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In this study, the rates of reoperation for stress urinary incontinence (SUI) and pelvic organ prolapse (POP) in women who underwent a mid-urethral sling (MUS) with or without concurrent colporrhaphy were evaluated. An academic faculty practice consortium database was used to identify a cohort of patients treated surgically for SUI with or without concurrent POP repair (apical, anterior, posterior, or a combination of the three) with or without hysterectomy between 2009 and 2011. A total of 20,484 patients matched the criteria. Of patients who underwent a MUS, 7.2% underwent secondary surgery, with a higher rate of 8.6% associated with those who underwent concurrent prolapse repair (Apical repair HR 1.84, p < .01; Anterior compartment repair HR 1.47, p < .01). Concurrent hysterectomy was associated with a lower hazard of secondary prolapse surgery (HR 0.48; p < .01) if the initial surgery involved a complete POP repair. Prolapse mesh repair resulted in a higher hazard of additional surgery (HR 1.43, p < .01). Medicaid insurance was also associated with an increased hazard ratio compared to commercial insurance for secondary surgery (HR 1.32, p < .01). For women undergoing MUS with complete prolapse repair, concurrent hysterectomy is associated with lower secondary surgery rates. Concurrent prolapse repair with mesh is associated with higher secondary surgery rates. Synopsis: For women undergoing MUS (mid-urethral sling) with complete prolapse repair, concurrent hysterectomy is associated with lower secondary surgery rates. Concurrent prolapse repair with mesh is associated with higher secondary surgery rates.Impact StatementWhat is already known on this subject? Stress urinary incontinence (SUI) and pelvic organ prolapse (POP) can present at the same time and negatively impact patients’ quality of life. There is little data regarding reoperation rates for patients who undergo both MUS and colporrhaphy in one setting.What do the results of this study add? This study found that patients who undergo concurrent MUS (mid-urethral sling) and complete POP repair with the addition of hysterectomy had a lower risk of secondary surgery.What are the implications of these findings for clinical practice and/or further research? Our data can be used by surgeons to counsel patients on the risks of re-operation for SUI for those who would like to undergo concurrent POP repair with or without hysterectomy. What is already known on this subject? Stress urinary incontinence (SUI) and pelvic organ prolapse (POP) can present at the same time and negatively impact patients’ quality of life. There is little data regarding reoperation rates for patients who undergo both MUS and colporrhaphy in one setting. What do the results of this study add? This study found that patients who undergo concurrent MUS (mid-urethral sling) and complete POP repair with the addition of hysterectomy had a lower risk of secondary surgery. What are the implications of these findings for clinical practice and/or further research? Our data can be used by surgeons to counsel patients on the risks of re-operation for SUI for those who would like to undergo concurrent POP repair with or without hysterectomy.

