Study of association between corneal shape parameters and axial length elongation during orthokeratology using image-pro plus software

BACKGROUND

The aim was to validate the correlation between corneal shape parameters and axial length growth (ALG) during orthokeratology using Image-Pro Plus (IPP) 6.0 software.

METHODS

This retrospective study used medical records of myopic children aged 8-13 years (n = 104) undergoing orthokeratology. Their corneal topography and axial length were measured at baseline and subsequent follow-ups after lens wear. Corneal shape parameters, including the treatment zone (TZ) area, TZ diameter, TZ fractal dimension, TZ radius ratio, eccentric distance, pupil area, and pupillary peripheral steepened zone(PSZ) area, were measured using IPP software. The impact of corneal shape parameters at 3 months post-orthokeratology visit on 1.5-year ALG was evaluated using multivariate linear regression analysis.

RESULTS

ALG exhibited significant associations with age, TZ area, TZ diameter, TZ fractal dimension, and eccentric distance on univariate linear regression analysis. Multivariate regression analysis identified age, TZ area, and eccentric distance as significantly correlated with ALG (all P < 0.01), with eccentric distance showing the strongest correlation (β = -0.370). The regressive equation was y = 1.870 - 0.235a + 0.276b - 0.370c, where y represents ALG, a represents age, b represents TZ area, and c represents eccentric distance; R2 = 0.27). No significant relationships were observed between the TZ radius ratio, pupillary PSZ area, and ALG.

CONCLUSIONS

IPP software proves effective in capturing precise corneal shape parameters after orthokeratology. Eccentric distance, rather than age or the TZ area, significantly influences ALG retardation.

End Group Engineering for Constructing A-D-A Fused-Ring Photosensitizers with Balanced Phototheranostics Performance

Phototheranostics continues to flourish in cancer treatment. Due to the competitive relationships between these photophysical processes of fluorescence emission, photothermal conversion, and photodynamic action, it is critical to balance them through subtle photosensitizer designs. Herein, it is provided a useful guideline for constructing A-D-A photosensitizers with superior phototheranostics performance. Various cyanoacetate group-modified end groups containing ester side chains of different length are designed to construct a series of A-D-A photosensitizers (F8CA1 ∼ F8CA4) to study the structure-property relationships. It is surprising to find that the photophysical properties of A-D-A photosensitizers can be precisely regulated by these tiny structural changes. The results reveal that the increase in the steric hindrance of ester side chains has positive impacts on their photothermal conversion capabilities, but adverse impacts on the fluorescence emission and photodynamic activities. Notably, these tiny structural changes lead to their different aggregation behavior. The molecule mechanisms are detailedly explained by theoretical calculations. Finally, F8CA2 nanoparticles with more balanced photophysical properties perform well in fluorescence imaging-guided photothermal and type I&II photodynamic synergistic cancer therapy, even under hypoxic conditions. Therefore, this work provides a novel practicable construction strategy for desired A-D-A photosensitizers.

Deuteration-enhanced neutron contrasts to probe amorphous domain sizes in organic photovoltaic bulk heterojunction films

An organic photovoltaic bulk heterojunction comprises of a mixture of donor and acceptor materials, forming a semi-crystalline thin film with both crystalline and amorphous domains. Domain sizes critically impact the device performance; however, conventional X-ray scattering techniques cannot detect the contrast between donor and acceptor materials within the amorphous intermixing regions. In this study, we employ neutron scattering and targeted deuteration of acceptor materials to enhance the scattering contrast by nearly one order of magnitude. Remarkably, the PM6:deuterated Y6 system reveals a new length scale, indicating short-range aggregation of Y6 molecules in the amorphous intermixing regions. All-atom molecular dynamics simulations confirm that this short-range aggregation is an inherent morphological advantage of Y6 which effectively assists charge extraction and suppresses charge recombination as shown by capacitance spectroscopy. Our findings uncover the amorphous nanomorphology of organic photovoltaic thin films, providing crucial insights into the morphology-driven device performance.

Susceptible bacteria can survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance

Antibiotic resistance and evasion are incompletely understood and complicated by the fact that murine interval dosing models do not fully recapitulate antibiotic pharmacokinetics in humans. To better understand how gastrointestinal bacteria respond to antibiotics, we colonized germ-free mice with a pan-susceptible genetically barcoded Escherichia coli clinical isolate and administered the antibiotic cefepime via programmable subcutaneous pumps, allowing closer emulation of human parenteral antibiotic dynamics. E. coli was only recovered from intestinal tissue, where cefepime concentrations were still inhibitory. Strikingly, "some" E. coli isolates were not cefepime resistant but acquired mutations in genes involved in polysaccharide capsular synthesis increasing their invasion and survival within human intestinal cells. Deleting wbaP involved in capsular polysaccharide synthesis mimicked this phenotype, allowing increased invasion of colonocytes where cefepime concentrations were reduced. Additionally, "some" mutant strains exhibited a persister phenotype upon further cefepime exposure. This work uncovers a mechanism allowing "select" gastrointestinal bacteria to evade antibiotic treatment.

Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration

Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of 2394 cases and 2393 controls for age-related macular degeneration (AMD) via whole-genome sequencing, with 46.9 million genetic variants. Our study reveals significant single-variant association signals at four loci and independent gene-based signals in CFH, C2, C3, and NRTN. Using data from the Exome Aggregation Consortium (ExAC) for a gene-based test, we demonstrate an enrichment of predicted rare loss-of-function variants in CFH, CFI, and an as-yet unreported gene in AMD, ORMDL2. Our method of using a large variant list without individual-level genotypes as an external reference provides a flexible and convenient approach to leverage the publicly available variant datasets to augment the search for rare variant associations, which can explain additional disease risk in AMD.

Genetic determinants underlying the progressive phenotype of β-lactam/β-lactamase inhibitor resistance in Escherichia coli

IMPORTANCE

The increased feasibility of whole-genome sequencing has generated significant interest in using such molecular diagnostic approaches to characterize difficult-to-treat, antimicrobial-resistant (AMR) infections. Nevertheless, there are current limitations in the accurate prediction of AMR phenotypes based on existing AMR gene database approaches, which primarily correlate a phenotype with the presence/absence of a single AMR gene. Our study utilized a large cohort of cephalosporin-susceptible Escherichia coli bacteremia samples to determine how increasing the dosage of narrow-spectrum β-lactamase-encoding genes in conjunction with other diverse β-lactam/β-lactamase inhibitor (BL/BLI) genetic determinants contributes to progressively more severe BL/BLI phenotypes. We were able to characterize the complexity of the genetic mechanisms underlying progressive BL/BLI resistance including the critical role of β-lactamase encoding gene amplification. For the diverse array of AMR phenotypes with complex mechanisms involving multiple genomic factors, our study provides an example of how composite risk scores may improve understanding of AMR genotype/phenotype correlations.

Deep learning of cell spatial organizations identifies clinically relevant insights in tissue images

Recent advancements in tissue imaging techniques have facilitated the visualization and identification of various cell types within physiological and pathological contexts. Despite the emergence of cell-cell interaction studies, there is a lack of methods for evaluating individual spatial interactions. In this study, we introduce Ceograph, a cell spatial organization-based graph convolutional network designed to analyze cell spatial organization (for example,. the cell spatial distribution, morphology, proximity, and interactions) derived from pathology images. Ceograph identifies key cell spatial organization features by accurately predicting their influence on patient clinical outcomes. In patients with oral potentially malignant disorders, our model highlights reduced structural concordance and increased closeness in epithelial substrata as driving features for an elevated risk of malignant transformation. In lung cancer patients, Ceograph detects elongated tumor nuclei and diminished stroma-stroma closeness as biomarkers for insensitivity to EGFR tyrosine kinase inhibitors. With its potential to predict various clinical outcomes, Ceograph offers a deeper understanding of biological processes and supports the development of personalized therapeutic strategies.

