Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis on Key Metabolic Pathways in Rhodotorula mucilaginosa Under Pb(II) Stress

Glycolysis (EMP), the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS) are critical metabolism pathways for microorganisms to obtain energy during the resistance to heavy metal (HM) stress. However, these pathways at the genetic level have not been elucidated to evaluate their cytoprotective functions for Rhodotorula mucilaginosa under Pb stress. ABSTRACT Rhodotorula mucilaginosa shows adaption to a broad range of Pb2+ stress. In this study, three key pathways, i.e., glycolysis (EMP), the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS), were investigated under 0–2,500 mg · L−1 Pb stress, primarily based on biochemical analysis and RNA sequencing. R. mucilaginosa cells showed similar metabolic response to low/medium (500/1000 mg · L−1) Pb2+ stress. High (2,500 mg · L−1) Pb2+ stress exerted severe cytotoxicity to R. mucilaginosa. The downregulation of HK under low-medium Pb2+ suggested a correlation with the low hexokinase enzymatic activity in vivo. However, IDH3, regulating a key step of circulation in TCA, was upregulated to promote ATP feedstock for downstream OXPHOS. Then, through activation of complex I & IV in the electron transport chain (ETC) and ATP synthase, ATP production was finally enhanced. This mechanism enabled fungal cells to compensate for ATP consumption under low-medium Pb2+ toxicity. Hence, R. mucilaginosa tolerance to such a broad range of Pb2+ concentrations can be attributed to energy adaption. In contrast, high Pb2+ stress caused ATP deficiency. Then, the subsequent degradation of intracellular defense systems further intensified Pb toxicity. This study correlated responses of EMP, TCA, and OXPHOS pathways in R. mucilaginosa under Pb stress, hence providing new insights into the fungal resistance to heavy metal stress. IMPORTANCE Glycolysis (EMP), the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS) are critical metabolism pathways for microorganisms to obtain energy during the resistance to heavy metal (HM) stress. However, these pathways at the genetic level have not been elucidated to evaluate their cytoprotective functions for Rhodotorula mucilaginosa under Pb stress. In this study, we investigated these three pathways based on biochemical analysis and RNA sequencing. Under low-medium (500–1,000 mg · L−1) Pb2+ stress, ATP production was stimulated mainly due to the upregulation of genes associated with the TCA cycle and the electron transport chain (ETC). Such an energy compensatory mechanism could allow R. mucilaginosa acclimation to a broad range of Pb2+ concentrations (up to 1000 mg · L−1). In contrast, high (2500 mg · L−1) Pb2+ stress exerted its excessive toxicity by provoking ATP deficiency and damage to intracellular resistance systems. This study provided new insights into R. mucilaginosa resistance to HM stress from the perspective of metabolism.
An experimental investigation of the influence of loneliness on changes in belongingness and desire to escape

Abstract Objective Loneliness is a well‐established risk factor for suicide in young adults, but the mechanisms involved are still unclear. Drawing on the Interpersonal Theory of Suicide, the Evolutionary Model of Loneliness, and Prospect Theory, we examined if high and low levels of loneliness are associated with different patterns of response to losses or gains of belongingness. Methods A sample of 188 students completed the UCLA‐Loneliness scale (version 3) and measures of suicide risk. Participants in the top and bottom tertiles of loneliness scores completed a computerized task designed to induce changes (gains, losses) or consistency in risk factors for suicide (belongingness, burdensomeness) over time, and examined the effect on desire to quit the task. Results The results showed that the high loneliness group exhibited a larger magnitude of effect on desire to quit from gaining belongingness than for losing belongingness. In contrast, the low loneliness group showed a larger change in desire to quit from losing belongingness than gaining belongingness. Conclusion The findings provide preliminary experimental support for distinct profiles of suicide risk based on prevailing levels of loneliness. The findings are discussed in relation to a need for increased precision in theoretical models of suicide and loneliness.
Ketogenic HMG‐CoA lyase and its product β‐hydroxybutyrate promote pancreatic cancer progression

