Correlation between metabolic syndrome and periurethral prostatic fibrosis: results of a prospective study.

BACKGROUND: Prostatic fibrosis, characterized by the accumulation of myofibroblasts and collagen deposition, is closely associated with LUTS and may lead to mechanical obstruction of the urethra. Additionally, Metabolic Syndrome (MetS), characterized by central obesity, high blood sugar, lipid metabolism disorders, and hypertension, is increasingly recognized as a proinflammatory condition linked to prostate inflammation. METHODS: Clinical data from 108 subjects who underwent transurethral resection of the prostate or bipolar plasmakinetic enucleation of the prostate were prospectively collected between June 2021 and August 2022. Patients were divided in two groups according to whether or not they had a diagnosis of MetS. Specimens were stained with Masson trichrome and the periurethral prostatic fibrosis extent was evaluated using quantitative morphometry. RESULTS: Forty-three patients (39.8%) were diagnosed with MetS. Patients with MetS showed a significantly greater extent of prostatic fibrosis than the others (68.1 ± 17.1% vs. 42.5 ± 18.2%, P < 0.001), and there was a positive correlation between the number of positive MetS parameters and the extent of prostatic fibrosis (R2 = 0.4436, P < 0.001). Multivariate regression analysis revealed that central obesity (B = 2.941, 95% confidence interval, 1.700-3.283), elevated fasting glucose (B = 1.036, 95% confidence interval, 0.293-1.780), reduced HDL cholesterol (B = 0.910, 95% confidence interval, 0.183-1.636) and elevated triglycerides (B = 1.666, 95% confidence interval, 0.824-2.508) were positively correlated to prostatic fibrosis. Elevated blood pressure, however, was unrelated to prostatic fibrosis (B = 0.009, 95% confidence interval, -0.664-0.683). CONCLUSIONS: The present findings suggest that prostatic fibrosis is positively correlated with MetS and its components including central obesity, elevated fasting glucose, reduced high density lipoprotein cholesterol and elevated triglycerides.

Comparative RNA-sequencing analysis of the prostate in a mouse model of benign prostatic hyperplasia with bladder outlet obstruction.

In ageing men, benign prostatic hyperplasia (BPH) is a chronic disease that leads to progressive lower urinary tract symptoms (LUTS) caused by obstruction of the bladder outlet (BOO). Patients with LUTS (such as increased frequency and urgency of urination) and complications of BOO (such as hydronephrosis and bladder stones) are at risk of serious health problems. BPH causes a rapidly rising burden of LUTS far exceeding that of other urological conditions. Treatment outcomes are unsatisfactory for BPH largely due to the lacking of fully understanding of the pathogenesis. Hormonal imbalances related to androgen and oestrogen can cause BPH, but the exact mechanism is still unknown, even the animal model is not fully understood. Additionally, there are no large-scale data to explain this mechanism. A BPH mouse model was established using mixed slow-release pellets of testosterone (T) and estradiol (E2), and we measured gene expression in mouse prostate tissue using RNA-seq, verified the results using qRT‒PCR, and used bioinformatics methods to analyse the differentially expressed genes (DEGs).

Comparative effectiveness of interventions for managing urological postoperative catheter-related bladder discomfort: a systematic review and network meta-analysis.

BACKGROUND: Catheter-related bladder discomfort (CRBD) is a common postoperative bladder pain syndrome. Many drugs and interventions for managing CRBD have been studied, but their comparative effectiveness remains controversial. We made a study to assess the comparative effectiveness of interventions included Ketorolac, Lidocaine, Chlorpheniramine, Gabapentin, Magnesium, Nefopam, Oxycodone, Parecoxib, Solifenacin, Tolterodine, Bupivancaine, Dexmedetomidine, Hyoscine N-butyl bromide, Ketamine, Penile nerve block on urological postoperative CRBD. METHODS: We performed a network meta-analysis via Aggregate Data Drug Inormation System software included 18 studies with 1816 patients and assessed the risk of bias by Cochrane Collaboration tool. The incidence of moderate to severe CRBD at 0, 1, and 6 h after surgery and the incidence severe CRBD at 1 h after surgery were compared. RESULT: The number of best rank is 0.48(Nefopam) and 0.22(Nefopam) in the incidence of moderate to severe CRBD at 1 h and incidence severe CRBD at 1 h. More than half of studies at unclear or high risk of bias. CONCLUSION: Nefopam reduced the incidence of CRBD and prevented severe events, but limited by the small number of studies for each intervention and heterogeneous patients.

lra: A long read aligner for sequences and contigs.

