Correction: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

[This corrects the article DOI: 10.1371/journal.pcbi.1007732.].

MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.

Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don't account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.

TIA Caused by Contrast Echocardiography in Patient with Platypnea-Orthodeoxia.

Platypnea-orthodeoxia syndrome (POS) is a rare clinical disorder characterized by dyspnea caused by the upright position and relieved at recumbent position. Few cases of POS and stroke were reported in literature, and the association between stroke and POS with evidence of patent foramen ovale (PFO) is rare. Stroke may occur in patients with cardiac shunt who undergo contrast echocardiography. We present a patient with POS who experienced transitory ischemic attack (TIA) most likely caused by injection of agitated saline microbubbles during screen for PFO. No case report of TIA/stroke during contrast echocardiography in patients with POS has previously been published.

High hyperopic LASIK with reduction of corneal prolateness to control induced spherical aberration.

PURPOSE: To evaluate visual outcomes of high hyperopic LASIK, using corneal aspherization to control the induced spherical aberration. SETTING: Fondation Ophtalmologique Adolphe de Rothschild. DESIGN: Prospective interventional case series. METHODS: Prospective interventional study of consecutive high hyperopes (≥+3D of Spherical Equivalent SE) undergoing LASIK with the WaveLight FS200 femtosecond and EX500 excimer laser platform. An aspheric ablation profile (planned change in corneal asphericity ΔQ = +0.2) was delivered using the Custom-Q nomogram (Alcon Laboratories, Inc., Fort Worth, TX) on an optical zone of ≥ 6.5mm centered near the corneal vertex. Uncorrected and best-corrected distance visual acuity (UDVA-BDVA), as well as changes in SE, corneal asphericity (ΔQ) and Higher order aberrations (HOAs), were analyzed preoperatively and on day1, 1, 3, 6, and 12 months. RESULTS: 117 eyes of 63 patients, (mean age of 30.1 ± 5.6 years), were included. Preoperatively and at 12 months postoperatively, the mean SE was 5.1 ± 1.1 D and 0.00 ± 0.7 D, respectively. 88% of eyes achieved 0 Log Mar or better UDVA at 12 months. One month after surgery, there was a statistically significant induction of positive spherical aberration decreasing progressively and significantly until the last visit (Preop SA4 = 0.09 ± 0.11 µm, Day 1 SA4 = 0.30 ± 0.32 µm, 12 Months SA4 = 0.08 ± 0.21 µm, p=0.056). Two eyes needed enhancement at 12 months. CONCLUSION: LASIK for high levels of hyperopia showed good outcomes mainly due to aspheric-customized ablation profile with a change of ΔQ = +0.2 in corneal asphericity.

Do GC/MS methods available for furan and alkylfurans in food provide comparable results? - An interlaboratory study and safety assessment of 2-pentylfuran in food.

A call for data on the occurrence of alkylfurans in food and feed from EFSA triggered the development of new methods to cover next to furan also 2- and 3-methylfuran, 2,5-dimethyl- and 2-ethylfuran as well as 2-pentylfuran. A significant variability was noticed when comparing analysis of 2-pentylfuran and furans in the same matrix performed by different laboratories. To assess the variability an interlaboratory study including eight laboratories was organised. The highest variabilities were observed when analysing cereals, with measurements of 2-pentylfuran indicating concentrations from 8 mg/kg up to more than 1000 mg/kg in the same sample. This study illustrates that the analysis of 2-pentylfuran requires special attention, and that additional method development would be necessary to ensure reliable and reproducible determination of 2-pentylfuran at contamination level. Moreover, a recent evaluation of the EFSA Panel on Food Additives and Flavourings indicates that concerns for genotoxicity, reason why it was grouped with the shorter alkylfurans, are now ruled out. We question the need and justification to include 2-pentylfuran in the analytical method as requested by EFSA, from both the analytical and the safety perspective.

Technique of corneal allogenic ring segment preparation using femtosecond laser: preclinical study on human corneal grafts.