Pancreatic ductal adenocarcinoma (PDA) tumor cells are deprived of oxygen and nutrients and therefore must adapt their metabolism to ensure proliferation. In some physiological states, cells rely on ketone bodies to satisfy their metabolic needs, especially during nutrient stress. Here, we show that PDA cells can activate ketone body metabolism and that β‐hydroxybutyrate (βOHB) is an alternative cell‐intrinsic or systemic fuel that can promote PDA growth and progression. PDA cells activate enzymes required for ketogenesis, utilizing various nutrients as carbon sources for ketone body formation. By assessing metabolic gene expression from spontaneously arising PDA tumors in mice, we find HMG‐CoA lyase (HMGCL), involved in ketogenesis, to be among the most deregulated metabolic enzymes in PDA compared to normal pancreas. In vitro depletion of HMGCL impedes migration, tumor cell invasiveness, and anchorage‐independent tumor sphere compaction. Moreover, disrupting HMGCL drastically decreases PDA tumor growth in vivo, while βOHB stimulates metastatic dissemination to the liver. These findings suggest that βOHB increases PDA aggressiveness and identify HMGCL and ketogenesis as metabolic targets for limiting PDA progression.
Whole-Genome Transformation of Yeast Promotes Rare Host Mutations with a Single Causative SNP Enhancing Acetic Acid Tolerance

Whole-genome (WG) transformation (WGT) with DNA from the same or another species has been used to obtain strains with superior traits. Very few examples have been reported in eukaryotes—most apparently involving integration of large fragments of foreign DNA into the host genome. We show that WGT of a haploid acetic acid-sensitive Saccharomyces cerevisiae strain with DNA from a tolerant strain, but not from nontolerant strains, generated many tolerant transformants, some of which were stable upon subculturing under nonselective conditions. ABSTRACT Whole-genome (WG) transformation (WGT) with DNA from the same or another species has been used to obtain strains with superior traits. Very few examples have been reported in eukaryotes—most apparently involving integration of large fragments of foreign DNA into the host genome. We show that WGT of a haploid acetic acid-sensitive Saccharomyces cerevisiae strain with DNA from a tolerant strain, but not from nontolerant strains, generated many tolerant transformants, some of which were stable upon subculturing under nonselective conditions. The most tolerant stable transformant contained no foreign DNA but only seven nonsynonymous single nucleotide polymorphisms (SNPs), of which none was present in the donor genome. The SNF4 mutation c. [805G→T], generating Snf4E269*, was the main causative SNP. Allele exchange of SNF4E269* or snf4Δ in industrial strains with unrelated genetic backgrounds enhanced acetic acid tolerance during fermentation under industrially relevant conditions. Our work reveals a surprisingly small number of mutations introduced by WGT, which do not bear any sequence relatedness to the genomic DNA (gDNA) of the donor organism, including the causative mutation. Spontaneous mutagenesis under protection of a transient donor gDNA fragment, maintained as extrachromosomal circular DNA (eccDNA), might provide an explanation. Support for this mechanism was obtained by transformation with genomic DNA of a yeast strain containing NatMX and selection on medium with nourseothricin. Seven transformants were obtained that gradually lost their nourseothricin resistance upon subculturing in nonselective medium. Our work shows that WGT is an efficient strategy for rapidly generating and identifying superior alleles capable of improving selectable traits of interest in industrial yeast strains.
Target-Dependent Coordinated Biogenesis of Secondary MicroRNAs by miR-146a Balances Macrophage Activation Processes

MicroRNAs (miRNAs) repress protein expression by binding to the target mRNAs. Exploring whether the expression of one miRNA can regulate the abundance and activity of other miRNAs, we noted the coordinated biogenesis of miRNAs in activated macrophages. miRNAs with higher numbers of binding sites (the “primary” miRNAs) induce expression of other miRNAs (“secondary” miRNAs) having binding sites on the 3′ untranslated region (UTR) of common target mRNAs. miR-146a-5p, in activated macrophages, acts as a “primary” miRNA that coordinates biogenesis of “secondary” miR-125b, miR-21, or miR-142-3p to target new sets of mRNAs to balance the immune responses. ABSTRACT MicroRNAs (miRNAs) repress protein expression by binding to the target mRNAs. Exploring whether the expression of one miRNA can regulate the abundance and activity of other miRNAs, we noted the coordinated biogenesis of miRNAs in activated macrophages. miRNAs with higher numbers of binding sites (the “primary” miRNAs) induce expression of other miRNAs (“secondary” miRNAs) having binding sites on the 3′ untranslated region (UTR) of common target mRNAs. miR-146a-5p, in activated macrophages, acts as a “primary” miRNA that coordinates biogenesis of “secondary” miR-125b, miR-21, or miR-142-3p to target new sets of mRNAs to balance the immune responses. During coordinated biogenesis, primary miRNA drives the biogenesis of secondary miRNA in a target mRNA- and Dicer1 activity-dependent manner. The coordinated biogenesis of miRNAs was observed across different cell types. The target-dependent coordinated miRNA biogenesis also ensures a cumulative mode of action of primary and secondary miRNAs on the secondary target mRNAs. Interestingly, using the “primary” miR-146a-5p-specific inhibitor, we could inhibit the target-dependent biogenesis of secondary miRNAs that can stop the miRNA-mediated buffering of cytokine expression and inflammatory response occurring in activated macrophages. Computational analysis suggests the prevalence of coordinated biogenesis of miRNAs also in other contexts in human and in mouse.
Cefiderocol- Compared to Colistin-Based Regimens for the Treatment of Severe Infections Caused by Carbapenem-Resistant Acinetobacter baumannii

