Miracle-dz/UniFAR-FTUs huggingface dataset:
Synergistic Effect of Cefazolin Plus Fosfomycin Against Staphylococcus aureus in vitro and in vivo in an Experimental Galleria mellonella Model

Objectives: This study investigated the synergistic in vitro and in vivo activity of cefazolin plus fosfomycin against methicillin-susceptible and methicillin-resistant S. aureus (MSSA and MRSA) to provide the basis for a potential treatment alternative. Methods: Antimicrobial susceptibility and in vitro synergy tests were performed with five MSSA and five MRSA isolates using the broth microdilution and chequerboard assays, respectively. The in vivo efficacy of cefazolin plus fosfomycin for the treatment of MRSA infections was assessed using the Galleria mellonella survival assay. Results: Using fractional inhibitory concentration index (FICI), the evaluated combination of cefazolin plus fosfomycin showed synergistic in vitro activity against all MSSA and MRSA isolates tested. In addition, cefazolin susceptibility was recovered in all MRSA isolates except one fosfomycin-resistant strain when combined with fosfomycin at readily achievable concentrations. The G. mellonella survival assay demonstrated highly synergistic in vivo activity of cefazolin plus fosfomycin, resulting in a 44–52% reduction in mortality when compared to cefazolin-alone and fosfomycin-alone, respectively. Conclusion: If susceptibility to fosfomycin is either confirmed or can be assumed based on local resistance patterns, combination therapy with cefazolin plus fosfomycin could be a valuable treatment option for empirical as well as targeted therapy of S. aureus and MRSA infections. Future studies proving the clinical significance of this combination therapy are therefore warranted.
Gravity Threshold and Dose Response Relationships: Health Benefits Using a Short Arm Human Centrifuge

Purpose Increasing the level of gravity passively on a centrifuge, should be equal to or even more beneficial not only to astronauts living in a microgravity environment but also to patients confined to bed. Gravity therapy (GT) may have beneficial effects on numerous conditions, such as immobility due to neuromuscular disorders, balance disorders, stroke, sports injuries. However, the appropriate configuration for administering the Gz load remains to be determined. Methods To address these issues, we studied graded G-loads from 0.5 to 2.0g in 24 young healthy, male and female participants, trained on a short arm human centrifuge (SAHC) combined with mild activity exercise within 40–59% MHR, provided by an onboard bicycle ergometer. Hemodynamic parameters, as cardiac output (CO), stroke volume (SV), mean arterial pressure (MAP), systolic blood pressure (SBP), diastolic blood pressure (DBP), and heart rate (HR) were analyzed, as well as blood gas analysis. A one-way repeated measures ANOVA and pairwise comparisons were conducted with a level of significance p < 0.05. Results Significant changes in heart rate variability (HRV) and its spectral components (Class, Fmax, and VHF) were found in all g loads when compared to standing (p < 0.001), except in 1.7 and 2.0g. There were significant changes in CO, cardiac index (CI), and cardiac power (CP) (p < 0.001), and in MAP (p = 0.003) at different artificial gravity (AG) levels. Dose-response curves were determined based on statistically significant changes in cardiovascular parameters, as well as in identifying the optimal G level for training, as well as the optimal G level for training. There were statistically significant gender differences in Cardiac Output/CO (p = 0.002) and Cardiac Power/CP (p = 0.016) during the AG training as compared to standing. More specifically, these cardiovascular parameters were significantly higher for male than female participants. Also, there was a statistically significant (p = 0.022) gender by experimental condition interaction, since the high-frequency parameter of the heart rate variability was attenuated during AG training as compared to standing but only for the female participants (p = 0.004). Conclusion The comprehensive cardiovascular evaluation of the response to a range of graded AG loads, as compared to standing, in male and female subjects provides the dose-response framework that enables us to explore and validate the usefulness of the centrifuge as a medical device. It further allows its use in precisely selecting personalized gravity therapy (GT) as needed for treatment or rehabilitation of individuals confined to bed.
Circadian control of heparan sulfate levels times phagocytosis of amyloid beta aggregates

