Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiome in Blood Samples From the General Population Recruited in the MARK-AGE Project: A Pilot Study

The presence of circulating microbiome in blood has been reported in both physiological and pathological conditions, although its origins, identities and function remain to be elucidated. This study aimed to investigate the presence of blood microbiome by quantitative real-time PCRs targeting the 16S rRNA gene. To our knowledge, this is the first study in which the circulating microbiome has been analyzed in such a large sample of individuals since the study was carried out on 1285 Randomly recruited Age-Stratified Individuals from the General population (RASIG). The samples came from several different European countries recruited within the EU Project MARK-AGE in which a series of clinical biochemical parameters were determined. The results obtained reveal an association between microbial DNA copy number and geographic origin. By contrast, no gender and age-related difference emerged, thus demonstrating the role of the environment in influencing the above levels independent of age and gender at least until the age of 75. In addition, a significant positive association was found with Free Fatty Acids (FFA) levels, leukocyte count, insulin, and glucose levels. Since these factors play an essential role in both health and disease conditions, their association with the extent of the blood microbiome leads us to consider the blood microbiome as a potential biomarker of human health.
Low-Dose Lactulose as a Prebiotic for Improved Gut Health and Enhanced Mineral Absorption

Although medium and high doses of lactulose are used routinely for the treatment of constipation and hepatic encephalopathy, respectively, a wealth of evidence demonstrates that, at low doses, lactulose can also be used as a prebiotic to stimulate the growth of health-promoting bacteria in the gastrointestinal tract. Indeed, multiple preclinical and clinical studies have shown that low doses of lactulose enhance the proliferation of health-promoting gut bacteria (e.g., Bifidobacterium and Lactobacillus spp.) and increase the production of beneficial metabolites [e.g., short-chain fatty acids (SCFAs)], while inhibiting the growth of potentially pathogenic bacteria (e.g., certain clostridia). SCFAs produced upon microbial fermentation of lactulose, the most abundant of which is acetate, are likely to contribute to immune regulation, which is important not only within the gut itself, but also systemically and for bone health. Low-dose lactulose has also been shown to enhance the absorption of minerals such as calcium and magnesium from the gut, an effect which may have important implications for bone health. This review provides an overview of the preclinical and clinical evidence published to date showing that low-dose lactulose stimulates the growth of health-promoting gut bacteria, inhibits the growth of pathogenic bacteria, increases the production of beneficial metabolites, improves mineral absorption, and has good overall tolerability. Implications of these data for the use of lactulose as a prebiotic are also discussed.
Prospective Exploratory Analysis of Angiogenic Biomarkers in Peripheral Blood in Advanced NSCLC Patients Treated With Bevacizumab Plus Chemotherapy: The ANGIOMET Study

Finding angiogenic prognostic markers in advanced non-small-cell lung cancer is still an unmet medical need. We explored a set of genetic variants in the VEGF-pathway as potential biomarkers to predict clinical outcomes of patients with non-small-cell lung cancer treated with chemotherapy plus bevacizumab. We prospectively analyzed the relationship between VEGF-pathway components with both pathological and prognostic variables in response to chemotherapy plus bevacizumab in 168 patients with non-squamous non-small-cell lung cancer. Circulating levels of VEGF and VEGFR2 and expression of specific endothelial surface markers and single-nucleotide polymorphisms in VEGF-pathway genes were analyzed. The primary clinical endpoint was progression-free survival. Secondary endpoints included overall survival and objective tumor response. VEGFR-1 rs9582036 variants AA/AC were associated with increased progression-free survival (p = 0.012 and p = 0.035, respectively), and with improved overall survival (p = 0.019) with respect to CC allele. Patients with VEGF-A rs3025039 harboring allele TT had also reduced mortality risk (p = 0.049) compared with the CC allele. The VEGF-A rs833061 variant was found to be related with response to treatment, with 61.1% of patients harboring the CC allele achieving partial treatment response. High pre-treatment circulating levels of VEGF-A were associated with shorter progression-free survival (p = 0.036). In conclusion, in this prospective study, genetic variants in VEGFR-1 and VEGF-A and plasma levels of VEGF-A were associated with clinical benefit, progression-free survival, or overall survival in a cohort of advanced non-squamous non-small-cell lung cancer patients receiving chemotherapy plus antiangiogenic therapy.
KEAP1/NFE2L2 Mutations of Liquid Biopsy as Prognostic Biomarkers in Patients With Advanced Non-Small Cell Lung Cancer: Results From Two Multicenter, Randomized Clinical Trials