It is computationally challenging to detect variation by aligning single-molecule sequencing (SMS) reads, or contigs from SMS assemblies. One approach to efficiently align SMS reads is sparse dynamic programming (SDP), where optimal chains of exact matches are found between the sequence and the genome. While straightforward implementations of SDP penalize gaps with a cost that is a linear function of gap length, biological variation is more accurately represented when gap cost is a concave function of gap length. We have developed a method, lra, that uses SDP with a concave-cost gap penalty, and used lra to align long-read sequences from PacBio and Oxford Nanopore (ONT) instruments as well as de novo assembly contigs. This alignment approach increases sensitivity and specificity for SV discovery, particularly for variants above 1kb and when discovering variation from ONT reads, while having runtime that are comparable (1.05-3.76×) to current methods. When applied to calling variation from de novo assembly contigs, there is a 3.2% increase in Truvari F1 score compared to minimap2+htsbox. lra is available in bioconda (https://anaconda.org/bioconda/lra) and github (https://github.com/ChaissonLab/LRA).

Identifying the pulsed neuron networks' structures by a nonlinear Granger causality method.

BACKGROUND: It is a crucial task of brain science researches to explore functional connective maps of Biological Neural Networks (BNN). The maps help to deeply study the dominant relationship between the structures of the BNNs and their network functions. RESULTS: In this study, the ideas of linear Granger causality modeling and causality identification are extended to those of nonlinear Granger causality modeling and network structure identification. We employed Radial Basis Functions to fit the nonlinear multivariate dynamical responses of BNNs with neuronal pulse firing. By introducing the contributions from presynaptic neurons and detecting whether the predictions for postsynaptic neurons' pulse firing signals are improved or not, we can reveal the information flows distribution of BNNs. Thus, the functional connections from presynaptic neurons can be identified from the obtained network information flows. To verify the effectiveness of the proposed method, the Nonlinear Granger Causality Identification Method (NGCIM) is applied to the network structure discovery processes of Spiking Neural Networks (SNN). SNN is a simulation model based on an Integrate-and-Fire mechanism. By network simulations, the multi-channel neuronal pulse sequence data of the SNNs can be used to reversely identify the synaptic connections and strengths of the SNNs. CONCLUSIONS: The identification results show: for 2-6 nodes small-scale neural networks, 20 nodes medium-scale neural networks, and 100 nodes large-scale neural networks, the identification accuracy of NGCIM with the Gaussian kernel function was 100%, 99.64%, 98.64%, 98.37%, 98.31%, 84.87% and 80.56%, respectively. The identification accuracies were significantly higher than those of a traditional Linear Granger Causality Identification Method with the same network sizes. Thus, with an accumulation of the data obtained by the existing measurement methods, such as Electroencephalography, functional Magnetic Resonance Imaging, and Multi-Electrode Array, the NGCIM can be a promising network modeling method to infer the functional connective maps of BNNs.

vamos: variable-number tandem repeats annotation using efficient motif sets.

Roughly 3% of the human genome is composed of variable-number tandem repeats (VNTRs): arrays of motifs at least six bases. These loci are highly polymorphic, yet current approaches that define and merge variants based on alignment breakpoints do not capture their full diversity. Here we present a method vamos: VNTR Annotation using efficient Motif Sets that instead annotates VNTR using repeat composition under different levels of motif diversity. Using vamos we estimate 7.4-16.7 alleles per locus when applied to 74 haplotype-resolved human assemblies, compared to breakpoint-based approaches that estimate 4.0-5.5 alleles per locus.

Remote interventions for informal caregivers of patients with stroke: a systematic review and meta-analysis.