Cefiderocol may represent a therapeutic option for carbapenem-resistant Acinetobacter baumannii (CRAB) infections, but clinical data are limited. This is an observational retrospective study conducted in the University Hospital of Pisa including consecutive patients with CRAB infections (January 2020 to August 2021). ABSTRACT Cefiderocol may represent a therapeutic option for carbapenem-resistant Acinetobacter baumannii (CRAB) infections, but clinical data are limited. This is an observational retrospective study conducted in the University Hospital of Pisa including consecutive patients with CRAB infections (January 2020 to August 2021). Patients were divided in two study groups according to the antibiotic treatment received: cefiderocol- and colistin-containing regimens. The primary outcome was the 30-day mortality. A Cox regression analysis was performed to identify factors independently associated with 30-day mortality. A propensity score analysis using inverse probability of treatment weighting (IPTW) was also performed. A total of 124 patients were included: 47 (37.9%) received cefiderocol, while 77 (62.1%) colistin-containing regimens. Overall, 79 (63.7%) patients had a bloodstream infection (BSI), 35 (28.5%) a ventilator-associated pneumonia (VAP) and 10 (8.1%) other infections. Thirty-day mortality was higher in patients receiving colistin- compared to those who received cefiderocol-containing regimens (55.8% versus 34%, P = 0.018). This difference was confirmed in patients with BSI, but not in those with VAP. On multivariable analysis, septic shock, SOFA score, and age were independently associated with 30-day mortality, while cefiderocol therapy was protective in an IPTW analysis (Hazard ratio 0.44, 95% confidence interval 0.22–0.66, P < 0.001). Nephrotoxicity was more common in the colistin group. Microbiological failure occurred in 17.4% of patients receiving cefiderocol versus 6.8% of those receiving colistin (P = 0.079). Among 8 cases in the cefiderocol group who experienced microbiological failure, 4 (50%) developed resistance to cefiderocol. Cefiderocol represents a promising therapeutic option in patients with severe CRAB infections. Randomized clinical trial in this specific patient population should confirm our findings.
Comparative structural analysis of the human and Schistosoma glutathione transferase dimer interface using selective binding of bromosulfophthalein

The binding channel of Schistosoma glutathione transferase (SGST) has been identified to possess a non‐substrate site implicated in enzyme inhibition. This binding channel is formed by the interface of the GST dimer. We produced a comparative characterization of the SGST dimer interface with respect to that of human GST (hGST) analogues using the selective binding of bromosulfophthalein (BSP). First, two SGST and three hGST structures were used as search queries to assemble a data set of 48 empirical GST structures. Sequence alignment to generate a universal residue indexing scheme was then performed, followed by local superposition of the dimer interface. Principal component analysis revealed appreciable variation of the dimer interface, suggesting the potential for selective inhibition of SGST. BSP was found to dock invariably in the dimer interface core pocket, placing it in proximity to the GST catalytic domains, through which it may exert its inhibitory behavior. Binding poses across the GST forms were distinguished with ligand interaction profiling, where SGST complexes showed stabilization of ligand aromatic‐ and sulfonate moieties, which altogether anchor the ligand and produce a tight association. In comparison, missing aromatic stabilization in the hGST complexes impart large bonding distances, causing mobile poses likely to dissociate. Altogether, this study illustrates the potential for selective inhibition of SGST, rationalizes the selective behavior of the BSP inhibitor, and produces a reliable metric for construction and validation of pharmacophore models of the SGST binding channel.
Preclinical Immunogenicity and Efficacy of Optimized O25b O-Antigen Glycoconjugates To Prevent MDR ST131 E. coli Infections

