Assessment of spatial brightness for a visual field in interior spaces based on indirect corneal illuminance.

Quantitative evaluation of spatial brightness has been difficult, mainly due to the lack of a metric that is both highly related to subjective evaluation and convenient to measure in the field. This work investigated the applicability of using indirect corneal illuminance to evaluate spatial brightness for a visual field in interior spaces. Three lighting scenes with different patterns of lighting distribution, which all delivered indirect light to the subjects, were compared against each other in pairs for spatial brightness. The corresponding indirect corneal illuminance required for each test scene to match the spatial brightness of the reference scene with a fixed corneal illuminance was obtained. The results showed that our proposed metric had a high correlation with subjective evaluation of spatial brightness even under very different patterns of lighting distribution. Furthermore, the proposed metric was compared with the prior metrics of MRSE and Lav,B40 in spatial brightness evaluation, and the former showed the best correlation with subjective judgments. Since the spatial brightness assessment for various visual fields together compose people's overall impression of an illuminated space, the proposed metric of indirect corneal illuminance, which combines both accuracy and convenience in measurement, could serve as a preferred metric for spatial brightness evaluation.

Optimized Sequencing Adaptors Enable Rapid and Real-Time Metagenomic Identification of Pathogens during Runtime of Sequencing.

BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers the promise of unbiased detection of emerging pathogens. However, in indexed sequencing, the sequential paradigm of data acquisition, demultiplexing, and analysis restrain read assignment in advance and real-time analysis, resulting in lengthy turnaround time for clinical metagenomic detection. METHODS: We described the utility of internal-index adaptors with different lengths of barcode in multiplex sequencing. The base composition for each position within these adaptors was well-balanced to ensure nucleotide diversity and optimal sequencing performance and to achieve the early assignment of reads by first sequencing the barcodes. Combined with an automated library preparation device, we delivered a rapid and real-time bioinformatics pathogen identification solution for the Illumina NextSeq platform. The diagnostic performance was evaluated by testing 153 lower respiratory tract specimens using mNGS in comparison to culture, 16S/internal transcribed spacer amplicon sequencing, and additional PCR-based tests. RESULTS: By calculating the average F1 scores of all read lengths under different threshold values, we established the optimal threshold for pathogens identification, and found that 36 bp was the optimal shortest read length for rapid mNGS analysis. Rapid detection had a negative percentage agreement and positive percentage agreement of 100% and 85.1% for bacteria and 97.4% and 80.3% for fungi, when compared to a composite standard. The rapid mNGS solution enabled accurate pathogen identification in about 9.1 to 10.1 h sample-to-answer turnaround time. CONCLUSIONS: Optimized internal index adaptors combined with a real-time analysis pipeline provide a potential tool for a first-line test in critically ill patients.

MicroRNA Profile of Human Bone Marrow Mesenchymal Stem Cells during Hepatic Differentiation and Therapy.

Background and Aims: MicroRNAs (miRNAs) play important roles in hepatocyte differentiation from human bone marrow mesenchymal stem cells (hBMSCs) and the therapeutic application in vivo. However, the mechanisms of miRNA regulation are still unknown. This study aimed to profile the miRNA basis for improving the function of hBMSC-differentiated hepatocyte-like cells (hBMSC-Heps). Methods: Characteristic miRNAs of hBMSC-Heps were identified by transcriptome sequencing and validated by quantitative real-time polymerase chain reaction (qRT-PCR). An in vivo hBMSC transplantation model was used to assess the regulatory effects of miRNAs on liver regeneration during hBMSC therapy in pigs with fulminant hepatic failure (FHF). The biological functions of significant miRNA molecules were confirmed by transfection of miRNA activators or inhibitors into hBMSCs during hepatogenic differentiation. Results: The transcriptome of hBMSC-Heps showed characteristics distinct from those of undifferentiated hBMSCs. A total of 77 miRNAs were significantly differentially expressed in hBMSC-Heps at day 10 and day 20 after hBMSC differentiation that were directly related to the functions of hepatocytes. Among the top 10 significantly differentially expressed and the top 10 most abundant miRNAs, nine miRNAs that exhibited a pattern of gradual change were chosen for further analysis. The expression of nine miRNAs was confirmed by qRT-PCR in vitro and showed the same changing trends in vivo in an hBMSC transplantation model in pigs. Functional experiments with these miRNAs showed that activators of hsa-miR-26b-5p and hsa-miR-148a-3p and an inhibitor of hsa-miR-423-3p were sufficient to improve the differentiation of hBMSCs into hepatocyte-like cells. Conclusions: Transcriptome profiles of miRNA revealed the basis of the differentiation and development of hBMSC-Heps. Manipulation of three miRNAs (hsa-miR-26b-5p, hsa-miR-148a-3p and hsa-miR-423-3p) significantly improved hepatocyte generation and liver regeneration, indicating the potential of these miRNAs for future clinical applications.