Alzheimer’s Disease (AD) is a neuroinflammatory disease characterized partly by the inability to clear, and subsequent build-up, of amyloid-beta (Aβ). Aβ clearance is regulated by several pathways and has a circadian component. However, the mechanism underlying the circadian clearance of Aβ has not been defined. Myeloid-based phagocytosis, a key mechanism in the metabolism of Aβ, is circadianly-regulated, presenting a potential mechanism for the circadian clearance of Aβ. In this work, we revealed that the phagocytosis of Aβ42 undergoes a daily oscillation that is dependent on the circadian clock. We found the circadian timing of global heparan sulfate proteoglycan (HSPG) biosynthesis was the molecular timer for the clock-controlled phagocytosis of Aβ and that both HSPG binding and Aβ42 aggregation were essential for this oscillation. These data highlight that circadian regulation in immune cells may play a role in the intricate relationship between the circadian clock and AD. Graphical Abstract
Differential regulation of developmental stages supports a linear model for C. elegans postembryonic development

The repetitive nature of C. elegans postembryonic development is considered an oscillatory process, a concept that has gained traction from regulation by a circadian clock gene homolog. Nevertheless, each larval stage has a defined duration and entails specific events. We have measured the duration of each stage of development for over 2,500 larvae, under varied environmental conditions known to alter overall developmental rate. Our results show that distinct developmental stages respond differently to environmental perturbations, including changes in temperature, in food quantity and quality, and amount of insulin signaling. Furthermore, our high-resolution measurement of the effect of temperature on the stage-specific duration of development has unveiled novel features of temperature dependence in C. elegans postembryonic development. Altogether, our results support a model of linear progression of C. elegans development, with the duration of each stage determined by a unique program.
Identification of a Shrimp E3 Ubiquitin Ligase TRIM50-Like Involved in Restricting White Spot Syndrome Virus Proliferation by Its Mediated Autophagy and Ubiquitination

Most tripartite motif (TRIM) family proteins are critical components of the autophagy machinery and play important roles in host defense against viral pathogens in mammals. However, the roles of TRIM proteins in autophagy and viral infection have not been studied in lower invertebrates, especially crustaceans. In this study, we first identified a TRIM50-like gene from Penaeus monodon (designated PmTRIM50-like), which, after a white spot syndrome virus (WSSV) challenge, was significantly upregulated at the mRNA and protein levels in the intestine and hemocytes. Knockdown of PmTRIM50-like led to an increase in the WSSV quantity in shrimp, while its overexpression led to a decrease compared with the controls. Autophagy can be induced by WSSV or rapamycin challenge and has been shown to play a positive role in restricting WSSV replication in P. monodon. The mRNA and protein expression levels of PmTRIM50-like significantly increased with the enhancement of rapamycin-induced autophagy. The autophagy activity induced by WSSV or rapamycin challenge could be inhibited by silencing PmTRIM50-like in shrimp. Further studies showed that rapamycin failed to induce autophagy or inhibit WSSV replication after knockdown of PmTRIM50-like. Moreover, pull-down and in vitro ubiquitination assays demonstrated that PmTRIM50-like could interact with WSSV envelope proteins and target them for ubiquitination in vitro. Collectively, this study demonstrated that PmTRIM50-like is required for autophagy and is involved in restricting the proliferation of WSSV through its ubiquitination. This is the first study to report the role of a TRIM family protein in virus infection and host autophagy in crustaceans.
Identification of Potentially Therapeutic Immunogenic Peptides From Paracoccidioides lutzii Species

