Probiotic Lactobacillus and Bifidobacterium Strains Counteract Adherent-Invasive Escherichia coli (AIEC) Virulence and Hamper IL-23/Th17 Axis in Ulcerative Colitis, but Not in Crohn's Disease

Hypersecretion of proinflammatory cytokines and dysregulated activation of the IL-23/Th17 axis in response to intestinal microbiota dysbiosis are key factors in the pathogenesis of inflammatory bowel diseases (IBD). In this work, we studied how Lactobacillus and Bifidobacterium strains affect AIEC-LF82 virulence mechanisms and the consequent inflammatory response linked to the CCR6-CCL20 and IL-23/Th17 axes in Crohn's disease (CD) and ulcerative colitis (UC) patients. All Lactobacillus and Bifidobacterium strains significantly reduced the LF82 adhesion and persistence within HT29 intestinal epithelial cells, inhibiting IL-8 secretion while not affecting the CCR6-CCL20 axis. Moreover, they significantly reduced LF82 survival within macrophages and dendritic cells, reducing the secretion of polarizing cytokines related to the IL-23/Th17 axis, both in healthy donors (HD) and UC patients. In CD patients, however, only B. breve Bbr8 strain was able to slightly reduce the LF82 persistence within dendritic cells, thus hampering the IL-23/Th17 axis. In addition, probiotic strains were able to modulate the AIEC-induced inflammation in HD, reducing TNF-\u3b1 and increasing IL-10 secretion by macrophages, but failed to do so in IBD patients. Interestingly, the probiotic strains studied in this work were all able to interfere with the IL-23/Th17 axis in UC patients, but not in CD patients. The different interaction mechanisms of probiotic strains with innate immune cells from UC and CD patients compared to HD suggest that testing on CD-derived immune cells may be pivotal for the identification of novel probiotic strains that could be effective also for CD patients

Make some noise: reliable and efficient single-step adversarial training

Recently, Wong et al. (2020) showed that adversarial training with single-step FGSM leads to a characteristic failure mode named catastrophic overfitting (CO), in which a model becomes suddenly vulnerable to multi-step attacks. Experimentally they showed that simply adding a random perturbation prior to FGSM (RS-FGSM) could prevent CO. However, Andriushchenko & Flammarion (2020) observed that RS-FGSM still leads to CO for larger perturbations, and proposed a computationally expensive regularizer (GradAlign) to avoid it. In this work, we methodically revisit the role of noise and clipping in single-step adversarial training. Contrary to previous intuitions, we find that using a stronger noise around the clean sample combined with \textit{not clipping} is highly effective in avoiding CO for large perturbation radii. We then propose Noise-FGSM (N-FGSM) that, while providing the benefits of single-step adversarial training, does not suffer from CO. Empirical analyses on a large suite of experiments show that N-FGSM is able to match or surpass the performance of previous state of-the-art GradAlign while achieving 3× speed-up

Effect of compost addition on arsenic uptake, morphological and physiological attributes of maize plants grown in contrasting soils

Contamination of soils with arsenic (As) represents a global environmental and health issue considering the entrance of toxic As in the human food chain. Although partially understood, addition of compost for the remediation of As-contaminated soils may result in distinct effects on plant growth and physiological attributes depending on compost-mediated potential mobility/sequestration of As in soils. This study explores the role of compost addition (C; 0, 1 and 2.5%) on morphological and gas exchange attributes and photosynthetic pigments (chlorophyll contents) of maize plants under As stress (0, 40, 80, 120 mg kg− 1), as well as soil As immobilization/mobilization in a pot experiment, using two contrasting soils. Results revealed that, in Narwala (sandy loam) soil, the addition of compost decreased shoot As concentration of maize plants (p < 0.05; 4.01–13.7 mg kg− 1 dry weight (DW)), notably at C2.5 treatment, with significant improvement in shoot dry biomass, gas exchange attributes and chlorophyll (a and b) contents, i.e., 1.33–1.82, 1.20–2.65 and 1.34–1.66 times higher, respectively, over C0 at all As levels. Contrastingly, in Shahkot (clay loam) soil, C2.5 treatment increased shoot As concentration (p < 0.05; 7.02–17.3 mg kg− 1 DW), and as such reduced the shoot dry biomass, gas exchange attributes and chlorophyll contents, compared to the control – rather C1 treatment was more effective and exhibited positive effect than C2.5. Considerably, at C2.5 treatment, phosphate extractable (bioavailable) soil As concentration was also found to be greater in the (post-experiment) Shahkot soil than that of Narwala soil (0.40–3.82 vs. 0.19–1.51 mg kg− 1, respectively). This study advanced our understanding to resolve the complex compost-As interactions in As-contaminated soils, which are imperative to understand for developing the effective and soil-specific remediation strategies

