Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Modification of TonB and Emergence of Small-Colony Phenotype in VIM- and NDM-Producing Escherichia coli following Cefiderocol Exposure In Vitro

Knowledge on resistance mechanisms toward cefiderocol, a novel siderophore-conjugated cephalosporin antibiotic, is still limited. Although the presence of New-Delhi metallo-β-lactamase has been demonstrated to facilitate the resistance development toward cefiderocol via siderophore receptor mutations in Enterobacter cloacae and Klebsiella pneumoniae, the impact of metallo-β-lactamases on facilitating such mutations in Escherichia coli is not yet elucidated. Our study aimed to study the effect of the presence of various β-lactamases, such as NDM-5, VIM-1, KPC-2, and OXA-48, on the development of cefiderocol resistance in E. coli. To this end, we performed liquid mating to transfer these β-lactamases onto a defined K-12 E. coli background (J53) and exposed these transconjugants to increasing cefiderocol concentrations in a serial passage experiment. Cefiderocol-resistant isolates were genotyped by whole-genome sequencing to investigate the underlying resistance mechanism. ABSTRACT Knowledge on resistance mechanisms toward cefiderocol, a novel siderophore-conjugated cephalosporin antibiotic, is still limited. Although the presence of New-Delhi metallo-β-lactamase has been demonstrated to facilitate the resistance development toward cefiderocol via siderophore receptor mutations in Enterobacter cloacae and Klebsiella pneumoniae, the impact of metallo-β-lactamases on facilitating such mutations in Escherichia coli is not yet elucidated. Our study aimed to study the effect of the presence of various β-lactamases, such as NDM-5, VIM-1, KPC-2, and OXA-48, on the development of cefiderocol resistance in E. coli. To this end, we performed liquid mating to transfer these β-lactamases onto a defined K-12 E. coli background (J53) and exposed these transconjugants to increasing cefiderocol concentrations in a serial passage experiment. Cefiderocol-resistant isolates were genotyped by whole-genome sequencing to investigate the underlying resistance mechanism. Cefiderocol-resistant isolates emerged only in isolates producing VIM-1 and NDM-5 metallo-β-lactamase, but not in those producing the serine β-lactamases KPC-2 and OXA-48. We observed two distinct morphological changes of the J53 E. coli strain exhibiting reduced colony size after insertions of transposable elements in the tonB gene leading to alterations in the TonB binding site and morphological changes consistent with the small-colony variant (SCV) phenotype due to mutations in the hemB and hemH genes. Passaging experiments suggested that these phenotypes were highly plastic. The SCV phenotype is attributed to immune evasion and decreased susceptibility toward antibiotics. The emergence of SCV following cefiderocol exposure may have clinical implications for bacterial clearance and warrants further investigation.
Correlation between the IgG/IgA Antibody Response against PEDV Structural Protein and Virus Neutralization

The humoral immune response plays an important role in virus neutralization. Against PEDV, both IgG and the mucosal immune component IgA play roles in virus neutralization. ABSTRACT Porcine epidemic diarrhea (PED) is a highly contagious intestinal infectious disease caused by porcine epidemic diarrhea virus (PEDV). Large-scale outbreaks of PEDV have caused huge economic losses to the pig industry since 2010. Neutralizing antibodies play a pivotal role in protecting piglets from enteric infections. However, there has been no systematic report on the correlations between neutralizing antibody titers (NTs) and absorbance values of IgG or IgA to all PEDV individual structural proteins in clinical serum, fecal, and colostrum samples. In this study, the spike protein S1 domain (S1), membrane protein (M), envelope protein (E), and nucleocapsid protein (N) of the variant PEDV strain AH2012/12 were expressed and purified by using the human embryonic kidney (HEK) 293F expression system. A total of 92 clinical serum samples, 46 fecal samples, and 33 colostrum samples were collected, and the correlations between IgG or IgA absorbance values and NTs were analyzed. R2 values revealed that anti-S1 IgA absorbance values show the highest agreement with NTs in all serum, fecal, and colostrum samples, followed by the N protein. The correlations between anti-E or M IgA and NTs were very low. However, in the colostrum samples, both IgG and IgA to S1 showed high correlations with NTs. In addition, compared with E and M, the highest correlations of IgA absorbance values were with N and S1 in serum and fecal samples. Overall, this study revealed the highest correlation between NTs and IgA to PEDV S1 protein. Therefore, the diagnostic method with anti-S1 IgA can be used as a powerful tool for assessing the immune status of pigs. IMPORTANCE The humoral immune response plays an important role in virus neutralization. Against PEDV, both IgG and the mucosal immune component IgA play roles in virus neutralization. However, which plays a more prominent role and whether there are differences in different tissue samples are not clearly reported. Additionally, the relationship between IgG and IgA against individual structural proteins and viral neutralization remains unclear. In this study, we systematically determined the relationship between IgG and IgA against all PEDV structural proteins and viral neutralization in different clinical samples and found the highest correlation between neutralization activity and IgA to PEDV S1 protein. Our data have important guiding implications in the evaluation of immune protection.
Intracellular metabolomics and microRNAomics unveil new insight into the regulatory network for potential biocontrol mechanism of stress‐tolerant Tricho‐fusants interacting with phytopathogen Sclerotium rolfsii Sacc