Paracoccidioidomycosis (PCM) is an endemic mycosis in Latin America caused by the thermodimorphic fungi of the genus Paracoccidioides spp. Paracoccidioides lutzii (PL) is one of the 5 species that constitute the Paracoccidioides genus. PL expresses low amounts of glycoprotein (Gp) 43 (PLGp43) and PLGp43 displays few epitopes in common with the P. brasiliensis (PB) immunodominant antigen PBGp43, which is commonly used for serological diagnosis of PCM. This difference in structure between the glycoproteins markedly reduces the efficiency of serological diagnosis in patients infected with PL. We previously demonstrated that peptide 10 (P10) from the PBGp43 induces protective immune responses in in vitro and in vivo models of PB PCM. Since, P10 has proven to be a promising therapeutic to combat PB, we sought to identify peptides in PL that could similarly be applied for the treatment of PCM. PL yeast cell proteins were isolated from PL: dendritic cell co-cultures and subjected to immunoproteomics. This approach identified 18 PL peptides that demonstrated in silico predictions for immunogenicity. Eight of the most promising peptides were synthesized and applied to lymphocytes obtained from peptide-immunized or PL-infected mice as well as to in vitro cultures with peptides or dendritic cells pulsed the peptides. The peptides LBR5, LBR6 and LBR8 efficiently promoted CD4+ and CD8+ T cell proliferation and dendritic cells pulsed with LBR1, LBR3, LBR7 or LBR8 stimulated CD4+ T cell proliferation. We observed increases of IFN-γ in the supernatants from primed T cells for the conditions with peptides without or with dendritic cells, although IL-2 levels only increased in response to LBR8. These novel immunogenic peptides derived from PL will be employed to develop new peptide vaccine approaches and the proteins from which they are derived can be used to develop new diagnostic assays for PL and possibly other Paracoccidioides spp. These findings identify and characterize new peptides with a promising therapeutic profile for future against this important neglected systemic mycosis.
Low cytotoxicity, and antiproliferative activity on cancer cells, of the plant Senna alata (Fabaceae)

Introduction: The leaves of Senna alata from the Fabaceae family have been used in folk medicine for the cure of skin disease. In this study, we tested the extract and fractions on brine shrimp lethality test and antiproliferative activity on cancer and normal cell lines. Objective: In this study, we assessed the cytotoxicity of S. alata using brine shrimp test and two cell lines. Methods: The 80 % ethanolic leaf extract and its fractions were examined for possible cytotoxic effect using sulforhodamine B (SRB) cytotoxicity assay towards breast cancer (MCF-7), normal (MCF10A) cell lines, and brine shrimp lethality test (BSLT). Results: The brine shrimp lethality bioassay exhibits no cytotoxicity even at high concentration (5 000 μg/mL). The LC50 for dichloromethane, chloroform, butanol, and aqueous were > 1 000 μg/mL (non-toxic). The IC50 for in vitro SRB cytotoxicity against MCF-7 for n-hexane was 0.013 μg/mL, which was considered highly toxic, while dichloromethane and chloroform recorded at 47.11 and 57.61 μg/mL, respectively after 72 hours exposure time although there was no cytotoxicity found on the normal cell line. Conclusion: This study shows that S. alata crude ethanolic leaf extract and its fractions potentially contain significant bioactive compounds that are safe from adverse effects, which proves the therapeutic application of S. alata in traditional remedy.
Capacity to erase gene occlusion is a defining feature distinguishing naive from primed pluripotency

Pluripotent stem cells can exist in either the naive state representing a developmental blank slate or the downstream primed state poised for differentiation. Currently, known differences between these two states are mostly phenomenological, and none can adequately explain why the two states should differ in developmental priming. Gene occlusion is a mode of epigenetic inactivation that renders genes unresponsive to their cognate transcriptional activators. It plays a crucial role in lineage restriction. Here, we report that a defining feature distinguishing the two pluripotent states lies in the ability of naive but not primed cells to erase occlusion. This “deocclusion” capacity requires Esrrb, a gene expressed only in the naive but not primed state. Notably, Esrrb silencing in the primed state is itself due to occlusion. Collectively, our data argue that the Esrrb-dependent deocclusion capacity in naive cells is key for sustaining naive pluripotency, and the loss of this capacity in the primed state via the occlusion of Esrrb poises cells for differentiation.
Spousal Care and Pain Among the Population Aged 65 Years and Older: A European Analysis

