A comprehensive performance evaluation, comparison, and integration of computational methods for detecting and estimating cross-contamination of human samples in cancer next-generation sequencing analysis.

Cross-sample contamination is one of the major issues in next-generation sequencing (NGS)-based molecular assays. This type of contamination, even at very low levels, can significantly impact the results of an analysis, especially in the detection of somatic alterations in tumor samples. Several contamination identification tools have been developed and implemented as a crucial quality-control step in the routine NGS bioinformatic pipeline. However, no study has been published to comprehensively and systematically investigate, evaluate, and compare these computational methods in the cancer NGS analysis. In this study, we comprehensively investigated nine state-of-the-art computational methods for detecting cross-sample contamination. To explore their application in cancer NGS analysis, we further compared the performance of five representative tools by qualitative and quantitative analyses using in silico and simulated experimental NGS data. The results showed that Conpair achieved the best performance for identifying contamination and predicting the level of contamination in solid tumors NGS analysis. Moreover, based on Conpair, we developed a Python script, Contamination Source Predictor (ConSPr), to identify the source of contamination. We anticipate that this comprehensive survey and the proposed tool for predicting the source of contamination will assist researchers in selecting appropriate cross-contamination detection tools in cancer NGS analysis and inspire the development of computational methods for detecting sample cross-contamination and identifying its source in the future.

Orientation transitions and chiral assemblies of para-terphenyl molecules on Cd(0001).

The interplay between orientation transition and chiral self-assemblies of para-terphenyl (P3P) molecules on the Cd(0001) surface has been investigated using low temperature scanning tunneling microscopy and density functional theory calculations. Three distinct molecular orientations have been discerned from the self-assembled thin films of P3P. At the low coverage, flat-lying molecules appear in the homochiral domains with the incommensurate registry to the substrate. With the coverage increasing, the incoming molecules are incorporated into the first layer with edge-on orientation and form the self-assembled zigzag chains. The alternative arrangement of zigzag chains with opposite chirality leads to the formation of a c(4 × 2) superstructure, in which the tilted molecules exhibit orientational frustration and fuzzy noises. The analysis of the tunneling spectra reveals that the electronic structure of P3P layers is contingent upon the hybridization between the electronic states of P3P molecules and the Cd(0001) surface. These results provide important insights into the interplay between orientational transition and chiral assembly of P3P molecules on metal substrates.

The tale of HORTON: Lessons learned in a decade of scientific software development.

HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade.

Grid: A Python library for molecular integration, interpolation, differentiation, and more.

Grid is a free and open-source Python library for constructing numerical grids to integrate, interpolate, and differentiate functions (e.g., molecular properties), with a strong emphasis on facilitating these operations in computational chemistry and conceptual density functional theory. Although designed, maintained, and released as a stand-alone Python library, Grid was originally developed for molecular integration, interpolation, and solving the Poisson equation in the HORTON and ChemTools packages. Grid is designed to be easy to use, extend, and maintain; this is why we use Python and adopt many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. We leverage popular scientific packages, such as NumPy and SciPy, to ensure high efficiency and optimized performance in grid development. This article is the official release note of the Grid library showcasing its unique functionality and scope.

Tenofovir disoproxil fumarate mediates neuronal injury by inducing neurotoxicity.