The present study employed microRNA (miRNA) sequencing and metabolome profiling of Trichoderma parental strains and fusants during normal growth and interaction with the phytopathogen Sclerotium rolfsii Sacc. In‐vitro antagonism indicated that abiotic stress‐tolerant Tricho‐fusant FU21 was examined as a potent biocontroller with mycoparasitic action after 10 days. During interaction with the test pathogen, the most abundant uprising intracellular metabolite was recognized as l‐proline, which corresponds to held‐down l‐alanine, associated with arginine and proline metabolism, biosynthesis of secondary metabolites, and nitrogen metabolism linked to predicted genes controlled by miRNAs viz., cel‐miR‐8210‐3p, hsa‐miR‐3613‐5p, and mml‐miR‐7174‐3p. The miRNAs‐ mml‐miR‐320c and mmu‐miR‐6980‐5p were found to be associated with phenylpropanoid biosynthesis, transcription factors, and signal transduction pathways, respectively, and were ascertained downregulated in potent FU21_IB compared with FU21_CB. The amino benzoate degradation and T cell receptor signaling pathways were regulated by miRNAs cel‐miR‐8210 and tca‐miR‐3824 as stress tolerance mechanisms of FU21. The intracellular metabolites l‐proline, maleic acid, d‐fructose, Myo‐inositol, arabinitol, d‐xylose, mannitol, and butane were significantly elevated as potential biocontrol and stress‐tolerant constituents associated with miRNA regulatory pathways in potent FU21_IB. A network analysis between regulatory miRNA‐predicted genes and intracellular metabolomics acknowledged possible biocontrol pathways/mechanisms in potent FU21_IB to restrain phytopathogen.
CTC1 OB-B interaction with TPP1 terminates telomerase and prevents telomere overextension

Abstract CST (CTC1-STN1-TEN1) is a telomere associated complex that binds ssDNA and is required for multiple steps in telomere replication, including termination of G-strand extension by telomerase and synthesis of the complementary C-strand. CST contains seven OB-folds which appear to mediate CST function by modulating CST binding to ssDNA and the ability of CST to recruit or engage partner proteins. However, the mechanism whereby CST achieves its various functions remains unclear. To address the mechanism, we generated a series of CTC1 mutants and studied their effect on CST binding to ssDNA and their ability to rescue CST function in CTC1−/− cells. We identified the OB-B domain as a key determinant of telomerase termination but not C-strand synthesis. CTC1-ΔB expression rescued C-strand fill-in, prevented telomeric DNA damage signaling and growth arrest. However, it caused progressive telomere elongation and the accumulation of telomerase at telomeres, indicating an inability to limit telomerase action. The CTC1-ΔB mutation greatly reduced CST-TPP1 interaction but only modestly affected ssDNA binding. OB-B point mutations also weakened TPP1 association, with the deficiency in TPP1 interaction tracking with an inability to limit telomerase action. Overall, our results indicate that CTC1-TPP1 interaction plays a key role in telomerase termination.
Acquisition time reduction in pediatric 99mTc‐DMSA planar imaging using deep learning