OBJECTIVES: It is unclear whether remote interventions are effective in improving outcomes of informal caregivers of patients who had a stroke. We synthesised evidence for the impact of remote interventions on informal caregivers of patients who had a stroke. Moreover, we also analysed its potential effects on patients who had a stroke. DESIGN: Systematic review and meta-analysis. DATA SOURCES: PubMed, Excerpta Medica Database, Web of Science, the Cochrane Library, China National Knowledge Infrastructure, Wanfang Database and China Science and Technology Journal Database were searched from inception up to 1 February 2022. ELIGIBILITY CRITERIA: We included randomised controlled trials (RCTs) that assessed the effect of remote interventions on informal caregivers who provide unpaid care for patients who had a stroke living at home compared with traditional interventions, including with respect to caregivers' mood, care burden, life satisfaction and perceived competence. Moreover, we considered the potential impact of remote interventions on the depressive and anxiety symptoms, functional rehabilitation and re-admission of patients who had a stroke. Only studies published in Chinese or English were included. We excluded studies of interventions aimed at healthcare professionals or patients who had a stroke and those that could not provide complete data. DATA EXTRACTION AND SYNTHESIS: Data analyses were performed using RevMan V.5.3. The Cochrane Collaboration risk of bias tool for RCTs was used to evaluate the quality of the included studies, and the review is reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. For continuous outcomes, we calculated the mean difference or standardised mean difference (SMD) and 95% CIs. The Grading of Recommendations, Assessment, Development, and Evaluations method was used to assess the certainty of the evidence. RESULTS: Eight RCTs with a total of 733 participants were included. Compared with traditional interventions, for informal caregivers, we found that remote interventions did not produce significant effects on depressive symptoms (SMD -0.04, 95% CI -0.24 to 0.15), anxiety symptoms (SMD -0.26, 95% CI -0.94 to 0.43), care burden (SMD -0.06, 95% CI -0.56 to 0.45), life satisfaction (SMD -0.16, 95% CI -0.43 to 0.11), or perceived competence (SMD 0.37, 95% CI -0.23 to 0.96). Similarly, for patients who had a stroke, remote interventions had no significant effect on depression (SMD 0.16, 95% CI -0.61 to 0.93) or anxiety symptoms (SMD -0.34, 95% CI -0.72 to 0.04). The effects of remote interventions on functional rehabilitation and re-admission in patients who had a stroke were evaluated by three studies and two studies, respectively, but the studies were too varied to combine their data in meta-analysis. CONCLUSIONS: Current evidence suggests that remote interventions for informal caregivers of patients who had a stroke have no significant superiority over traditional interventions. However, the quality of the included studies was low and more high-quality evidence is required to determine the possible impacts of remote interventions. PROSPERO REGISTRATION NUMBER: CRD42022313544.

Disparities in COVID-19 clinical studies from high-income and low-and middle-income countries.

OBJECTIVES: To examine the disparities between COVID-19 studies conducted in high-income countries (HICs) and low-and middle-income countries (LMICs). METHODS: We used the International Clinical Trials Registry Platform to identify COVID-19-related studies registered from December 31, 2019 to December 31, 2021. The World Bank definition was used to classify countries as high-, upper-middle-, lower-middle-, and low-income. The last three were considered to be LMICs. We examined the disparities in response speed, classification of medicines and vaccines, and registration and results reporting compliance between COVID-19 studies conducted in HICs and LMICs. RESULTS: We included 12,396 COVID-19 studies, with 6631 (53.5%) from HICs. HIC-registered studies reached a peak of 1039 in April 2020, whereas LMICs had only 440 studies. Of the 6969 interventional trials, those from HICs showed higher registration compliance (2199, 62.3% vs 1979, 57.6%, P <0.001) and results reporting compliance (hazard ratio 0.39, 95% confidence interval 0.28-0.55, P < 0.001) than LMICs. HICs also conducted significantly more small-molecule drug (956, 57.5% vs 868, 41.2%, P <0.001) and messenger RNA vaccine trials (135, 32.9% vs 19, 4.8%, P <0.001) than LMICs. CONCLUSION: HICs conducted COVID-19 trials with faster response speed and higher registration and publication compliance and produced more innovative pharmaceutical and vaccine products to combat COVID-19 than LMICs.

Abnormal Function in Dentate Nuclei Precedes the Onset of Psychosis: A Resting-State fMRI Study in High-Risk Individuals.