OVOL2 sustains postnatal thymic epithelial cell identity

Distinct pathways and molecules may support embryonic versus postnatal thymic epithelial cell (TEC) development and maintenance. Here, we identify a mechanism by which TEC numbers and function are maintained postnatally. A viable missense allele (C120Y) of Ovol2, expressed ubiquitously or specifically in TECs, results in lymphopenia, in which T cell development is compromised by loss of medullary TECs and dysfunction of cortical TECs. We show that the epithelial identity of TECs is aberrantly subverted towards a mesenchymal state in OVOL2-deficient mice. We demonstrate that OVOL2 inhibits the epigenetic regulatory BRAF-HDAC complex, specifically disrupting RCOR1-LSD1 interaction. This causes inhibition of LSD1-mediated H3K4me2 demethylation, resulting in chromatin accessibility and transcriptional activation of epithelial genes. Thus, OVOL2 controls the epigenetic landscape of TECs to enforce TEC identity. The identification of a non-redundant postnatal mechanism for TEC maintenance offers an entry point to understanding thymic involution, which normally begins in early adulthood.

Unsupervised domain adaptation for nuclei segmentation: Adapting from hematoxylin & eosin stained slides to immunohistochemistry stained slides using a curriculum approach

BACKGROUND AND OBJECTIVE

Unsupervised domain adaptation (UDA) is a powerful approach in tackling domain discrepancies and reducing the burden of laborious and error-prone pixel-level annotations for instance segmentation. However, the domain adaptation strategies utilized in previous instance segmentation models pool all the labeled/detected instances together to train the instance-level GAN discriminator, which neglects the differences among multiple instance categories. Such pooling prevents UDA instance segmentation models from learning categorical correspondence between source and target domains for accurate instance classification; METHODS: To tackle this challenge, we propose an Instance Segmentation CycleGAN (ISC-GAN) algorithm for UDA multiclass-instance segmentation. We conduct extensive experiments on the multiclass nuclei recognition task to transfer knowledge from hematoxylin and eosin to immunohistochemistry stained pathology images. Specifically, we fuse CycleGAN with Mask R-CNN to learn categorical correspondence with image-level domain adaptation and virtual supervision. Moreover, we utilize Curriculum Learning to separate the learning process into two steps: (1) learning segmentation only on labeled source data, and (2) learning target domain segmentation with paired virtual labels generated by ISC-GAN. The performance was further improved through experiments with other strategies, including Shared Weights, Knowledge Distillation, and Expanded Source Data.

RESULTS

Comparing to the baseline model or the three UDA instance detection and segmentation models, ISC-GAN illustrates the state-of-the-art performance, with 39.1% average precision and 48.7% average recall. The source codes of ISC-GAN are available at https://github.com/sdw95927/InstanceSegmentation-CycleGAN.

CONCLUSION

ISC-GAN adapted knowledge from hematoxylin and eosin to immunohistochemistry stained pathology images, suggesting the potential for reducing the need for large annotated pathological image datasets in deep learning and computer vision tasks.

Osteosarcoma Explorer: A Data Commons With Clinical, Genomic, Protein, and Tissue Imaging Data for Osteosarcoma Research

PURPOSE

Osteosarcoma research advancement requires enhanced data integration across different modalities and sources. Current osteosarcoma research, encompassing clinical, genomic, protein, and tissue imaging data, is hindered by the siloed landscape of data generation and storage.

MATERIALS AND METHODS

Clinical, molecular profiling, and tissue imaging data for 573 patients with pediatric osteosarcoma were collected from four public and institutional sources. A common data model incorporating standardized terminology was created to facilitate the transformation, integration, and load of source data into a relational database. On the basis of this database, a data commons accompanied by a user-friendly web portal was developed, enabling various data exploration and analytics functions.

RESULTS

The Osteosarcoma Explorer (OSE) was released to the public in 2021. Leveraging a comprehensive and harmonized data set on the backend, the OSE offers a wide range of functions, including Cohort Discovery, Patient Dashboard, Image Visualization, and Online Analysis. Since its initial release, the OSE has experienced an increasing utilization by the osteosarcoma research community and provided solid, continuous user support. To our knowledge, the OSE is the largest (N = 573) and most comprehensive research data commons for pediatric osteosarcoma, a rare disease. This project demonstrates an effective framework for data integration and data commons development that can be readily applied to other projects sharing similar goals.

CONCLUSION

The OSE offers an online exploration and analysis platform for integrated clinical, molecular profiling, and tissue imaging data of osteosarcoma. Its underlying data model, database, and web framework support continuous expansion onto new data modalities and sources.

Ceftolozane/tazobactam heteroresistance in cystic fibrosis-related Pseudomonas aeruginosa infections

Objectives

Cystic fibrosis (CF) patients are often colonized with Pseudomonas aeruginosa. During treatment, P. aeruginosa can develop subpopulations exhibiting variable in vitro antimicrobial (ABX) susceptibility patterns. Heteroresistance (HR) may underlie reported discrepancies between in vitro susceptibility results and clinical responses to various ABXs. Here, we sought to examine the presence and nature of P. aeruginosa polyclonal HR (PHR) and monoclonal HR (MHR) to ceftolozane/tazobactam in isolates originating from CF pulmonary exacerbations.

Methods

This was a single-centre, non-controlled study. Two hundred and forty-six P. aeruginosa isolates from 26 adult CF patients were included. PHR was defined as the presence of different ceftolozane/tazobactam minimum inhibitory concentration (MIC) values among P. aeruginosa isolates originating from a single patient specimen. Population analysis profiles (PAPs) were performed to assess the presence of MHR, defined as ≥4-fold change in the ceftolozane/tazobactam MIC from a single P. aeruginosa colony.

Results

Sixteen of 26 patient specimens (62%) contained PHR P. aeruginosa populations. Of these 16 patients, 6 (23%) had specimens in which PHR P. aeruginosa isolates exhibited ceftolozane/tazobactam MICs with categorical differences (i.e. susceptible versus resistant) compared to results reported as part of routine care. One isolate, PSA 1311, demonstrated MHR. Canonical ceftolozane/tazobactam resistance genes were not found in the MHR isolates (MHR PSA 1311 or PHR PSA 6130).

Conclusions

Ceftolozane/tazobactam PHR exists among P. aeruginosa isolates in this work, and approximately a quarter of these populations contained isolates with ceftolozane/tazobactam susceptibiilty interpretations different from what was reported clinically, supporting concerns surrounding the utility of traditional susceptibility testing methodology in the setting of CF specimens. Genome sequencing of isolates with acquired MHR to ceftolozane/tazobactam revealed variants of unknown significance. Future work will be centred on determining the significance of these mutations to better understand these data in clinical context.

Development of LOX-1 Antibody Modified Immuno-liposomes as Drug Carriers to Macrophages in Atherosclerotic Lesions

We developed a drug delivery system for atherosclerotic lesions using immuno-liposomes. We focused on enhancing the delivery efficiency of the liposomes to macrophages in atherosclerotic lesions by antibody modification of lectinlike oxidized low-density lipoproteins (LDL) receptor 1 (LOX-1). The cellular accumulation of the liposomes in foam cells induced by oxidized LDL (oxLDL) in Raw264 mouse macrophages was evaluated. The cellular accumulation of LOX-1 antibody modified liposomes in oxLDL-induced foam cells and untreated Raw264 cells was significantly higher compared with that of unmodified liposomes. The liposomes were also administered intravenously to Apoeshl mice as an atherosclerosis model. Frozen sections were prepared from the mouse aortas and observed by confocal laser microscopy. The distribution of LOX-1 antibody modified liposomes in the atherosclerotic regions of Apoeshl mice was significantly greater compared with that of unmodified liposomes. The results suggest that LOX-1 antibody modified liposomes can target foam cells in atherosclerotic lesions, providing a potential route for delivering various drugs with pharmacological effects or detecting atherosclerotic foci for the diagnosis of atherosclerosis.

