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The Journal of Urology Mar 2022After radical prostatectomy (RP), clinical complaints of new onset storage symptoms may be related to anastomotic strictures or may accommodate for stress urinary...
PURPOSE
After radical prostatectomy (RP), clinical complaints of new onset storage symptoms may be related to anastomotic strictures or may accommodate for stress urinary incontinence; however, a subgroup of men will experience storage symptoms in the absence of stricture or stress urinary incontinence. As therapies for overactive bladder have improved, we sought to assess the prevalence, natural history and risk factors of storage dysfunction in continent men.
MATERIALS AND METHODS
We retrospectively analyzed urinary symptom questionnaires completed by patients who were continent prior to RP and did not have postoperative anastomotic strictures at our institution from 2002 to 2019. storage dysfunction, assessed as new onset or worsening urgency or frequency, was assessed at 6, 12, 18 and 24 months after RP, and association between it and patient and preoperative factors was determined.
RESULTS
A total of 2,619 patients were included in the final analysis. An initial 34% of patients reported storage symptoms at 6 months, which decreased to 26% at later followup. We found evidence that minimally invasive surgery and nonWhite race were associated with reporting worsening symptoms. The association between postoperative hematoma and worsening symptoms was less conclusive but was of clear clinical relevance (OR 3.15; 95% CI 1.04, 9.54; p=0.042).
CONCLUSIONS
A significant number of RP patients experience storage symptoms. Patients who underwent minimally invasive surgery are at higher risk. At-risk patients should be counseled on the incidence of storage symptoms and offered early treatment per overactive bladder guidelines.
Topics: Hematoma; Humans; Incidence; Male; Middle Aged; Nocturia; Postoperative Complications; Prostatectomy; Prostatic Neoplasms; Retrospective Studies; Surveys and Questionnaires; Urinary Bladder, Overactive
PubMed: 34694923
DOI: 10.1097/JU.0000000000002312 -
BMC Bioinformatics Apr 2023RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of...
BACKGROUND
RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore presents a major barrier for researchers to adopt best-practice methods and up-to-date versions of software.
RESULTS
Here we present a streamlined and universal de novo transcriptome assembly and annotation pipeline, transXpress, implemented in Snakemake. transXpress supports two popular assembly programs, Trinity and rnaSPAdes, and allows parallel execution on heterogeneous cluster computing hardware.
CONCLUSIONS
transXpress simplifies the use of best-practice methods and up-to-date software for de novo transcriptome assembly, and produces standardized output files that can be mined using SequenceServer to facilitate rapid discovery of new genes and proteins in non-model organisms.
Topics: Transcriptome; Sequence Analysis, RNA; RNA-Seq; Software; Gene Expression Profiling; Molecular Sequence Annotation
PubMed: 37016291
DOI: 10.1186/s12859-023-05254-8 -
Frontiers in Cardiovascular Medicine 2021Extra-pulmonary vein triggers can play a significant role in atrial fibrillation recurrence after catheter ablation. We explored the characteristics of the...
Extra-pulmonary vein triggers can play a significant role in atrial fibrillation recurrence after catheter ablation. We explored the characteristics of the extra-pulmonary vein (PV) triggers in and repeat atrial fibrillation (AF) catheter ablation (AFCA). We included 2,118 patients who underwent a AFCA (women 27.6%, 59.2 ± 10.9 years old, paroxysmal AF 65.9%) and 227 of them conducted repeat procedures. All included patients underwent isoproterenol provocation tests at the end of the procedure, and then we analyzed extra-PV triggers-related factors. Extra-PV triggers were documented in 11.7% of patients undergoing AFCA (1.22 ± 0.46 foci per patient) and 28.6% undergoing repeat AFCA (1.49 ± 0.73 foci per patient). Older age and higher LA volume index in procedures and women, diabetes, and higher parasympathetic nerve activity (heart rate variability) in repeat-AFCA were independently associated with the existence of extra-PV triggers. The septum (19.9%), coronary sinus (14.7%), and superior vena cava (11.2%) were common extra-PV foci. Among 46 patients who were newly found to have mappable extra-PV triggers upon repeat procedures, 15 (32.6%) matched with the previous focal or empirical extra-PV ablation sites. The rate of AF recurrence was significantly higher in patients with extra-PV triggers than in those without after (HR 1.91, 95% CI 1.54-2.38, < 0.001) and repeat procedures (HR 2.68, 95% CI 1.63-4.42, < 0.001). Extra-PV triggers were commonly found in AF patients with significant remodeling and previous empirical extra-PV ablation. The existence of extra-PV triggers was independently associated with poorer rhythm outcomes after the and repeat AFCA.