Alterations of the human gut microbiome in liver cirrhosis.

Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.

Transcriptome Profiling Reveals Distinct Phenotype of Human Bone Marrow Mesenchymal Stem Cell-derived Hepatocyte-like cells.

Background: Human bone marrow mesenchymal stem cell-derived hepatocyte-like cells (hBMSC-HLCs) are a promising alternative for primary human hepatocytes (HHs) for treating liver disease. However, the molecular characteristics of HLCs remain unclear. Here, we aimed to clarify the transcriptome characteristics of hBMSC-HLCs for future clinical application. Materials and Methods: hBMSCs were isolated from the bone marrow of healthy volunteers and differentiated into hepatocytes. mRNA sequencing was used in the transcriptome profiling of hBMSC-HLCs, with hBMSCs and HHs as controls. Results: hBMSC-HLCs exhibited a polygonal morphology, glycogen accumulation and albumin expression. A total of 630 upregulated and 1082 downregulated genes were observed in hBMSC-HLCs and HHs compared with undifferentiated hBMSCs. The upregulated genes were mainly involved in hepatic metabolism and inflammatory and immune responses. The downregulated genes were mainly associated with stem cell characteristics (multipotent differentiation, cell cycle regulation, etc.). Confirmatory qRT-PCR of 9 upregulated and 9 downregulated genes with log2 fold changes > 5 showed similar results. In vivo transdifferentiation of hBMSCs in pigs with fulminant hepatic failure confirmed the similarly upregulated expression of 5 hepatogenic genes (TDO2, HP, SERPINA3, LBP and SAA1), showing a 150-fold change in liver tissues at 7 days after hBMSC transplantation. These 5 genes mainly contributed to liver metabolism and inflammation. Conclusion: hBMSC-HLCs possess a hepatic transcriptome profile and express hepatic-specific genes in vitro and in vivo, which might be useful for future clinical applications. The five upregulated genes identified herein could be potential biomarkers for the characterization of hBMSC-HLCs.

Quantitative evaluation of human bone mesenchymal stem cells rescuing fulminant hepatic failure in pigs.

OBJECTIVE: Stem cell transplantation provides a promising alternative for the treatment of fulminant hepatic failure (FHF). However, it lacks fundamental understanding of stem cells' activities. Our objective was to clarify stem cell-recipient interactions for overcoming barriers to clinical application. DESIGN: We used an in-house large-animal (pig) model of FHF rescue by human bone marrow mesenchymal stem cells (hBMSCs) and profiled the cells' activities. The control and transplantation groups of pigs (n=15 per group) both received a D-galactosamine (D-Gal) injection (1.5 g/kg). The transplantation group received hBMSCs via intraportal vein infusion (3×106 cells/kg) immediately after D-Gal administration. The stem cell-recipient interactions were quantitatively evaluated by biochemical function, cytokine array, metabolite profiling, transcriptome sequencing and immunohistochemistry. RESULTS: All pigs in the control group died within an average of 3.22 days, whereas 13/15 pigs in the transplantation group lived >14 days. The cytokine array and metabolite profiling analyses revealed that hBMSC transplantation suppressed D-Gal-induced life-threatening cytokine storms and stabilised FHF within 7 days, while human-derived hepatocytes constituted only ∼4.5% of the pig hepatocytes. The functional synergy analysis of the observed profile changes indicated that the implanted hBMSCs altered the pigs' cytokine responses to damage through paracrine effects. Delta-like ligand 4 was validated to assist liver restoration in both pig and rat FHF models. CONCLUSIONS: Our results delineated an integrated model of the multifaceted interactions between stem cells and recipients, which may open a new avenue to the discovery of single molecule-based therapeutics that simulate stem cell actions.