Tay-Sachs Disease: Two Novel Rare HEXA Mutations from Pakistan and Morocco

Background: Tay-Sachs disease (TSD) is a rare autosomalrecessive genetic disorder characterized by progressive destruction of nerve cells in the brain and spinal cord. It is caused by genetic variations in the HEXA gene leading to a deficiency of β hexosaminidase A (HEXA) isoenzyme activity. This study aimed to identify causative gene variants in 3 unrelated consanguineous families presented with TSD from Pakistan and Morocco. / Methods: Detailed clinical investigations were carried out on probands in 3 unrelated consanguineous families of Pakistani and Moroccan origin. Targeted gene sequencing and Whole Exome Sequencing (WES) were performed for variant identification. Candidate variants were checked for co-segregation with the phenotype using Sanger sequencing. Public databases including ExAC, GnomAD, dbSNP and the 1,000 Genome Project were searched to determine frequencies of the alleles. Conservation of the missense variants was ensured by aligning orthologous protein sequences from diverse vertebrate species. / Results: We report on 3 children presented with Tay-Sachs Disease. The β hexosaminidaseA enzyme activity was reduced in the Pakistani patient in one of the pedigrees. Genetic testing revealed 2 novel homozygous variants (p.Asp386Alafs*13 and p.Trp266Gly) in the gene HEXA in Pakistani and Moroccan patients respectively.The third family of Pakistani origin revealed a previously reported variant (p.Tyr427Ilefs*5) in HEXA. p.Tyr427Ilefs*5 is the most commonly occurring pathogenic variationin Ashkenazi but was not reported in Pakistani population. / Conclusion: Our study further expands the ethnic and mutational spectrum of Tay-Sachs disease emphasizing the usefulness of WES as a powerful diagnostic tool where enzymatic activity is not performed for Tay-Sachs disease. The study recommends targeted screening for these mutations (p.Tyr427Ilefs5) for cost effective testing of TSD patients. Further, the study would assist in carrier testing and prenatal diagnosis of the affected families

A Search Strategy for Detecting Duodenoscope-Associated Infections:A Retrospective Observational Study

Background: Duodenoscope-associated infections (DAIs) are exogenous infections resulting from the use of contaminated duodenoscopes. Though numerous outbreaks of DAI have involved multidrug-resistant micro-organisms (MDROs), outbreaks involving non-MDROs are also likely to occur. Detection challenges arise as these infections often resolve before culture or because causative strains are not retained for comparison with duodenoscope strains. Aim: To identify and analyse DAIs spanning a seven-year period in a tertiary care medical centre. Methods: This was a retrospective observational study. Duodenoscope cultures positive for gastrointestinal flora between March 2015 and September 2022 were paired with duodenoscope usage data to identify patients exposed to contaminated duodenoscopes. Analysis encompassed patients treated after a positive duodenoscope culture and those treated within the interval from a negative to a positive culture. Patient identification numbers were cross-referenced with a clinical culture database to identify patients developing infections with matching micro-organisms within one year of their procedure. A ‘pair’ was established upon a species-level match between duodenoscope and patient cultures. Pairs were further analysed via antibiogram comparison, and by whole-genome sequencing (WGS) to determine genetic relatedness. Findings: Sixty-eight pairs were identified; of these, 21 exhibited matching antibiograms which underwent WGS, uncovering two genetically closely related pairs categorized as DAIs. Infection onset occurred up to two months post procedure. Both causative agents were non-MDROs. Conclusion: This study provides crucial insights into DAIs caused by non-MDROs and it highlights the challenge of DAI recognition in daily practice. Importantly, the delayed manifestation of the described DAIs suggests a current underestimation of DAI risk.</p

