Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Apple Root-Associated Endophytic Streptomyces pulveraceus Strain ES16 by an OSMAC-Assisted Metabolomics Approach

The One Strain Many Compounds approach (OSMAC) is a powerful and comprehensive method that enables the chemo-diversity evaluation of microorganisms. This is achieved by variations of physicochemical cultivation parameters and by providing biotic and abiotic triggers to mimic microorganisms' natural environment in the lab. This approach can reactivate the silent biosynthetic routes of specific metabolites typically not biosynthesized under standard laboratory conditions. In the present study, we combined the OSMAC approach with static headspace solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS), high-performance liquid chromatography-high-resolution tandem mass spectrometry (HPLC-HRMSn), and matrix-assisted laser desorption/ionization high-resolution mass spectrometry imaging (MALDI-HRMSI) to evaluate the chemoecological significance of an apple root-associated endophytic Streptomyces pulveraceus strain ES16. We employed the OSMAC approach by cultivating the endophyte in six different media conditions and performed temporal studies over 14 days. Analysis of the volatilome revealed that only under stressful conditions associated with sporulation, endophytic S. pulveraceus ES16 produces geosmin, a volatile semiochemical known to attract the soil arthropods Collembola (springtails) specifically. Subsequently, targeted metabolic profiling revealed polycyclic tetramate macrolactams (PTMs) production by the endophyte under stress, which are bioactive against various pathogens. Additionally, the endophyte produced the iron-chelating siderophore, mirubactin, under the same conditions. The structures of the compounds were evaluated using HRMSn and by comparison with literature data. Finally, MALDI-HRMSI revealed the produced compounds' spatial-temporal distribution over 14 days. The compounds were profusely secreted into the medium after production. Our results indicate that endophytic S. pulveraceus ES16 can release the signal molecule geosmin, chemical defense compounds such as the PTMs, as well as the siderophore mirubactin into the host plant apoplast or the soil for ecologically meaningful purposes, which are discussed.
Revisiting Human-Agent Communication: The Importance of Joint Co-construction and Understanding Mental States

The study of human-human communication and the development of computational models for human-agent communication have diverged significantly throughout the last decade. Yet, despite frequently made claims of “super-human performance” in, e.g., speech recognition or image processing, so far, no system is able to lead a half-decent coherent conversation with a human. In this paper, we argue that we must start to re-consider the hallmarks of cooperative communication and the core capabilities that we have developed for it, and which conversational agents need to be equipped with: incremental joint co-construction and mentalizing. We base our argument on a vast body of work on human-human communication and its psychological processes that we reason to be relevant and necessary to take into account when modeling human-agent communication. We contrast those with current conceptualizations of human-agent interaction and formulate suggestions for the development of future systems.
Identification of Suitable Biomass Torrefaction Operation Envelops for Auto-Thermal Operation

Auto-thermal operation of biomass torrefaction can help avoid additional heat investment and the associated costs to the system. This work provides a general method for relating the feedstock-specific parameters to the energy balance and pre-diagnosing the potential of auto-thermal for different biomass torrefaction and pyrolysis systems. Both solid and gas thermal properties under various torrefaction conditions and their influences to the torrefaction system energy balances are considered. Key parameters that influence the process auto-thermal operation are analyzed, which include torrefaction reaction heat, torrefaction conditions, drying method, biomass species, and inert N2 flowrate. Equations of torgas and biomass higher heating values (HHVs), as well as the torrefaction reaction heat at different operating conditions are developed. It is found that torgas and biomass HHVs increase with torrefaction temperature and biomass weight loss. Torrefaction reaction heat has a linear relationship with the biomass weight loss, with a positive slope at 250–260°C, and a negative slope at 270–300°C, which indicates that torrefaction shifts from endothermic to exothermic at ∼270°C. Applying advanced drying technology and avoiding the use of N2 can help the system achieve auto-thermal operation at lower torrefaction temperature and residence time, thus leading to a higher process energy efficiency and product yield. This is the first work to relate the micro level element changes of biomass to the macro level process energy balances of the torrefaction system. This work is important in design and operation of the torrefaction system in both pilot and industrial scales to improve process efficiency and predict product quality in a reliable and economic manner.
Mathematical Model of Glucagon Kinetics for the Assessment of Insulin-Mediated Glucagon Inhibition During an Oral Glucose Tolerance Test