A Deep Learning Approach for Histology-Based Nucleus Segmentation and Tumor Microenvironment Characterization

Microscopic examination of pathology slides is essential to disease diagnosis and biomedical research. However, traditional manual examination of tissue slides is laborious and subjective. Tumor whole-slide image (WSI) scanning is becoming part of routine clinical procedures and produces massive data that capture tumor histologic details at high resolution. Furthermore, the rapid development of deep learning algorithms has significantly increased the efficiency and accuracy of pathology image analysis. In light of this progress, digital pathology is fast becoming a powerful tool to assist pathologists. Studying tumor tissue and its surrounding microenvironment provides critical insight into tumor initiation, progression, metastasis, and potential therapeutic targets. Nucleus segmentation and classification are critical to pathology image analysis, especially in characterizing and quantifying the tumor microenvironment (TME). Computational algorithms have been developed for nucleus segmentation and TME quantification within image patches. However, existing algorithms are computationally intensive and time consuming for WSI analysis. This study presents Histology-based Detection using Yolo (HD-Yolo), a new method that significantly accelerates nucleus segmentation and TME quantification. We demonstrate that HD-Yolo outperforms existing WSI analysis methods in nucleus detection, classification accuracy, and computation time. We validated the advantages of the system on 3 different tissue types: lung cancer, liver cancer, and breast cancer. For breast cancer, nucleus features by HD-Yolo were more prognostically significant than both the estrogen receptor status by immunohistochemistry and the progesterone receptor status by immunohistochemistry. The WSI analysis pipeline and a real-time nucleus segmentation viewer are available at https://github.com/impromptuRong/hd_wsi.

ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data

Motivation

Spatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing and visualizing large image datasets together with molecular information.

Results

We introduce ScopeViewer, a browser-based software designed to overcome these challenges. ScopeViewer offers the following functionalities: (1) It visualizes large image data and associated annotations at various zoom levels, allowing for intricate exploration of the data; (2) It enables dual interactive viewing of the original images along with their annotations, providing a comprehensive understanding of the context; (3) It displays spatial molecular features with optimized bandwidth, ensuring a smooth user experience; and (4) It bolsters data security by circumventing data transfers.

Availability

ScopeViewer is available at: https://datacommons.swmed.edu/scopeviewer.

Deep Learning of Cell Spatial Organizations Identifies Clinically Relevant Insights in Tissue Images

Recent advancements in tissue imaging techniques have facilitated the visualization and identification of various cell types within physiological and pathological contexts. Despite the emergence of cell-cell interaction studies, there is a lack of methods for evaluating individual spatial interactions. In this study, we introduce Ceograph, a novel cell spatial organization-based graph convolutional network designed to analyze cell spatial organization (i.e. the cell spatial distribution, morphology, proximity, and interactions) derived from pathology images. Ceograph identifies key cell spatial organization features by accurately predicting their influence on patient clinical outcomes. In patients with oral potentially malignant disorders, our model highlights reduced structural concordance and increased closeness in epithelial substrata as driving features for an elevated risk of malignant transformation. In lung cancer patients, Ceograph detects elongated tumor nuclei and diminished stroma-stroma closeness as biomarkers for insensitivity to EGFR tyrosine kinase inhibitors. With its potential to predict various clinical outcomes, Ceograph offers a deeper understanding of biological processes and supports the development of personalized therapeutic strategies.

IsoAnalytics: a single-cell proteomics web server

Motivation

Single-cell proteomics provide unprecedented resolution to examine biological processes. Customized data analysis and facile data visualization are crucial for scientific discovery. Further, user-friendly data analysis and visualization software that is easily accessible for the general scientific community is essential.

Results

We have created a web server, IsoAnalytics, that gives users without computational or bioinformatics background the ability to directly analyze and interactively visualize data obtained from the Isoplexis single cell technology platform. We envision this open-sourced web server will increase research productivity and serve as a free, competitive alternative for single-cell proteomics research.

Availability and implementation

IsoAnalytics is free and available at: https://cdc.biohpc.swmed.edu/isoplexis/ and is implemented in Python, with all major browsers supported. Code for IsoAnalytics is free and available at: https://github.com/zhanxw/Isoplexis_Data_Analysis.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

End Group Nonplanarization Enhances Phototherapy Efficacy of A-D-A Fused-Ring Photosensitizer for Tumor Phototherapy

Enhancing the phototherapy efficacy of organic photosensitizers through molecular design is a fascinating but challenging task. Herein, we propose a simple design strategy to first realize the generation of superoxide anion radical (O₂^•-) by A-D-A fused-ring photosensitizers. Through replacing one cyano group of traditional end group with an ester group, we designed a novel nonplanar end group (A unit) to synthesize a novel A-D-A photosensitizer F8CA. In a comparison with its counterpart F8CN with the traditional end group, F8CA displays more loose packing and larger spin-orbit coupling constants. The F8CA nanoparticles showed higher photodynamic activities with the generation capability of singlet oxygen (¹O₂), hydroxyl radical (^•OH), and O₂^•-, while F8CN nanoparticles could only generate ¹O₂ and ^•OH. In addition, F8CA nanoparticles still remain high photothermal conversion efficiency (61%). As a result, F8CA nanoparticles perform well in hypoxia-tolerant tumor phototherapy. This study brings an effective design thought for A-D-A photosensitizers.

Enhanced Pathology Image Quality with Restore-Generative Adversarial Network

Whole slide imaging is becoming a routine procedure in clinical diagnosis. Advanced image analysis techniques have been developed to assist pathologists in disease diagnosis, staging, subtype classification, and risk stratification. Recently, deep learning algorithms have achieved state-of-the-art performances in various imaging analysis tasks, including tumor region segmentation, nuclei detection, and disease classification. However, widespread clinical use of these algorithms is hampered by their performances often degrading due to image quality issues commonly seen in real-world pathology imaging data such as low resolution, blurring regions, and staining variation. Restore-Generative Adversarial Network (GAN), a deep learning model, was developed to improve the imaging qualities by restoring blurred regions, enhancing low resolution, and normalizing staining colors. The results demonstrate that Restore-GAN can significantly improve image quality, which leads to improved model robustness and performance for existing deep learning algorithms in pathology image analysis. Restore-GAN has the potential to be used to facilitate the applications of deep learning models in digital pathology analyses.

Spatial Transcriptomics Arena (STAr): an Integrated Platform for Spatial Transcriptomics Methodology Research

The emerging field of spatially resolved transcriptomics (SRT) has revolutionized biomedical research. SRT quantifies expression levels at different spatial locations, providing a new and powerful tool to interrogate novel biological insights. An essential question in the analysis of SRT data is to identify spatially variable (SV) genes; the expression levels of such genes have spatial variation across different tissues. SV genes usually play an important role in underlying biological mechanisms and tissue heterogeneity. Currently, several computational methods have been developed to detect such genes; however, there is a lack of unbiased assessment of these approaches to guide researchers in selecting the appropriate methods for their specific biomedical applications. In addition, it is difficult for researchers to implement different existing methods for either biological study or methodology development. Furthermore, currently available public SRT datasets are scattered across different websites and preprocessed in different ways, posing additional obstacles for quantitative researchers developing computational methods for SRT data analysis. To address these challenges, we designed Spatial Transcriptomics Arena (STAr), an open platform comprising 193 curated datasets from seven technologies, seven statistical methods, and analysis results. This resource allows users to retrieve high-quality datasets, apply or develop spatial gene detection methods, as well as browse and compare spatial gene analysis results. It also enables researchers to comprehensively evaluate SRT methodology research in both simulated and real datasets. Altogether, STAr is an integrated research resource intended to promote reproducible research and accelerate rigorous methodology development, which can eventually lead to an improved understanding of biological processes and diseases. STAr can be accessed at https://lce.biohpc.swmed.edu/star/ .