Purpose The KEAP1-NFE2L2 (Kelch-like ECH-associated protein 1 (KEAP1)-Nuclear factor (erythroid-derived 2)-like 2 (NFE2L2)) mutations are associated with resistance to chemotherapy or immunotherapy in non-small cell lung cancer (NSCLC). Conversely, it has been reported that NFE2L2 mutations potentiate improved clinical outcome with immunotherapy. However, therapeutic benefits for patients with KEAP1/NFE2L2 mutations remain unclear. The purpose of this study was to investigate the association between KEAP1/NFE2L2 and NSCLC prognosis, and to explore whether immunotherapy can improve prognosis in populations with KEAP1/NFE2L2 mutations. Experimental Design The impact of KEAP1/NFE2L2 mutations on survival outcomes in NSCLC patients received immunotherapy and chemotherapy was verified in the randomized phase II/III POPLAR/OAK trials (blood-based sequencing, bNGS cohort, POPLAR (n = 211) and OAK (n = 642)). The Cancer Genome Atlas (TCGA) NSCLC cohort (n=998) and an in-house Chinese NSCLC cohort (n=733) was used For the analysis of immune-related markers. Results Compared with KEAP1/NFE2L2 wild-type, patients with KEAP1/NFE2L2 mutations were significantly associated with poorer overall survival (OS, HR = 1.97, 95% CI 1.48–2.63, P < 0.001) on atezolizumab and docetaxel (HR = 1.66, 95% CI 1.28–2.16, P < 0.001). In KEAP1/NFE2L2 mutant group, there was no significant difference in median OS between atezolizumab and docetaxel (HR 0.74, 95% CI 0.53–1.03, P = 0.07). NFE2L2/KEAP1 mutations were significantly associated with higher TMB values and PD-L1 expression in the OAK/POPLAR and in-house Chinese NSCLC cohorts. GSEA revealed that KEAP1/NFE2L2mutant subgroup was associated with deficient infiltration of CD4+ T cells, NK T cells and natural Treg cells, and lower expression of DNA damage response genes in TCGA NSCLC cohort. Conclusions Our study revealed that patients with KEAP1/NFE2L2 mutations have a worse prognosis than wild-type patients, both on immunotherapy and chemotherapy. In addition, in patients with KEAP1/NFE2L2 mutations, immunotherapy did not significantly improve prognosis compared to chemotherapy.
Distribution of HCV Genotypes Among People Who Inject Drugs in Tunisia: New Evidence for Scaling Up Prevention and Treatment Toward National Elimination Goal

Little is known about the distribution of hepatitis C virus (HCV) genotypes among people who inject drugs (PWID) in North African countries, including Tunisia. This study aims to describe HCV genotypes circulating among Tunisian PWID. A cross-sectional study was conducted, and 128 HCV-positive PWID were recruited between 2018 and 2019 from community-based harm reduction centers. After informed consent, sociodemographic characteristics and risk behavior data were obtained using an interviewer-administrated questionnaire. Blood samples were collected for further serological and molecular testing. Overall, five women and 123 men were included. The median age was 39.5 years. The majority of PWID (56.3%) had less than a secondary level of education, were single (57%), were unemployed (65.6%), were incarcerated at least once (93.0%), and had a history of residency in at least one foreign country (50.8%). During the previous 12 months, 82.0% reported having reused syringes at least once, 43.8% shared syringes at least once, while 56.2% had at least one unprotected sexual relation, and 28.1% had more than two different sexual partners. Tattooing was reported among 60.2%. All positive results for HCV-infection by rapid testing were confirmed by enzyme-linked immunosorbent assay (ELISA). HCV-RNA was detectable in 79.7%. Genotyping showed a predominance of genotype 1 (52%) followed by genotype 3 (34%) and genotype 4 (10%). Four patients (4%) had an intergenotype mixed infection. Subtyping showed the presence of six different HCV subtypes as follows: 1a (53.2%), 1b (6.4%), 3a (33.0%), 4a (3.2%), and 4d (4.3%). This is the first study describing circulating HCV genotypes among PWID in Tunisia. The distribution of HCV genotypes is distinct from the general population with a predominance of subtypes 1a and 3a. These findings can be used to guide national efforts aiming to optimize the access of PWID to relevant HCV prevention and treatment measures including pangenotypic regimens for patients infected with HCV genotype 3.
Tissue Multiplex Analyte Detection in Anatomic Pathology – Pathways to Clinical Implementation