PURPOSE: To describe a new technique for preparing corneal allogenic ring segments (CAIRSs) using femtosecond laser technology. SETTING: Hospital Foundation Adolphe de Rothschild-Noémie de Rothschild institute, Paris, France. DESIGN: Preclinical study conducted on human corneal grafts. METHODS: The corneal grafts were mounted on an artificial chamber pressurizer (ACP) with preset constant pressure, and the FSL was used to create a circular annulus with specific dimensions. The resulting CAIRSs were analyzed for their thickness and width after air drying. RESULTS: A total of 25 CAIRSs were prepared using the FSL. The mean width and thickness of the CAIRSs were 803 ± 77 µm and 83 ± 16 µm, respectively. Statistical analysis revealed no significant differences in width among the various quadrants of each CAIRS or between different CAIRSs. Significantly thicker CAIRSs were obtained with a higher ACP pressure. CONCLUSIONS: The technique of CAIRS preparation using FSL technology and controlled artificial anterior chamber pressure demonstrated reproducibility and precision. This approach holds the potential for customizing and personalizing CAIRSs based on individual corneal characteristics.

Descemet Membrane Endothelial Keratoplasty-Induced Refractive Shift and Descemet Membrane Endothelial Keratoplasty-Induced Intraocular Lens Calculation Error.

PURPOSE: The aim of this study was to determine the mechanisms leading to the refractive shift and intraocular lens calculation error induced by Descemet membrane endothelial keratoplasty (DMEK), using ocular biometry and corneal elevation tomography data. METHODS: This is a retrospective, monocentric cohort study. Eyes which underwent uncomplicated DMEK surgery with available pre-DMEK and post-DMEK Scheimpflug rotating camera data (Pentacam, Oculus, Wetzlar, Germany) were considered for inclusion with an age-matched control group of healthy corneas. Cataract surgery data were collected for triple-DMEK cases. DMEK-induced refractive shift (DIRS) and intraocular lens calculation error (DICE) were calculated. Pearson r correlation coefficient was calculated between each corneal parameter variation and both DIRS and DICE. RESULTS: DIRS was calculable for 49 eyes from 43 patients. It was 30.61% neutral, 53.06% hyperopic (36.73% > 1D), and 16.32% myopic (6.12% > 1 D). DICE was calculable for 30 eyes of 26 patients: It was 46.67% neutral, 40.00% hyperopic (10.00% > 1D), and 13.33% myopic (3.33% > 1D). DIRS and DICE were mainly associated with variations in PRC/ARC ratio, anterior average radii of curvature (ARC), posterior average radii of curvature (PRC), and posterior Q. CONCLUSIONS: Our results suggest that ARC variations, PRC/ARC ratio variations, PRC variations, and posterior Q variations are the most influential parameters for both DIRS and DICE. We suggest that a distinction between those different phenomenons, both currently described as "hyperopic shift" in the literature, should be made by researchers and clinicians.

Long-Term Follow-Up of Descemet Stripping Only: Data Up to 7 Years Postoperatively.

PURPOSE: The aim of this study was to report long-term follow-up of eyes undergoing Descemet stripping only (DSO). METHODS: This was a retrospective study including 26 eyes of 20 patients undergoing DSO between December 2015 and November 2022. Eligibility criteria included peripheral endothelial cell count (ECC) >1000 cells/mm2 and symptoms caused by central guttata. Patients underwent a central circular 4-mm descemetorhexis using a reverse Sinskey hook and a pair of descemetorhexis forceps using a peeling technique. Three parameters were measured before surgery and at last follow-up: best-corrected visual acuity (BCVA), central corneal thickness (CCT), and ECC measured centrally and at the periphery. RESULTS: The mean age was 73 ± 9 years [52-90 years]. The average follow-up period was 23.7 ± 24.8 months [3-84]. Twenty-two eyes responded to DSO with 20 female eyes (91%) and 2 male eyes (9%). The mean postoperative BCVA improved from 0.3 ± 0.17 logMAR to 0.09 ± 0.13 logMAR (P value <0.05). The mean postoperative CCT decreased from 588 ± 41 µm to 546 ± 50 µm (P-value <0.05). The mean postoperative central ECC was 780 ± 257 cells/mm2 [484-1500]. Peripheral ECC decreased postoperatively (1837 ± 407 cells/mm2 preoperatively to 864 ± 340 cells/mm2 postoperatively, P value >0.05). Peripheral endothelial cell polymegathism was stable (average of 26.8% ± 6.8% preoperatively and 30.2% ± 14% postoperatively). Average peripheral endothelial cells polymorphism decreased postoperatively (63.1 ± 20.5% preoperatively to 33% ± 25% postoperatively, P value >0.05). Four eyes did not show improvement after DSO and underwent Descemet membrane endothelial keratoplasty surgery. There were 3 men (75%) and 1 women (25%). The preoperative trend was for nonresponders to have lower BCVA, higher CCT, more abnormal peripheral polymorphism, and polymegathism. CONCLUSIONS: The results of this study, with up to 7 years follow up, demonstrate the durability of DSO.