Glucagon is secreted from the pancreatic alpha cells and plays an important role in the maintenance of glucose homeostasis, by interacting with insulin. The plasma glucose levels determine whether glucagon secretion or insulin secretion is activated or inhibited. Despite its relevance, some aspects of glucagon secretion and kinetics remain unclear. To gain insight into this, we aimed to develop a mathematical model of the glucagon kinetics during an oral glucose tolerance test, which is sufficiently simple to be used in the clinical practice. The proposed model included two first-order differential equations -one describing glucagon and the other describing C-peptide in a compartment remote from plasma - and yielded a parameter of possible clinical relevance (i.e., SGLUCA(t), glucagon-inhibition sensitivity to glucose-induced insulin secretion). Model was validated on mean glucagon data derived from the scientific literature, yielding values for SGLUCA(t) ranging from -15.03 to 2.75 (ng of glucagon·nmol of C-peptide-1). A further validation on a total of 100 virtual subjects provided reliable results (mean residuals between -1.5 and 1.5 ng·L-1) and a negative significant linear correlation (r = -0.74, p < 0.0001, 95% CI: -0.82 – -0.64) between SGLUCA(t) and the ratio between the areas under the curve of suprabasal remote C-peptide and glucagon. Model reliability was also proven by the ability to capture different patterns in glucagon kinetics. In conclusion, the proposed model reliably reproduces glucagon kinetics and is characterized by sufficient simplicity to be possibly used in the clinical practice, for the estimation in the single individual of some glucagon-related parameters.
Meaning in Life Mediates Between Emotional Deregulation and Eating Disorders Psychopathology: A Research From the Meaning-Making Model of Eating Disorders

Emotional dysregulation, age, gender, and obesity are transdiagnostic risk factors for the development and maintenance of eating disorders (EDs). Previous studies found that patients with ED had less meaning in life than the non-clinical population, and that meaning in life acted as a buffer in the course of ED; however, to the data, there are no studies about the mediator role of meaning in life in association between the emotional dysregulation and the ED psychopathology. Objective: To analyze the mediating role of meaning in life in the relationship between emotional dysregulation and the ED psychopathology in three samples with diverse risk factors for ED. Method: Sample 1, n = 153 undergraduate young women; sample 2, n = 122 participants with obesity; and sample 3, n = 292 participants with ED. Multiple mediation analysis was performed. Results: Sample 1: meaning in life showed a mediation effect between emotional dysregulation and the ED psychopathology (direct effect β = 0.390, p < 0.05) (indirect effect β = 0.227, p < 0.05), body satisfaction (direct effect β = −0.017, p < 0.05) (indirect effect β = −0.013, p < 0.01), and depression symptoms (direct effect β = 1.112, p < 0.001) (indirect effect β = 0.414, p < 0.001); sample 2: meaning in life showed a mediation effect between emotional dysregulation and binge eating and purging behaviors (direct effect β = 0.194, p < 0.01) (indirect effect β = 0.054, p < 0.05) and depression symptoms (direct effect β = 0.357, p < 0.001) (indirect effect β = 0.063, p < 0.05); sample 3: meaning in life showed a mediation effect between emotional dysregulation and the ED psychopathology (direct effect β = 0.884, p < 0.001) (indirect effect β = 0.252, p < 0.007), body satisfaction (direct effect β = −0.033, p < 0.05) (indirect effect β = −0.021, p < 0.001), borderline symptoms (direct effect β = 0.040, p < 0.001) (indirect effect β = 0.025, p < 0.001), and hopelessness (direct effect β = 0.211, p < 0.001) (indirect effect β = 0.087, p < 0.001). Conclusions: These studies suggest the importance of considering meaning in life as a variable in the onset and maintenance of ED.
Psoriasis and Diabetes, a Dangerous Association: Evaluation of Insulin Resistance, Lipid Abnormalities, and Cardiovascular Risk Biomarkers