Abstract Purpose Given the potential risk of motion artifacts, acquisition time reduction is desirable in pediatric 99mTc‐dimercaptosuccinic acid (DMSA) scintigraphy. The aim of this study was to evaluate the performance of predicted full‐acquisition‐time images from short‐acquisition‐time pediatric 99mTc‐DMSA planar images with only 1/5th acquisition time using deep learning in terms of image quality and quantitative renal uptake measurement accuracy. Methods One hundred and fifty‐five cases that underwent pediatric 99mTc‐DMSA planar imaging as dynamic data for 10 min were retrospectively collected for the development of three deep learning models (DnCNN, Win5RB, and ResUnet), and the generation of full‐time images from short‐time images. We used the normalized mean squared error (NMSE), peak signal‐to‐noise ratio (PSNR), and structural similarity index metrics (SSIM) to evaluate the accuracy of the predicted full‐time images. In addition, the renal uptake of 99mTc‐DMSA was calculated, and the difference in renal uptake from the reference full‐time images was assessed using scatter plots with Pearson correlation and Bland–Altman plots. Results The predicted full‐time images from the deep learning models showed a significant improvement in image quality compared to the short‐time images with respect to the reference full‐time images. In particular, the predicted full‐time images obtained by ResUnet showed the lowest NMSE (0.4 [0.4−0.5] %) and the highest PSNR (55.4 [54.7−56.1] dB) and SSIM (0.997 [0.995−0.997]). For renal uptake, an extremely high correlation was achieved in all short‐time and three predicted full‐time images (R 2 > 0.999 for all). The Bland–Altman plots showed the lowest bias (−0.10) of renal uptake in ResUnet, while short‐time images showed the lowest variance (95% confidence interval: −0.14, 0.45) of renal uptake. Conclusions Our proposed method is capable of producing images that are comparable to the original full‐acquisition‐time images, allowing for a reduction of acquisition time/injected dose in pediatric 99mTc‐DMSA planar imaging.
A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level

RNA alternative splicing, a post-transcriptional stage in eukaryotes, is crucial in cellular homeostasis and disease processes. Due to the rapid development of the next-generation sequencing (NGS) technology and the flood of NGS data, the detection of differential splicing from RNA-seq data has become mainstream. A range of bioinformatic tools has been developed. However, until now, an independent and comprehensive comparison of available algorithms/tools at the event level is still lacking. Here, 21 different tools are subjected to systematic evaluation, based on simulated RNA-seq data where exact differential splicing events are introduced. We observe immense discrepancies among these tools. SUPPA, DARTS, rMATS and LeafCutter outperforme other event-based tools. We also examine the abilities of the tools to identify novel splicing events, which shows that most event-based tools are unsuitable for discovering novel splice sites. To improve the overall performance, we present two methodological approaches i.e. low-expression transcript filtering and tool-pair combination. Finally, a new protocol of selecting tools to perform differential splicing analysis for different analytical tasks (e.g. precision and recall rate) is proposed. Under this protocol, we analyze the distinct splicing landscape in the DUX4/IGH subgroup of B-cell acute lymphoblastic leukemia and uncover the differential splicing of TCF12. All codes needed to reproduce the results are available at https://github.com/mhjiang97/Benchmarking_DS.
Whole-genome sequencing of Shigella for surveillance purposes shows (inter)national relatedness and multidrug resistance in isolates from men who have sex with men