Analytical integrate-and-fire neuron models with conductance-based dynamics and realistic postsynaptic potential time course for event-driven simulation strategies.

In a previous paper (Rudolph & Destexhe, 2006), we proposed various models, the gIF neuron models, of analytical integrate-and-fire (IF) neurons with conductance-based (COBA) dynamics for use in event-driven simulations. These models are based on an analytical approximation of the differential equation describing the IF neuron with exponential synaptic conductances and were successfully tested with respect to their response to random and oscillating inputs. Because they are analytical and mathematically simple, the gIF models are best suited for fast event-driven simulation strategies. However, the drawback of such models is they rely on a nonrealistic postsynaptic potential (PSP) time course, consisting of a discontinuous jump followed by a decay governed by the membrane time constant. Here, we address this limitation by conceiving an analytical approximation of the COBA IF neuron model with the full PSP time course. The subthreshold and suprathreshold response of this gIF4 model reproduces remarkably well the postsynaptic responses of the numerically solved passive membrane equation subject to conductance noise, while gaining at least two orders of magnitude in computational performance. Although the analytical structure of the gIF4 model is more complex than that of its predecessors due to the necessity of calculating future spike times, a simple and fast algorithmic implementation for use in large-scale neural network simulations is proposed.

Discordant Keratoconus in Monozygotic Twins.

We report a case of discordant keratoconus (KC) in a set of monozygotic twins with contrasting environmental risk factors. Twin one had bilateral, asymmetrical KC. He reported significant eye rubbing using his knuckles during his night-shift work as an emergency doctor. His usual sleeping position on the left side corresponded to the most affected eye. Twin two had normal corneas, with no evidence of KC. He reported mild infrequent eye rubbing, daytime work pattern, and a supine sleeping position. This case report highlights the influence of environmental and behavioural factors in the development of KC, in particular eye rubbing, night work, and sleeping position, in two individuals sharing identical genetic inheritance.

A multi-residue pesticide determination in fatty food commodities by modified QuEChERS approach and gas chromatography-tandem mass spectrometry.

A QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) based multi-residue method has been developed and validated for the extraction and determination of pesticides in fatty matrices by gas chromatography tandem mass spectrometry. Extraction and clean-up were performed according to QuEChERS principles widely used for non-fatty matrices, with main difference, a higher solvent/sample- ratio followed by a 6-fold preconcentration step, ensuring good extractability and sensitivity. A validation according to SANTE guidelines was performed using a olive and sunflower oils mixture 1:1, w/w as representative matrix, at 2 concentration levels (5 and 50 µg/kg) targeting 176 GC-amenable pesticides. Most compounds fulfilled the validation criteria, with a limit of quantification of 5 µg/kg for 137 compounds , and of 50 µg/kg for 24 compounds. Afterwards, the method performance was tested in six different fatty matrices with 73-90% of the analytes fulfilling the performance criteria at 5 µg/kg depending on the matrix.

Descemet's membrane endothelial keratoplasty (DMEK) rejection following COVID-19 infection: A case report.

PURPOSE: To report the first known case of Descemet's Membrane Endothelial Keratoplasty (DMEK) graft rejection following COVID19 infection. OBSERVATION: A 60-year-old woman with a history of DMEK for Fuch's dystrophy, presented with redness and vision loss in her operated eye 18 months after surgery. Further clinical history revealed systemic symptoms consistent with COVID19, which had started 3 weeks prior to the onset of ocular symptoms. Examination revealed graft rejection, despite patient compliance with maintenance topical corticosteroid therapy. Serological testing was positive for SARS-CoV-2 IgG. The patient responded well to intensive treatment with systemic, periocular and topical corticosteroids, and reversal of graft rejection was achieved. Two months later, there was a recurrence of graft rejection while on maintenance therapy with cyclosporin 2% and topical corticosteroids. The same intensive immunosuppressive treatment protocol was followed, and reversal of graft rejection was again achieved. CONCLUSION AND IMPORTANCE: We believe that COVID-19 infection was a causative factor in this patient DMEK rejection. By highlighting this case, we hope to raise awareness amongst ophthalmologists of potential graft complications following COVID19 infection.

Quantification of furan and 5 alkylfurans with complete separation of 2-ethylfuran and 2,5-dimethylfuran isomers in cereals, coffee and Infant products by GC-MS.