Impact of the antiproliferative agent ciclopirox olamine treatment on stem cell proteome

AIM: To investigate the proteome changes of stem cells due to ciclopirox olamine (CPX) treatment compared to control and retinoic acid treated cells. METHODS: Stem cells (SCs) are cells, which have the ability to continuously divide and differentiate into various other kinds of cells. Murine embryonic stem cells (ESCs) and multipotent adult germline stem cells (maGSCs) were treated with CPX, which has been shown to have an antiproliferative effect on stem cells, and compared to stem cells treated with retinoic acid (RA), which is known to have a differentiating effect on stem cells. Classical proteomic techniques like 2-D gel electrophoresis and differential in-gel electrophoresis (DIGE) were used to generate 2D protein maps from stem cells treated with RA or CPX as well as from non-treated stem cells. The resulting 2D gels were scanned and the digitalized images were collated with the help of Delta 2D software. The differentially expressed proteins were analyzed by a MALDI-TOF-TOF mass spectrometer, and the identified proteins were investigated and categorized using bioinformatics. RESULTS: Treatment of stem cells with CPX, a synthetic antifungal clinically used to treat superficial mycoses, resulted in an antiproliferative effect in vitro, without impairment of pluripotency. To understand the mechanisms induced by CPX treatments which results in arrest of cell cycle without any marked effect on pluripotency, a comparative proteomics study was conducted. The obtained data revealed that the CPX impact on cell proliferation was accompanied with a significant alteration in stem cell proteome. By peptide mass fingerprinting and tandem mass spectrometry combined with searches of protein sequence databases, a set of 316 proteins was identified, corresponding to a library of 125 non-redundant proteins. With proteomic analysis of ESCs and maGSCs treated with CPX and RA, we could identify more than 90 single proteins, which were differently expressed in both cell lines. We could highlight, that CPX treatment of stem cells, with subsequent proliferation inhibition, resulted in an alteration of the expression of 56 proteins compared to non-treated cells, and 54 proteins compared to RA treated cells. Bioinformatics analysis of the regulated proteins demonstrated their involvement in various biological processes. To our interest, a number of proteins have potential roles in the regulation of cell proliferation either directly or indirectly. Furthermore the classification of the altered polypeptides according to their main known/postulated functions revealed that the majority of these proteins are involved in molecular functions like nucleotide binding and metal ion binding, and biological processes like nucleotide biosynthetic processes, gene expression, embryonic development, regulation of transcription, cell cycle processes, RNA and mRNA processing. Proteins, which are involved in nucleotide biosynthetic process and proteolysis, were downregulated in CPX treated cells compared to control, as well as in RA treated cells, which may explain the cell cycle arrest. Moreover, proteins which were involved in cell death, positive regulation of biosynthetic process, response to organic substance, glycolysis, anti-apoptosis, and phosphorylation were downregulated in RA treated cells compared to control and CPX treated cells. CONCLUSION: The CPX treatment of SCs results in downregulation of nucleotide binding proteins and leads to cell cycle stop without impairment of pluripotency

Countering Calcium Blooming With Personalized Contrast Media Injection Protocols: The 1-2-3 Rule for Photon-Counting Detector CCTA