Background: Multiplex tissue analysis has revolutionized our understanding of the tumor microenvironment (TME) with implications for biomarker development and diagnostic testing. Multiplex labeling is used for specific clinical situations, but there remain barriers to expanded use in anatomic pathology practice. Methods: We review immunohistochemistry (IHC) and related assays used to localize molecules in tissues, with reference to United States regulatory and practice landscapes. We review multiplex methods and strategies used in clinical diagnosis and in research, particularly in immuno-oncology. Within the framework of assay design and testing phases, we examine the suitability of multiplex immunofluorescence (mIF) for clinical diagnostic workflows, considering its advantages and challenges to implementation. Results: Multiplex labeling is poised to radically transform pathologic diagnosis because it can answer questions about tissue-level biology and single-cell phenotypes that cannot be addressed with traditional IHC biomarker panels. Widespread implementation will require improved detection chemistry, illustrated by InSituPlex technology (Ultivue, Inc., Cambridge, MA) that allows coregistration of hematoxylin and eosin (H&E) and mIF images, greater standardization and interoperability of workflow and data pipelines to facilitate consistent interpretation by pathologists, and integration of multichannel images into digital pathology whole slide imaging (WSI) systems, including interpretation aided by artificial intelligence (AI). Adoption will also be facilitated by evidence that justifies incorporation into clinical practice, an ability to navigate regulatory pathways, and adequate health care budgets and reimbursement. We expand the brightfield WSI system “pixel pathway” concept to multiplex workflows, suggesting that adoption might be accelerated by data standardization centered on cell phenotypes defined by coexpression of multiple molecules. Conclusion: Multiplex labeling has the potential to complement next generation sequencing in cancer diagnosis by allowing pathologists to visualize and understand every cell in a tissue biopsy slide. Until mIF reagents, digital pathology systems including fluorescence scanners, and data pipelines are standardized, we propose that diagnostic labs will play a crucial role in driving adoption of multiplex tissue diagnostics by using retrospective data from tissue collections as a foundation for laboratory-developed test (LDT) implementation and use in prospective trials as companion diagnostics (CDx).
Development of Preschoolers’ Understanding of Zero

While knowledge on the development of understanding positive integers is rapidly growing, the development of understanding zero remains not well-understood. Here, we test several components of preschoolers’ understanding of zero: Whether they can use empty sets in numerical tasks (as measured with comparison, addition, and subtraction tasks); whether they can use empty sets soon after they understand the cardinality principle (cardinality-principle knowledge is measured with the give-N task); whether they know what the word “zero” refers to (tested in all tasks in this study); and whether they categorize zero as a number (as measured with the smallest-number and is-it-a-number tasks). The results show that preschoolers can handle empty sets in numerical tasks as soon as they can handle positive numbers and as soon as, or even earlier than, they understand the cardinality principle. Some also know that these sets are labeled as “zero. ” However, preschoolers are unsure whether zero is a number. These results identify three components of knowledge about zero: operational knowledge, linguistic knowledge, and meta-knowledge. To account for these results, we propose that preschoolers may understand numbers as the properties of items or objects in a set. In this view, zero is not regarded as a number because an empty set does not include any items, and missing items cannot have any properties, therefore, they cannot have the number property either. This model can explain why zero is handled correctly in numerical tasks even though it is not regarded as a number.
Effect of Estrogen on Heteronemin-Induced Anti-proliferative Effect in Breast Cancer Cells With Different Estrogen Receptor Status