Alkylfurans have been found concurrently to furan in thermally processed food and might add to the overall exposure, thereby increase the health concern. The analytical methods developed for these compounds are based on gas chromatography separation coupled to mass spectrometry. Two of those alkylfurans, 2,5-dimethylfuran and 2-ethylfuran, are isomers, for which accurate quantification require either complete chromatographic separation or tandem mass spectrometry (MS/MS) selectivity. A new chromatographic method is reported using the Supelco Equity-1 column, demonstrating complete baseline separation of these two isomers, with a shorter runtime when using single mass spectrometry. Full validation was performed successfully for furan, 2- and 3-methylfuran, 2-ethylfuran, 2,5-dimethylfuran and 2-pentylfuran on different food matrices with recovery rates in the range of 80-110 %, repeatability below 14%, intermediate reproducibility below 22% as well as expanded uncertainty under 50%.

Determining the Theoretical Effective Lens Position of Thick Intraocular Lenses for Machine Learning-Based IOL Power Calculation and Simulation.

Purpose: To describe a formula to back-calculate the theoretical position of the principal object plane of an intraocular lens (IOL), as well as the theoretical anatomic position in a thick lens eye model. A study was conducted to ascertain the impact of variations in design and IOL power, on the refractive outcomes of cataract surgery. Methods: A schematic eye model was designed and manipulated to reflect changes in the anterior and posterior radii of an IOL, while keeping the central thickness and paraxial powers static. Modifications of the shape factor (X) of the IOL affects the thick lens estimated effective lens position (ELP). Corresponding postoperative spherical equivalent (SE) were computed for different IOL powers (-5 diopters [D], 5 D, 15 D, 25 D, and 35 D) with X ranging from -1 to +1 by 0.1. Results: The impact of the thick lens estimated effective lens position shift on postoperative refraction was highly dependent on the optical power of the IOL and its thickness. Design modifications could theoretically induce postoperative refraction variations between approximately 0.50 and 3.0 D, for implant powers ranging from 15 D to 35 D. Conclusions: This work could be of interest for researchers involved in the design of IOL power calculation formulas. The importance of IOL geometry in refractive outcomes, especially for short eyes, should challenge the fact that these data are not usually published by IOL manufacturers. Translational Relevance: The back-calculation of the estimated effective lens position is central to intraocular lens calculation formulas, especially for artificial intelligence-based optical formulas, where the algorithm can be trained to predict this value.

The PEARL-DGS Formula: The Development of an Open-source Machine Learning-based Thick IOL Calculation Formula.

PURPOSE: To describe an open-source, reproducible, step-by-step method to design sum-of-segments thick intraocular lens (IOL) calculation formulas, and to evaluate a formula built using this methodology. DESIGN: Retrospective, multicenter case series METHODS: A set of 4242 eyes implanted with Finevision IOLs (PhysIOL, Liège, Belgium) was used to devise the formula design process and build the formula. A different set of 677 eyes from the same center was kept separate to serve as a test set. The resulting formula was evaluated on the test set as well as another independent data set of 262 eyes. RESULTS: The lowest standard deviation (SD) of prediction errors on Set 1 were obtained with the PEARL-DGS formula (±0.382 D), followed by K6 and Olsen (±0.394 D), EVO 2.0 (±0.398 D), RBF 3.0, and BUII (±0.402 D). The formula yielding the lowest SD on Set 2 was the PEARL-DGS (±0.269 D), followed by Olsen (±0.272 D), K6 (±0.276 D), EVO 2.0 (±0.277 D), and BUII (±0.301 D). CONCLUSION: Our methodology achieved an accuracy comparable to other state-of-the-art IOL formulas. The open-source tools provided in this article could allow other researchers to reproduce our results using their own data sets, with other IOL models, population settings, biometric devices, and measured, rather than calculated, posterior corneal radius of curvature or sum-of-segments axial lengths.

Liquid chromatography/tandem mass spectrometry assay for the absolute quantification of the expected circulating apelin peptides in human plasma.