Additional file 1: Fig. S1. Ranked genes by median normalized read counts in units of Log2 counts per million (Log2CPM) in the subcortical white matter of the pre-frontal cortex (PFCw), and gray matter of the superior temporal sulcus (STS), caudate nucleus (CN), and hippocampus (HP) of uninfected animals. Dotted lines indicate location of marker genes associated with neurons (MAP2), astrocytes (GFAP), microglia (P2RY12), and oligodendrocytes (MOG) within ranked distribution. Fig. S2. T-stochastic neighborhood embedding analysis (t-SNE) of gene expression profiles from the pre-frontal cortex white matter (black), superior temporal sulcus (blue), caudate nucleus (red), and hippocampus (green) of uninfected animals. Outlier sample [Animal 43661 pre-frontal cortex white matter] is included. Symbols represent individual animals. Circles indicate 95% confidence intervals. Fig. S3. Regional eigengene expression and corresponding top fifteen most significantly enriched (p < 0.01 by Fisher’s exact test) biological processes GO terms within region specific modules (PFCw-specific [MEmagenta, MEmidnightblue], STS-specific [MEtan], CN-specific [MEpurple, MEred], HP-specific [MEsalmon]) determined by weighted gene co-expression network analysis from uninfected animals. *p < 0.05 by linear mixed effects model (region effect). Boxplots represent quartiles. Fig. S4. Normalized read counts of genes encoding for chemokines in the STS (blue), PFCw (black), CN (red), and HP (green) of uninfected animals. Expression levels are displayed in normalized read counts in units of Log2 counts per million (Log2CPM). Brackets indicate structural chemokine classes. Fig. S5. Log2 Fold change of genes regulating inflammatory processes and synaptic functions between SHIV infected and uninfected animals in all brain regions (gray), STS (blue), and PFCw (red). Dotted line indicates a fold change of 1. Fig. S6. T-stochastic neighborhood embedding (t-SNE) analysis of gene expression profiles from SHIV infected and uninfected animals. (Left) t-SNE plot indicates clustering of gene expression profiles by region and SHIV infection status (SHIV infected [pink], uninfected [black]) with removal of outlier sample [Animal 43661 Pre-frontal cortex white matter]. (Right) t-SNE plot shows all samples including the outlier with data points indicating regions (pre-frontal cortex white matter (P), superior temporal sulcus [S], caudate nucleus [C], hippocampus [H]) and infection status (color) and individual animals (symbols). Circles indicate 95% confidence intervals. Fig. S7 Expression levels of genes (expressed as normalized read counts in units of Log2 Counts per million [CPM]) related to synaptic functions, endoplasmic reticulum stress, and ATP synthase subunits in the PFCw of SHIV infected (red) and uninfected (gray) animals. Violin plots indicate quartiles. P values determined by linear mixed effects model. Table S1 Animal/Sample Data. Animal information—Animal ID, Sex, Age, SHIV infection status, and medical cull rationale. Sample Information—Sample ID, Sample Code, Tissue identity, Tissue weight (mg), purified RNA absorbance ratios (A260/A280 and A260/A230), and sample RNA yield. Table S3. Reagents used for flow cytometric analysis.

The prenatal period is a critical window for the development of autism spectrum disorder (ASD). The relationship between prenatal nutrients and gestational gene expression in mothers of children later diagnosed with ASD or non-typical development (Non-TD) is poorly understood. Maternal blood collected prospectively during pregnancy provides insights into the effects of nutrition, particularly one-carbon metabolites, on gene pathways and neurodevelopment. Genome-wide transcriptomes were measured with microarrays in 300 maternal blood samples in Markers of Autism Risk in Babies-Learning Early Signs. Sixteen different one-carbon metabolites, including folic acid, betaine, 5'-methyltretrahydrofolate (5-MeTHF), and dimethylglycine (DMG) were measured. Differential expression analysis and weighted gene correlation network analysis (WGCNA) were used to compare gene expression between children later diagnosed as typical development (TD), Non-TD and ASD, and to one-carbon metabolites. Using differential gene expression analysis, six transcripts (TGR-AS1, SQSTM1, HLA-C, and RFESD) were associated with child outcomes (ASD, Non-TD, and TD) with genome-wide significance. Genes nominally differentially expressed between ASD and TD significantly overlapped with seven high confidence ASD genes. WGCNA identified co-expressed gene modules significantly correlated with 5-MeTHF, folic acid, DMG, and betaine. A module enriched in DNA methylation functions showed a suggestive protective association with folic acid/5-MeTHF concentrations and ASD risk. Maternal plasma betaine and DMG concentrations were associated with a block of co-expressed genes enriched for adaptive immune, histone modification, and RNA processing functions. These results suggest that the prenatal maternal blood transcriptome is a sensitive indicator of gestational one-carbon metabolite status and changes relevant to children's later neurodevelopmental outcomes. LAY SUMMARY: Pregnancy is a time when maternal nutrition could interact with genetic risk for autism spectrum disorder. Blood samples collected during pregnancy from mothers who had a prior child with autism were examined for gene expression and nutrient metabolites, then compared to the diagnosis of the child at age three. Expression differences in gene pathways related to the immune system and gene regulation were observed for pregnancies of children with autism and non-typical neurodevelopment and were associated with maternal nutrients.