Aims: Psoriasis is an immune-mediated dermatosis with cardio-metabolic comorbidities. The aim of this study was to assess insulin-resistance, lipid abnormalities, and cardiovascular risk biomarkers in psoriatic patients with or without type 2 diabetes mellitus (T2DM). Methods and materials: We enrolled 425 patients: 86 psoriatics, 69 psoriatics with T2DM, 120 T2DM patients, and 150 healthy subjects. We measured the Psoriasis Area and Severity Index (PASI), body mass index (BMI), insulin-resistance parameters [glycosylated hemoglobin (HbA1c), fasting plasma glucose (FPG), fasting plasma insulin (FPI), and with homeostasis model assessment index (HOMA index)], lipidic panel, plasminogen activator inhibitor-1 (PAI-1), homocysteine, soluble adhesion molecules, matrix metalloproteinase, and adipocytokines. Results: FPG, HbA1c, and HOMA-IR were higher in diabetics with psoriasis (p < 0.0001) than in psoriatics. FPI levels were higher in diabetics with psoriasis than in diabetics and psoriatics (p < 0.0001), and higher in psoriatics than controls (p < 0.0001). Psoriatics and diabetics with psoriasis showed higher triglyceride and LDL-C levels (p < 0.0001) than diabetics. Homocysteine was higher in psoriatics and diabetics with psoriasis (p < 0.0001) than in diabetics. PAI-1 was higher in diabetics with psoriasis than diabetics (p < 0.01). sICAM-1 and sVCAM-1 were higher in diabetics with psoriasis than diabetics (p < 0.001 and p < 0.01) and psoriatics (p < 0.001 and p < 0.0001). Visfatin and resistin were lower in psoriatics (p < 0.0001) and in diabetics with psoriasis (p < 0.001 and p < 0.0001, respectively) than diabetics. Conclusions: A limitation of this study is that there is a significant difference in mean age between controls and other study groups: the lack of matching between case and control groups may interfere with the external validity of the study findings. Despite this, the study highlights a pathogenetic link between psoriasis, considered a pre-diabetic condition, and diabetes. Insulin-resistance seems to be the keystone of psoriasis comorbidities. Psoriasis reinforces diabetes, causing a greater cardiometabolic risk.
Peptidoglycan Recognition Peptide 2 Aggravates Weight Loss in a Murine Model of Chemotherapy-Induced Gastrointestinal Toxicity

Introduction: Chemotherapy-induced gastrointestinal toxicity (CIGT) is a frequent, severe and dose-limiting side effect. Few treatments have proven effective for CIGT. CIGT is characterized by activation of the nuclear factor kappa B pathway which, leads to upregulation of proinflammatory cytokines. The innate immune protein peptidoglycan recognition peptide 2 (PGLYRP2) binds to and hydrolyzes microbial peptidoglycan. Expression of PGLYRP2 is upregulated in the intestine of chemotherapy-treated piglets. In this experimental study, we investigated the role of Pglyrp2 in the development and severity of murine CIGT. Methods: Pglyrp2 wildtype and Pglyrp2 knockout mice received intraperitoneal injections of chemotherapy (Doxorubicin 20 mg/kg) to induce CIGT. Weight was monitored daily, and animals were euthanized after 2 or 7 days. Expression of proinflammatory cytokines in the jejunum was measured by quantitative real-time polymerase-chain reaction and enzyme-linked immunosorbent assay. Villus height, crypt depth, and histologic inflammation were evaluated on haematoxylin and eosin stained tissue specimens. Results: Chemotherapeutic treatment induced weight loss (p < 0.05), shortening of the small intestine (p < 0.05), elongation of villus height (p < 0.05), increased crypt depth (p < 0.05), and led to elevated mRNA levels of II1β (p < 0.05), II6 (p < 0.05), and Tnf (p < 0.001) at day 2. Protein levels of IL1β, IL6, and TNFα did not change after exposure to chemotherapy. Doxorubicin treated wildtype mice had a more pronounced weight loss compared to knockout mice from day 3 to day 7 (D3-D6: p < 0.05 and D7: p < 0.01). No other phenotypic differences were detected. Conclusion: Pglyrp2 aggravates chemotherapy-induced weight loss but does not induce a specific pattern of inflammation and morphological changes in the small intestine.
Exploring the Effect of Collective Cultural Attributes on Covid-19-Related Public Health Outcomes