PubMed: 34805314
DOI: 10.3389/fcvm.2021.759967 -
Scientific Data May 2023Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed...
Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Attitude to disperse is unevenly distributed among individuals within populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here, we assembled and annotated the first de novo transcriptome of the head tissues of Salamandra salamandra from individuals, representative of distinct behavioral profiles. We obtained 1,153,432,918 reads, which were successfully assembled and annotated. The high-quality of the assembly was confirmed by three assembly validators. The alignment of contigs against the de novo transcriptome led to a mapping percentage higher than 94%. The homology annotation with DIAMOND led to 153,048 (blastx) and 95,942 (blastp) shared contigs, annotated on NR, Swiss-Prot and TrEMBL. The domain and site protein prediction led to 9850 GO-annotated contigs. This de novo transcriptome represents reliable reference for comparative gene expression studies between alternative behavioral types, for comparative gene expression studies within Salamandra, and for whole transcriptome and proteome studies in amphibians.
Topics: Animals; Gene Expression Profiling; Genetic Association Studies; High-Throughput Nucleotide Sequencing; Larva; Molecular Sequence Annotation; Salamandra; Transcriptome
PubMed: 37244908
DOI: 10.1038/s41597-023-02217-9 -
Frontiers in Immunology 2022To examine the production time, type, and MFI of post-transplantation HLA antibodies, and their effects on haplo-HSCT outcomes, we retrospectively included 116 patients...
To examine the production time, type, and MFI of post-transplantation HLA antibodies, and their effects on haplo-HSCT outcomes, we retrospectively included 116 patients who were negative for pre-existing HLA antibodies. In total, 322 serum samples from pre-transplantation to post-transplantation were dynamically tested by Luminex and single-antigen bead reagents. Patients were divided into: HLA antibody persistently negative group (group 1), the HLA antibody transiently positive group (group 2), the HLA antibody non-persistently positive group (group 3), and the HLA antibody persistently positive group (group 4). Group 4 included DSA+non-DSA (NDSA) (group 4a) and NDSA (group 4b) groups. The detection rate of HLA antibodies was 75.9% (88/116). The median MFI for HLA antibodies was 2439 (1033-20162). The incidence of II-IV aGvHD was higher in group 2 than in group 1 (52.6% vs 17.9%, P < 0.01); in group 4a than in group 1 (87.5% vs 17.9%, P < 0.001); and in group 4a than in group 4b (87.5% vs 40.0%, P = 0.001). The DFS (37.5% vs 85.7%, P < 0.01) and OS (37.5% vs 85.7%, P < 0.01) of group 4a were lower than those of group 1. The DFS (48.0% vs 85.7%, P < 0.01) and OS (56.0% vs 85.7%, P = 0.03) of group 4b were lower than those of group 1. Multivariate analysis showed that HLA antibody being transiently positive (HR: 5.30; 95% CI: 1.71-16.42, P = 0.01) and persistently positive (HR: 5.67; 95% CI: 2.00-16.08, P < 0.01) were both associated with a higher incidence of II-IV aGvHD. Persistently positive HLA antibodies were a risk factor for reduced DFS (HR: 6.57; 95% CI: 2.08-20.70, P < 0.01) and OS (HR: 5.51; 95% CI: 1.73-17.53, P < 0.01). DSA and NDSA can be detected since 15 days after haplo-HSCT in patients without pre-existing HLA antibodies, and affect aGvHD, DFS, and OS. Haplo-HSCT patients must be monitored for HLA antibodies changes for appropriate preventive clinical management, and we recommend that 1-month post-transplantation is the best test time point.
Topics: Humans; Retrospective Studies; Hematologic Neoplasms; Antibodies; Risk Factors; Hematopoietic Stem Cell Transplantation
PubMed: 36532004
DOI: 10.3389/fimmu.2022.1047200 -
Frontiers in Physiology 2022Embryonic-to-neonatal development in chicken is characterized by high rates of lipid oxidation in the late-term embryonic liver and high rates of lipogenesis in the...
