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Shaun O’Hagan,1,2 Niamh Galway,3 Michael D Shields,3,4 Peter Mallett,1,4 Helen E Groves1,2 1Paediatric Infectious Diseases, Royal Belfast Hospital for Sick Children, Belfast, Northern Ireland; 2Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, Northern Ireland; 3Paediatric Respiratory Medicine, Royal Belfast Hospital for Sick Children, Belfast, Northern Ireland; 4Centre for Medical Education, Queen’s University Belfast School of Medicine, Belfast, Northern IrelandCorrespondence: Helen E Groves, Email h.groves@qub.ac.ukAbstract: Respiratory Syncytial Virus (RSV) is a major global cause of childhood morbidity and mortality. Palivizumab, a monoclonal antibody that provides passive immunity against RSV, is currently licensed for prophylactic use in specific “high-risk” populations, including congenital heart disease, bronchopulmonary dysplasia and prematurity. Available research suggests palivizumab use in these high-risk populations can lead to a reduction in RSV-related hospitalization. However, palivizumab has not been demonstrated to reduce mortality, adverse events or length of hospital stay related to RSV. In this article, we review the management of RSV, indications for palivizumab prophylaxis, the safety, cost-effectiveness and efficacy of this preventative medication, and emerging therapeutics that could revolutionize future prevention of this significant pathogen.Keywords: RSV, palivizumab, efficacy, safety, future directions

Jenny Xue Tian,1 Stephen O’Hagan2 1Ophthalmology Department, Cairns Base Hospital, Cairns, QLD, Australia; 2Ophthalmology, James Cook University, Cairns, QLD, Australia Abstract: To report a rare case of bilateral granulomatous chorioretinitis complicated by bilateral peripapillary choroidal neovascular membranes. This is the first reported case in Australia where intravitreal injections of anti-vascular endothelial growth factor ranibizumab were used to successfully treat choroidal neovascular membrane caused by granulomatous chorioretinitis. This is also the first reported case in Australia of Toxocara polymerase chain reaction being performed on intraocular fluids. Keywords: granulomatous chorioretinitis, ocular toxocariasis, neovascular membrane, anti-VEGF

Thomas P Moloney,1 Stephen O’Hagan,1 Lawrence Lee2,3 1Department of Ophthalmology, Cairns Hospital, Cairns, QLD, Australia; 2City Eye Centre, Brisbane, QLD, Australia; 3Associate Professor of Ophthalmology, School of Medicine, University of Queensland, Brisbane, QLD, Australia Abstract: Gyrate atrophy of the choroid and retina is a rare chorioretinal dystrophy inherited in an autosomal recessive pattern. We describe the first documented case of gyrate atrophy from Australia in a 56-year-old woman with a history of previous diagnosis of retinitis pigmentosa and worsening night vision in her right eye over several years. She was myopic and bilaterally pseudophakic, and fundus examination revealed pale optic discs and extensive peripheral chorioretinal atrophy exposing bare sclera bilaterally with only small islands of normal-appearing retina at each posterior pole. Visual field testing showed grossly constricted fields, blood testing showed hyperornithinemia, and further questioning revealed consanguinity between the patient’s parents. We then used the patient’s typical retinal findings of gyrate atrophy to demonstrate the potential use of ultrawide-field fundus photography and angiography in diagnosis and monitoring response in future treatment. Keywords: gyrate atrophy, ultrawide-field retinal photography, angiography, retinal photography, hyperornithinemia

This case study highlights the clinical importance of ovarian vein thrombosis in the context of pelvic surgery for benign gynaecological conditions and the role of imaging, particularly computed tomography with reformatting, in confirming the diagnosis. [ABSTRACT FROM AUTHOR]

Background: In 2021 we launched the BronchStart study, which collected information on 17,899 presentations in children with serious respiratory tract infections following the release of lockdown restrictions. Our study informed the Joint Committee on Vaccination and Immunisation's decision to recommend the introduction maternal respiratory syncytial virus (RSV) vaccination, which was introduced in the United Kingdom in August/September 2024., Study Question: We modified our original protocol to conduct a United Kingdom-wide assessment of maternal vaccination against RSV., Methods and Likely Impact: We will conduct a multi-centre study, utilising the PERUKI network used in the original BronchStart study, to assess the effectiveness of maternal vaccination using a test-negative study design. We will gather detailed clinical information on children admitted with bronchiolitis in the post-RSV vaccination era, and understand possible reasons for incomplete vaccine uptake., Competing Interests: No competing interests were disclosed., (Copyright: © 2024 Williams TC et al.)