Background: Spousal care is the most important source of informal care in old age. Nevertheless, despite the growing importance of this issue, the association between providing spousal care inside the household and pain remains unexplored in Europe. Objective and Methods: This study aims to estimate the prevalence of pain reported by spouse caregivers aged 65 plus that provide care inside the household and to investigate the association between providing spousal care and pain. Data from 17 European countries that participated in wave 6 of the Survey of Health, Aging and Retirement in Europe (SHARE) is used. The analyses are based on 26,301 respondents aged 65 years and older who provide informal care inside the household to their spouse/partner exclusively (N = 1,895) or do not provide any informal care (inside or outside the household) (24,406). Descriptive statistics and multilevel logistic regressions (individual-level as level 1, and country as level 2) were performed. Results: Overall, spouse caregivers report pain more often (63.4%) than their non-caregiver‘s counterparts (50.3%). Important differences in the prevalence of pain among spouse caregivers were found between countries, with Portugal (80.3%), Spain (74.6%), France (73%), Italy (72.4%), and Slovenia (72.1) showing the highest prevalence of pain, and Denmark (36%), Switzerland (41.5) and Sweden (42.3%), the lowest. Results from multilevel logistic regressions show that European individuals aged 65+ who provide spousal care have an increased likelihood of reporting pain (OR 1.30; CI = 1.13–1.48). Conclusion: Our results suggest that in Europe, spouse caregivers aged 65+ are at greater risk of experiencing pain. Therefore, European policymakers should consider spouse caregivers as a health priority group, and take measures to ensure they receive comprehensive health and socio-economic support.
Cell-envelope synthesis is required for surface-to-mass coupling, which determines dry-mass density in Bacillus subtilis

Cells must increase their volumes in response to biomass growth to maintain intracellular mass density, the ratio of dry mass to cell volume, within physiologically permissive bounds. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. Recently, we demonstrated that the Gram-negative bacterium Escherichia coli expands cell-surface area rather than volume in proportion to mass. Here, we investigate the regulation of cell-volume growth in the evolutionarily distant Bacillus subtilis. First, we demonstrate that the coupling of surface growth to mass growth is conserved in B. subtilis. Therefore, mass density changes with cell shape at the single-cell level. Interestingly, mass density varies by more than 30% when we systematically change cell width by modulation of cell-wall insertion, without any effect on mass-growth rate. Second, we demonstrate that the coupling of surface- and mass growth is broken if peptidoglycan or membrane synthesis are inhibited. Once transient perturbations are relieved, the surface-to-mass ratio is rapidly restored. In conclusion, we demonstrate that surface-to-mass coupling is a conserved principle for volume regulation in bacteria, and that envelope synthesis provides an important link between surface growth and biomass growth in B. subtilis.
Cancer Mutational Processes Vary in Their Association with Replication Timing and Chromatin Accessibility

Many mutational processes associate with early or late replication timing regions independently of chromatin accessibility, enabling development of a focused identification approach to improve mutational signature detection. Cancer somatic mutations are the product of multiple mutational and repair processes, both of which are tightly associated with DNA replication. Distinctive patterns of somatic mutation accumulation, termed mutational signatures, are indicative of processes sustained within tumors. However, the association of various mutational processes with replication timing (RT) remains an open question. In this study, we systematically analyzed the mutational landscape of 2,787 tumors from 32 tumor types separately for early and late replicating regions using sequence context normalization and chromatin data to account for sequence and chromatin accessibility differences. To account for sequence differences between various genomic regions, an artificial genome–based approach was developed to expand the signature analyses to doublet base substitutions and small insertions and deletions. The association of mutational processes and RT was signature specific: Some signatures were associated with early or late replication (such as SBS7b and SBS7a, respectively), and others had no association. Most associations existed even after normalizing for genome accessibility. A focused mutational signature identification approach was also developed that uses RT information to improve signature identification; this approach found that SBS16, which is biased toward early replication, is strongly associated with better survival rates in liver cancer. Overall, this novel and comprehensive approach provides a better understanding of the etiology of mutational signatures, which may lead to improved cancer prevention, diagnosis, and treatment. Significance: Many mutational processes associate with early or late replication timing regions independently of chromatin accessibility, enabling development of a focused identification approach to improve mutational signature detection.
Different Cultivation Environments Affect the Yield, Bacterial Community and Metabolites of Cordyceps cicadae