Embryonic-to-neonatal development in chicken is characterized by high rates of lipid oxidation in the late-term embryonic liver and high rates of lipogenesis in the neonatal liver. This rapid remodeling of hepatic mitochondrial and cytoplasmic networks occurs without symptoms of hepatocellular stress. Our objective was to characterize the metabolic phenotype of the embryonic and neonatal liver and explore whether these metabolic signatures are preserved in primary cultured hepatocytes. Plasma and liver metabolites were profiled using mass spectrometry based metabolomics on embryonic day 18 (ed18) and neonatal day 3 (nd3). Hepatocytes from ed18 and nd3 were isolated and cultured, and treated with insulin, glucagon, growth hormone and corticosterone to define hormonal responsiveness and determine their impacts on mitochondrial metabolism and lipogenesis. Metabolic profiling illustrated the clear transition from the embryonic liver relying on lipid oxidation to the neonatal liver upregulating lipogenesis. This metabolic phenotype was conserved in the isolated hepatocytes from the embryos and the neonates. Cultured hepatocytes from the neonatal liver also maintained a robust response to insulin and glucagon, as evidenced by their contradictory effects on lipid oxidation and lipogenesis. In summary, primary hepatocytes from the embryonic and neonatal chicken could be a valuable tool to investigate mechanisms regulating hepatic mitochondrial metabolism and lipogenesis.
PubMed: 35530509
DOI: 10.3389/fphys.2022.870451 -
European Journal of Human Genetics :... Jan 2021By performing whole-genome sequencing in a Swedish cohort of 71 parent-offspring trios, in which the child in each family is affected by systemic lupus erythematosus...
By performing whole-genome sequencing in a Swedish cohort of 71 parent-offspring trios, in which the child in each family is affected by systemic lupus erythematosus (SLE, OMIM 152700), we investigated the contribution of de novo variants to risk of SLE. We found de novo single nucleotide variants (SNVs) to be significantly enriched in gene promoters in SLE patients compared with healthy controls at a level corresponding to 26 de novo promoter SNVs more in each patient than expected. We identified 12 de novo SNVs in promoter regions of genes that have been previously implicated in SLE, or that have functions that could be of relevance to SLE. Furthermore, we detected three missense de novo SNVs, five de novo insertion-deletions, and three de novo structural variants with potential to affect the expression of genes that are relevant for SLE. Based on enrichment analysis, disease-affecting de novo SNVs are expected to occur in one-third of SLE patients. This study shows that de novo variants in promoters commonly contribute to the genetic risk of SLE. The fact that de novo SNVs in SLE were enriched to promoter regions highlights the importance of using whole-genome sequencing for identification of de novo variants.
Topics: Adolescent; Adult; Child; Female; Gene Frequency; Humans; Lupus Erythematosus, Systemic; Male; Middle Aged; Mutation, Missense; Polymorphism, Single Nucleotide; Promoter Regions, Genetic
PubMed: 32724065
DOI: 10.1038/s41431-020-0698-5 -
Children (Basel, Switzerland) Dec 2021The available endoscopic techniques for ureterocele decompression include laser puncture (LP), electrosurgical incision (ES), and cold-knife incision. This systematic... (Review)
Review
De Novo Vesicoureteral Reflux Following Ureterocele Decompression in Children: A Systematic Review and Meta-Analysis Comparing Laser Puncture versus Electrosurgical Incision Techniques.
BACKGROUND
The available endoscopic techniques for ureterocele decompression include laser puncture (LP), electrosurgical incision (ES), and cold-knife incision. This systematic review was performed to compare the efficacy of LP versus ES techniques with special emphasis on de novo VUR.
METHODS
Four databases were systematically searched by the authors. The inclusion criteria were all comparative studies in which ureterocele decompression was performed by either LP or ES endoscopic techniques. Outcomes including the incidence of de novo VUR, the need for endoscopic retreatment of the ureterocele, and the need for secondary surgical procedures were studied. Risk ratios (RR) were calculated for all outcomes and the Mantel-Haenszel method was utilized for the estimation of pooled RR. The methodological quality was assessed by the Downs and Black scale.