The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae . Of the 385 compounds transported by yeast, we selected six compounds ( viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999)., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Møller-Hansen, Sáez-Sáez, van der Hoek, Dyekjær, Christensen, Wright Muelas, O’Hagan, Kell and Borodina.)

Introduction: Plain radiographs remain a first-line trauma investigation. Most trauma radiographs worldwide are reported by junior doctors. This study assesses the accuracy of after-hour acute trauma radiograph reporting by emergency centre (EC) doctors in an African district hospital., Methods: An institutional review board approved retrospective descriptive study over two consecutive weekends in February 2020. The radiologist report on the admission radiographs of adult trauma patients was compared with the initial EC interpretation. The accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) for EC interpretation were calculated with 95% confidence intervals (95%CI). The association between reporting accuracy and anatomical region, mechanism of injury, time of investigation, and the number of abnormalities per radiograph was assessed., Results: 140 radiographs were included, of which 49 (35%) were abnormal. EC doctors recorded (95%CI) 77% (69-84%) accuracy, 38% (25-54%) sensitivity, 97% (91-99%) specificity, 86% (65-95%) PPV and 76% (71-80%) NPV. Performance was associated with the anatomical region (p=0.02), mechanism of injury (p=<0.01) time of day (p=0.04) and the number of abnormalities on the film (p=<0.01). The highest sensitivity was achieved in reports of the appendicular skeleton (42%) and in the setting of simple blunt trauma (62%). Overall accuracy was in line with the range (44%-99%) reported in the international literature., Discussion: Accurate reporting of acute trauma radiographs is challenging. Key factors impact performance. Further training of junior doctors in this area of clinical practice is recommended. Future work should focus on assessing the impact of such training on reporting performance., Competing Interests: The authors declare no conflicts of interest., (© 2022 Published by Elsevier B.V. on behalf of African Federation for Emergency Medicine.)

Stereotype threat has been proposed as one cause of gender differences in post-compulsory mathematics participation. Danaher and Crandall argued, based on a study conducted by Stricker and Ward, that enquiring about a student's gender after they had finished a test, rather than before, would reduce stereotype threat and therefore increase the attainment of women students. Making such a change, they argued, could lead to nearly 5000 more women receiving AP Calculus AB credit per year. We conducted a preregistered conceptual replication of Stricker and Ward's study in the context of the UK Mathematics Trust's Junior Mathematical Challenge, finding no evidence of this stereotype threat effect. We conclude that the 'silver bullet' intervention of relocating demographic questions on test answer sheets is unlikely to provide an effective solution to systemic gender inequalities in mathematics education., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: At the time the study was conducted, Steven O’Hagan was employed as the Deputy Director of the UK Mathematics Trust. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Our previous work demonstrated that two commonly used fluorescent dyes that were accumulated by wild-type Escherichia coli MG1655 were differentially transported in single-gene knockout strains, and also that they might be used as surrogates in flow cytometric transporter assays. We summarize the desirable properties of such stains, and here survey 143 candidate dyes. We eventually triage them (on the basis of signal, accumulation levels and cost) to a palette of 39 commercially available and affordable fluorophores that are accumulated significantly by wild-type cells of the 'Keio' strain BW25113, as measured flow cytometrically. Cheminformatic analyses indicate both their similarities and their (much more considerable) structural differences. We describe the effects of pH and of the efflux pump inhibitor chlorpromazine on the accumulation of the dyes. Even the 'wild-type' MG1655 and BW25113 strains can differ significantly in their ability to take up such dyes. We illustrate the highly differential uptake of our dyes into strains with particular lesions in, or overexpressed levels of, three particular transporters or transporter components ( yhjV , yihN and tolC ). The relatively small collection of dyes described offers a rapid, inexpensive, convenient and informative approach to the assessment of microbial physiology and phenotyping of membrane transporter function.