Immune checkpoint blockade induces gut microbiota translocation that augments extraintestinal antitumor immunity

Gut microbiota, specifically gut bacteria, are critical for effective immune checkpoint blockade therapy (ICT) for cancer. The mechanisms by which gut microbiota augment extraintestinal anticancer immune responses, however, are largely unknown. Here, we find that ICT induces the translocation of specific endogenous gut bacteria into secondary lymphoid organs and subcutaneous melanoma tumors. Mechanistically, ICT induces lymph node remodeling and dendritic cell (DC) activation, which facilitates the translocation of a selective subset of gut bacteria to extraintestinal tissues to promote optimal antitumor T cell responses in both the tumor-draining lymph nodes (TDLNs) and the primary tumor. Antibiotic treatment results in decreased gut microbiota translocation into mesenteric lymph nodes (MLNs) and TDLNs, diminished DC and effector CD8+ T cell responses, and attenuated responses to ICT. Our findings illuminate a key mechanism by which gut microbiota promote extraintestinal anticancer immunity.

Triplets with a Twist: Ultrafast Intersystem Crossing in a Series of Electron Acceptor Materials Driven by Conformational Disorder

Control over the populations of singlet and triplet excitons is key to organic semiconductor technologies. In different contexts, triplets can represent an energy loss pathway that must be managed (i.e., solar cells, light-emitting diodes, and lasers) or provide avenues to improve energy conversion (i.e., photon upconversion and multiplication systems). A key consideration in the interplay of singlet and triplet exciton populations in these systems is the rate of intersystem crossing (ISC). In this work, we design, measure, and model a series of new electron acceptor molecules and analyze them using a combination of ultrafast transient absorption and ultrafast broadband photoluminescence spectroscopies. We demonstrate that intramolecular triplet formation occurs within several hundred picoseconds in solution and is accelerated considerably in the solid state. Importantly, ISC occurs with sufficient rapidity to compete with charge formation in modern organic solar cells, implicating triplets in intrinsic exciton loss channels in addition to charge recombination. Density functional theory calculations reveal that ISC occurs in triplet excited states characterized by local deviations from orbital π-symmetry associated with rotationally flexible thiophene rings. In disordered films, structural distortions, therefore, result in significant increases in spin-orbit coupling, enabling rapid ISC. We demonstrate the generality of this proposal in an oligothiophene model system where ISC is symmetry-forbidden and show that conformational disorder introduced by the formation of a solvent glass accelerates ISC, outweighing the lower temperature and increased viscosity. This proposal sheds light on the factors responsible for facile ISC and provides a simple framework for molecular control over spin states.

Susceptible bacteria survive antibiotic treatment in the mammalian gastrointestinal tract without evolving resistance

In vitro systems have provided great insight into the mechanisms of antibiotic resistance. Yet, in vitro approaches cannot reflect the full complexity of what transpires within a host. As the mammalian gut is host to trillions of resident bacteria and thus a potential breeding ground for antibiotic resistance, we sought to better understand how gut bacteria respond to antibiotic treatment in vivo . Here, we colonized germ-free mice with a genetically barcoded antibiotic pan-susceptible Escherichia coli clinical isolate and then administered the antibiotic cefepime via programmable subcutaneous pumps which allowed for closer emulation of human parenteral antibiotic pharmacokinetics/dynamics. After seven days of antibiotics, we were unable to culture E. coli from feces. We were, however, able to recover barcoded E. coli from harvested gastrointestinal (GI) tissue, despite high GI tract and plasma cefepime concentrations. Strikingly, these E. coli isolates were not resistant to cefepime but had acquired mutations â€" most notably in the wbaP gene, which encodes an enzyme required for the initiation of the synthesis of the polysaccharide capsule and lipopolysaccharide O antigen - that increased their ability to invade and survive within intestinal cells, including cultured human colonocytes. Further, these E. coli mutants exhibited a persister phenotype when exposed to cefepime, allowing for greater survival to pulses of cefepime treatment when compared to the wildtype strain. Our findings highlight a mechanism by which bacteria in the gastrointestinal tract can adapt to antibiotic treatment by increasing their ability to persist during antibiotic treatment and invade intestinal epithelial cells where antibiotic concentrations are substantially reduced.

IsoAnalytics: A Single-cell Proteomics Web Server

Motivation

Single-cell proteomics provide unprecedented resolution to examine biological processes. Customized data analysis and facile data visualization are crucial for scientific discovery. Further, userfriendly data analysis and visualization software that is easily accessible for the general scientific community is essential.

Results

We have created a web server, IsoAnalytics , that gives users without computational or bioinformatics background the ability to directly analyze and interactively visualize data obtained from the Isoplexis single cell technology platform. We envision this open-sourced web server will increase research productivity and serve as a free, competitive alternative for single-cell proteomics research.

Contact

Andrew.Koh@utsouthwestern.edu and Xiaowei.Zhan@utsouthwestern.edu.

Availability

IsoAnalytics is free and available at: https://cdc.biohpc.swmed.edu/isoplexis/ and is implemented in Python, with all major browsers supported. Code for IsoAnalytics is free and available at: https://github.com/zhanxw/Isoplexis_Data_Analysis .

Supplementary Information

Supplementary data are available at Bioinformatics online.

Quasi-Homojunction Organic Nonfullerene Photovoltaics Featuring Fundamentals Distinct from Bulk Heterojunctions

In contrast to classical bulk heterojunction (BHJ) in organic solar cells (OSCs), the quasi-homojunction (QHJ) with extremely low donor content (≤10 wt.%) is unusual and generally yields much lower device efficiency. Here, representative polymer donors and nonfullerene acceptors are selected to fabricate QHJ OSCs, and a complete picture for the operation mechanisms of high-efficiency QHJ devices is illustrated. PTB7-Th:Y6 QHJ devices at donor:acceptor (D:A) ratios of 1:8 or 1:20 can achieve 95% or 64% of the efficiency obtained from its BHJ counterpart at the optimal D:A ratio of 1:1.2, respectively, whereas QHJ devices with other donors or acceptors suffer from rapid roll-off of efficiency when the donors are diluted. Through device physics and photophysics analyses, it is observed that a large portion of free charges can be intrinsically generated in the neat Y6 domains rather than at the D/A interface. Y6 also serves as an ambipolar transport channel, so that hole transport as also mainly through Y6 phase. The key role of PTB7-Th is primarily to reduce charge recombination, likely assisted by enhancing quadrupolar fields within Y6 itself, rather than the previously thought principal roles of light absorption, exciton splitting, and hole transport.

Clinically undetected polyclonal heteroresistance among Pseudomonas aeruginosa isolated from cystic fibrosis respiratory specimens

BACKGROUND

Pseudomonas aeruginosa infection is the leading cause of death among patients with cystic fibrosis (CF) and a common cause of difficult-to-treat hospital-acquired infections. P. aeruginosa uses several mechanisms to resist different antibiotic classes and an individual CF patient can harbour multiple resistance phenotypes.