In the Netherlands, more than half of domestic shigellosis cases are among men who have sex with men (MSM), particularly in the Amsterdam region. However, there is limited insight into which Shigella strains circulate in the Netherlands. Our objective was to assess the added value of whole-genome sequencing (WGS)-based surveillance for Shigella . To this end, we determined the relatedness among Shigella spp. isolates from patients in the Amsterdam region, as well as in an international context, including antimicrobial resistance markers, using WGS. The following criteria were used: it should provide insight into (1) clustering of shigellosis cases and the affected population, (2) the extent of admixture of MSM-associated isolates with those from the broader population and (3) the presence of antimicrobial resistance. It should then lead to more opportunities for targeted control measures. For this study, Shigella isolates from three laboratories in the Amsterdam region obtained between February 2019 and October 2021 were subjected to Illumina WGS at the National Institute for Public Health and the Environment (RIVM). Raw data were quality-checked and assembled, the Shigella serotype was determined with ShigaTyper, and antimicrobial resistance markers were detected using ResFinder and PointFinder. For Shigella sonnei , subclades were determined using Mykrobe. Relatedness of isolates, including 21 international reference genomes, was assessed with core genome multilocus sequence typing. In total, 109 isolates were included, of which 27 were from females (25 %) and 66 were from males (61 %), with which the majority (n=48, 73 %) being from MSM. No information on sex was available for the remaining 16 cases. The WGS data for all isolates, comprising 55 S . sonnei , 52 Shigella flexneri , 1 Shigella boydii and 1 Shigella dysenteriae , met the quality criteria. In total, 14 clusters containing 51 isolates (49 %) were identified, with a median cluster size of 2.5 cases (range: 2–15). Nine out of 14 clusters were MSM-associated, and 8 clusters (57 %) were travel-related. Six of the MSM clusters were related to international reference genomes. The prevalence of antimicrobial resistance markers was higher among isolates from MSM than non-MSM patients, particularly for ciprofloxacin (89 vs 33 %) and azithromycin (58 vs 17 %). In conclusion, about half of Shigella spp. patients were part of a cluster, of which a substantial part were related to international reference genomes, particularly among MSM, and a high prevalence of antimicrobial resistance markers was found. These findings indicate widespread international circulation of Shigella spp. , particularly among MSM, with multidrug resistance that hampers treatment of patients. Moreover, the results of this study led to the implementation of a national WGS-based laboratory surveillance programme for Shigella spp. that started in April 2022.
The effect of weight loss following 18 months of lifestyle intervention on brain age assessed with resting-state functional connectivity

Background: Obesity negatively impacts multiple bodily systems, including the central nervous system. Retrospective studies that estimated chronological age from neuroimaging have found accelerated brain aging in obesity, but it is unclear how this estimation would be affected by weight loss following a lifestyle intervention. Methods: In a sub-study of 102 participants of the Dietary Intervention Randomized Controlled Trial Polyphenols Unprocessed Study (DIRECT-PLUS) trial, we tested the effect of weight loss following 18 months of lifestyle intervention on predicted brain age based on magnetic resonance imaging (MRI)-assessed resting-state functional connectivity (RSFC). We further examined how dynamics in multiple health factors, including anthropometric measurements, blood biomarkers, and fat deposition, can account for changes in brain age. Results: To establish our method, we first demonstrated that our model could successfully predict chronological age from RSFC in three cohorts (n=291;358;102). We then found that among the DIRECT-PLUS participants, 1% of body weight loss resulted in an 8.9 months’ attenuation of brain age. Attenuation of brain age was significantly associated with improved liver biomarkers, decreased liver fat, and visceral and deep subcutaneous adipose tissues after 18 months of intervention. Finally, we showed that lower consumption of processed food, sweets and beverages were associated with attenuated brain age. Conclusions: Successful weight loss following lifestyle intervention might have a beneficial effect on the trajectory of brain aging. Funding: The German Research Foundation (DFG), German Research Foundation - project number 209933838 - SFB 1052; B11, Israel Ministry of Health grant 87472511 (to I Shai); Israel Ministry of Science and Technology grant 3-13604 (to I Shai); and the California Walnuts Commission 09933838 SFB 105 (to I Shai).
Glycation reduces the binding dynamics of aflatoxin B1 to human serum albumin: a comprehensive spectroscopic and computational investigation