PURPOSE: Highly active antiretroviral therapy (HAART) is an accepted treatment option for patients with virus infection. Mounting evidence indicated that persistent HAART treatment is implicated with increased morbidity of HIV-associated neurocognitive disorders (HAND) in patients. Tenofovir disoproxil fumarate (TDF), a novel nucleotide reverse transcriptase inhibitor (NRTI), was used in patients with HIV co-infected with HBV. And it is still a vital first-line antiretroviral compounds in HAART. However, whether persistent treatment with TDF is involved in HAND development remains to be further elucidated. In this study, we aimed to discuss the neurotoxicity of TDF. METHODS: We used SH-SY5Y cells and primary neuronal cells to evaluate the neurotoxicity of TDF in vitro. The cytotoxicity of TDF on SH-SY5Y cells and primary neuronal cells was evaluated by the cell viability and LDH levels by MTT assay and LDH kit, respectively. Hoechst 33342 staining, TUNEL assay and flow cytometry were performed to evaluate the cells apoptosis. The intracellular reactive oxygen species (ROS) and malondialdehyde (MDA) production were measured by commercial kits. In addition, the activation level of caspase-3 was evaluated using spectrophotometry and western blotting. RESULTS: Our results showed that TDF treatment significantly induced cell viability and induced apoptosis of SH-SY5Y cells and primary neuronal cells. Furthermore, the ROS levels and MDA productions were significantly up-regulated in nerve cells treated with TDF.  CONCLUSION: Our findings indicated that TDF may induce neuronal cell apoptosis through increasing the intracellular ROS and the expression level of caspase-3, which may be related to the increasing prevalence of HAND.

Adsorption configurations and electronic properties of self-assembled C60and C70molecules on a semiconductor CuSe monolayer with periodic nanopores.

Two-dimensional (2D) supramolecular self-assembly architectures are considered one of the most significant and challenging topics in nanotechnology and modern organic chemistry. The study of these processes on surfaces is vital to achieving a higher degree of control in the design of supramolecular architecture. Herein, we report on the 2D self-assembly monolayer architectures based on C60and C70molecules on a semiconductor CuSe monolayer with periodic nanopores, which are essential for providing ideas for surface template chemistry. With the aid of low-temperature scanning tunneling microscopy/spectroscopy (LT-STM/STS) and density functional theory (DFT) calculation methods, we systematically investigate the adsorption configurations and electronic properties of C60and C70on CuSe monolayer with periodic nanopores. Our results show that both the C60and C70molecules above the nanopores will fall into the nanopores, while those on the CuSe surface will show well-defined self-assembly with various adsorption configurations. Besides, through STS measurement, the lowest unoccupied molecular orbitals (LUMOs) and characteristic peaks of fullerene molecules will be slightly different due to different adsorption configurations. This work helps us to study the adsorption behavior of the fullerene family on various kinds of semiconductor substrates, and also provides vigorous support for the development of fullerene electrical devices in the future.

27-gauge microincision vitrectomy surgery compared with 25-gauge microincision vitrectomy surgery on wound closure and need for wound suture and other postoperative parameters in the treatment of vitreoretinal disease: A meta-analysis.

We performed a meta-analysis to evaluate the effect of 27-gauge microincision vitrectomy surgery compared with 25-gauge microincision vitrectomy surgery on wound closure and the need for wound suture and other postoperative parameters in the treatment of vitreoretinal disease. A systematic literature search up to June 2022 was performed and 1264 subjects with the vitreoretinal disease at the baseline of the studies; 562 of them were using the 27-gauge microincision vitrectomy surgery, and 722 were using 25-gauge microincision vitrectomy surgery. Odds ratio (OR), and mean difference (MD) with 95% confidence intervals (CIs) were calculated to assess the effect of 27-gauge microincision vitrectomy surgery compared with 25-gauge microincision vitrectomy surgery on wound closure and the need for wound suture and other postoperative parameters in the treatment of vitreoretinal disease using the dichotomous, and contentious methods with a random or fixed-effect model. The 27-gauge microincision vitrectomy surgery subjects had a significantly lower intraoperative and postoperative wound complication (OR, 6.66; 95% CI, 0.46-0.95, P = .02), and wound suture number (OR, 0.38; 95% CI, 0.20-0.71, P = .002), and best corrected visual acuity (MD, -0.03; 95% CI, -0.05 to -0.001, P = .02) compared with 25-gauge microincision vitrectomy surgery in subjects with vitreoretinal disease. However, 27-gauge microincision vitrectomy surgery subjects had no significant difference in the wound closure time (MD, -8.45; 95% CI, -23.44 to 6.55, P = .27), operation time (MD, 0.85; 95% CI, -1.17 to 2.86, P = .41), intraocular pressure at postoperative day 1 (MD, 0.42; 95% CI, -1.45-2.28, P = .66), primary anatomical success rate (OR, 0.83; 95% CI, 0.42-1.63, P = .58), and central macular thickness (MD, 1.81; 95% CI, -21.76 to 25.37, P = .88) compared to 25-gauge microincision vitrectomy surgery in subjects with vitreoretinal disease. The 27-gauge microincision vitrectomy surgery subjects had a significantly lower intraoperative and postoperative wound complication, wound suture number, and best corrected visual acuity, and no significant difference in the wound closure time, operation time, intraocular pressure at postoperative day 1, primary anatomical success rate, and central macular thickness compared to 25-gauge microincision vitrectomy surgery in subjects with vitreoretinal disease. The analysis of outcomes should be with caution because of the low sample size of 12 out of 15 studies in the meta-analysis and a low number of studies in certain comparisons.