OBJECTIVES

To determine the rates and distribution of polyclonal heteroresistance (PHR) in P. aeruginosa by random, prospective evaluation of respiratory cultures from CF patients at a large referral centre over a 1 year period.

METHODS

We obtained 28 unique sputum samples from 19 CF patients and took multiple isolates from each, even when morphologically similar, yielding 280 unique isolates. We performed antimicrobial susceptibility testing (AST) on all isolates and calculated PHR on the basis of variability in AST in a given sample. We then performed whole-genome sequencing on 134 isolates and used a machine-learning association model to interrogate phenotypic PHR from genomic data.

RESULTS

PHR was identified in most sampled patients (n = 15/19; 79%). Importantly, resistant phenotypes were not detected by routine AST in 26% of patients (n = 5/19). The machine-learning model, using the extended sampling, identified at least one genetic variant associated with phenotypic resistance in 94.3% of isolates (n = 1392/1476).

CONCLUSION

PHR is common among P. aeruginosa in the CF lung. While traditional microbiological methods often fail to detect resistant subpopulations, extended sampling of isolates and conventional AST identified PHR in most patients. A machine-learning tool successfully identified at least one resistance variant in almost all resistant isolates by leveraging this extended sampling and conventional AST.

[Clinical and StAR genetic characteristics of 33 children with congenital lipoid adrenal hyperplasia]

Objective: To analyze the clinical and genetic characteristics of 33 children with congenital lipoid adrenal hyperplasia (CLAH) caused by StAR gene defects. Methods: The clinical, biochemical, genetic, and follow-up (until December 2021) data of 33 children diagnosed with CLAH from 2006 to 2021 were retrospectively analyzed in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine. Results: Of the 33 children with CLAH, 17 had a karyotype of 46, XX and 16 had a karyotype of 46, XY; 31 were female and 2 were male by social gender. Classic type and non-classic type were found in 30 and 3 children respectively. The age at diagnosis was 9.0 (3.0, 34.5) months. All the 30 cases with classic CLAH presented within the first year of life with skin hyperpigmentation (28 cases, 93%), vomiting and(or) diarrhea (19 cases, 63%), no increase in body weight (8 cases, 27%), elevated adrenocorticotropic hormone levels (21cases (70%)>275 pmol/L), decreased cortisol levels (47 (31,126) nmol/L), hyponatremia ((126±13) mmol/L), hyperkalemia ((5.7±1.1) mmol/L), and normal 17α-hydroxyprogesterone levels (30 cases, 100%). All these with classic CLAH exhibited female external genitalia. Three children with non-classic CLAH (including 2 cases of 46, XY and 1 case of 46, XX) also showed signs and symptoms of adrenal insufficiency, but 2 of them had an age of onset later than 1 year of age, including 1 case of 46, XY with male external genitalia and 1 case of 46, XX with female external genitalia. The other 46, XY patient with non-classic CLAH presented with adrenal insufficiency at 2 months of age, showing micropenis and hypospadias. In the 17 females with 46, XX, 4 older than 10 years of age showed spontaneous pubertal development. A total of 25 StAR gene pathogenic variants were identified in 33 patients, with p.Q258* (18/66, 27%), p.K236Tfs*47 (8/66, 12%) and p.Q77* (6/66, 9%) being the common variantion. Six novel variants were found, including c.358T>G, c.713_714del, c.125del, c.745-1G>A, c.179-2A>C, and exon 1 deletion. Conclusions: Patients with classic CLAH typically present with signs and symptoms of primary adrenal insufficiency in the early infancy period and female external genitalia. p.Q258*, p.K236Tfs*47 and p.Q77* are common variants in CLAH patients.

Simultaneously Enhancing Exciton/Charge Transport in Organic Solar Cells by an Organoboron Additive

Efficient exciton diffusion and charge transport play a vital role in advancing the power conversion efficiency (PCE) of organic solar cells (OSCs). Here, a facile strategy is presented to simultaneously enhance exciton/charge transport of the widely studied PM6:Y6-based OSCs by employing highly emissive trans-bis(dimesitylboron)stilbene (BBS) as a solid additive. BBS transforms the emissive sites from a more H-type aggregate into a more J-type aggregate, which benefits the resonance energy transfer for PM6 exciton diffusion and energy transfer from PM6 to Y6. Transient gated photoluminescence spectroscopy measurements indicate that addition of BBS improves the exciton diffusion coefficient of PM6 and the dissociation of PM6 excitons in the PM6:Y6:BBS film. Transient absorption spectroscopy measurements confirm faster charge generation in PM6:Y6:BBS. Moreover, BBS helps improve Y6 crystallization, and current-sensing atomic force microscopy characterization reveals an improved charge-carrier diffusion length in PM6:Y6:BBS. Owing to the enhanced exciton diffusion, exciton dissociation, charge generation, and charge transport, as well as reduced charge recombination and energy loss, a higher PCE of 17.6% with simultaneously improved open-circuit voltage, short-circuit current density, and fill factor is achieved for the PM6:Y6:BBS devices compared to the devices without BBS (16.2%).

Analysis of KIR gene variants in The Cancer Genome Atlas and UK Biobank using KIRCLE

BACKGROUND

Natural killer (NK) cells represent a critical component of the innate immune system's response against cancer and viral infections, among other diseases. To distinguish healthy host cells from infected or tumor cells, killer immunoglobulin receptors (KIR) on NK cells bind and recognize Human Leukocyte Antigen (HLA) complexes on their target cells. However, NK cells exhibit great diversity in their mechanism of activation, and the outcomes of their activation are not yet understood fully. Just like the HLAs they bind, KIR receptors exhibit high allelic diversity in the human population. Here we provide a method to identify KIR allele variants from whole exome sequencing data and uncover novel associations between these variants and various molecular and clinical correlates.

RESULTS

In order to better understand KIRs, we have developed KIRCLE, a novel method for genotyping individual KIR genes from whole exome sequencing data, and used it to analyze approximately sixty-thousand patient samples in The Cancer Genome Atlas (TCGA) and UK Biobank. We were able to assess population frequencies for different KIR alleles and demonstrate that, similar to HLA alleles, individuals' KIR alleles correlate strongly with their ethnicities. In addition, we observed associations between different KIR alleles and HLA alleles, including HLA-B*53 with KIR3DL2*013 (Fisher's exact FDR = 7.64e-51). Finally, we showcased statistically significant associations between KIR alleles and various clinical correlates, including peptic ulcer disease (Fisher's exact FDR = 0.0429) and age of onset of atopy (Mann-Whitney U FDR = 0.0751).

CONCLUSIONS

We show that KIRCLE is able to infer KIR variants accurately and consistently, and we demonstrate its utility using data from approximately sixty-thousand individuals from TCGA and UK Biobank to discover novel molecular and clinical correlations with KIR germline variants. Peptic ulcer disease and atopy are just two diseases in which NK cells may play a role beyond their "classical" realm of anti-tumor and anti-viral responses. This tool may be used both as a benchmark for future KIR-variant-inference algorithms, and to better understand the immunogenomics of and disease processes involving KIRs.

MB-SupCon: Microbiome-based Predictive Models via Supervised Contrastive Learning

Human microbiome consists of trillions of microorganisms. Microbiota can modulate the host physiology through molecule and metabolite interactions. Integrating microbiome and metabolomics data have the potential to predict different diseases more accurately. Yet, most datasets only measure microbiome data but without paired metabolome data. Here, we propose a novel integrative modeling framework, Microbiome-based Supervised Contrastive Learning Framework (MB-SupCon). MB-SupCon integrates microbiome and metabolome data to generate microbiome embeddings, which can be used to improve the prediction accuracy in datasets that only measure microbiome data. As a proof of concept, we applied MB-SupCon on 720 samples with paired 16S microbiome data and metabolomics data from patients with type 2 diabetes. MB-SupCon outperformed existing prediction methods and achieved high average prediction accuracies for insulin resistance status (84.62%), sex (78.98%), and race (80.04%). Moreover, the microbiome embeddings form separable clusters for different covariate groups in the lower-dimensional space, which enhances data visualization. We also applied MB-SupCon on a large inflammatory bowel disease study and observed similar advantages. Thus, MB-SupCon could be broadly applicable to improve microbiome prediction models in multi-omics disease studies.