It is known that at least some fluorophores can act as 'surrogate' substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the 'natural' substrates of 'orphan' transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly 'drug-like', and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores along with standard fingerprinting methods and the Tanimoto similarity metric. Results: The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug, as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the "quantitative estimate of drug likeness" technique. It is concluded that this set of fluorophores does overlap with a significant part of both the drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities.

We address the problem of generating novel molecules with desired interaction properties as a multi-objective optimization problem. Interaction binding models are learned from binding data using graph convolution networks (GCNs). Since the experimentally obtained property scores are recognised as having potentially gross errors, we adopted a robust loss for the model. Combinations of these terms, including drug likeness and synthetic accessibility, are then optimized using reinforcement learning based on a graph convolution policy approach. Some of the molecules generated, while legitimate chemically, can have excellent drug-likeness scores but appear unusual. We provide an example based on the binding potency of small molecules to dopamine transporters. We extend our method successfully to use a multi-objective reward function, in this case for generating novel molecules that bind with dopamine transporters but not with those for norepinephrine. Our method should be generally applicable to the generation in silico of molecules with desirable properties.

Molecular similarity is an elusive but core "unsupervised" cheminformatics concept, yet different "fingerprint" encodings of molecular structures return very different similarity values, even when using the same similarity metric. Each encoding may be of value when applied to other problems with objective or target functions, implying that a priori none are "better" than the others, nor than encoding-free metrics such as maximum common substructure (MCSS). We here introduce a novel approach to molecular similarity, in the form of a variational autoencoder (VAE). This learns the joint distribution p(z|x) where z is a latent vector and x are the (same) input/output data. It takes the form of a "bowtie"-shaped artificial neural network. In the middle is a "bottleneck layer" or latent vector in which inputs are transformed into, and represented as, a vector of numbers (encoding), with a reverse process (decoding) seeking to return the SMILES string that was the input. We train a VAE on over six million druglike molecules and natural products (including over one million in the final holdout set). The VAE vector distances provide a rapid and novel metric for molecular similarity that is both easily and rapidly calculated. We describe the method and its application to a typical similarity problem in cheminformatics.

We recently introduced the Gini coefficient (GC) for assessing the expression variation of a particular gene in a dataset, as a means of selecting improved reference genes over the cohort ('housekeeping genes') typically used for normalisation in expression profiling studies. Those genes (transcripts) that we determined to be useable as reference genes differed greatly from previous suggestions based on hypothesis-driven approaches. A limitation of this initial study is that a single (albeit large) dataset was employed for both tissues and cell lines. We here extend this analysis to encompass seven other large datasets. Although their absolute values differ a little, the Gini values and median expression levels of the various genes are well correlated with each other between the various cell line datasets, implying that our original choice of the more ubiquitously expressed low-Gini-coefficient genes was indeed sound. In tissues, the Gini values and median expression levels of genes showed a greater variation, with the GC of genes changing with the number and types of tissues in the data sets. In all data sets, regardless of whether this was derived from tissues or cell lines, we also show that the GC is a robust measure of gene expression stability. Using the GC as a measure of expression stability we illustrate its utility to find tissue- and cell line-optimised housekeeping genes without any prior bias, that again include only a small number of previously reported housekeeping genes. We also independently confirmed this experimentally using RT-qPCR with 40 candidate GC genes in a panel of 10 cell lines. These were termed the Gini Genes. In many cases, the variation in the expression levels of classical reference genes is really quite huge (e.g. 44 fold for GAPDH in one data set), suggesting that the cure (of using them as normalising genes) may in some cases be worse than the disease (of not doing so). We recommend the present data-driven approach for the selection of reference genes by using the easy-to-calculate and robust GC.