Multivalent O-antigen polysaccharide glycoconjugate vaccines are under development to prevent invasive infections caused by pathogenic Enterobacteriaceae. Sequence type 131 (ST131) Escherichia coli of serotype O25b has emerged as the predominant lineage causing invasive multidrug-resistant extraintestinal pathogenic E. coli (ExPEC) infections. We observed the prevalence of E. coli O25b ST131 among a contemporary collection of isolates from U.S. bloodstream infections from 2013 to 2016 (n = 444) and global urinary tract infections from 2014 to 2017 (n = 102) to be 25% and 24%, respectively. ABSTRACT Multivalent O-antigen polysaccharide glycoconjugate vaccines are under development to prevent invasive infections caused by pathogenic Enterobacteriaceae. Sequence type 131 (ST131) Escherichia coli of serotype O25b has emerged as the predominant lineage causing invasive multidrug-resistant extraintestinal pathogenic E. coli (ExPEC) infections. We observed the prevalence of E. coli O25b ST131 among a contemporary collection of isolates from U.S. bloodstream infections from 2013 to 2016 (n = 444) and global urinary tract infections from 2014 to 2017 (n = 102) to be 25% and 24%, respectively. To maximize immunogenicity of the serotype O25b O antigen, we investigated glycoconjugate properties, including CRM197 carrier protein cross-linking (single-end versus cross-linked “lattice”) and conjugation chemistry (reductive amination chemistry in dimethyl sulfoxide [RAC/DMSO] versus ((2-((2-oxoethyl)thio)ethyl)carbamate [eTEC] linker). Using opsonophagocytic assays (OPAs) to measure serum functional antibody responses to vaccination, we observed that higher-molecular-mass O25b long-chain lattice conjugates showed improved immunogenicity in mice compared with long- or short-chain O antigens conjugated via single-end attachment. The lattice conjugates protected mice from lethal challenge with acapsular O25b ST131 strains as well as against hypervirulent O25b isolates expressing K5 or K100 capsular polysaccharides. A single 1-μg dose of long-chain O25b lattice conjugate constructed with both chemistries also elicited robust serum IgG and OPA responses in cynomolgus macaques. Our findings show that key properties of the O-antigen carrier protein conjugate such as saccharide epitope density and degree of intermolecular cross-linking can significantly enhance functional immunogenicity.
Parsing Immune Correlates of Protection Against SARS-CoV-2 from Biomedical Literature

After the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, identification of immune correlates of protection (CoPs) have become increasingly important to understand the immune response to SARS-CoV-2. The vast amount of preprint and published literature related to COVID-19 makes it challenging for researchers to stay up to date on research results regarding CoPs against SARS-CoV-2. To address this problem, we developed a machine learning classifier to identify papers relevant to CoPs and a customized named entity recognition (NER) model to extract terms of interest, including CoPs, vaccines, assays, and animal models. A user-friendly visualization tool was populated with the extracted and normalized NER results and associated publication information including links to full-text articles and clinical trial information where available. The goal of this pilot project is to provide a basis for developing real-time informatics platforms that can inform researchers with scientific insights from emerging research.
Dexmedetomidine attenuates hypoxia‐induced cardiomyocyte injury by promoting telomere/telomerase activity: Possible involvement of ERK1/2‐Nrf2 signaling pathway

