Auritidibacter ignavus, an Emerging Pathogen Associated with Chronic Ear Infections.

We describe detection of the previously rarely reported gram-positive bacterium Auritidibacter ignavus in 3 cases of chronic ear infections in Germany. In all 3 cases, the patients had refractory otorrhea. Although their additional symptoms varied, all patients had an ear canal stenosis and A. ignavus detected in microbiologic swab specimens. A correct identification of A. ignavus in the clinical microbiology laboratory is hampered by the inability to identify it by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Also, the bacterium might easily be overlooked because of its morphologic similarity to bacterial species of the resident skin flora. We conclude that a high index of suspicion is warranted to identify A. ignavus and that it should be particularly considered in patients with chronic external otitis who do not respond clinically to quinolone ear drop therapy.

Patch endothelial keratoplasty for corneal perforations secondary to ocular surface disease: case series.

BACKGROUND: Corneal perforation is an ophthalmic emergency. The conventional management of corneal perforation can be associated with severe complications especially in patients with ocular surface disease. Endothelial keratoplasty has been suggested as an alternative surgical technique for the management of corneal perforations. We present a case series of nine patients with corneal perforation and ocular surface disease managed with secondary patch endothelial keratoplasty. METHODS: This is a retrospective case series of nine patch endothelial keratoplasties performed between 2016 and 2022 at a quaternary eye hospital in Australia. The surgical technique is similar to conventional endothelial keratoplasty except descemetorhexis was not performed. RESULTS: A total of 9 cases were treated during the review period. Eight of the nine cases had an improvement in visual acuity. One case failed to achieve corneal tectonic objective. CONCLUSION: Patch endothelial keratoplasty is a safe secondary procedure for the management of corneal perforations in patients with ocular surface disease.

miRNATissueAtlas2: an update to the human miRNA tissue atlas.

Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing the expression of miRNAs across organs in the human body. Here, we present an updated resource containing sequencing data of 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling the organs from the same bodies minimizes intra-individual variability and facilitates the making of a precise high-resolution body map of the non-coding transcriptome. The data allow shedding light on the organ- and organ system-specificity of piwi-interacting RNAs (piRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs) and other non-coding RNAs. As use case of our resource, we describe the identification of highly specific ncRNAs in different organs. The update also contains 58 samples from six tissues of the Tabula Muris collection, allowing to check if the tissue specificity is evolutionary conserved between Homo sapiens and Mus musculus. The updated resource of 87 252 non-coding RNAs from nine non-coding RNA classes for all organs and organ systems is available online without any restrictions (https://www.ccb.uni-saarland.de/tissueatlas2).

Encyclopedia of tools for the analysis of miRNA isoforms.

RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.

The use of donor scleral patch in ophthalmic surgery.

Scleral tissue has been in use in ophthalmology for many years although indications for use have varied. We retrospectively reviewed scleral transplant tissue requests over a 12 month period at a local eye bank and confirmed a small but significant demand for the use of scleral tissue. Iatrogenic surgical complications are the primary indication for use. Our understanding of the indications and outcomes of scleral graft procedures is derived from case reports and small cohort series. We reviewed the current literature on existing indications for its use and discuss the relative outcomes. To our knowledge this represents the first review of scleral transplant indications and further summarises usage rates in the Lions NSW Eye Bank which may provide practical information for those surgeons who use scleral tissue and Eye Banks who supply it.

Implementation of Organ Culture storage of donor corneas: a 3 year study of its impact on the corneal transplant wait list at the Lions New South Wales Eye Bank.

Organ Culture corneal storage offers an extended storage time and increased donor pool and tissue assessment opportunities. In September 2011, the Lions New South Wales Eye Bank (LNSWEB) moved from hypothermic storage to Organ Culture corneal storage. This study evaluates the impact of implementation of Organ Culture on donor eye retrieval and the corneal transplant waiting list over a 3 year period in NSW, Australia. Retrospective review of the LNSWEB data from September 2011 to August 2014. Tissue collection, waiting list and tissue utilization data were recorded. The data from September 2008 to August 2011 for Optisol-GS storage was used for comparison. The annual donor and cornea collection rate increased 35 % and 44 % respectively with Organ Culture compared to Optisol-GS storage. The utilization rate of corneal tissue increased from 73.4 % with hypothermic storage to 77.2 % with Organ Culture storage. The transplant wait list decreased by 77.3 % from September 2011 to August 2014 and correlated with the increased rate of corneal transplantation (r = -0.9381, p < 0.0001). No other factors impacting the wait list changed over this period. Corneas not used from either storage method were due to unacceptable endothelial cell density/viability. The contamination rate of corneas stored in Organ Culture medium was low at 1.74 %. The Organ Culture storage method increases the corneal donor pool available to Eye banks. The practical benefits of the extended storage time and increased donor assessment opportunities have directly led to an increase in corneal utilization rate and a significant decrease in recipient wait list time.

Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease.

The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA-target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson's disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ).

Forecasting football injuries by combining screening, monitoring and machine learning.