Dysregulation of the kynurenine pathway (KP) leads to imbalances in neuroactive metabolites associated with the pathogenesis of several neurodegenerative disorders, including Huntington's disease (HD). Inhibition of the enzyme kynurenine 3-monooxygenase (KMO) in the KP normalises these metabolic imbalances and ameliorates neurodegeneration and related phenotypes in several neurodegenerative disease models. KMO is thus a promising candidate drug target for these disorders, but known inhibitors are not brain permeable. Here, 19 new KMO inhibitors have been identified. One of these ( 1 ) is neuroprotective in a Drosophila HD model but is minimally brain penetrant in mice. The prodrug variant ( 1b ) crosses the blood-brain barrier, releases 1 in the brain, thereby lowering levels of 3-hydroxykynurenine, a toxic KP metabolite linked to neurodegeneration. Prodrug 1b will advance development of targeted therapies against multiple neurodegenerative and neuroinflammatory diseases in which KP likely plays a role, including HD, Alzheimer's disease, and Parkinson's disease., Competing Interests: Competing interestsThe authors declare no competing non-financial interests but the following competing financial interests: a patent (new compounds and uses) from the University of Leicester and University of Manchester by N.S.S. and F.G. is pending, application number 1719327.7.

Time-critical management is of particular significance in the trauma and emergency setting, where intervals from patient arrival to diagnostic imaging and from imaging to radiology report are key determinants of outcome. This study, based in the Trauma and Emergency Unit of a large, tertiary-level African hospital with a fully digital radiology department, assessed the impact of increased workload on computerised tomography (CT) efficiency. Sequential, customised searches of the institutional radiology information system (RIS) were conducted to define two weekends in 2016 with the lowest and highest emergency CT workloads, respectively. The electronic RIS timestamps defining the intervals between key steps in the CT workflow were extracted and analysed for each weekend. With the exception of radiologist reporting time, workflow steps were significantly prolonged by increased workload. This study highlights the potential role of the integrated digital radiology system in enabling a detailed analysis of imaging workflow, thereby facilitating the identification and appropriate management of bottlenecks.

Background: While it is has been proven that tranexamic acid (TXA) reduces blood loss in primary total hip and knee arthroplasty (THA and TKA), there is little published evidence on the use of TXA beyond 3 h post-operatively. Most blood loss occurs after wound closure and the primary aim of this study is to determine if the use of oral TXA post-operatively for up to 24 h will reduce calculated blood loss at 48 h beyond an intra-operative intravenous bolus alone following primary THA and TKA. To date, most TXA studies have excluded patients with a history of thromboembolic disease., Methods/design: This is a phase IV, single-centred, open-label, parallel-group, randomised controlled trial. Participants are randomised to one of three groups: group 1, an intravenous (IV) bolus of TXA peri-operatively plus oral TXA post-operatively for 24 h; group 2, an IV bolus of TXA peri-operatively or group 3, standard care (no TXA). Eligible participants, including those with a history of thromboembolic disease, are allocated to these groups with a 2:2:1 allocation ratio. The primary outcome is the indirectly calculated blood loss 48 h after surgery. Researchers and patients are not blinded to the treatment; however, staff processing blood samples are. Originally 1166 participants were required to complete this study, 583 THA and 583 TKA. However, following an interim analysis after 100 THA and 100 TKA participants had been recruited to the study, the data monitoring ethics committee recommended stopping group 3 (standard care)., Discussion: TRAC-24 will help to determine whether an extended TXA dosing regimen can further reduce blood loss following primary THA and TKA. By including patients with a history of thromboembolic disease, this study will add to our understanding of the safety profile of TXA in this clinical situation., Trial Registration: ISRCTN registry, ISRCTN58790500 . Registered on 3 June 2016, EudraCT: 2015-002661-36.

A 35-year-old man presented after a high-speed motor vehicle accident and the driver's side curtain air bag causing blunt force trauma rupturing his right globe. The tangential force of the air bag resulted in an unusual arcuate horseshoe-shaped rupture through the lateral rectus insertion, causing avulsion of the muscle and tearing the sclera, with the apices of the tear extending anteriorly towards the limbus. Repair of the globe rupture was undertaken, and secondary vitrectomy revealed that the scleral tear had not involved the retina abutting the ora serrata. Silicone oil tamponade was used to fill the globe and the postoperative best corrected vision was 6/9. This is the first reported case of a ruptured globe caused by a side curtain air bag, resulting in a uniquely shaped arcuate scleral wound combined with lateral rectus avulsion, not associated with rhegmatogenous retinal damage, and is the first air bag-related globe rupture with scleral involvement to report a final best-corrected visual acuity better than 6/60., Competing Interests: Competing interests: None declared., (© BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