RESULTS
Five studies were considered for systematic review, while four of them were included in the meta-analysis. Out of 202 children, 67 developed de novo VUR. Significantly lower rates of reflux were observed in the LP group vis-a-vis ES group (RR = 0.17, 95% CI 0.09 to 0.32, 0.00001). Endoscopic retreatment rates ( = 20) demonstrated no significant difference among the two patient groups (RR = 0.66, 95% CI 0.26-1.68, = 0.38). A total of 46 secondary procedures were performed in 170 children, mostly ureteral re-implantations, with a significantly lower need of secondary surgeries following LP versus ES (RR = 0.26, 95% CI 0.13-0.49, 0.0001). The risk of bias in the included studies was low-to-moderate.
CONCLUSIONS
When compared to the ES technique, the LP technique is associated with a significantly low incidence of de novo VUR and requirement for secondary surgeries (particularly anti-reflux surgeries). Endoscopic retreatment rates showed no significant difference between the two techniques. However, due to the moderate risk of bias in two out of four included studies, randomized controlled trials are needed in the future.
PubMed: 35053634
DOI: 10.3390/children9010010 -
Computational and Structural... 2022Various deep learning-based architectures for molecular generation have been proposed for drug design. The flourish of the molecular generation methods and...
Various deep learning-based architectures for molecular generation have been proposed for drug design. The flourish of the molecular generation methods and applications has created a great demand for the visualization and functional profiling for the generated molecules. An increasing number of publicly available chemogenomic databases sets good foundations and creates good opportunities for comprehensive profiling of the de novo library. In this paper, we present DenovoProfiling, a webserver dedicated to library visualization and functional profiling. Currently, DenovoProfiling contains six modules: (1) identification & visualization module for chemical structure visualization and identify the reported structures, (2) chemical space module for chemical space exploration using similarity maps, principal components analysis (PCA), drug-like properties distribution, and scaffold-based clustering, (3) ADMET prediction module for predicting the ADMET properties of the molecules, (4) molecular alignment module for three dimensional molecular shape analysis, (5) drugs mapping module for identifying structural similar drugs, and (6) target & pathway module for identifying the reported targets and corresponding functional pathways. DenovoProfiling could provide structural identification, chemical space exploration, drug mapping, and target & pathway information. The comprehensive annotated information could give users a clear picture of their library and could guide the further selection of candidates for chemical synthesis and biological confirmation. DenovoProfiling is freely available at http://denovoprofiling.xielab.net.
PubMed: 36016718
DOI: 10.1016/j.csbj.2022.07.045 -
Frontiers in Cellular Neuroscience 2022The prevalence of cerebral microbleeds (CMBs) is significantly higher in patients with atrial fibrillation (AF) than in those without AF. CMBs in patients with AF have...
BACKGROUND
The prevalence of cerebral microbleeds (CMBs) is significantly higher in patients with atrial fibrillation (AF) than in those without AF. CMBs in patients with AF have been reported to be primarily of the lobar type, but the exact cause of this remains unknown. We investigated the possibility that hemorrhagic transformation of embolic microinfarction can account for lobar CMBs.
METHODS
A total of 101 patients who underwent ablation therapy for AF were prospectively registered, and 72 patients completed the assessment with MRI 6 months after catheter ablation. Brain MRI, including diffusion-weighted imaging (DWI) and susceptibility-weighted imaging (SWI), were examined at 1-3 days (baseline) and 6 months after catheter ablation. We quantitatively evaluated the spatial and temporal distribution of embolic microinfarctions and CMBs.
RESULTS
Of the 101 patients, 68 were enrolled in this study. Fifty-nine patients (86.8%) showed embolic microinfarctions on baseline DWI immediately after catheter ablation. There were 137 CMBs in SWI, and 96 CMBs were of the lobar type. Six months later, there were 208 CMBs, including 71 CMBs, and 60 of 71 (84.5%) were of the lobar type. Of the 71 CMBs, 56 (78.9%) corresponded to the location of previous embolic microinfarctions found on baseline DWI. The platelet count was significantly lower and hematocrit/hemoglobin and Fazekas score were higher in the group with CMBs than in the group without CMBs.
CONCLUSION
CMBs frequently appeared after catheter ablation therapy. Our results suggest that embolic microinfarction can cause lobar CMBs.
PubMed: 35237131
DOI: 10.3389/fncel.2022.818288