The principles, design and applications of fused-ring electron acceptors

Fused-ring electron acceptors (FREAs) have a donor-acceptor-donor structure comprising an electron-donating fused-ring core, electron-accepting end groups, π-bridges and side chains. FREAs possess beneficial features, such as feasibility to tailor their structures, high property tunability, strong visible and near-infrared light absorption and excellent n-type semiconducting characteristics. FREAs have initiated a revolution to the field of organic solar cells in recent years. FREA-based organic solar cells have achieved unprecedented efficiencies, over 20%, which breaks the theoretical efficiency limit of traditional fullerene acceptors (~13%), and boast potential operational lifetimes approaching 10 years. Based on the original studies of FREAs, a variety of new structures, mechanisms and applications have flourished. In this Review, we introduce the fundamental principles of FREAs, including their structures and inherent electronic and physical properties. Next, we discuss the way in which the properties of FREAs can be modulated through variations to the electronic structure or molecular packing. We then present the current applications and consider the future areas that may benefit from developments in FREAs. Finally, we conclude with the position of FREA chemistry, reflecting on the challenges and opportunities that may arise in the future of this burgeoning field.

[Disease spectrum analysis of children with inherited metabolic diseases detected by gas chromatography-mass spectrometry of urinary organic acids]

Objective: To investigate the spectrum of amino acid, organic acid, and fatty acid oxidative metabolic diseases in children diagnosed by detecting urinary organic acid levels using gas chromatography-mass spectrometry. Methods: From January 2005 to December 2021, clinical data of 2 461 children diagnosed with inherited metabolic diseases (IMD) by gas chromatography-mass spectrometry, in combination with tandem mass spectrometry and genetic testing in Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine were retrospectively analyzed. Results: Among 2 461 children, 1 446 were male and 1 051 were female. A total of 32 types of IMD were detected among 2 461 patients, which included 10 amino acid disorders in 662 cases (26.9%), 6 common diseases were hyperphenylalaninemia, citrin deficiency, ornithine carbamoyltransferase deficiency, maple syrup urine disease, alkaptonuria, and tyrosinemia-I, 17 types of organic acidemias in 1 683 cases (68.4%), 6 common diseases were methylmalonic acidemia, propionic acidemia, valeric acidemia-type Ⅰ, isovaleric acidemia, 3-methylcrotonyl-CoA carboxylase deficiency and multiple carboxylase deficiency and 5 fatty acid β oxidative defects in 116 cases (4.7%), 2 common diseases were multiple acyl-CoA dehydrogenase deficiency and short-chain acyl-CoA dehydrogenase deficiency). Conclusion: Among the diseases diagnosed by analyzing urinary organic acid profiling with gas chromatography-mass spectrometry, the most common are organic acidemias, followed by amino acid disorders and fatty acid oxidation defects.

Free charge photogeneration in a single component high photovoltaic efficiency organic semiconductor

Organic photovoltaics (OPVs) promise cheap and flexible solar energy. Whereas light generates free charges in silicon photovoltaics, excitons are normally formed in organic semiconductors due to their low dielectric constants, and require molecular heterojunctions to split into charges. Recent record efficiency OPVs utilise the small molecule, Y6, and its analogues, which – unlike previous organic semiconductors – have low band-gaps and high dielectric constants. We show that, in Y6 films, these factors lead to intrinsic free charge generation without a heterojunction. Intensity-dependent spectroscopy reveals that 60–90% of excitons form free charges at AM1.5 light intensity. Bimolecular recombination, and hole traps constrain single component Y6 photovoltaics to low efficiencies, but recombination is reduced by small quantities of donor. Quantum-chemical calculations reveal strong coupling between exciton and CT states, and an intermolecular polarisation pattern that drives exciton dissociation. Our results challenge how current OPVs operate, and renew the possibility of efficient single-component OPVs.

When light hits organic semiconductors, bound charge pairs, called excitons, are usually produced. Here, the authors show that in the best performing organic solar material to date, free charges, rather than excitons, are directly created by light.

Revealing the Sole Impact of Acceptor's Molecular Conformation to Energy Loss and Device Performance of Organic Solar Cells through Positional Isomers

Two new fused-ring electron acceptor (FREA) isomers with nonlinear and linear molecular conformation, m-BAIDIC and p-BAIDIC, are designed and synthesized. Despite the similar light absorption range and energy levels, the two isomers exhibit distinct electron reorganization energies and molecular packing motifs, which are directly related to the molecular conformation. Compared with the nonlinear acceptor, the linear p-BAIDIC shows more ordered molecular packing and higher crystallinity. Furthermore, p-BAIDIC-based devices exhibit reduced nonradiative energy loss and improved charge transport mobilities. It is beneficial to enhance the open-circuit voltage (V_OC ) and short-current current density (J_SC ) of the devices. Therefore, the linear FREA, p-BAIDIC yields a relatively higher efficiency of 7.71% in the binary device with PM6, in comparison with the nonlinear m-BAIDIC. When p-BAIDIC is incorporated into the binary PM6/BO-4Cl system to form a ternary system, synergistic enhancements in V_OC , J_SC , fill factor (FF), and ultimately a high efficiency of 17.6% are achieved.

Pushing the Efficiency of High Open-Circuit Voltage Binary Organic Solar Cells by Vertical Morphology Tuning

The tuning of vertical morphology is critical and challenging for organic solar cells (OSCs). In this work, a high open-circuit voltage (V_OC ) binary D18-Cl/L8-BO system is attained while maintaining the high short-circuit current (J_SC ) and fill factor (FF) by employing 1,4-diiodobenzene (DIB), a volatile solid additive. It is suggested that DIB can act as a linker between donor or/and acceptor molecules, which significantly modifies the active layer morphology. The overall crystalline packing of the donor and acceptor is enhanced, and the vertical domain sizes of phase separation are significantly decreased. All these morphological changes contribute to exciton dissociation, charge transport, and collection. Therefore, the best-performing device exhibits an efficiency of 18.7% with a V_OC of 0.922 V, a J_SC of 26.6 mA cm^-2 , and an FF of 75.6%. As far as it is known, the V_OC achieved here is by far the highest among the reported OSCs with efficiencies over 17%. This work demonstrates the high competence of solid additives with two iodine atoms to tune the morphology, particularly in the vertical direction, which can become a promising direction for future optimization of OSCs.

Towards High-Performance Semitransparent Organic Photovoltaics: Dual-Functional p-Type Soft Interlayer

Semitransparent organic photovoltaics (OPVs) have drawn significant attention for their promising potential in the field of building integrated photovoltaics such as energy-generating greenhouses. However, the conflict between the need to attain satisfying average visible transmittances for greenhouse applications and the need to maintain high power conversion efficiencies is limiting the commercialization of semitransparent OPVs. A major manifestation of this issue is the undermining of charge carrier extraction efficiency when opaque, visible-light-absorbing electrodes are substituted with semitransparent ones. Here, we incorporated a dual-function p-type compatible interlayer to modify the interface of the hole-transporting layer and the ultrathin electrode of the semitransparent devices. We find that the p-type interlayer not only enhances the charge carrier extraction of the electrode but also increases the light transmittance in the wavelength range of 400-450 nm, which covers most of the photosynthetic absorption spectrum. The modified semitransparent devices reach a power conversion efficiency of 13.7% and an average visible transmittance of 22.2%.