Circ_HIPK3 alleviates CoCl2-induced apoptotic injury in neuronal cells by depending on the regulation of the miR-222-3p/DUSP19 axis.

Circular RNA (circRNA) homeodomain-interacting protein kinase 3 (circ_HIPK3) has recently reported as regulator in spinal cord injury (SCI). The regulatory mechanism of circ_HIPK3 in SCI was further researched in this study. Circ_HIPK3 expression was inhibited by CoCl2 in AGE1.HN cells. The CoCl2-induced cell cycle arrest, cell proliferation inhibition and apoptosis promotion were mitigated by overexpression of circ_HIPK3. Circ_HIPK3 could target miR-222-3p and circ_HIPK3 repressed the CoCl2-induced neuronal cell injury by sponging miR-222-3p. DUSP19 was a target gene of miR-222-3p and circ_HIPK3 affected the expression of DUSP19 via binding to miR-222-3p. The regulation of circ_HIPK3 in CoCl2-induced injury of AGE1.HN cells was associated with the upregulation of DUSP19. Circ_HIPK3 acted as a pathogenic inhibitor in the progression of SCI via the miR-222-3p-mediated DUSP19 upregulation.

IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files.

IOData is a free and open-source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane-wave density-functional-theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand-alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third-party) molecular quantum chemistry and solid-state density-functional-theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.

Quantitative and semi-quantitative assessment of synovitis on MRI and the relationship with symptoms in symptomatic knee osteoarthritis.

OBJECTIVES: Synovitis in symptomatic knee OA (KOA) is common and is associated with joint symptoms. Optimal synovial measurement on MRI is, however, unclear. Our aims were to examine the relationship between MRI measures of synovitis and knee symptoms in symptomatic KOA. METHODS: Data from a randomized, multicentre, placebo-controlled trial (UK-VIDEO) of vitamin-D therapy in symptomatic KOA were utilized. Participants reported knee symptoms using WOMAC at baseline and annually. On contrast-enhanced (CE) MRI, synovial thickness was measured using established, semi-quantitative methods whilst synovial tissue volume (STV) was assessed as absolute STV (aSTV) and relative to the width of femoral condyle (rSTV). STV of the infrapatellar region was also assessed. Associations between synovial measures and symptoms were analysed using multiple linear regression modelling. RESULTS: No linear association was observed between knee symptoms and synovitis thickness scores. Whole-joint aSTV (0.88, 95% CI: 0.17, 1.59) and infrapatellar aSTV (5.96, 95% CI: 1.22, 10.7) were positively associated with knee pain. Whole-joint rSTV had a stronger association with pain (7.96, 95% CI: 2.60, 13.33) and total scores (5.63, 95% CI: 0.32, 10.94). Even stronger associations were found for infrapatellar rSTV with pain (55.47, 95% CI: 19.99, 90.96), function (38.59, 95% CI: 2.1, 75.07) and total scores (41.64, 95% CI: 6.56, 76.72). CONCLUSIONS: Whole-joint and site-specific infrapatellar STV measures on CE-MRI were associated with knee pain, respectively. Volumes relative to the size of the femoral condyle may be promising outcome measures in KOA trials.