Revitalizing the Frens Method To Synthesize Uniform, Quasi-Spherical Gold Nanoparticles with Deliberately Regulated Sizes from 2 to 330 nm.

In this work, we have successfully developed a new and consistent model to describe the growth of gold nanoparticles (Au NPs) via citrate reduction of auric acid (HAuCl4) by carefully assessing the temporal evolution of the NP sizes and surface charges by means of dynamic light scattering (DLS) and zeta-potential measurements. The new model demonstrates that the nucleation and growth of the Au NPs occur exclusively in the particles of the complexes of Au(+) ions and sodium acetone dicarboxylate (SAD) derived from the citrate/HAuCl4 redox reaction, which proceeds as described by the classic LaMer model. Concomitant with the Au NP growing therein, the Au(+)/SAD complex particles undergo reversible agglomeration with the reaction time, which may result in an abnormal color change of the reaction media but have little impact on the Au NP growth. Built on the new model, we have successfully produced monodisperse quasi-spherical Au NPs with sizes precisely regulated from 2 to 330 nm via simple citrate reduction in a one-pot manner. To date, highly uniform Au NPs with sizes spanning such a large size range could not be formed otherwise even via deliberately controlled seeded growth methods.

Effect of latent heat in boiling water on the synthesis of gold nanoparticles of different sizes by using the Turkevich method.

The Turkevich method, involving the reduction of HAuCl4 with citrate in boiling water, allows the facile production of monodisperse, quasispherical gold nanoparticles (AuNPs). Although, it is well-known that the size of the AuNPs obtained with the same recipe vary slightly (as little as approximately 4 nm), but noticeably, from one report to another, it has rarely been studied. The present work demonstrates that this size variation can be reconciled by the small, but noticeable, effect that the latent heat in boiling water has on the size of the AuNPs obtained by using the Turkevich method. The increase in latent heat during water boiling caused an approximately 3 nm reduction in the size of the as-prepared AuNPs; this reduction in size is mainly a result of accelerated nucleation driven by the extra heat. It was further demonstrated that, the heating temperature can be utilized as an additional measure to adjust the growth rate of AuNPs during the reduction of HAuCl4 with citrate in boiling water. Therefore, the latent heat of boiling solvents may provide one way to control nucleation and growth in the synthesis of monodisperse nanoparticles.

Human bone marrow mesenchymal stem cell-derived hepatocytes express tissue inhibitor of metalloproteinases 4 and follistatin.