Identifying players or circumstances associated with an increased risk of injury is fundamental for successful risk management in football. So far, time-constant and volatile risk factors are generally considered separately in either a screening (constant) or a monitoring (volatile) approach each resulting in a restricted set of explanatory variables. Consequently, improvements in predictive accuracy may be expected when screening and monitoring data are combined, especially when analysed with current machine learning (ML) techniques.This trial was designed as a prospective observational cohort study aiming to forecast non-contact time-loss injuries in male professional football (soccer). Injuries were registered according to the Fuller consensus. Gradient boosting with ROSE upsampling within a leave-one-out cross-validation was used for data analysis. The hierarchical data structure was considered throughout. Different splits of the original dataset were used to probe the robustness of results.Data of 88 players from 4 teams and 51 injuries could be analysed. The cross-validated performance of the gradient boosted model (ROC area under the curve 0.61) was promising and higher compared to models without integration of screening data. Importantly, holdout test set performance was similar (ROC area under the curve 0.62) indicating prospect of generalizability to new cases. However, the variation of predictive accuracy and feature importance with different splits of the original dataset reflects the relatively low number of events.It is concluded that ML-based injury forecasting based on the integration of screening and monitoring data is promising. However, external prospective verification and continued model development are required.

Evaluating patients' satisfaction level after using 3D printed PEEK facial implants in repairing maxillofacial deformities.

Background: it is generally the case in any traumatic accident where a loss in hard tissue occurs to preform restorative plastic surgery, as there are many materials and approaches used to restore the loss, this research sheds the light on the use of one such material and approach being 3D printed facial implants manufactured from PolyEther Ether Ketone (PEEK) and to evaluate the level of patients' satisfaction following the use of said method in repairing maxillofacial deformities. Materials and methods: a research sample consisting of 10 patients with facial deformities underwent maxillofacial reconstructive surgery between 2020 and 2021 in the Department of Oral and Maxillofacial Surgery in the Tishreen University Hospital - Latakia - Syria. All patients underwent Computed Tomography (CT) scans, then the design of the required facial implant was carried out, the final form of the facial implant was printed from PolyEther Ether Ketone (PEEK), and then surgical work was performed, a check-up after 3 months of the surgical procedure was carried out to evaluate the level of satisfaction on a scale of 1-5. Results: The results from the 10 patients showed a good level of satisfaction except in one case where the facial implant had to be removed due to recurrent infection where the patient showed no signs of response to medicinal treatment following the surgery. Conclusions: this research suggests that the use of 3D printed PEEK facial implants to be very agreeable in terms of functionality and aesthetics in treating various facial deformities.

Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial.

The composition of the gut microbiota is linked to multiple diseases, including Parkinson's disease (PD). Abundance of bacteria producing short-chain fatty acids (SCFAs) and fecal SCFA concentrations are reduced in PD. SCFAs exert various beneficial functions in humans. In the interventional, monocentric, open-label clinical trial "Effects of Resistant Starch on Bowel Habits, Short Chain Fatty Acids and Gut Microbiota in Parkinson'sDisease" (RESISTA-PD; ID: NCT02784145), we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch (RS). We enrolled 87 subjects in three study-arms: 32 PD patients received RS (PD + RS), 30 control subjects received RS, and 25 PD patients received solely dietary instructions. We performed paired-end 100 bp length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB. RS was well-tolerated. In the PD + RS group, fecal butyrate concentrations increased significantly, and fecal calprotectin concentrations dropped significantly after 8 weeks of RS intervention. Clinically, we observed a reduction in non-motor symptom load in the PD + RS group. The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups, including bacteria producing SCFAs. Reference-free analysis suggested punctual, yet pronounced differences in the metagenomic signature in the PD + RS group. RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD. The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies, also investigating whether RS is able to modify the clinical course of PD.

Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies.

High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.

Supply and Demand of Domestic Corneal Tissue and Its Implications on Export Potential-Using Australia as an Example.

PURPOSE: Corneal tissue importation is only possible if another country is able to export corneas without impacting its own domestic demand. Currently, there is little evidence to indicate whether export nations have such surplus capacity and in a position to export. To explore this concept, we examined our nation, Australia, which is reported to routinely decline donations because of its ability to meet domestic corneal transplant demand. Our research offers insights and opportunities for Australia and other nations to evaluate their domestic and international supply and allocation of corneal tissue in this space. METHOD: We collated 12 months of data on collected and noncollected donations, through participating Australian Eye Banks. The explanation of why some known donors were declined or not pursued indicated if demand was met and potential surplus-for-export levels. RESULTS: There were 7.5% (n = 11,889) of deaths in Australia that were notified to Australian Eye Banks during our reporting period. Of those, 9.3% (n = 1106/11,889) were recovered and allocated, 15.7% (n = 1863/11,889) were known but declined, and 75% (n = 8920/11,889) were not pursued. Of those that were declined, 64.3% (n = 1197/1863) were declined because of limitations with service/manpower at the eye bank, whereas 35.7% (n = 666/1863) were declined because demand was met. CONCLUSIONS: Australia did not meet demand all the time, during our data period. There were adequate quantities of potential donors to support increasing recovery for domestic allocation and provide for exportation without hindrance to Australian demand. Further examination of domestic supply and demand cycles and the export process is required before routine exportation.

Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective.

The predominance of bacterial taxa in the gut, was examined in view of the putative antimicrobial peptide sequences (AMPs) within their proteomes. The working assumption was that compatible bacteria would share homology and thus immunity to their putative AMPs, while competing taxa would have dissimilarities in their proteome-hidden AMPs. A network-based method ("Bacterial Wars") was developed to handle sequence similarities of predicted AMPs among UniProt-derived protein sequences from different bacterial taxa, while a resulting parameter ("Die" score) suggested which taxa would prevail in a defined microbiome. T he working hypothesis was examined by correlating the calculated Die scores, to the abundance of bacterial taxa from gut microbiomes from different states of health and disease. Eleven publicly available 16S rRNA datasets and a dataset from a full shotgun metagenomics served for the analysis. The overall conclusion was that AMPs encrypted within bacterial proteomes affected the predominance of bacterial taxa in chemospheres.

Factors Affecting Corneal Organ Culture Contamination: A 6-year Study at the New South Wales Tissue Bank.

PURPOSE: To report the rate of microbial contamination and analyze possible risk factors for contamination of banked corneas stored using the organ culture method. METHODS: Data from the New South Wales Tissue Banks incorporating the Lions NSW Eye Bank, between September 1, 2011, and November 30, 2017, were reviewed retrospectively. All corneas collected during this period and stored in organ culture storage media were tested for microbial contamination. The influence of potential factors on the rate of contamination was analyzed using the χ test and logistic regression using generalized estimating equations. RESULTS: A total of 4410 corneas were included in this study, of which 110 were medium culture positive, representing a microbial contamination rate of 2.5%. The main contaminants were Candida species followed by Staphylococcus species. Corneal tissue collected in summer and autumn had a significantly higher contamination rate (P = 0.006). All other factors studied were not shown to have a statistically significant association with contamination after accounting for within-pair correlation and confounders. CONCLUSIONS: A relatively low contamination rate of 2.5% observed in our study reflects the stringent laboratory protocols, strict donor selection criteria, and high level of experience among staff at the Lions NSW Eye Bank. Our study demonstrated that the season of collection had a strong association with the rate of organ culture contamination. Because Candida species contributed the largest percentage of contamination, specific measures to reduce and eliminate fungal proliferation should be considered by eye banks particularly in warm seasons.

Schistosomiasis Sustained Control Program in Ethnic Groups Around Ninefescha (Eastern Senegal).

Schistosomiasis is the second most significant parasitic disease in children in several African countries. For this purpose, the "Programme National de Lutte contre les Bilharzioses" (PNLB) was developed in partnership with the World Health Organization (WHO) to control this disease in Senegal. However, geographic isolation of Bedik ethnic groups challenged implementation of the key elements of the schistosomiasis program in eastern Senegal, and therefore, a hospital was established in Ninefescha to improve access to health care as well as laboratory support for this population. The program we have implemented from 2008 in partnership with the PNLB/WHO involved campaigns to 1) evaluate schistosomiasis prevalence in children of 53 villages around Ninefescha hospital, 2) perform a mass drug administration following the protocol established by the PNLB in school-aged children, 3) monitor annual prevalence, 4) implement health education campaigns, and 5) oversee the building of latrines. This campaign led to a drop in schistosomiasis prevalence but highlighted that sustainable schistosomiasis control by praziquantel treatment, awareness of the use of latrines, and inhabitants' voluntary commitment to the program are crucial to improve Schistosoma elimination. Moreover, this study revealed that preschool-aged children, for whom praziquantel was not recommended until 2014 in Senegal, constituted a significant reservoir for the parasite.

Link Conditions for Simplifying Meshes with Embedded Structures.

Interactive visualization applications benefit from simplification techniques that generate good-quality coarse meshes from high-resolution meshes that represent the domain. These meshes often contain interesting substructures, called embedded structures, and it is desirable to preserve the topology of the embedded structures during simplification, in addition to preserving the topology of the domain. This paper describes a proof that link conditions, proposed earlier, are sufficient to ensure that edge contractions preserve the topology of the embedded structures and the domain. Excluding two specific configurations, the link conditions are also shown to be necessary for topology preservation. Repeated application of edge contraction on an extended complex produces a coarser representation of the domain and the embedded structures. An extension of the quadric error metric is used to schedule edge contractions, resulting in a good-quality coarse mesh that closely approximates the input domain and the embedded structures.

A vida intensa de François Lamasson / François Lamasson's intense life

Dados biográficos breves mas abrangentes, homenagem póstuma que lhe dedica seu discípulo G.P. Poisson. O Texto foi publicado originalmente na revista L'Homéopathie Française, número 8, em 1975, ano da morte de François Lamasson, nosso patrono.