Estrogen (E2) has multiple functions in breast cancers including stimulating cancer growth and interfering with chemotherapeutic efficacy. Heteronemin, a marine sesterterpenoid-type natural product, has cytotoxicity on cancer cells. Breast cancer cell lines, MCF-7 and MDA-MB-231, were used for investigating mechanisms involved in inhibitory effect of E2 on heteronemin-induced anti-proliferation in breast cancer cells with different estrogen receptor (ER) status. Cytotoxicity was detected by cell proliferation assay and flow cytometry, gene expressions were determined by qPCR, mechanisms were investigated by Western blot and Mitochondrial ROS assay. Heteronemin exhibited potent cytotoxic effects against both ER-positive and ER-negative breast cancer cells. E2 stimulated cell growth in ER-positive breast cancer cells. Heteronemin induced anti-proliferation via suppressing activation of ERK1/2 and STAT3. Heteronemin suppressed E2-induced proliferation in both breast cancer cells although some gene expressions and anti-proliferative effects were inhibited in the presence of E2 in MCF-7 and MDA-MB-231 cells with a higher concentration of heteronemin. Heteromenin decreased the Bcl-2/Bax ratio to inhibit proliferation in MDA-MB-231 but not in MCF-7 cells. Both heteronemin and E2 increased mitochondrial reactive oxygen species but combined treatment reversed superoxide dismutase (SOD)s accumulation in MCF-7 cells. Heteronemin caused G0/G1 phase arrest and reduced the percentage of cells in the S phase to suppress cancer cell growth. In conclusion, Heteronemin suppressed both ER-positive and ER-negative breast cancer cell proliferation. Interactions between E2 and heteronemin in signal transduction, gene expressions, and biological activities provide insights into the complex pathways by which anti-proliferation is induced by heteronemin in E2-replete environments.
Red and White Meat Intake in Relation to Mental Disorders in Iranian Adults

Background: The association between meat consumption and mental disorders is less investigated in Iranian population. We examined the association between meat consumption and prevalence of symptoms of depression, anxiety, and psychological distress in Iranian adults. Methods: This cross-sectional study included 3,362 participants aged 18–55 years old. A dish-based 106-item semiquantitative food frequency questionnaire (FFQ) was used to assess usual dietary intake of study population. Hospital Anxiety and Depression Scale (HADS) and General Health Questionnaire (GHQ), all validated in Iranian population, were applied to collect data on symptoms of anxiety, depression, and psychological distress, respectively. Results: The prevalence of symptoms of depression, anxiety, and psychological distress in the study population was 28.6, 13.6, and 22.6%, respectively. After considering potential confounders, individuals in the top quartile of red meat intake had 43% increased risk of depression symptoms [odds ratio (OR) = 1.43; 95% CI: 1.09–1.89] compared to those in the first quartile. No significant relation was observed between red meat intake and anxiety or psychological distress symptoms. White meat consumption was not associated with mental disorders. Stratified analysis by sex showed that male participants in the highest quartile of red meat intake had 92% greater risk of depression symptoms (95% CI: 1.17–3.15) than those individuals in the lowest category. Red and white meat intake was not associated with mental disorders in women. In overweight or obese individuals, despite lack of any association between red meat intake and mental disorders, high intake of white meat was associated with a lower odds of psychological distress symptoms (OR = 0.64; 95% CI: 0.42–0.99) and a lower risk of depression symptoms (OR = 0.68; 95% CI: 0.45–1.00). In normal-weight participants, those in the highest quartile of red meat intake had greater odds for depression symptoms than those in the lowest quartile (OR = 1.66; 95% CI: 1.14–2.42). Conclusions: We found that red meat consumption was associated with increased risk of depression symptoms, especially in men, and normal-weight participants. In overweight or obese participants, white meat intake was inversely associated with psychological distress symptoms.
Functional Characterization of Olfactory Receptors in the Thyroid Gland

Olfactory receptors (ORs) are almost ubiquitously expressed in the human body. However, information about their functions in these tissues is lacking. To date, no functional characterization of expressed ORs in the human thyroid has been performed. In this study, we detected and compared the expression of OR2H2 and OR2W3 in healthy and malignant cell lines and their corresponding tissues, respectively. We demonstrated that stimulation of ORs by their specific ligand resulted in a transient increase in intracellular calcium and cAMP concentrations. In the case of OR2H2, the downstream signaling cascade analysis revealed that adenylate cyclase (AC) and phosphoinositide phospholipase C (PLC) were involved. Furthermore, OR2H2 and OR2W3 activation affected migration, proliferation, and invasion. These are the first insights that ORs influence physiology-relevant processes in the healthy and malignant thyroid.
The Role of Short-Chain Fatty Acids and Bile Acids in Intestinal and Liver Function, Inflammation, and Carcinogenesis

During the past decade, researchers have investigated the role of microbiota in health and disease. Recent findings support the hypothesis that commensal bacteria and in particular microbiota-derived metabolites have an impact on development of inflammation and carcinogenesis. Major classes of microbial-derived molecules such as short-chain fatty acids (SCFA) and secondary bile acids (BAs) were shown to have immunomodulatory potential in various autoimmune, inflammatory as well as cancerous disease models and are dependent on diet-derived substrates. The versatile mechanisms underlying both beneficial and detrimental effects of bacterial metabolites comprise diverse regulatory pathways in lymphocytes and non-immune cells including changes in the signaling, metabolic and epigenetic status of these. Consequently, SCFAs as strong modulators of immunometabolism and histone deacetylase (HDAC) inhibitors have been investigated as therapeutic agents attenuating inflammatory and autoimmune disorders. Moreover, BAs were shown to modulate the microbial composition, adaptive and innate immune response. In this review, we will discuss the recent findings in the field of microbiota-derived metabolites, especially with respect to the molecular and cellular mechanisms of SCFA and BA biology in the context of intestinal and liver diseases.
Hydrogen Sulfide Alleviates Alkaline Salt Stress by Regulating the Expression of MicroRNAs in Malus hupehensis Rehd. Roots

Malus hupehensis Rehd. var. pingyiensis Jiang (Pingyi Tiancha, PYTC) is an excellent apple rootstock and ornamental tree, but its tolerance to salt stress is weak. Our previous study showed that hydrogen sulfide (H2S) could alleviate damage in M. hupehensis roots under alkaline salt stress. However, the molecular mechanism of H2S mitigation alkaline salt remains to be elucidated. MicroRNAs (miRNAs) play important regulatory roles in plant response to salt stress. Whether miRNAs are involved in the mitigation of alkaline salt stress mediated by H2S remains unclear. In the present study, through the expression analysis of miRNAs and target gene response to H2S and alkaline salt stress in M. hupehensis roots, 115 known miRNAs (belonging to 37 miRNA families) and 15 predicted novel miRNAs were identified. In addition, we identified and analyzed 175 miRNA target genes. We certified the expression levels of 15 miRNAs and nine corresponding target genes by real-time quantitative PCR (qRT-PCR). Interestingly, H2S pretreatment could specifically induce the downregulation of mhp-miR408a expression, and upregulated mhp-miR477a and mhp-miR827. Moreover, root architecture was improved by regulating the expression of mhp-miR159c and mhp-miR169 and their target genes. These results suggest that the miRNA-mediated regulatory network participates in the process of H2S-mitigated alkaline salt stress in M. hupehensis roots. This study provides a further understanding of miRNA regulation in the H2S mitigation of alkaline salt stress in M. hupehensis roots.
Beyond Deforestation: Carbon Emissions From Land Grabbing and Forest Degradation in the Brazilian Amazon

Carbon losses from forest degradation and disturbances are significant and growing sources of emissions in the Brazilian Amazon. Between 2003 and 2019, degradation and disturbance accounted for 44% of forest carbon losses in the region, compared with 56% from deforestation (forest clearing). We found that land tenure played a decisive role in explaining these carbon losses, with Undesignated Public Forests and Other Lands (e.g., private properties) accounting for the majority (82%) of losses during the study period. Illegal deforestation and land grabbing in Undesignated Public Forests widespread and increasingly are important drivers of forest carbon emissions from the region. In contrast, indigenous Territories and Protected Natural Areas had the lowest emissions, demonstrating their effectiveness in preventing deforestation and maintaining carbon stocks. These trends underscore the urgent need to develop reliable systems for monitoring and reporting on carbon losses from forest degradation and disturbance. Together with improved governance, such actions will be crucial for Brazil to reduce pressure on standing forests; strengthen Indigenous land rights; and design effective climate mitigation strategies needed to achieve its national and international climate commitments.