Towards High-Performance Semitransparent Organic Photovoltaics: Dual-Functional p-Type Soft Interlayer

Semitransparent organic photovoltaics (OPVs) have drawn significant attention for their promising potential in the field of building integrated photovoltaics such as energy-generating greenhouses. However, the conflict between the need to attain satisfying average visible transmittances for greenhouse applications and the need to maintain high power conversion efficiencies is limiting the commercialization of semitransparent OPVs. A major manifestation of this issue is the undermining of charge carrier extraction efficiency when opaque, visible-light-absorbing electrodes are substituted with semitransparent ones. Here, we incorporated a dual-function p-type compatible interlayer to modify the interface of the hole-transporting layer and the ultrathin electrode of the semitransparent devices. We find that the p-type interlayer not only enhances the charge carrier extraction of the electrode but also increases the light transmittance in the wavelength range of 400-450 nm, which covers most of the photosynthetic absorption spectrum. The modified semitransparent devices reach a power conversion efficiency of 13.7% and an average visible transmittance of 22.2%.

Printing fabrication of large-area non-fullerene organic solar cells

Organic solar cells (OSCs) based on a bulk heterojunction structure exhibit inherent advantages, such as low cost, light weight, mechanical flexibility, and easy processing, and they are emerging as a potential renewable energy technology. However, most studies are focused on lab-scale, small-area (<1 cm²) devices. Large-area (>1 cm²) OSCs still exhibit considerable efficiency loss during upscaling from small-area to large-area, which is a big challenge. In recent years, along with the rapid development of high-performance non-fullerene acceptors, many researchers have focused on developing large-area non-fullerene-based devices and modules. There are three essential issues in upscaling OSCs from small-area to large-area: fabrication technology, equipment development, and device component processing strategy. In this review, the challenges and solutions in fabricating high-performance large-area OSCs are discussed in terms of the abovementioned three aspects. In addition, the recent progress of large-area OSCs based on non-fullerene electron acceptors is summarized.

[HBx promotes ubiquitination and degradation of ZO1 and increases the migration and invasion of liver cancer cells]

Objective: To study the effect of hepatitis B virus X protein (HBx) expression level on migration and invasion of zonula occludens protein-1 (ZO-1) in HepG2 liver cancer cells. Methods: Liver cancer cells were transfected with HBV full gene plasmid (pcDNA3.1-HBV1. 1 or pcDNA3.1-HBV1.3), empty plasmid (pcDNA3.1) and HBV-encoded protein plasmids (pHBc, pHBs, pHBp and pHBx), respectively. Western blot and RT-PCR were used to detect ZO1 protein and mRNA levels. Immunoprecipitation was used to detect transfected pHBx. Western blot was used to detect ZO1 ubiquitination levels. Transwell chambers were used to assess cell migration and invasion. Cell proliferation and lactate dehydrogenase assay was used to detect siRNA transfecting targeting ZO1. Flow cytometry was used to detect cell apoptosis and cycle. The data was compared between two and multiple groups by using an independent sample t-test and one-way analysis of variance. Results: Compared with the empty plasmid, ZO1 protein level in HepG2 cells after transiently transfected with pHBV1.1 and pHBV1.3 was decreased by 42.99% ± 6.8% and 55.0% 5 ± 4.56%, respectively, and their mRNA levels did not change significantly. ZO1 protein level in Huh7 cells was decreased by 17.46% ± 4.94% and 47.53% ± 3.38%, respectively. ZO1 protein level after transfection with pHBx was decreased by 47.02% ± 3.4%, while the ZO1 protein level after transfection with pHBc, pHBs and pHBp did not change significantly. ZO1 mRNA level was unaffected with pHBx transfection. ZO1 ubiquitin level and cell migration and invasion ability in HepG2 cells was significantly increased with transfected pHBx. HepG2 cells proliferation, apoptosis and cycle after transfection with ZO1-targeted siRNA did not change significantly, but the migration and invasion ability were significantly increased. Conclusion: HBx can increase the migration and invasion of liver cancer cells by promoting the ubiquitination and degradation of ZO1 protein level.

Uncovering the out-of-plane nanomorphology of organic photovoltaic bulk heterojunction by GTSAXS

The bulk morphology of the active layer of organic solar cells (OSCs) is known to be crucial to the device performance. The thin film device structure breaks the symmetry into the in-plane direction and out-of-plane direction with respect to the substrate, leading to an intrinsic anisotropy in the bulk morphology. However, the characterization of out-of-plane nanomorphology within the active layer remains a grand challenge. Here, we utilized an X-ray scattering technique, Grazing-incident Transmission Small-angle X-ray Scattering (GTSAXS), to uncover this new morphology dimension. This technique was implemented on the model systems based on fullerene derivative (P3HT:PC71BM) and non-fullerene systems (PBDBT:ITIC, PM6:Y6), which demonstrated the successful extraction of the quantitative out-of-plane acceptor domain size of OSC systems. The detected in-plane and out-of-plane domain sizes show strong correlations with the device performance, particularly in terms of exciton dissociation and charge transfer. With the help of GTSAXS, one could obtain a more fundamental perception about the three-dimensional nanomorphology and new angles for morphology control strategies towards highly efficient photovoltaic devices.

Fast Response Organic Tandem Photodetector for Visible and Near-Infrared Digital Optical Communications

Organic photodetectors (OPDs), which usually work as photodiodes, photoconductors, or phototransistors, have emerged as candidates for next-generation light sensing. However, low response speed caused by low carrier mobility and resistance-capacitance (RC) time constant, severely hinders the commercialization of OPDs. Herein, the authors demonstrate a state-of-the-art OPD with a record response speed of 146.8 ns by employing tandem structure to simultaneously reduce both the carrier transit time and RC time constant of the device, which is faster than that of previously reported OPDs as far as they know. Moreover, benefitting from the multi-level barrier enhancement and voltage division engendered by tandem structure, an ultralow noise current of 7.82 × 10^-14 A Hz^-1/2 is obtained, as well as a wide detection range in 300-1000 nm. In addition, the tandem OPDs are successfully integrated into the optical communication system as signal receivers, demonstrating the precise digital signal communication from visible to near-infrared light. It is believed that tandem OPDs have promising application potential in the wireless transmission system.

Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases

The X Chromosome plays an important role in human development and disease. However, functional genomic and disease association studies of X genes greatly lag behind autosomal gene studies, in part owing to the unique biology of X-Chromosome inactivation (XCI). Because of XCI, most genes are only expressed from one allele. Yet, ∼30% of X genes “escape” XCI and are transcribed from both alleles, many only in a proportion of the population. Such interindividual differences are likely to be disease relevant, particularly for sex-biased disorders. To understand the functional biology for X-linked genes, we developed X-Chromosome inactivation for RNA-seq (XCIR), a novel approach to identify escape genes using bulk RNA-seq data. Our method, available as an R package, is more powerful than alternative approaches and is computationally efficient to handle large population-scale data sets. Using annotated XCI states, we examined the contribution of X-linked genes to the disease heritability in the United Kingdom Biobank data set. We show that escape and variable escape genes explain the largest proportion of X heritability, which is in large part attributable to X genes with Y homology. Finally, we investigated the role of each XCI state in sex-biased diseases and found that although XY homologous gene pairs have a larger overall effect size, enrichment for variable escape genes is significantly increased in female-biased diseases. Our results, for the first time, quantitate the importance of variable escape genes for the etiology of sex-biased disease, and our pipeline allows analysis of larger data sets for a broad range of phenotypes.