BACKGROUND & AIMS: Human bone marrow mesenchymal stem cell (hBMSC) transplantation is expected to become an alternative regenerative technique for liver diseases. However, the mechanism by which hBMSCs differentiate into hepatocytes is still unclear. The aim of this study was to establish the specific characteristics of hBMSC-derived hepatocytes (hBMSC-Heps) for future clinical applications. METHODS: Potential hBMSC-Hep biomarkers were screened using cytokine arrays. Significant biomarkers were then validated by enzyme-linked immunosorbent assay (ELISA) in vitro and in an in vivo xenotransplantation model in fulminant hepatic failure (FHF) pigs. RESULTS: After 20 days of differentiation, the expression levels of tissue inhibitor of metalloproteinases 4 (TIMP-4) and follistatin (FST) in functional hBMSC-Heps were significantly increased, whereas those of activin A, osteoprotegerin and platelet-derived growth factor α polypeptide (PDGF-A) were significantly decreased. The high levels of TIMP-4 and FST were validated by ELISA in hBMSC-Heps grown in differentiation medium. The in vivo xenotransplantation model in FHF pigs showed that the serum levels of TIMP-4 and FST were significantly increased 6 h after hBMSC transplantation and reached their highest levels at 24 and 48 h, respectively, after hBMSC transplantation. Immunohistochemistry confirmed that TIMP-4 and FST were expressed in cultured hBMSC-Heps and in implanted hBMSC-Heps in pig livers. CONCLUSIONS: The transdifferentiation of hBMSCs into hepatocytes is associated with the expression of TIMP-4 and FST. TIMP-4 and FST represent potential novel biomarkers for the characterisation of hBMSC-Heps and may be useful for future clinical applications.

Synthesis of monodisperse, quasi-spherical silver nanoparticles with sizes defined by the nature of silver precursors.

Monodisperse, quasi-spherical silver nanoparticles (Ag NPs) with controlled sizes have been produced directly in water via adding the aqueous solutions of the mixtures of AgNO3 and sodium citrate to boiling aqueous solutions of ascorbic acid (AA). Different compounds, including NaCl, NaBr, KI, Na2SO4, Na2CO3, Na2S, and Na3PO4, are added to the AgNO3/citrate mixture solutions to form new silver compounds with fairly low solubility in water, which are used as precursors instead of soluble Ag(+) ions to synthesize Ag NPs via AA/citrate reduction. This enables us not only to produce monodisperse, quasi-spherical Ag NPs but also to tune the sizes of the resulting NPs from 16 to 30 nm according to the potential of new silver precursors as well as the concentrations of anions.

Synthesis of polyaniline-coated carbon nanotubes and study on their pH-sensitive conductivity.

We report the synthesis of polyaniline-coated-carbon nanotubes (PANI-c-CNTs) composites by using water-soluble CNTs with phenyl sulfonate groups as templates. A series of characterizations including transmission electron microscopy (TEM), Fourier-Transform Infrared Spectroscopy (FTIR) and UV-vis spectroscopy were conducted to investigate the formation of PANI coating on the surfaces of the CNTs. The thickness of PANI coating in the PANI-c-CNTs composites was controlled by adjusting concentrations of aniline and CNTs. The conductivities of PANI-c-CNTs composites were measured by using conductive atomic force microscopy (c-AFM). It was found that the conductivities of PANI-c-CNTs composites were remarkably affected after doping and dedoping process of PANI coating by different pH solution. Therefore, our preliminary result indicates that as-prepared PANI-c-CNTs composites may be used as gas sensor such as HCl and NH3 vapor.

A Machine learning model for predicting sepsis based on an optimized assay for microbial cell-free DNA sequencing.

OBJECTIVE: To integrate an enhanced molecular diagnostic technique to develop and validate a machine-learning model for diagnosing sepsis. METHODS: We prospectively enrolled patients suspected of sepsis from August 2021 to August 2023. Various feature selection algorithms and machine learning models were used to develop the model. The best classifier was selected using 5-fold cross validation set and then was applied to assess the performance of the model in the testing set. Additionally, we employed the Shapley Additive exPlanations (SHAP) method to illustrate the effects of the features. RESULTS: We established an optimized mNGS assay and proposed using the copies of microbe-specific cell-free DNA per milliliter of plasma (CPM) as the detection signal to evaluate the real burden, with strong precision and high accuracy. In total, 237 patients were eligible for participation, which were randomly assigned to either the training set (70 %, n = 165) or the testing set (30 %, n = 72). The random forest classifier achieved accuracy, AUC and F1 scores of 0.830, 0.918 and 0.856, respectively, outperforming other machine learning models in the training set. Our model demonstrated clinical interpretability and achieved good prediction performance in differentiating between bacterial sepsis and non-sepsis, with an AUC value of 0.85 and an average precision of 0.91 in the testing set. Based on the SHAP value, the top nine features of the model were PCT, CPM, CRP, ALB, SBPmin, RRmax, CREA, PLT and HRmax. CONCLUSION: We demonstrated the potential of machine-learning approaches for predicting bacterial sepsis based on optimized mcfDNA sequencing assay accurately.