The expression levels of SLC or ABC membrane transporter transcripts typically differ 100- to 10,000-fold between different tissues. The Gini coefficient characterizes such inequalities and here is used to describe the distribution of the expression of each transporter among different human tissues and cell lines. Many transporters exhibit extremely high Gini coefficients even for common substrates, indicating considerable specialization consistent with divergent evolution. The expression profiles of SLC transporters in different cell lines behave similarly, although Gini coefficients for ABC transporters tend to be larger in cell lines than in tissues, implying selection. Transporter genes are significantly more heterogeneously expressed than the members of most non-transporter gene classes. Transcripts with the stablest expression have a low Gini index and often differ significantly from the "housekeeping" genes commonly used for normalization in transcriptomics/qPCR studies. PCBP1 has a low Gini coefficient, is reasonably expressed, and is an excellent novel reference gene. The approach, referred to as GeneGini, provides rapid and simple characterization of expression-profile distributions and improved normalization of genome-wide expression-profiling data., (Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.)

Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles. We examined the functional potential of mucus and stool microbial communities in the mdr1a -/- mouse model of colitis and littermate controls using PICRUSt on 16S rRNA sequencing data. Our findings indicate that despite changes in microbial composition, microbial functional pathways were stable before and during the development of mucosal inflammation. LC-MS-based metabolic phenotyping (metabotyping) in urine samples confirmed that metabolite profiles in mdr1a -/- mice were remarkably unaffected by development of intestinal inflammation and there were no differences in previously published metabolic markers of IBD. Metabolic profiles did, however, discriminate the colitis-prone mdr1a -/- genotype from controls. Our results indicate resilience of the metabolic network irrespective of inflammation. Importantly as metabolites differentiated genotype, genotype-differentiating metabolites could potentially predict IBD risk.

The transport of drug molecules is mainly determined by the distribution of influx and efflux transporters for which they are substrates. To enable tissue targeting, we sought to develop the idea that we might affect the transporter-mediated disposition of small-molecule drugs via the addition of a second small molecule that of itself had no inhibitory pharmacological effect but that influenced the expression of transporters for the primary drug. We refer to this as a "binary weapon" strategy. The experimental system tested the ability of a molecule that on its own had no cytotoxic effect to increase the toxicity of the nucleoside analog gemcitabine to Panc1 pancreatic cancer cells. An initial phenotypic screen of a 500-member polar drug (fragment) library yielded three "hits." The structures of 20 of the other 2,000 members of this library suite had a Tanimoto similarity greater than 0.7 to those of the initial hits, and each was itself a hit (the cheminformatics thus providing for a massive enrichment). We chose the top six representatives for further study. They fell into three clusters whose members bore reasonable structural similarities to each other (two were in fact isomers), lending strength to the self-consistency of both our conceptual and experimental strategies. Existing literature had suggested that indole-3-carbinol might play a similar role to that of our fragments, but in our hands it was without effect; nor was it structurally similar to any of our hits. As there was no evidence that the fragments could affect toxicity directly, we looked for effects on transporter transcript levels. In our hands, only the ENT1-3 uptake and ABCC2,3,4,5, and 10 efflux transporters displayed measurable transcripts in Panc1 cultures, along with a ribonucleoside reductase RRM1 known to affect gemcitabine toxicity. Very strikingly, the addition of gemcitabine alone increased the expression of the transcript for ABCC2 (MRP2) by more than 12-fold, and that of RRM1 by more than fourfold, and each of the fragment "hits" served to reverse this. However, an inhibitor of ABCC2 was without significant effect, implying that RRM1 was possibly the more significant player. These effects were somewhat selective for Panc cells. It seems, therefore, that while the effects we measured were here mediated more by efflux than influx transporters, and potentially by other means, the binary weapon idea is hereby fully confirmed: it is indeed possible to find molecules that manipulate the expression of transporters that are involved in the bioactivity of a pharmaceutical drug. This opens up an entirely new area, that of chemical genomics-based drug targeting.