AimsMachine learning (ML) binary classification in diagnostic histopathology is an area of intense investigation. Several assumptions, including training image quality/format and the number of training images required, appear to be similar in many studies irrespective of the paucity of supporting evidence. We empirically compared training image file type, training set size, and two common convolutional neural networks (CNNs) using transfer learning (ResNet50 and SqueezeNet).Methods and resultsThirty haematoxylin and eosin (H&E)-stained slides with carcinoma or normal tissue from three tissue types (breast, colon, and prostate) were photographed, generating 3000 partially overlapping images (1000 per tissue type). These lossless Portable Networks Graphics (PNGs) images were converted to lossy Joint Photographic Experts Group (JPG) images. Tissue type-specific binary classification ML models were developed by the use of all PNG or JPG images, and repeated with a subset of 500, 200, 100, 50, 30 and 10 images. Eleven models were generated for each tissue type, at each quantity of training images, for each file type, and for each CNN, resulting in 924 models. Internal accuracies and generalisation accuracies were compared. There was no meaningful significant difference in accuracies between PNG and JPG models. Models trained with more images did not invariably perform better. ResNet50 typically outperformed SqueezeNet. Models were generalisable within a tissue type but not across tissue types.ConclusionsLossy JPG images were not inferior to lossless PNG images in our models. Large numbers of unique H&E-stained slides were not required for training optimal ML models. This reinforces the need for an evidence-based approach to best practices for histopathological ML.

P values for correlation of miRNA expression in RNA extracted from blood samples from canine patients with normal bladders, Table S2. P values for correlation of miRNA expression in RNA extracted from urine samples from canine patients with normal bladders, Table S3. P values for correlation of miRNA expression in RNA extracted from blood samples from canine patients with LUTD, Table S4. P values for correlation of miRNA expression in RNA extracted from urine samples from canine patients with LUTD, Table S5. P values for correlation miRNA expression in RNA extracted from blood samples from canine patients with TCC, Table S6. P values for correlation of miRNA expression in RNA extracted from urine samples from canine patients with TCC. (DOCX 28 kb)

Objective: To evaluate the patterns of impact of neoadjuvant chemotherapy (NAC) on renal function across the initial year following treatment for muscle-invasive bladder cancer (MIBC) with radical cystectomy (RC). Methods: We reviewed the charts of 241 patients who underwent RC for urothelial carcinoma of the bladder between 2003-14 at our institution. Renal function was evaluated at multiple time points (pre-chemotherapy, pre-operatively, post-operatively, 6-12months follow-up), and then classified by CKD staging. Univariable and multivariable logistic regression analyses were performed to determine relationship between NAC and change in CKD stage. Results: Of the 241 patients who underwent RC for urothelial carcinoma of the bladder, 66 (27%) received NAC and 175 (73%) did not. In multivariable analysis, NAC was significantly associated with adecrease of at least one CKD stage from baseline to post-op (p = 0.009), but not to the 6-12months follow-up time point (p = 0.050). The loss of GFR in the NAC cohort occurs up-front with chemotherapy, but the peri-operative course is similar to those who underwent cystectomy alone. Of the 15 NAC patients (26.8%) who were Stage 3 CKD prior to chemotherapy, none progressed to ahigher stage CKD. Conclusion: NAC is associated with an initial decline in GFR, which then remains stable through the first year following RC. Despite an initial insult, patients receiving NAC are not vulnerable to further deterioration. When appropriately selected, NAC does not appear to result in aclinically significant deterioration of renal function.

Fibrodysplasia ossificans progressiva (FOP) leads to disabling heterotopic ossification (HO) from episodic flare-ups. However, the natural history of FOP flare-ups is poorly understood. A 78-question survey on FOP flare-ups, translated into 15 languages, was sent to 685 classically-affected patients in 45 countries (six continents). Five hundred patients or knowledgeable informants responded (73%; 44% males, 56% females; ages: 1 to 71 years; median: 23 years). The most common presenting symptoms of flare-ups were swelling (93%), pain (86%), or decreased mobility (79%). Seventy-one percent experienced a flare-up within the preceding 12 months (52% spontaneous; 48% trauma-related). Twenty-five percent of those who had received an intramuscular injection reported an immediate flare-up at the injection site, 84% of whom developed HO. Axial flare-ups most frequently involved the back (41.6%), neck (26.4%), or jaw (19.4%). Flare-ups occurred more frequently in the upper limbs before 8 years of age, but more frequently in the lower limbs thereafter. Appendicular flare-ups occurred more frequently at proximal than at distal sites without preferential sidedness. Seventy percent of patients reported functional loss from a flare-up. Thirty-two percent reported complete resolution of at least one flare-up and 12% without any functional loss (mostly in the head or back). The most disabling flare-ups occurred at the shoulders or hips. Surprisingly, 47% reported progression of FOP without obvious flare-ups. Worldwide, 198 treatments were reported; anti-inflammatory agents were most common. Seventy-five percent used short-term glucocorticoids as a treatment for flare-ups at appendicular sites. Fifty-five percent reported that glucocorticoids improved symptoms occasionally whereas 31% reported that they always did. Only 12% reported complete resolution of a flare-up with glucocorticoids. Forty-three percent reported rebound symptoms within 1 to 7 days after completing a course of glucocorticoids. This study is the first comprehensive global assessment of FOP flare-ups and establishes a critical foundation for the design and evaluation of future clinical trials.