Dexmedetomidine (Dex), an α2‐adrenergic receptor (α2‐AR) agonist, possesses cardioprotection against ischemic/hypoxic injury, but the exact mechanism is not fully elucidated. Since telomere/telomerase dysfunction is involved in myocardial ischemic damage, the present study aimed to investigate whether Dex ameliorates cobalt chloride (CoCl2; a hypoxia mimic agent in vitro)‐induced the damage of H9c2 cardiomyocytes by improving telomere/telomerase dysfunction and further explored the underlying mechanism focusing on extracellular signal‐regulated kinase (ERK1/2)‐NF‐E2‐related factor 2 (Nrf2) signaling pathway. The result showed that Dex increased cell viability, decreased apoptosis, and reduced cardiomyocyte hypertrophy as illustrated by the decreases in cell surface area and the biomarker levels for cardiac hypertrophy including atrial natriuretic peptide, brain natriuretic peptide, and myosin heavy chain β messenger RNA (mRNA) and protein in CoCl2‐exposed H9c2 cells. Intriguingly, Dex increased the telomere length and telomerase activity as well as telomere reverse transcriptase protein and mRNA levels in H9c2 cells exposed to CoCl2, indicating that Dex promotes telomere/telomerase function under hypoxia. In addition, Dex remarkably diminished the reactive oxygen species generation, reduced malondialdehyde content, and increased antioxidative signaling as evidenced by the increases in superoxide dismutase and plasma glutathione peroxidase activities. Furthermore, Dex increased the ratio of P‐ERK1/2/T‐ERK1/2 and P‐Nrf2/T‐Nrf2 and enhanced Nrf2 nuclear translocation in CoCl2‐subjected H9c2 cells, suggesting that Dex promotes the activation of the ERK1/2‐Nrf2 signaling pathway. These novel findings indicated that Dex attenuates myocardial ischemic damage and reduces myocardial hypertrophy by promoting telomere/telomerase function, which may be associated with the activation of the ERK1/2‐Nrf2 signaling pathway in vitro.
Contrast-enhanced double inversion recovery sequence for patients with multiple sclerosis: feasibility of subtraction images between pre- and post-contrast images

Background Few reports have examined the feasibility of a post-contrast double inversion recovery (DIR) magnetic resonance (MR) sequence in patients with multiple sclerosis (MS) because of partial or complete signal loss of enhancing MS lesions. Purpose To compare subtracted images of DIR (pre-contrast – post-contrast DIR images) with contrast enhanced T1-weighted (CE-T1W) images in the depiction of contrast enhancement of MS lesions. Material and Methods In total, 27 patients were included. Two neuroradiologists interpreted both images of CE-T1W imaging and subtracted DIR, and interpretation of the images was classified into a score of 1–5 (from 5, definitely superior contrast of lesions on DIR subtraction compared to conventional CE-T1W imaging, to 1, definitely superior contrast of lesions on CE-T1W imaging. The interrater agreement (κ coefficient) was measured. The signal-to-noise ratio (SNR) and contrast-noise-ratio (CNR) of the lesion were compared. Results A significant difference (P < 0.001) in scoring was seen between conventional CE-T1W imaging (2.1 ± 1.5 with one reviewer and 2.4 ± 1.5 with the other) and DIR subtraction (4.4 ± 1.0 with one reviewer and 4.7 ± 0.8 with the other). SNR from conventional CE-T1W imaging (24.8 ± 14.7) was significantly superior to that from DIR subtraction (4.0 ± 1.0; P < 0.001). CNR in DIR subtraction (326.4 ± 250.0) was significantly superior to that in conventional CE-T1W imaging (0.8 ± 5.5; P < 0.001). For interrater agreement in the evaluation of contrast enhancement of the lesions, κ coefficients were 0.84 for conventional CE-T1W imaging and 0.72 for DIR subtraction. Conclusion Subtracted DIR image enables more obvious contrast enhancement of the MS lesions compared with conventional CE-T1W imaging.
Do entrustment scales make a difference in the inter-rater reliability of the workplace-based assessment?

ABSTRACT Background A workplace-based assessment (WBA) is used to assess learners’ competencies in their workplaces. Many workplace assessment tools are available and validated to assess various constructs. The implementation of workplace-based assessment requires proper training of the staff. Objective This study aimed to explore the impact of staff training on WBA practices and evaluate the inter-rater reliability of these practices while using entrustment scales, performance descriptors, and personal judgment. Design A quasi-experimental study, in which the staff members of the orthopedic department were invited to participate in a training program on the use of entrustment scales and assessment descriptors within the WBA tools. As a response to the training, subjective judgment was replaced by entrustment scales and performance descriptors in a trauma course offered by the orthopedic department. The inter-rater reliability of the WBA was evaluated using various rating scales. Results The entrustment scales had higher inter-rater reliability of the assessment tools than performance descriptors and the personal judgment. Conclusion The inter-rater reliability was highest when using entrustment scales for WBAs, which could indicate that the entrustment scales achieve good psychometric properties as regards consistency among different raters. Thus, they decrease the confounding effect of differences in assessors. They may also give a clearer image of the actual academic level of the learners.