OBJECTIVE: The cerebellum serves a wide range of functions and is suggested to be composed of discrete regions dedicated to unique functions. We recently developed a new parcellation of the dentate nuclei (DN), the major output nuclei of the cerebellum, which optimally divides the structure into 3 functional territories that contribute uniquely to default-mode, motor-salience, and visual processing networks as indexed by resting-state functional connectivity (RsFc). Here we test for the first time whether RsFc differences in the DN, precede the onset of psychosis in individuals at risk of developing schizophrenia. METHODS: We used the magnetic resonance imaging (MRI) dataset from the Shanghai At Risk for Psychosis study that included subjects at high risk to develop schizophrenia (N = 144), with longitudinal follow-up to determine which subjects developed a psychotic episode within 1 year of their functional magnetic resonance imaging (fMRI) scan (converters N = 23). Analysis used the 3 functional parcels (default-mode, salience-motor, and visual territory) from the DN as seed regions of interest for whole-brain RsFc analysis. RESULTS: RsFc analysis revealed abnormalities at baseline in high-risk individuals who developed psychosis, compared to high-risk individuals who did not develop psychosis. The nature of the observed abnormalities was found to be anatomically specific such that abnormal RsFc was localized predominantly in cerebral cortical networks that matched the 3 functional territories of the DN that were evaluated. CONCLUSIONS: We show for the first time that abnormal RsFc of the DN may precede the onset of psychosis. This new evidence highlights the role of the cerebellum as a potential target for psychosis prediction and prevention.

Haplotype-resolved diverse human genomes and integrated analysis of structural variation.

Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates.

In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research.   The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at  https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.

Isolation and characterization of CD105+/CD90+ subpopulation in breast cancer MDA-MB-231 cell line.

BACKGROUND: The epithelial-mesenchymal transition (EMT) generates cells with properties of stem cells, if that happened, the stem cell should be with mesenchymal property. This study aimed to identify a group of cells with mesenchymal stem cell (MSC)-like characteristics in breast cancer bone metastatic cell line MDA-MB-231, moreover, the relevance between breast cancer stem cells and the EMT was observed. CD105 and CD90, identified as the standards of MSCs, were used for the identification. METHODS: The CD105+/CD90+ and CD105-/CD90- subpopulation of MDA-MB-231 cells were detected and sorted by flow cytometry. MSC-like characteristics in cell proliferation, migration and cell cycle were investigated here by MTT asaay, transwell migration assay, and PI staining respectively. The expression profiles of some stem cell-associated genes were also observed by quantitative real time PCR. RESULTS: Around 0.99% and 90.77% of parental cells were identified as CD105+/CD90+ and CD105-/CD90- cell subpopulations respectively. The CD105+/CD90+ cells exhibited stronger migratory capacity as compared to parental and CD105-/CD90- cells, while less CD105+/CD90+ cells were arrested in the S phase. Besides, pluripotent stem cell factors, like Oct-4, Nanog, Klf4 and Sox-2, were all upregulated in CD105+/CD90+ cells, with also proliferation increase, as compared with other two populations. CONCLUSION: The CD105+/CD90+ subpopulation from breast cancer MDA-MB-231 cells was proven to possess "mesenchymal stem cell-like" characteristics, and its high migratory ability might be associated with EMT. Moreover, using the surface markers of CD105 and CD90 for the identification of MSCs might provide new theoretical basis for the recurrence and metastasis of breast cancer.

A novel cyclic pentapeptide, H-10, inhibits B16 cancer cell growth and induces cell apoptosis.

Sansalvamide A, a cyclic depsipeptide isolated from a marine fungus of the Fusarium genus, exhibits significant antitumor activity. In the present study, H-10 (molecular formula, C38H55N5O6; molecular weight, 677.8732), a novel sansalvamide A derivative, demonstrated an inhibitory effect on the proliferation of murine melanoma B16 cells. It was confirmed that H-10 induced the apoptosis of the B16 cells. The inhibitory rate of various concentrations of H-10 on the B16 cells was measured by sulforhodamine B colorimetric assay, and the results revealed that the inhibitory effect of H-10 on the B16 cells occurred in a concentration-dependent manner. In addition, a growth curve model of the B16 cells treated with 50 µM H-10 revealed that the effect of H-10 also occurred in a time-dependent manner. The apoptotic morphology of the B16 cells was observed using an optical microscope. Following the treatment of the cells with 50 µM H-10 for 24 h, the cell apoptosis rate was analyzed using flow cytometry. The expression levels of caspase-3, -8 and -9 were analyzed by western blot analysis, and the results indicated that H-10 may induce the apoptosis of B16 cells.