Search

Abstract 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

Abstract 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.

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

Abstract 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.

The downhole working conditions of oil fields are harsh and complex, and the working performance of tools is affected by erosion and wear after being washed by sand laden mud. In order to improve the service life of downhole tools and optimize the material with excellent anti-erosion properties, the anti-erosion properties of three common metal materials are studied in this paper. By analogy with the difficulty of abrasive water jet cutting materials, the erosion wear ability of sand laden mud on the shell of downhole tools is equivalent evaluated, and the time dimension is shortened, which is prone to analyze the erosion wear resistance of different materials. Then, a numerical model of abrasive particles impact on the material surface, based on the finite element method–smoothed particle hydrodynamics coupled method, is established, the deformation and material removal amount of different materials under the same erosion condition are compared and analyzed, and the reasons for the difference in anti-erosion properties of different materials are quantitatively analyzed from the microscopic point of view. The results showed that under the same erosion conditions, the material removal amount 40CrNi2Mo < 45Steel < Ti6Al4V, and the anti-erosion properties decreases sequentially, which is not affected by erosion velocity V (jet pressure P) and waterjet sand ratio ζ. Among them, the material deformation and removal of 40CrNi2Mo and 45Steel are similar, and the anti-erosion properties of the two are approximately the same.

Isogeometric analysis (IGA) is an effective numerical method for connecting computer-aided design and engineering, which has been widely applied in various aspects of computational mechanics. IGA involves Galerkin and collocation formulations. Exploiting the same high-order non-uniform rational B-spline (NURBS) bases that span the physical domain and the solution space leads to increased accuracy and fast computation. Although IGA Galerkin provides optimal convergence, IGA collocation performs better in terms of the ratio of accuracy to computational time. Without numerical integration, by working directly with the strong form of the partial differential equation over the physical domain defined by NURBS geometry, the derivatives of the NURBS-expressed numerical solution at some chosen collocation points can be calculated. In this study, we survey the methodological framework and the research prospects of IGA. The collocation schemes in the IGA collocation method that affect the convergence performance are addressed in this paper. Recent studies and application developments are reviewed as well.

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.

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).

Isogeometric analysis (IGA) is introduced to establish the direct link between computer-aided design and analysis. It is commonly implemented by Galerkin formulations (isogeometric Galerkin, IGA-G) through the use of nonuniform rational B-splines (NURBS) basis functions for geometric design and analysis. Another promising approach, isogeometric collocation (IGA-C), working directly with the strong form of the partial differential equation (PDE) over the physical domain defined by NURBS geometry, calculates the derivatives of the numerical solution at the chosen collocation points. In a typical IGA, the knot vector of the NURBS numerical solution is only determined by the physical domain. A new perspective on the IGA method is proposed in this study to improve the accuracy and convergence of the solution. Solving the PDE with IGA can be regarded as fitting the load function defined on the NURBS geometry (right-hand side) with derivatives of the NURBS numerical solution (left-hand side).Moreover, the design of the knot vector has a close relationship to the NURBS functions to be fitted in the area of data fitting in geometric design. Therefore, the detected feature points of the load function are integrated into the initial knot vector of the physical do main to construct the new knot vector of the numerical solution. Then, they are connected seamlessly with the IGA-C framework for its great potential combining the accuracy and smoothness merits with the computational efficiency, which we call isogeometric collocation by fitting load function (IGACL). In numerical experiments, we implement our method to solve 1D, 2D, and 3D PDEs and demonstrate the improvement in accuracy by comparing it with the standard IGA-C method.We also verify the superiority in the accuracy of our knot selection scheme when employed in the IGA-G method, which we call isogeometric Galerkin by fitting load function (IGA-GL). [ABSTRACT FROM AUTHOR]

This paper takes Hejiaou river region as the research object by time-space mutual substitution method to probe biodiversity and biomass of 29 sample abandoned lands. The results show that: (1) Biodiversity of vegetation changes along with the abandoned age of biomass. Simpson index, Shannon-Weiner index, Margalef richness index and Pielou evenness index reach the maximum when the abandoned age is 10 or 11 years. And biomass increases along with the growth of the abandoned age. (2) Biodiversity and biomass of different site types vary from one to another. For Simpson index, sunny slope>cloudy slope>semi-cloudy slope>semi-sunny slope. For Shannon-Weiner index and Pielou evenness index, sunny slope>cloudy slope>semi-sunny slope>semi-cloudy slope. For Margalef richness index, semi-sunny slope>semi-cloudy slope>cloudy slope>sunny slope. For biomass, cloudy slope>semi-cloudy slope>sunny slope>semi-sunny slope. The difference among Simpson index, Margalef richness index and Pielou evenness index is not apparent in terms of site type. But sunny slope and semi-cloudy slope of Shannon-Weiner index are distinguished from each other (p<0.05). And there is a great difference among biomass of four site types (p<0.05). (3) Simpson index, Shannon-Weiner index, Margalef richness index and Pielou evenness index have no linear correlation with biomass, indicating that biodiversity and biomass are not correlated. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The article discusses research which investigated human genomic structural variants (SV). Topics explored include the genetic variation of the haplotype human genome assemblies presented, the use of single-cell DNA template strand sequencing to cluster assembled contigs into chromosome clusters, and the analysis of SV complex patterns, distribution, and mechanisms.