BackgroundOver 40% of male and ∼16% of female carriers of a premutation FMR1 allele (55-200 CGG repeats) will develop fragile X-associated tremor/ataxia syndrome, an adult onset neurodegenerative disorder, while about 20% of female carriers will developfragile X-associated primary ovarian insufficiency. Marked elevation in FMR1 mRNA transcript levels has been observed with premutation alleles, and RNA toxicity due to increased mRNA levels is the leading molecular mechanism proposed for these disorders. However, although the FMR1 gene undergoes alternative splicing, it is unknown whether all or only some of the isoforms are overexpressed in premutation carriers and which isoforms may contribute to the premutation pathology.MethodsTo address this question, we have applied a long-read sequencing approach using single-molecule real-time (SMRT) sequencing and qRT-PCR.ResultsOur SMRT sequencing analysis performed on peripheral blood mononuclear cells, fibroblasts and brain tissue samples derived from premutation carriers and controls revealed the existence of 16 isoforms of 24 predicted variants. Although the relative abundance of all mRNA isoforms was significantly increased in the premutation group, as expected based on the bulk increase in mRNA levels, there was a disproportionate (fourfold to sixfold) increase, relative to the overall increase in mRNA, in the abundance of isoforms spliced at both exons 12 and 14, specifically Iso10 and Iso10b, containing the complete exon 15 and differing only in splicing in exon 17.ConclusionsThese findings suggest that RNA toxicity may arise from a relative increase of all FMR1 mRNA isoforms. Interestingly, the Iso10 and Iso10b mRNA isoforms, lacking the C-terminal functional sites for fragile X mental retardation protein function, are the most increased in premutation carriers relative to normal, suggesting a functional relevance in the pathology of FMR1-associated disorders.

BackgroundGreater than 200 CGG repeats in the 5'UTR of the FMR1 gene lead to epigenetic silencing and lack of the FMR1 protein, causing fragile X Syndrome. Individual carriers of a premutation (PM) allele with 55-200 CGG repeats are typically unmethylated and can present with clinical features defined as FMR1-associated conditions.MethodsBlood samples from 17 male PM carriers were assessed clinically and molecularly by Southern blot, western blot, PCR and QRT-PCR. Blood and brain tissue from an additional 18 PM males were also similarly examined. Continuous outcomes were modelled using linear regression and binary outcomes were modelled using logistic regression.ResultsMethylated alleles were detected in different fractions of blood cells in all PM cases (n=17). CGG repeat numbers correlated with percent of methylation and mRNA levels and, especially in the upper PM range, with greater number of clinical involvements. Inter-tissue/intra-tissue somatic instability and differences in percent methylation were observed between blood and fibroblasts (n=4) and also observed between blood and different brain regions in three of the 18 PM cases examined. CGG repeat lengths in lymphocytes remained unchanged over a period of time ranging from 2 to 6 years, three cases for whom multiple samples were available.ConclusionsIn addition to CGG size instability, individuals with a PM expanded allele can exhibit methylation and display more clinical features likely due to RNA toxicity and/or FMR1 silencing. The observed association between CGG repeat length and percent of methylation with the severity of the clinical phenotypes underscores the potential value of methylation in affected PM to further understand penetrance, inform diagnosis and expand treatment options.