Infections and deaths associated with COVID-19 show a high degree of heterogeneity across different populations. A thorough understanding of population-level predictors of such outcomes is crucial for devising better-targeted and more appropriate public health preparedness measures. While demographic, economic, and health-system capacity have featured prominently in recent work, cultural, and behavioral characteristics have largely been overlooked. However, cultural differences shape both the public policy response and individuals' behavioral responses to the crisis in ways that can impact infection dynamics and key health outcomes. To address this gap, we used meta-analytic methods to explore the global variability of three public health outcomes (i.e., crude test positivity, case/infection fatality, and mortality risk) during the first wave of the pandemic. This set of analyses identified several cultural/behavioral attributes (e.g., uncertainty avoidance and long-term vs. short-term normative orientation) as independent predictors of public health outcomes after adjusting for key demographic, political, economic, and health-system-related predictors; which were robust in sensitivity analyses. In conclusion, this study clearly demonstrates that cultural attributes do in fact account for some of the global disparities in COVID-19-attributed health outcomes. As a consequence, policymakers should more explicitly consider a society's cultural attributes alongside other important parameters such as demographic characteristics and health system constraints in order to develop better tailored and more effective policy responses.
The Role of Relational Entitlement, Self-Disclosure and Perceived Partner Responsiveness in Predicting Couple Satisfaction: A Daily-Diary Study

Recent research has investigated how the sense of relational entitlement (SRE, the extent to which a person expects that his/her needs and wishes will be fulfilled by the romantic partner) diminishes couple satisfaction, but little is known about how SRE affects the daily quality of close, romantic relationships. Moreover, the evidence on how SRE interacts with other features of a satisfying relationship (such as the variables of the interpersonal process model of relationships—self-disclosure, perceived partner disclosure, and perceived partner responsiveness) is scarce. Using an electronic daily diary, we examined 99 couples (198 participants) for 7 days, with two daily measurements for each partner. We used a dyadic double intercept multilevel model, which simultaneously computes effects for men and women. We tested a model where one partner's daily couple satisfaction was predicted by their overall levels of SRE (excessive, restricted, and assertive) and by their daily and overall levels of self-disclosure, perceived partner self-disclosure, and perceived partner responsiveness. The model also included person-level interactions and cross-level interactions between the SRE types and variables of the interpersonal process model of relationships for each gender. The analysis indicated that person-level excessive SRE lowers couple satisfaction. Also, day and person-level perceived partner responsiveness and person-level self-disclosure are related to couple satisfaction, but the latter association is significant only for men. Finally, we found some significant person-level interactions that account for changes in couple satisfaction. For men, the links between couple satisfaction, excessive and restricted SRE were moderated by self-disclosure and perceived partner responsiveness, respectively, perceived partner self-disclosure and perceived partner responsiveness. For women, the associations between couple satisfaction, restricted and assertive SRE were moderated by self-disclosure, respectively, perceived partner self-disclosure. This study advances our understanding of the general implications of SRE in the dynamics of couple relationships. More specifically, it shows how SRE interacts with other couple-specific variables in shaping day-to-day couple satisfaction. The theoretical and clinical implications for couple therapy are discussed.
Evidence of Age-Related Hemodynamic and Functional Connectivity Impairment: A Resting State fMRI Study

