linking defects in mast cell activation with host interferon responses correlates with more severe outcomes in COVID-19. Further characterisation of this pathway could help inform better treatment for vulnerable individuals.
An efficient transformation method for genome editing of elite bread wheat cultivars

An efficient genetic transformation protocol is necessary to edit genes for trait improvement directly in elite bread wheat cultivars. We used a protein fusion between a wheat growth-regulating factor 4 (GRF4) and its interacting factor (GIF1) to develop a reproducible genetic transformation and regeneration protocol, which we then used to successfully transform elite bread wheat cultivars Baj, Kachu, Morocco, Reedling, RL6077, and Sujata in addition to the experimental cultivar Fielder. Immature embryos were transformed with the vector using particle bombardment method. Transformation frequency increased nearly 60-fold with the GRF4-GIF1-containing vectors as compared to the control vector and ranged from ~5% in the cultivar Kachu to 13% in the cultivar RL6077. We then edited two genes that confer resistance against leaf rust and powdery mildew directly in the aforementioned elite cultivars. A wheat promoter, TaU3 or TaU6, to drive the expression of guide RNA was effective in gene editing whereas the OsU3 promoter failed to generate any edits. Editing efficiency was nearly perfect with the wheat promoters. Our protocol has made it possible to edit genes directly in elite wheat cultivars and would be useful for gene editing in other wheat varieties, which have been recalcitrant to transformation thus far.
Novel mutations in PLCZ1 lead to early embryonic arrest as a male factor

Early embryonic arrest is one of the causes of assist reproduction technology (ART) failure. We have previously reported that the first sperm-derived genetic factor, ACTL7a mutations, could lead to early embryonic arrest. However, whether there are other male genetic factors associated with early embryonic arrest remains elusive. Here, we reported bi-allelic mutations in PLCZ1, a well-known causal gene of total fertilization failure, in four infertile males. Among these mutations, p.403_404del, p.I489S, and p.W536X were newly reported in this study. Histological and Western blotting analysis of the patients’ sperm indicated these variants as loss-of-function mutations. These patients manifested normal conventional semen parameters and ultra-structures in sperm heads. However, among four in vitro fertilization (IVF) cycles, 81.8% (18/22) of the oocytes were polyspermic fertilized, which was rarely reported in PLCZ1-related male patients. In the following six ICSI cycles, artificial oocyte activation (AOA) was applied and successfully rescued the fertilization failure and polyspermy phenotypes, with 31.3% (15/48) of the MII oocytes normally fertilized. However, 60.0% (9/15) of these normally fertilized zygotes were arrested at 2–5-cell stage, with one failing to cleave, indicating that PLCZ1 was not only necessary for fertilization, but also crucial for early embryonic development. However, these rescued zygotes showed a lower potential in developing into blastocysts when cultured in vitro. Thus, fresh cleavage transfer was tried and two live births were successfully achieved thereafter. In conclusion, this study provided novel mutations in PLCZ1 gene to expand the pathogenic mutational spectrum in male infertility and demonstrated that PLCZ1 was a crucial sperm-related genetic factor for early embryonic arrest. We also proposed that cleavage transfer after ICSI and AOA treatment could be a potential treatment method for male patients carrying bi-allelic mutations in PLCZ1.
Well-posedness for the fourth-order Schrödinger equations with quadratic nonlinearity

This paper is concerned with 1-D quadratic semilinear fourth-order Schrödinger equations. Motivated by the quadratic Schrödinger equations in the pioneer work of Kenig-Ponce-Vega [12], three bilinearities uv, uv, uv for functions u, v : R× [0, T ] 7→ C are sharply estimated in function spaces Xs,b associated to the fourth-order Schrödinger operator i∂t + ∆ − ε∆. These bilinear estimates imply local wellposedness results for fourth-order Schrödinger equations with quadratic nonlinearity. To establish these bilinear estimates, we derive a fundamental estimate on dyadic blocks for the fourth-order Schrödinger from the [k, Z]-multiplier norm argument of Tao [20]. AMS Subject Classification: 35Q40, 35Q55, 47J35
LINC00426 is a potential immune phenotype-related biomarker and an overall survival predictor in PAM50 luminal B breast cancer

Background: Breast cancer (BRCA) represents the most frequent diagnosed malignancy in women worldwide. Despite treatment advances, BRCAs eventually develop resistance to targeted therapies, resulting in poor prognosis. The identification of new biomarkers, like immune-related long non-coding RNAs (lncRNAs), could contribute to the clinical management of BRCA patients. In this report, we evaluated the LINC00426 expression in PAM50 BRCA subtypes from two clinical independent cohorts (BRCA-TCGA and GEO-GSE96058 datasets). Methods and results: Using Cox regression models and Kaplan-Meier survival analyses, we identified that LINC00426 expression was a consistent overall survival (OS) predictor in luminal B (LB) BRCA patients. Subsequently, differential gene expression and gene set enrichment analyses identified that LINC00426 expression was associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression was correlated with the infiltration level of diverse immune cell populations, alongside immune checkpoint and cytolytic activity-related gene expression. Conclusion: This evidence suggests that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA.