Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and immunological characterization of cuproptosis-related molecular clusters in idiopathic pulmonary fibrosis disease

Background Idiopathic pulmonary fibrosis (IPF) has attracted considerable attention worldwide and is challenging to diagnose. Cuproptosis is a new form of cell death that seems to be associated with various diseases. However, whether cuproptosis-related genes (CRGs) play a role in regulating IPF disease is unknown. This study aims to analyze the effect of CRGs on the progression of IPF and identify possible biomarkers. Methods Based on the GSE38958 dataset, we systematically evaluated the differentially expressed CRGs and immune characteristics of IPF disease. We then explored the cuproptosis-related molecular clusters, the related immune cell infiltration, and the biological characteristics analysis. Subsequently, a weighted gene co-expression network analysis (WGCNA) was performed to identify cluster-specific differentially expressed genes. Lastly, the eXtreme Gradient Boosting (XGB) machine-learning model was chosen for the analysis of prediction and external datasets validated the predictive efficiency. Results Nine differentially expressed CRGs were identified between healthy and IPF patients. IPF patients showed higher monocytes and monophages M0 infiltration and lower naive B cells and memory resting T CD4 cells infiltration than healthy individuals. A positive relationship was found between activated dendritic cells and CRGs of LIPT1, LIAS, GLS, and DBT. We also identified cuproptosis subtypes in IPF patients. Go and KEGG pathways analysis demonstrated that cluster-specific differentially expressed genes in Cluster 2 were closely related to monocyte aggregation, ubiquitin ligase complex, and ubiquitin-mediated proteolysis, among others. We also constructed an XGB machine model to diagnose IPF, presenting the best performance with a relatively lower residual and higher area under the curve (AUC= 0.700) and validated by external validation datasets (GSE33566, AUC = 0.700). The analysis of the nomogram model demonstrated that XKR6, MLLT3, CD40LG, and HK3 might be used to diagnose IPF disease. Further analysis revealed that CD40LG was significantly associated with IPF. Conclusion Our study systematically illustrated the complicated relationship between cuproptosis and IPF disease, and constructed an effective model for the diagnosis of IPF disease patients.
Antifungal activity of volatile and non-volatile metabolites of endophytes of Chloranthus elatior Sw.

Agriculture crops that have fungal infections suffer significant economic losses and reduced crop output. Chemical fungicides are used to tackle the problem, although this has additional detrimental side effects. There is an urgent need for safe and novel antifungals. Volatiles from plant-beneficial endophytic fungi are considered promising alternatives for the biological control of fungal pathogens as a sustainable approach in an agroecosystem. In the present investigation, a volatile-emitting sterile endophytic fungus, Diaporthe sp. CEL3 with bio-fumigation activity, was isolated from leaves of the ethnomedicinal plant Chloranthus elatior Sw. , collected from the Passighat forest of North-East India. The camphor odor volatiles of CEL3 showed an inhibitory effect against eight fungal pathogens in vitro and minimized the infections of Monilinia fructicola, a causal agent of cherry fruit rot, in VOC-exposed cherry fruits. Rhizoctonia solani, Botrytis cinerea, Pythium ultimum, and M. fructicola were maximally inhibited up to 51.5%, 55.8%, 61.9%, and 78.5%, respectively, in comparison to control by the volatiles. Another isolate, CEL7, identified as Curvularia sp. , synthesized non-volatile, soluble antifungal metabolites in its cell-free extracts and exhibited antifungal action. Bioassay-guided fractionation revealed the presence of imidazole compounds- (2-aminoethyl)-1H-imidazole-2-carbaldehyde, Pyrazole 4, 5 imidazole, 1-formyl 3-ethyl, phenol compounds-Phenol, 4-[2-(methylamino) ethyl]-, 6-Nitro-3-chlorophenol, Phenol, 2,4,6-tri-tert-butyl-, etc., in the cell-free extracts, with a MIC value of 250–2,000 µg ml−1. Optimum VOC emission was achieved in a modified PDA medium with instantly smashed potato (150 g L−1), dextrose (20 g L−1), wheat husk (20 g L−1), and yeast extract (20 g L−1), with additional salts. Interestingly, endophytic CEL3 emitted different types of volatiles, and trans-verbenol (32.25%), geraniol (30.32%), trans-ocimenol (12.90%), and mentha-4,8-diene (5.16%) were the prime ones. These VOCs cause lethal leakage of protein and necessary intracellular molecules from the fungal pathogens. Thus, CEL3 could potentially be used as a bio-fumigating agent to control post-harvest infections caused by fungal pathogens. This study opens a new approach to the use of endophytic fungi in biocontrol.
The brain is not mental! coupling neuronal and immune cellular processing in human organisms

Significant efforts have been made in the past decades to understand how mental and cognitive processes are underpinned by neural mechanisms in the brain. This paper argues that a promising way forward in understanding the nature of human cognition is to zoom out from the prevailing picture focusing on its neural basis. It considers instead how neurons work in tandem with other type of cells (e.g., immune) to subserve biological self-organization and adaptive behavior of the human organism as a whole. We focus specifically on the immune cellular processing as key actor in complementing neuronal processing in achieving successful self-organization and adaptation of the human body in an ever-changing environment. We overview theoretical work and empirical evidence on “basal cognition” challenging the idea that only the neuronal cells in the brain have the exclusive ability to “learn” or “cognize. ” The focus on cellular rather than neural, brain processing underscores the idea that flexible responses to fluctuations in the environment require a carefully crafted orchestration of multiple cellular and bodily systems at multiple organizational levels of the biological organism. Hence cognition can be seen as a multiscale web of dynamic information processing distributed across a vast array of complex cellular (e.g., neuronal, immune, and others) and network systems, operating across the entire body, and not just in the brain. Ultimately, this paper builds up toward the radical claim that cognition should not be confined to one system alone, namely, the neural system in the brain, no matter how sophisticated the latter notoriously is.
A robust approach to multiple change-point estimation in an AR(1) process

We consider the problem of multiple change-point estimation in the mean of a Gaussian AR(1) process. Taking into account the dependence structure does not allow us to use the dynamic programming algorithm, which is the only algorithm giving the optimal solution in the independent case. We propose a robust estimator of the autocorrelation parameter, which is consistent and satisfies a central limit theorem. Then, we propose to follow the classical inference approach, by plugging this estimator in the criteria used for change-points estimation. We show that the asymptotic properties of these estimators are the same as those of the classical estimators in the independent framework. The same plug-in approach is then used to approximate the modified BIC and choose the number of segments. This method is implemented in the R package AR1seg and is available from the Comprehensive R Archive Network (CRAN). This package is used in the simulation section in which we show that for finite sample sizes taking into account the dependence structure improves the statistical performance of the change-point estimators and of the selection criterion.
The mechanism of ferroptosis in early brain injury after subarachnoid hemorrhage

Subarachnoid hemorrhage (SAH) is a cerebrovascular accident with an acute onset, severe disease characteristics, and poor prognosis. Within 72 hours after the occurrence of SAH, a sequence of pathological changes occur in the body including blood-brain barrier breakdown, cerebral edema, and reduced cerebrovascular flow that are defined as early brain injury (EBI), and it has been demonstrated that EBI exhibits an obvious correlation with poor prognosis. Ferroptosis is a novel programmed cell death mode. Ferroptosis is induced by the iron-dependent accumulation of lipid peroxides and reactive oxygen species (ROS). Ferroptosis involves abnormal iron metabolism, glutathione depletion, and lipid peroxidation. Recent study revealed that ferroptosis is involved in EBI and is significantly correlated with poor prognosis. With the gradual realization of the importance of ferroptosis, an increasing number of studies have been conducted to examine this process. This review summarizes the latest work in this field and tracks current research progress. We focused on iron metabolism, lipid metabolism, reduction systems centered on the GSH/GPX4 system, other newly discovered GSH/GPX4-independent antioxidant systems, and their related targets in the context of early brain injury. Additionally, we examined certain ferroptosis regulatory mechanisms that have been studied in other fields but not in SAH. A link between death and oxidative stress has been described. Additionally, we highlight the future research direction of ferroptosis in EBI of SAH, and this provides new ideas for follow-up research.
Sous-groupes compacts maximaux des groupes de Lie

© Association des collaborateurs de Nicolas Bourbaki, 1952, tous droits réservés. L’accès aux archives du séminaire Bourbaki (http://www.bourbaki. ens.fr/) implique l’accord avec les conditions générales d’utilisation (http://www.numdam.org/conditions). Toute utilisation commerciale ou impression systématique est constitutive d’une infraction pénale. Toute copie ou impression de ce fichier doit contenir la présente mention de copyright.
What’s the key for success? Translocation, growth and thermal stress mitigation in the Mediterranean coral Cladocora caespitosa (Linnaeus, 1767)

Marine heat waves (MHWs) are affecting corals populations, advocating their inclusion in restoration actions since conservation measures may be not sufficient. Cladocora caespitosa is a Mediterranean reef-building, long-living species, with low recruitment rate and high juvenile mortality, leading to the need for its inclusion in international and European legislations. The aim of this study, conducted in the southern Tyrrhenian Sea, was to test the translocation of several C. caespitosa colonies thriving on an artificial substrate intended for demolition, applying transplantation techniques. Thirty-four colonies were transplanted in May 2018, and monitored over 4 years, to check for their persistence and health status. The shaded position of the recipient site resulted adequate, considering that colony survival rates were as high as 82.4%, 70.6% and 55.9% in October 2018, January 2020 and October 2022, respectively. Colonies presented signs of suffering only after the high temperatures occurred during summer 2022, with a decreasing rate of -2.5 ± 0.4 corallite/month. To better interpret the documented survival rates, 40 fragments of C. caespitosa were reared in aquaria to test temperature and light effects on growth rates and resistance to thermal stress, simulating a MHW and exacerbating the dim-light natural conditions of the recipient site, exposing half of the fragments to complete darkness. Only bigger fragments produced new corallites, with a rate of 1.3 ± 0.3 corallites/month, like the natural growth rate obtained in the field before the thermal anomaly, highlighting the suitability of ex-situ rearing as a potential tool to supply restoration project. After 5-days at 28.5°C, all fragments survived, despite showing tissue retraction, shorter tentacles, lower responsiveness, and zooxanthellae density variation. Overall, our results highlighted a promising plasticity of C. caespitosa in the field, representing a good candidate for restoration purposes. In aquaria this adaptive potential has been tested on a single genotype and more tests are needed to assess the intraspecific variability of these responses. A first insight into the species-based siting selection was provided to ensure the success of a restoration action. Our results point out the importance of knowing life history traits and ecological optima to design proper management and restoration measures.
Glucagon-like peptide-1: a multi-faceted anti-inflammatory agent

Inflammation contributes to many chronic conditions. It is often associated with circulating pro-inflammatory cytokines and immune cells. GLP-1 levels correlate with disease severity. They are often elevated and can serve as markers of inflammation. Previous studies have shown that oxytocin, hCG, ghrelin, alpha-MSH and ACTH have receptor-mediated anti-inflammatory properties that can rescue cells from damage and death. These peptides have been studied well in the past century. In contrast, GLP-1 and its anti-inflammatory properties have been recognized only recently. GLP-1 has been proven to be a useful adjuvant therapy in type-2 diabetes mellitus, metabolic syndrome, and hyperglycemia. It also lowers HbA1C and protects cells of the cardiovascular and nervous systems by reducing inflammation and apoptosis. In this review we have explored the link between GLP-1, inflammation, and sepsis.
Transcriptome and co-expression network analysis reveals the molecular mechanism of inosine monophosphate-specific deposition in chicken muscle

The inosine monophosphate (IMP) content in chicken meat is closely related to muscle quality and is an important factor affecting meat flavor. However, the molecular regulatory mechanisms underlying the IMP-specific deposition in muscle remain unclear. This study performed transcriptome analysis of muscle tissues from different parts, feeding methods, sexes, and breeds of 180-day-old Jingyuan chickens, combined with differential expression and weighted gene co-expression network analysis (WGCNA), to identify the functional genes that regulate IMP deposition. Out of the four comparison groups, 1,775, 409, 102, and 60 differentially expressed genes (DEGs) were identified, of which PDHA2, ACSS2, PGAM1, GAPDH, PGM1, GPI, and TPI1 may be involved in the anabolic process of muscle IMP in the form of energy metabolism or amino acid metabolism. WGCNA identified 11 biofunctional modules associated with IMP deposition. The brown, midnight blue, red, and yellow modules were strongly correlated with IMP and cooking loss (p < 0.05). Functional enrichment analysis showed that glycolysis/gluconeogenesis, arginine and proline metabolism, and pyruvate metabolism, regulated by PYCR1, SMOX, and ACSS2, were necessary for muscle IMP-specific deposition. In addition, combined analyses of DEGs and four WGCNA modules identified TGIF1 and THBS1 as potential candidate genes affecting IMP deposition in muscle. This study explored the functional genes that regulate muscle development and IMP synthesis from multiple perspectives, providing an important theoretical basis for improving the meat quality and molecular breeding of Jingyuan chickens.
A case-control study about markers of stress in normal-/overweight women with polycystic ovary syndrome and in controls

Background Polycystic ovary syndrome (PCOS) is linked to an elevated risk of psychological disorders, decreased quality of life and emotional distress. Serum cortisol as a potential stress marker has been found to be increased in women with PCOS. The aim of this study was to evaluate both saliva stress markers and subjective psychological distress in women with PCOS. Methods In a prospective case-control study, 31 PCOS women and 31 healthy controls were included. Salivary cortisol, and metanephrines were collected in the morning and in the evening. Emotional distress and quality of life were assessed by means of the Perceived Stress Scale (PSS-10) and the Short Form-36 (SF-36). Multivariable generalized linear models were applied to test the influence of various parameters on numerical outcome parameters. Results After correction for age and body mass index (BMI), there were no statistically significant differences of salivary biomarkers between PCOS women and healthy controls (p>0.05). PCOS patients revealed significantly higher increased PSS total scores and lower quality of life in all SF-36 modules apart from pain (p< 0.05). The PSS total score was positively correlated to prolactin in PCOS women (r= 0.450; p= 0.011). In overweight/obese PCOS patients, a higher BMI, a higher Ferriman Gallwey score and higher age significantly predicted the PSS total score (p< 0.05). Conclusion Stress measured by salivary biomarkers did not differ between PCOS women and healthy controls, whereas stress scores evaluated by questionnaires were significantly greater in women with PCOS. A higher BMI, hirsutism and a higher age seem to be the main modulators of subjective stress in PCOS. Prolactin might serve as a biomarker for chronic stress in PCOS women.
Gut microbiota variation of a tropical oil-collecting bee species far exceeds that of the honeybee

Introduction Interest for bee microbiota has recently been rising, alleviating the gap in knowledge in regard to drivers of solitary bee gut microbiota. However, no study has addressed the microbial acquisition routes of tropical solitary bees. For both social and solitary bees, the gut microbiota has several essential roles such as food processing and immune responses. While social bees such as honeybees maintain a constant gut microbiota by direct transmission from individuals of the same hive, solitary bees do not have direct contact between generations. They thus acquire their gut microbiota from the environment and/or the provision of their brood cell. To establish the role of life history in structuring the gut microbiota of solitary bees, we characterized the gut microbiota of Centris decolorata from a beach population in Mayagüez, Puerto Rico. Females provide the initial brood cell provision for the larvae, while males patrol the nest without any contact with it. We hypothesized that this behavior influences their gut microbiota, and that the origin of larval microbiota is from brood cell provisions. Methods We collected samples from adult females and males of C. decolorata (n = 10 each, n = 20), larvae (n = 4), and brood cell provisions (n = 10). For comparison purposes, we also sampled co-occurring female foragers of social Apis mellifera (n = 6). The samples were dissected, their DNA extracted, and gut microbiota sequenced using 16S rRNA genes. Pollen loads of A. mellifera and C. decolorata were analyzed and interactions between bee species and their plant resources were visualized using a pollination network. Results While we found the gut of A. mellifera contained the same phylotypes previously reported in the literature, we noted that the variability in the gut microbiota of solitary C. decolorata was significantly higher than that of social A. mellifera. Furthermore, the microbiota of adult C. decolorata mostly consisted of acetic acid bacteria whereas that of A. mellifera mostly had lactic acid bacteria. Among C. decolorata, we found significant differences in alpha and beta diversity between adults and their brood cell provisions (Shannon and Chao1 p < 0.05), due to the higher abundance of families such as Rhizobiaceae and Chitinophagaceae in the brood cells, and of Acetobacteraceae in adults. In addition, the pollination network analysis indicated that A. mellifera had a stronger interaction with Byrsonima sp. and a weaker interaction with Combretaceae while interactions between C. decolorata and its plant resources were constant with the null model. Conclusion Our data are consistent with the hypothesis that behavioral differences in brood provisioning between solitary and social bees is a factor leading to relatively high variation in the microbiota of the solitary bee.
Insight into the metabolic potential and ecological function of a novel Magnetotactic Nitrospirota in coral reef habitat

Magnetotactic bacteria (MTB) within the Nitrospirota phylum play important roles in biogeochemical cycles due to their outstanding ability to biomineralize large amounts of magnetite magnetosomes and intracellular sulfur globules. For several decades, Nitrospirota MTB were believed to only live in freshwater or low-salinity environments. While this group have recently been found in marine sediments, their physiological features and ecological roles have remained unclear. In this study, we combine electron microscopy with genomics to characterize a novel population of Nitrospirota MTB in a coral reef area of the South China Sea. Both phylogenetic and genomic analyses revealed it as representative of a novel genus, named as Candidatus Magnetocorallium paracelense XS-1. The cells of XS-1 are small and vibrioid-shaped, and have bundled chains of bullet-shaped magnetite magnetosomes, sulfur globules, and cytoplasmic vacuole-like structures. Genomic analysis revealed that XS-1 has the potential to respire sulfate and nitrate, and utilize the Wood–Ljungdahl pathway for carbon fixation. XS-1 has versatile metabolic traits that make it different from freshwater Nitrospirota MTB, including Pta-ackA pathway, anaerobic sulfite reduction, and thiosulfate disproportionation. XS-1 also encodes both the cbb3-type and the aa3-type cytochrome c oxidases, which may function as respiratory energy-transducing enzymes under high oxygen conditions and anaerobic or microaerophilic conditions, respectively. XS-1 has multiple copies of circadian related genes in response to variability in coral reef habitat. Our results implied that XS-1 has a remarkable plasticity to adapt the environment and can play a beneficial role in coral reef ecosystems.
Humans need only 200 ms to generate posture-specific muscle activation patterns for successful vertical jumps in reaction to an auditory trigger

Introduction It is currently unknown how the central nervous system controls ballistic whole-body movements like vertical jumps. Here we set out to study the time frame of generating muscle activation patterns for maximum-effort jumps from different initial postures. Methods We had ten healthy male participants make a slow countermovement from an upright position and initiate a maximal vertical jump as soon as possible following an auditory trigger. The trigger was produced when hip height dropped below one of three preselected values, unknown in advance to the participant, so that the participant was uncertain about the posture from which to initiate the jump. Furthermore, we determined the ensuing bottom postures reached during jumps, and from these postures had the participants perform maximum-effort squat jumps in two conditions: whenever they felt ready, or as soon as possible following an auditory trigger. Kinematics and ground reaction forces were measured, and electromyograms were collected from gluteus maximus, biceps femoris, rectus femoris, vastus lateralis, gastrocnemius and soleus. For each muscle, we detected activation onsets, as well as reaction times defined as the delay between trigger onset and activation onset. Results In the jumps preceded by a slow countermovement, the posture from which to initiate the jump was unknown before trigger onset. Nevertheless, in these jumps, posture-specific muscle activation patterns were already released within 200 ms after trigger onset and reaction times were not longer and jump heights not less than in squat jumps from corresponding bottom postures. Discussion Our findings suggest that the generation of muscle activation patterns for jumping does not start before trigger onset and requires only about 200 ms.