Apelin peptides are of great interest owing to their involvement in physiological and pathological processes and they have been proposed as novel biomarkers for heart failure. The plasma concentrations of bioactive peptides of 12 (apelin-12), 13 (apelin-13) and pyroglutamyl apelin-13 (apelin-p13), 17 (apelin-17) and 36 (apelin-36) amino acids are reported to range from 20 to 4000 pg/mL in healthy subjects. As standard immunoassays cannot specifically quantify each apelin peptide, we have developed a sensitive and targeted multiplexed liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for each plasma apelin fragment. The approach was based on a cation-exchange extraction step of apelin forms present in human plasma. Apelin-12, -13, -p13, -17 and -36 were quantified using a triple quadrupole mass spectrometer operating in the multiple reaction monitoring mode. Stable isotope-labeled internal standards were used for quantification. Following assay validation, apelin peptide stability in plasma was investigated. Ten plasma samples from healthy donors were analyzed both with a standard immunoassay and with our LC/MS/MS method. The immunoassay results for the ten healthy donors showed immunoreactive plasma apelin concentrations ranging from 208 to 466 pg/mL. The lower limits of detection of our LC/MS/MS assay ranged from 10 to 50 pg/mL for apelin-12, -13, -p13, -17, and -36. Surprisingly, none of the five expected circulating forms of apelin was detected. These results question the nature and/or the concentration of circulating apelin peptides as well as the specificity of the immunoassays that have hitherto been used for clinical applications.

Detection of Furan and five Alkylfurans, including 2-Pentylfuran, in various Food Matrices.

Next to furan, other alkylfurans such as 2- and 3-methylfuran, 2-ethylfuran, 2,5-dimethylfuran, and 2-pentylfuran have been found concurrently in thermal processed food and fruit juices. To ensure an accurate quantification of these compounds, a method based on isotope dilution using all six respective internal standards and gas chromatography coupled to mass spectrometry was developed. Two injection techniques, static head space (HS) and solid phase micro extraction (SPME), were tested and compared for their performance. Validation was based on a single laboratory validation under repeatability condition. Good data for both techniques in baby food and cereals were obtained. Furthermore, validation was conducted successfully on fruit juices and infant formula using SPME injection and on coffee using HS injection. LOQ for all matrices was established at 5 µg/kg and 200 µg/kg in coffee samples, which corresponds to the lowest fortification level. Recovery was between 80 % and 110 % and repeatability obtained below 16 % at 50 µg/kg (7.4 % at 10 mg/kg for coffee samples), except few slight outliers.

Thermal degradation of 2-furoic acid and furfuryl alcohol as pathways in the formation of furan and 2-methylfuran in food.

This study reports the heat-induced formation of furan by decarboxylation of 2-furoic acid, and 2-methylfuran by dehydration of furfuryl alcohol under dry conditions. Model systems were incubated at temperatures up to 190 °C, followed by quantitative determination of furan and 2-methylfuran performed by isotope dilution headspace gas chromatography-mass spectrometry. Results show that 2-furoic acid decarboxylation and furfuryl alcohol dehydration are activated as from about 140-160 °C. Furfuryl alcohol and 2-furoic acids were measured in a selection of roasted coffee products by isotope dilution liquid chromatography-high resolution mass spectrometry, and the data evidenced a strong correlation between the two compounds, suggesting an intimate mechanistic relationship between them. The possible oxidation of furfuryl alcohol to furfural and 2-furoic acid in heated food is raised with particular emphasis on coffee roasting. These findings are relevant for better understanding the formation of furan and alkylfurans in food, and ultimately opening avenues for mitigation.

Surface-isomerization dynamics of trans-stilbene molecules adsorbed on Si(100)-2 x 1.

Photoinduced trans-cis isomerization studies of stilbene molecules in the gas phase have led to a precise understanding of the corresponding molecular dynamics. Yet, when such molecules are adsorbed on surfaces, these reactions are expected to be strongly modified as compared to what is know in the gas phase. In this work, a low temperature (5 K) scanning tunneling microscope (STM) is used to image the trans-stilbene molecules deposited on a Si(100)-2 x 1 surface at 12 K. trans-Stilbene undergoes conformational changes during the adsorption process such that four different stilbene conformers are observed: trans-stilbene (TS), cis-stilbene (CS), and two new conformers I(1) and I(2). Furthermore, electronic excitation of individual stilbene molecules, by means of tunnel electrons, is shown to activate specific reversible molecular surface isomerization (TS <--> I(1) and CS <--> I(2)) combined with diffusion across the surface. Calculated STM topographies, using the tight binding method, indicate that the CS and TS molecules are physisorbed. The molecular conformations of the surface isomers I(1) and I(2) are suggested to be analogous to transient states conformations of the stilbene molecule when stabilized by the silicon surface. The measurements of the molecular surface isomerization and diffusion reaction yields are used to build a qualitative potential energy surface of the various stilbene reactions. The molecular surface-isomerization dynamics is shown to be influenced by the type of dopant (n or p). This is related to surface charging, which reveals modifications in the stilbene ionization potential.