Purpose: To assess age-related changes in intrinsic functional brain connectivity and hemodynamics during adulthood in the context of the retrogenesis hypothesis, which states that the rate of age-related changes is higher in late-myelinating (prefrontal, lateral-posterior temporal) cerebrocortical areas as compared to early myelinating (parietal, occipital) regions. In addition, to examine the dependence of age-related changes upon concurrent subclinical depression symptoms which are common even in healthy aging. Methods: Sixty-four healthy adults (28 men) aged 23–79 years (mean 45.0, SD = 18.8 years) were examined. Resting-state functional MRI (rs-fMRI) time series were used to compute voxel-wise intrinsic connectivity contrast (ICC) maps reflecting the strength of functional connectivity between each voxel and the rest of the brain. We further used Time Shift Analysis (TSA) to estimate voxel-wise hemodynamic lead or lag for each of 22 ROIs from the automated anatomical atlas (AAL). Results: Adjusted for depression symptoms, gender and education level, reduced ICC with age was found primarily in frontal, temporal regions, and putamen, whereas the opposite trend was noted in inferior occipital cortices (p < 0.002). With the same covariates, increased hemodynamic lead with advancing age was found in superior frontal cortex and thalamus, with the opposite trend in inferior occipital cortex (p < 0.002). There was also evidence of reduced coupling between voxel-wise intrinsic connectivity and hemodynamics in the inferior parietal cortex. Conclusion: Age-related intrinsic connectivity reductions and hemodynamic changes were demonstrated in several regions—most of them part of DMN and salience networks—while impaired neurovascular coupling was, also, found in parietal regions. Age-related reductions in intrinsic connectivity were greater in anterior as compared to posterior cortices, in line with implications derived from the retrogenesis hypothesis. These effects were affected by self-reported depression symptoms, which also increased with age.
Periodic Fluctuations in the Incidence of Gastrointestinal Cancer

Purpose Native stem cells can be periodically replaced during short and long epigenetic intervals. Cancer-prone new stem cells might bring about periodic (non-stochastic) carcinogenic events rather than stochastic events. We investigated the epigenetic non-stochastic carcinogenesis by analyzing regular fluctuations in lifelong cancer incidence. Materials and Methods Korean National Cancer Screening Program data were collected between 2009 and 2016. Non-linear and log-linear regression models were applied to comparatively evaluate non-stochastic and stochastic increases in cancer incidence. Prediction performances of regression models were measured by calculating the coefficient of determination, R2. Results The incidence of gastric and colorectal cancers fluctuated regularly during both short (8 years) and long (20 years) intervals in the non-linear regression model and increased stochastically in the log-linear regression model. In comparison between the 20-year interval fluctuation model and the stochastic model, R2 values were higher in the 20-year interval fluctuation model of men with gastric cancer (0.975 vs. 0.956), and in the stochastic model of men with colorectal cancer (0.862 vs. 0.877) and women with gastric cancer (0.837 vs. 0.890) and colorectal cancer (0.773 vs. 0.809). Men with gastric cancer showed a high R2 value (0.973) in the 8-year interval fluctuation model as well. Conclusion Lifelong incidence of gastrointestinal cancer tended to fluctuate during short and long intervals, especially in men with gastric cancer, suggesting the influence of an epigenetic schedule.
Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

Buffalo is a luxurious genetic resource with multiple utilities (as a dairy, draft, and meat animal) and economic significance in the tropical and subtropical regions of the globe. The excellent potential to survive and perform on marginal resources makes buffalo an important source for nutritious products, particularly milk and meat. This study was aimed to investigate the evolutionary relationship, physiochemical properties, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in river and swamp buffalo. Phylogenetic, gene structure, motif, and conserved domain analysis revealed the evolutionarily conserved nature of the casein genes in buffalo and other closely related species. Results indicated that casein proteins were unstable, hydrophilic, and thermostable, although αs1-CN, β-CN, and κ-CN exhibited acidic properties except for αs2-CN, which behaved slightly basic. Comparative analysis of amino acid sequences revealed greater variation in the river buffalo breeds than the swamp buffalo indicating the possible role of these variations in the regulation of milk traits in buffalo. Furthermore, we identified lower transcription activators STATs and higher repressor site YY1 distribution in swamp buffalo, revealing its association with lower expression of casein genes that might subsequently affect milk production. The role of the main motifs in controlling the expression of casein genes necessitates the need for functional studies to evaluate the effect of these elements on the regulation of casein gene function in buffalo.