Abstract Aflatoxin B1 (AFB1), a potent mutagen, is synthesized by Aspergillus parasiticus and Aspergillus flavus. Human serum albumin (HSA) is a globular protein with diverse roles. As AFB1 is ingested with food and is transported in the body via blood, it becomes pertinent to comprehend the effect of the binding of this toxin on the structure and conformation of HSA, which may help to get insight into the toxic effect of the exposure of the mycotoxin. In this study, multi-spectroscopic approaches have been used to evaluate the binding efficiency of AFB1 with both the native HSA (nHSA) and the glycated HSA (gHSA). Steady-state fluorescence spectroscopy reveals the static type of fluorescence quenching in the fluorescence emission spectra of nHSA and gHSA in the presence of AFB1. The binding constant (Kb) is calculated to be 6.88 × 104 M−1 for nHSA, while a reduced Kb value of 2.95 × 104 M−1 has been obtained for gHSA. The circular dichroism study confirms the change in the secondary structure of nHSA and gHSA in the presence of AFB1, followed by alterations in the melting temperature (Tm) of nHSA and gHSA. In silico computational findings envisaged the amino acid residues and bonds involved in the binding of nHSA and gHSA with AFB1. The comprehensive study analyzes the binding effectiveness of AFB1 with nHSA and gHSA and shows reduced binding of AFB1 to gHSA. Communicated by Ramaswamy H. Sarma HIGHLIGHTS As revealed by UV-absorption spectroscopy, the hyperchromic effect was more prominent in nHSA than gHSA in the presence of AFB1. The binding constant (Kb) obtained for the nHSA-AFB1 complex was 6.88 × 104 M−1, and the gHSA-AFB1 complex yielded Kb value of 2.95 × 104 M−1. Negative enthalpy change (ΔH) and entropy change (ΔS) suggested hydrogen bonding and van der Waals interaction as stabilizing forces of nHSA-AFB1 and gHSA-AFB1 complex. Site markers displacement assay suggested Sudlow’s site I as the binding site for AFB1 in nHSA and gHSA. Circular dichroism study showed that AFB1 induced secondary structural changes in nHSA and gHSA. Melting temperature (Tm) increased in nHSA and decreased in gHSA in the presence of AFB1. Molecular docking results confirmed Lys-195, Arg-222 and Arg-257 as hydrogen bonding residues in the nHSA-AFB1 complex and Arg-222 and Lys-199 residues were involved in hydrogen bonding in the gHSA-AFB1 complex.
Sleep Patterns and the Risk of Acute Stroke

Background and Objectives Symptoms of sleep disturbance are common and may represent important modifiable risk factors of stroke. We evaluated the association between a spectrum of sleep disturbance symptoms and the risk of acute stroke in an international setting. Methods The INTERSTROKE study is an international case-control study of patients presenting with first acute stroke and controls matched by age (±5 years) and sex. Sleep symptoms in the previous month were assessed through a questionnaire. Conditional logistic regression estimated the association between sleep disturbance symptoms and acute stroke, expressed as odds ratios (ORs) and 95% CIs. The primary model adjusted for age, occupation, marital status, and modified Rankin scale at baseline, with subsequent models adjusting for potential mediators (behavioral/disease risk factors). Results Overall, 4,496 matched participants were included, with 1,799 of them having experienced an ischemic stroke and 439 an intracerebral hemorrhage. Short sleep (<5 hours: OR 3.15, 95% CI 2.09–4.76), long sleep (>9 hours: OR 2.67, 95% CI 1.89–3.78), impaired quality (OR 1.52, 95% CI 1.32–1.75), difficulty getting to sleep (OR 1.32, 95% CI 1.13–1.55) or maintaining sleep (OR 1.33, 95% CI 1.15–1.53), unplanned napping (OR 1.48, 95% CI 1.20–1.84), prolonged napping (>1 hour: OR 1.88, 95% CI 1.49–2.38), snoring (OR 1.91, 95% CI 1.62–2.24), snorting (OR 2.64, 95% CI 2.17–3.20), and breathing cessation (OR 2.87, 95% CI 2.28–3.60) were all significantly associated with an increased odds of acute stroke in the primary model. A derived obstructive sleep apnea score of 2–3 (2.67, 2.25–3.15) and cumulative sleep symptoms (>5: 5.38, 4.03–7.18) were also associated with a significantly increased odds of acute stroke, with the latter showing a graded association. After an extensive adjustment, significance was maintained for most of the symptoms (not difficulty getting to/maintaining sleep and unplanned napping), with similar findings for stroke subtypes. Discussion We found that sleep disturbance symptoms were common and associated with a graded increased risk of stroke. These symptoms may be a marker of increased individual risk or represent independent risk factors. Future clinical trials are warranted to determine the efficacy of sleep interventions in stroke prevention.