Cordyceps cicadae is an entomogenous fungus with important uses in traditional Chinese medicine. However, its wild resources have not met consumers’ demand due to excessive harvesting practices. Artificial cultivation is therefore an important alternative, but research on cultivating C. cicadae in natural habitats has not been reported. In this study, we aimed to explore the viability of cultivating C. cicadae in a natural habitat, in the soil of Pinus massoniana forest. We assessed and compared the yield, metabolite contents and bacterial community composition of C. cicadae grown in the Antheraea pernyi pupae at different growth stages, and under different cultivation conditions, in the soil of a natural habitat and in sterile glass bottles. Our results showed that cultivating C. cicadae in a natural habitat is feasible, with up to 95% of pupae producing C. cicadae fruiting bodies. The content of nitrogen compounds (amino acids) in C. cicadae cultivated in a natural habitat was significantly higher than in glass bottles, while the yield and carbon compound (mannitol and polysaccharide) and nucleoside (cordycepin and adenosine) contents were lower. Different bacterial genera were enriched in C. cicadae at different growth stages and cultivation environments, and these bacterial genera were closely related to metabolites contents during growth. This study demonstrated the viability of a novel cultivation method of C. cicadae, which could be used as an alternative to wild stocks of this fungus. These findings provided new insights into the growth mechanism of C. cicadae and its interaction with soil microorganisms.
Mesenchymal Stem Cells in Gastric Cancer: Vicious but Hopeful

Tumor progression depends on the collaborative interactions between tumor cells and the surrounding stroma. First-line therapies direct against cancer cells may not reach a satisfactory outcome, such as gastric cancer (GC), with high risk of recurrence and metastasis. Therefore, novel treatments and drugs target the effects of stroma components are to be promising alternatives. Mesenchymal stem cells (MSC) represent the decisive components of tumor stroma that are found to strongly affect GC development and progression. MSC from bone marrow or adjacent normal tissues express homing profiles in timely response to GC-related inflammation signals and anchor into tumor bulks. Then the newly recruited “naïve” MSC would achieve phenotype and functional alternations and adopt the greater tumor-supporting potential under the reprogramming of GC cells. Conversely, both new-comers and tumor-resident MSC are able to modulate the tumor biology via aberrant activation of oncogenic signals, metabolic reprogramming and epithelial-to-mesenchymal transition. And they also engage in remodeling the stroma better suited for tumor progression through immunosuppression, pro-angiogenesis, as well as extracellular matrix reshaping. On the account of tumor tropism, MSC could be engineered to assist earlier diagnosis of GC and deliver tumor-killing agents precisely to the tumor microenvironment. Meanwhile, intercepting and abrogating vicious signals derived from MSC are of certain significance for the combat of GC. In this review, we mainly summarize current advances concerning the reciprocal metabolic interactions between MSC and GC and their underlying therapeutic implications in the future.
Validity of a food frequency questionnaire for the estimation of total polyphenol intake estimates and its major food sources in the Japanese population: the JPHC FFQ Validation Study

Abstract We examine the validity and reproducibility of a food frequency questionnaire (FFQ) in a subsample of participants in the Japan Public Health Center-based Prospective Cohort Study using a database of polyphenol-containing foods commonly consumed in the Japanese population. Participants of the validation study were recruited from two different cohorts. In Cohort I, 215 participants completed a 28-d dietary record (DR) and the FFQ, and in Cohort II, 350 participants completed DRs and the FFQ. The total polyphenol intake estimated from the 28-d DR and FFQ were log-transformed and adjusted for energy intake by the residual method. Spearman correlation coefficients (CCs) between estimates from the FFQ and 28-d DR as well as two FFQs administered at a 1-year interval were computed. Median intakes of dietary polyphenols calculated from the DRs were 1172 mg/d for men and 1024 mg/d for women in Cohort I, and 1061 mg/d for men and 942 mg/d for women in Cohort II. The de-attenuated CCs for polyphenol intake between the DR and FFQ were 0⋅47 for men and 0⋅37 for women in Cohort I and 0⋅44 for men and 0⋅50 for women in Cohort II. Non-alcoholic beverages were the main contributor to total polyphenol intake in both men and women, accounting for 50 % of total polyphenol intake regardless of cohort and gender, followed by alcoholic beverages and seasoning and spices in men, and seasoning and spices, fruits and other vegetables in women. The present study showed that this FFQ had moderate validity and reproducibility and is suitable for use in future epidemiological studies.