[Analysis of six children with 3-methylglutaconic aciduria]

Objective: To explore the clinical characteristics, genotypes and long-term outcomes of individuals with 3-methylglutaconic aciduria. Methods: The clinical features, biochemical data, genetic test results and treatment outcomes of six children with 3-methylglutaconic aciduria admitted to the Department of Endocrinology, Genetics and Metabolism, Xinhua Hospital from February 2017 to February 2019 were retrospectively analyzed and the Gesell developmental diagnosis schedule was performed to evaluate the development of four patients. Results: Among 6 children with 3-methylglutaconic aciduria 2 were males and 4 were females.Four cases had 3-methylglutaconic aciduria type Ⅰ and 2 cases had 3-methylglutaconic aciduria with deafness,encephalopathy, and Leigh-like syndrome. Five of 6 patients were detected by newborn screening among whom 4 remained asymptomatic, and only one had a postmortem diagnosis. Among them, 4 patients remained asymptomatic, while two presented with clinical symptoms such as jaundice and dyspnea and the age of disease onset was 1 and 2 days respectively. The concentration of 3-methylglutaconic acid in urine of all affected individuals was between 22.38 and 77.09 mmol/molCr, which was above the normal value. Genetic tests were performed for all patients. Eleven variants were identified in 2 genes, of which 10 variants were novel and only c.442C>T p.(R148X) has been previously reported; Seven variants (c.656-2delA, EX5-EX6 Del, c.942+3A>G, c.373C>T p.(R125W), c.895-3C>G, c.667C>T p.(R223X) and c.894+5G>A) were in AUH gene. The others (c.548G>A p.(R138Q), c.442C>T p.(R148X), c.1339C>T p.(R447X) and c.973dupA p.(M325Nfs*5) were in SERAC1 gene. After being treated with leucine diet restriction and L-carnitine, 4 patients with AUH gene variation who were from asymptomatic phase developed normally, whereas those 2 patients with SERAC1 gene variation had a poor prognosis. During the follow-up, 2 patients exhibited varying degrees of psychomotor retardation, the rest had normal course of development. Conclusions: There are significant clinical heterogeneities among individuals with 3-methylglutaconic aciduria. The most common pathogenic variants are splicing variations, followed by nonsense, missense and frameshift mutations. Leucine-free diet and oral L-carnitine therapy are effective for some patients. Newborn screening is essential for early diagnosis and improvement of prognosis.

Enrichment of Autotrophic Denitrifiers From Anaerobic Sludge Using Sulfurous Electron Donors

This study compared the rates and microbial community development in batch bioassays on autotrophic denitrification using elemental sulfur (S0), pyrite (FeS2), thiosulfate (S2O3 2-), and sulfide (S2-) as electron donor. The performance of two inocula was compared: digested sludge (DS) from a wastewater treatment plant of a dairy industry and anaerobic granular sludge (GS) from a UASB reactor treating dairy wastewater. All electron donors supported the development of a microbial community with predominance of autotrophic denitrifiers during the enrichments, except for sulfide. For the first time, pyrite revealed to be a suitable substrate for the growth of autotrophic denitrifiers developing a microbial community with predominance of the genera Thiobacillus, Thioprofundum, and Ignavibacterium. Thiosulfate gave the highest denitrification rates removing 10.94 mM NO3 - day-1 and 8.98 mM NO3 - day-1 by DS and GS, respectively. This was 1.5 and 6 times faster than elemental sulfur and pyrite, respectively. Despite the highest denitrification rates observed in thiosulfate-fed enrichments, an evaluation of the most relevant parameters for a technological application revealed elemental sulfur as the best electron donor for autotrophic denitrification with a total cost of 0.38 € per m3 of wastewater treated.

Spatial molecular profiling: platforms, applications and analysis tools

Molecular profiling technologies, such as genome sequencing and proteomics, have transformed biomedical research, but most such technologies require tissue dissociation, which leads to loss of tissue morphology and spatial information. Recent developments in spatial molecular profiling technologies have enabled the comprehensive molecular characterization of cells while keeping their spatial and morphological contexts intact. Molecular profiling data generate deep characterizations of the genetic, transcriptional and proteomic events of cells, while tissue images capture the spatial locations, organizations and interactions of the cells together with their morphology features. These data, together with cell and tissue imaging data, provide unprecedented opportunities to study tissue heterogeneity and cell spatial organization. This review aims to provide an overview of these recent developments in spatial molecular profiling technologies and the corresponding computational methods developed for analyzing such data.

[Effects of pressure steam sterilization times on the accuracy of the digital intraoral scanning data]

Objective: To provide a scientific basis for the standardized operation of clinical disinfection by comparing and analyzing the influence of disinfection times on the accuracy of digital intraoral scanning. Methods: The author prepared 10 brand-new intraoral scanning heads (Trios, 3Shape, Denmark), scan the same plaster standard dentition model after 1, 20, 40, and 60 times of pressure steam sterilization, and obtained the data of four groups of experimental groups A, B, C, D, and scan the model 5 times repeatedly after each disinfection cycle of each scanning head. A model scanner (D2000, 3Shape, Denmark) was used to scan the standard dentition model, and the scan results were used as the control group data. Vernier calipers and measurement software were used to measure the arch length (the distance between the mesial cheek tips of the first molars on both sides of the maxillary) and the front and back length (the distance from the tongue protrusion of the right incisor to the buccal tip of the first molar on the right of the upper jaw) of the plaster model and the data of the 4 experimental groups. The line distance results of the 4 groups of experimental groups were compared for statistical analysis, and the trueness and precision values of the 4 groups of experimental groups were compared for statistical analysis. Results: The length of the arch across the 4 experimental groups increased with the increase in the number of disinfection (P<0.05), and there were statistical differences compared with the measurement results of the plaster model (P<0.05); the differences in the length of the dental arch were not statistically significant (P>0.05). The treness of the 4 experimental groups is statistically significant (P<0.05), and the trueness was from high to low in order of group A [(114.85±3.75) μm], group B [(124.65±3.85) μm], group C [(131.45±3.04) μm] and group D [(144.64±3.34) μm]; the precision of the 4 experimental groups was not statistically significant (P>0.05). Conclusions: The number of times of pressure steam sterilization can affect the accuracy of the scanning results of the digital intraoral scanner, and with the increase of the number of sterilizations, the error of the scanning results also tends to increase. The number of sterilizations has no effect on the repeatability of the digital scanning results. The increase in the number of times of pressure steam sterilization affects the accross of the arch but has no effect on the length of the dental arch, and the range of change of the length of the arch is within the clinically acceptable range. After 60 times of pressure steam sterilization, the accuracy of digital scan data can still meet clinical needs.

MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data

In microbiome research, metagenomic sequencing generates enormous amounts of data. These data are typically classified into taxa for taxonomy analysis, or into genes for functional analysis. However, a joint analysis where the reads are classified into taxa-specific genes is often overlooked. To enable the analysis of this biologically meaningful feature, we developed a novel bioinformatic toolkit, MetaPrism, which can analyze sequence reads for a set of joint taxa/gene analyses to: 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) compare the abundances between groups; and 4) build prediction models for clinical outcome. We illustrated these functions using a published microbiome metagenomics dataset from patients treated with immune checkpoint inhibitor therapy and showed the joint features can serve as potential biomarkers to predict therapeutic responses. MetaPrism is a toolkit for joint taxa and gene analysis. It offers biological insights on the taxa-specific genes on top of the taxa-alone or gene-alone analysis.

MetaPrism is open-source software and freely available at https://github.com/jiwoongbio/MetaPrism. The example script to reproduce the manuscript is also provided in the above code repository.