OBJECTIVE Photon-counting detector computed tomography (PCD-CT) enables spectral data acquisition of CT angiographies allowing for reconstruction of virtual monoenergetic images (VMIs) in routine practice. Specifically, it has potential to reduce the blooming artifacts associated with densely calcified plaques. However, calcium blooming and iodine attenuation are inversely affected by energy level (keV) of the VMIs, creating a challenge for contrast media (CM) injection protocol optimization. A pragmatic and simple rule for calcium-dependent CM injection protocols is investigated and proposed for VMI-based coronary CT angiography with PCD-CT. MATERIALS AND METHODS A physiological circulation phantom with coronary vessels including calcified lesions (maximum CT value >700 HU) with a 50% diameter stenosis was injected into at iodine delivery rates (IDRs) of 0.3, 0.5, 0.7, 1.0, 1.5, 2.0, 2.5, and 3.0 g I/s. Images were acquired using a first-generation dual-source PCD-CT and reconstructed at various VMI levels (between 45 and 190 keV). Iodine attenuation in the coronaries was measured at each IDR for each keV, and blooming artifacts from the calcified lesions were assessed including stenosis grading error (as % overestimation vs true lumen). The IDR to achieve 300 HU at each VMI level was then calculated and compared with stenosis grading accuracy to establish a general rule for CM injection protocols. RESULTS Plaque blooming artifacts and intraluminal iodine attenuation decreased with increasing keV. Fixed windowing (representing absolute worst case) resulted in stenosis overestimation from 77% ± 4% at 45 keV to 5% ± 2% at 190 keV, whereas optimized windowing resulted in overestimation from 29% ± 3% at 45 keV to 4% ± 1% at 190 keV. The required IDR to achieve 300 HU showed a strong linear correlation to VMI energy (R2 = 0.98). Comparison of this linear plot versus stenosis grading error and blooming artifact demonstrated that multipliers of 1, 2, and 3 times the reference IDR for theoretical clinical regimes of no, moderate, and severe calcification density, respectively, can be proposed as a general rule. CONCLUSIONS This study provides a proof-of-concept in an anthropomorphic phantom for a simple pragmatic adaptation of CM injection protocols in coronary CT angiography with PCD-CT. The 1-2-3 rule demonstrates the potential for reducing the effects of calcium blooming artifacts on overall image quality

Homozygosity mapping reveals novel and known mutations in Pakistani families with inherited retinal dystrophies.

Inherited retinal dystrophies are phenotypically and genetically heterogeneous. This extensive heterogeneity poses a challenge when performing molecular diagnosis of patients, especially in developing countries. In this study, we applied homozygosity mapping as a tool to reduce the complexity given by genetic heterogeneity and identify disease-causing variants in consanguineous Pakistani pedigrees. DNA samples from eight families with autosomal recessive retinal dystrophies were subjected to genome wide homozygosity mapping (seven by SNP arrays and one by STR markers) and genes comprised within the detected homozygous regions were analyzed by Sanger sequencing. All families displayed consistent autozygous genomic regions. Sequence analysis of candidate genes identified four previously-reported mutations in CNGB3, CNGA3, RHO, and PDE6A, as well as three novel mutations: c.2656C &gt; T (p.L886F) in RPGRIP1, c.991G &gt; C (p.G331R) in CNGA3, and c.413-1G &gt; A (IVS6-1G &gt; A) in CNGB1. This latter mutation impacted pre-mRNA splicing of CNGB1 by creating a -1 frameshift leading to a premature termination codon. In addition to better delineating the genetic landscape of inherited retinal dystrophies in Pakistan, our data confirm that combining homozygosity mapping and candidate gene sequencing is a powerful approach for mutation identification in populations where consanguineous unions are common

Securing recruitment and obtaining informed consent in minority ethnic groups in the UK

Background: Previous health research has often explicitly excluded individuals from minority ethnic backgrounds due to perceived cultural and communication difficulties, including studies where there might be language/literacy problems in obtaining informed consent. This study addressed these difficulties by developing audio-recorded methods of obtaining informed consent and recording data. This report outlines 1) our experiences with securing recruitment to a qualitative study investigating alternative methods of data collection, and 2) the development of a standardised process for obtaining informed consent from individuals from minority ethnic backgrounds whose main language does not have an agreed written form. Methods: Two researchers from South Asian backgrounds recruited adults with Type 2 diabetes whose main language was spoken and not written, to attend a series of focus groups. A screening tool was used at recruitment in order to assess literacy skills in potential participants. Informed consent was obtained using audio-recordings of the patient information and recording patients' verbal consent. Participants' perceptions of this method of obtaining consent were recorded. Results: Recruitment rates were improved by using telephone compared to face-to-face methods. The screening tool was found to be acceptable by all potential participants. Audio-recorded methods of obtaining informed consent were easy to implement and accepted by all participants. Attrition rates differed according to ethnic group. Snowballing techniques only partly improved participation rates. Conclusion: Audio-recorded methods of obtaining informed consent are an acceptable alternative to written consent in study populations where literacy skills are variable. Further exploration of issues relating to attrition is required, and a range of methods may be necessary in order to maximise response and participation