In previous work, we have assessed the structural similarities between marketed drugs ('drugs') and endogenous natural human metabolites ('metabolites' or 'endogenites'), using 'fingerprint' methods in common use, and the Tanimoto and Tversky similarity metrics, finding that the fingerprint encoding used had a dramatic effect on the apparent similarities observed. By contrast, the maximal common substructure (MCS), when the means of determining it is fixed, is a means of determining similarities that is largely independent of the fingerprints, and also has a clear chemical meaning. We here explored the utility of the MCS and metrics derived therefrom. In many cases, a shared scaffold helps cluster drugs and endogenites, and gives insight into enzymes (in particular transporters) that they both share. Tanimoto and Tversky similarities based on the MCS tend to be smaller than those based on the MACCS fingerprint-type encoding, though the converse is also true for a significant fraction of the comparisons. While no single molecular descriptor can account for these differences, a machine learning-based analysis of the nature of the differences (MACCS&#95;Tanimoto vs MCS&#95;Tversky) shows that they are indeed deterministic, although the features that are used in the model to account for this vary greatly with each individual drug. The extent of its utility and interpretability vary with the drug of interest, implying that while MCS is neither 'better' nor 'worse' for every drug-endogenite comparison, it is sufficiently different to be of value. The overall conclusion is thus that the use of the MCS provides an additional and valuable strategy for understanding the structural basis for similarities between synthetic, marketed drugs and natural intermediary metabolites.

Background: Previous studies compared the molecular similarity of marketed drugs and endogenous human metabolites (endogenites), using a series of fingerprint-type encodings, variously ranked and clustered using the Tanimoto (Jaccard) similarity coefficient (TS). Because this gives equal weight to all parts of the encoding (thence to different substructures in the molecule) it may not be optimal, since in many cases not all parts of the molecule will bind to their macromolecular targets. Unsupervised methods cannot alone uncover this. We here explore the kinds of differences that may be observed when the TS is replaced-in a manner more equivalent to semi-supervised learning-by variants of the asymmetric Tversky (TV) similarity, that includes α and β parameters., Results: Dramatic differences are observed in (i) the drug-endogenite similarity heatmaps, (ii) the cumulative "greatest similarity" curves, and (iii) the fraction of drugs with a Tversky similarity to a metabolite exceeding a given value when the Tversky α and β parameters are varied from their Tanimoto values. The same is true when the sum of the α and β parameters is varied. A clear trend toward increased endogenite-likeness of marketed drugs is observed when α or β adopt values nearer the extremes of their range, and when their sum is smaller. The kinds of molecules exhibiting the greatest similarity to two interrogating drug molecules (chlorpromazine and clozapine) also vary in both nature and the values of their similarity as α and β are varied. The same is true for the converse, when drugs are interrogated with an endogenite. The fraction of drugs with a Tversky similarity to a molecule in a library exceeding a given value depends on the contents of that library, and α and β may be "tuned" accordingly, in a semi-supervised manner. At some values of α and β drug discovery library candidates or natural products can "look" much more like (i.e., have a numerical similarity much closer to) drugs than do even endogenites., Conclusions: Overall, the Tversky similarity metrics provide a more useful range of examples of molecular similarity than does the simpler Tanimoto similarity, and help to draw attention to molecular similarities that would not be recognized if Tanimoto alone were used. Hence, the Tversky similarity metrics are likely to be of significant value in many general problems in cheminformatics.

Background: Conjunctival myxomas are rare, benign, connective tissue tumours that classically present as slow-growing, painless, well-circumscribed masses (Arch Ophthalmol 124:735-8, 2006; Case Rep Ophthalmol 3:145-50, 2012). There have been 29 cases reported in the literature (Arch Ophthalmol 124:735-8, 2006; Malays J Med Sci 20(1):92-4, 2013; Case Rep Ophthalmol 3:145-50, 2012; Middle East Afr J Ophthalmol 19(3):353-3, 2012). We present a case with atypical features, and emphasize the importance of excisional biopsies for diagnosing indeterminate conjunctival lesions., Case Presentation: A 32 year old Korean woman presented with a 5 mm × 7 mm × 3 mm pedunculated firm cystic lesion on the inferior palpebral conjunctiva of her right lower eyelid. The lesion had rapidly enlarged over the course of a week. She gave a history of uncomplicated bilateral epiblepharon correction performed in Korea three months prior. There were no systemic features, or family history of genetic conditions. The lesion was excised under local anaesthesia and reported to be a conjunctival myxoma. The clinical and histopathological features of this lesion were consistent with previous reports on conjunctival myxoma (Arch Ophthalmol 124:735-8, 2006; Arch Ophthalmol 101:1416-20, 1983; Case Rep Ophthalmol 3:145-50, 2012; Am J Ophthalmol 102(1):80-84, 1986). The unusual features of this case were, the rapid growth of the lesion - with the previously documented mean time before presentation being 34 months (range 3 months - 24 years) (Arch Ophthalmol 124:735-8, 2006; Case Rep Ophthalmol 3:145-50, 2012); the location of the lesion in the inferior palpebral conjunctiva - 93 % of previously reported cases had occurred in the bulbar conjunctiva (Arch Ophthalmol 124:735-8, 2006; Case Rep Ophthalmol 3:145-50, 2012); and its occurrence in association with recent eyelid surgery - which has never been reported., Conclusion: This case of conjunctival myxoma adds to the small number of documented cases, by demonstrating an atypical presentation. Conjunctival myxomas can occur in association with the Carney Complex, which is an autosomal dominant syndrome associated with benign tumours, spotty mucocutaneous pigmentation, and endocrine overactivity (Ophthalmic Surg Lasers Imaging 39(6):514-6, 2008). Ophthalmic manifestations of the Carney Complex have been found to precede vascular embolic events secondary to cardiac myxoma, thus early diagnosis of conjunctival myxoma can prevent potentially devastating consequences (Ophthalmic Surg Lasers Imaging 39(6):514-6, 2008). The different presentations of this rare tumour emphasise the importance of excisional biopsies in diagnosing indeterminate conjunctival lesions; and its association with cardiac myxoma, highlights the need for cardiac investigations in all patients who present with conjunctival myxoma (J Ophthalmol (1);1-5, 2014; Ophthalmic Surg Lasers Imaging 39(6):514-6, 2008).

We bring together fifteen, nonredundant, tabulated collections (amounting to 696 separate measurements) of the apparent permeability (P app) of Caco-2 cells to marketed drugs. While in some cases there are some significant interlaboratory disparities, most are quite minor. Most drugs are not especially permeable through Caco-2 cells, with the median P app value being some 16 ⋅ 10(-6) cm s(-1). This value is considerably lower than those (1,310 and 230 ⋅ 10(-6) cm s(-1)) recently used in some simulations that purported to show that P app values were too great to be transporter-mediated only. While these values are outliers, all values, and especially the comparatively low values normally observed, are entirely consistent with transporter-only mediated uptake, with no need to invoke phospholipid bilayer diffusion. The apparent permeability of Caco-2 cells to marketed drugs is poorly correlated with either simple biophysical properties, the extent of molecular similarity to endogenous metabolites (endogenites), or any specific substructural properties. In particular, the octanol:water partition coefficient, logP, shows negligible correlation with Caco-2 permeability. The data are best explained on the basis that most drugs enter (and exit) Caco-2 cells via a multiplicity of transporters of comparatively weak specificity.

Background: A recent comparison showed the extensive similarities between the structural properties of metabolites in the reconstructed human metabolic network ("endogenites") and those of successful, marketed drugs ("drugs")., Results: Clustering indicated the related but differential population of chemical space by endogenites and drugs. Differences between the drug-endogenite similarities resulting from various encodings and judged by Tanimoto similarity could be related simply to the fraction of the bitstrings set to 1. By extracting drug/endogenite substructures, we develop a novel family of fingerprints, the Drug Endogenite Substructure (DES) encodings, based on the ranked frequency of the various substructures. These provide a natural assessment of drug-endogenite likeness, and may be used as descriptors with which to derive quantitative structure-activity relationships (QSARs)., Conclusions: "Drug-endogenite likeness" seems to have utility, and leads to a simple, novel and interpretable substructure-based molecular encoding for cheminformatics.