Preparation of porous hollow polyaniline microspheres and study on their in vitro release behavior.

We report the synthesis of porous hollow polyaniline (PANI) microspheres loaded with Acid Red 8 dye (200-600 nm diameters under different reaction conditions) by using spherically mesoporous aggregates of Fe3O4 particles as soft templates and ammonium persulfate (APS) as the oxidant at 2.5 degrees C. Since the as-prepared spherical aggregates of Fe3O4 particles are readily dissolved in acidic aqueous solution, these spherical aggregates can be treated as soft template for the fabrication of hollow spheres. This process is therefore more convenient than other reported methods which require the post-treatment to remove the templates under strict conditions. The influence of the synthetic conditions on the formation and size of PANI microspheres was investigated. The morphology was confirmed by transmission electron microscopy (TEM). The chemical and electronic structures of the PANI microspheres were also studied by FTIR and UV-Vis spectrometry, respectively. The experimental in vitro release showed that these porous hollow PANI microspheres provided a controlled release of the entrapped dye, which was regulated by pH. Furthermore, the releasing behavior was qualitatively explained based on effective dissociation constant as a function of the pH.

Genome sequence of Staphylococcus capitis QN1, which causes infective endocarditis.

Staphylococcus capitis is a subtype of coagulase-negative staphylococci (CoNS) which could emerge as a significant pathogen causing infective endocarditis, prosthetic valve endocarditis, and late-onset sepsis. We isolated S. capitis strain QN1 from the skin swab sample of a female. Here we prepared a genome sequence for this strain consisting of 30 contigs totaling 2,430,101 bases and a GC content of 32.76%.

Whole-genome sequence of Staphylococcus hominis, an opportunistic pathogen.

Staphylococcus hominis is a commensal coagulase-negative species of staphylococci. It has been considered a presumptive and opportunistic pathogen that causes nosocomial infections in humans. Here we present the draft genome sequence of S. hominis ZBW5, a multidrug-resistant strain isolated from a human skin sample, which provides opportunities to understand the mechanism and genetic basis of its pathogenesis.

Effects of methyl halide flux characteristics following Spartina alterniflora invasion in a seaward direction in a temperate salt marsh, China.

In this study, we explored the source-sink characteristics of methyl halide (CH3X; X = Cl, Br, I) in coastal wetlands located in temperate regions, and identified key factors affecting the spatio-temporal variation of CH3X during the invasion of Spartina alterniflora. We used static chamber-gas chromatography to monitor CH3X fluxes in the S. alterniflora area and bare flat area of the Jiaozhou Bay salt marsh for a long time from August 2015 to May 2017. Our results indicated that CH3X emissions showed obvious seasonal and diurnal variations. The S. alterniflora area was a source of CH3X, with higher fluxes in the spring and autumn seasons. CH3X fluxes were higher during the daytime than at night, and the diurnal difference in CH3Br was the most significant (4.51 times). The bare flat area was mainly a sink for CH3X, and the maximum absorption flux occurred in summer. At this time, the microbial activity was greater, and the consumption rate during the day was higher than that at night. Extreme linear correlations existed between the fluxes of CH3Cl, CH3Br, and CH3I (P < 0.01), indicating that the production and consumption of the three gases were likely to have similar mechanisms and were affected by the same factors. S. alterniflora invasion increased CH3X emissions and shifted the original bare flat area from a sink to a source of CH3X. The biomass of S. alterniflora, especially the leaf, significantly affects CH3X fluxes. Additionally, S. alterniflora increased the content of total organic carbon, total sulfur, available sulfur, and iron (III) in the soil, which were the main factors promoting the source-sink transformation of CH3X. Based on the current invasive area of S. alterniflora in China, we estimated that the annual emissions of CH3Cl, CH3Br, and CH3I from S. alterniflora into the troposphere were 9.04 × 106, 2.42 × 105 and 2.06 × 105 mol, respectively.

Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model.

Metagenomic next-generation sequencing (mNGS) can accurately detect pathogens in clinical samples. However, wet-lab contamination constrains mNGS analysis and may result in erroneous interpretation of results. Many existing methods rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS tests. By generation of a pretrained profile of common laboratory contaminants, we developed an mNGS noise-filtering model based on the inverse linear relationship between microbial sequencing reads and sample library concentration, named the background elimination and correction by library concentration-normalized (BECLEAN) model. Its efficacy was evaluated with bacteria- and yeast-spiked samples and 28 cerebrospinal fluid (CSF) specimens. The diagnostic accuracy, precision, sensitivity, and specificity of BECLEAN with reference to conventional methods and diagnosis were 92.9%, 86.7%, 100%, and 86.7%, respectively. BECLEAN led to a dramatic reduction of background noise without affecting the true-positive rate and thus can provide a time-saving and convenient tool in various clinical settings. IMPORTANCE Most of the existing methods to remove wet-lab contamination rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS testing in individual cases. In clinical settings, only a handful of samples might be sequenced in a run. The lab-specific microbiome can complicate existing statistical approaches for removing contamination from small-scale clinical metagenomic sequencing data sets; thus, use of a preliminary lab-specific training set is necessary. Our study provides a rapid and accurate background-filtering tool for clinical metagenomic sequencing by generation of a pretrained profile of common laboratory contaminants. Notably, our work demonstrates that the inverse linear relationship between microbial sequencing reads and library concentration can serve to identify true contaminants and evaluate the relative abundance of a taxon in samples by comparing the observed microbial reads to the model-predicted value. Our findings extend the previously published research and demonstrate confirmatory results in clinical settings.

Simultaneous Detection of Pathogens and Tumors in Patients With Suspected Infections by Next-Generation Sequencing.

Background: Differential diagnosis of patients with suspected infections is particularly difficult, but necessary for prompt diagnosis and rational use of antibiotics. A substantial proportion of these patients have non-infectious diseases that include malignant tumors. This study aimed to explore the clinical value of metagenomic next-generation sequencing (mNGS) for tumor detection in patients with suspected infections. Methods: A multicenter, prospective case study involving patients diagnosed with suspected infections was conducted in four hospitals in Shanghai, China between July 2019 and January 2020. Based upon mNGS technologies and chromosomal copy number variation (CNV) analysis on abundant human genome, a new procedure named Onco-mNGS was established to simultaneously detect pathogens and malignant tumors in all of the collected samples from patients. Results: Of 140 patients screened by Onco-mNGS testing, 115 patients were diagnosed with infections; 17 had obvious abnormal CNV signals indicating malignant tumors that were confirmed clinically. The positive percent agreement and negative percent agreement of mNGS testing compared to clinical diagnosis was 53.0% (61/115) and 60% (15/25), vs. 20.9% (24/115) and 96.0% (24/25), respectively, for conventional microbiological testing (both P <0.01). Klebsiella pneumoniae (14.8%, 9/61) was the most common pathogen detected by mNGS, followed by Escherichia coli (11.5%, 7/61) and viruses (11.5%, 7/61). The chromosomal abnormalities of the 17 cases included genome-wide variations and local variations of a certain chromosome. Five of 17 patients had a final confirmed with malignant tumors, including three lung adenocarcinomas and two hematological tumors; one patient was highly suspected to have lymphoma; and 11 patients had a prior history of malignant tumor. Conclusion: This preliminary study demonstrates the feasibility and clinical value of using Onco-mNGS to simultaneously search for potential pathogens and malignant tumors in patients with suspected infections.

Tricyclo-hex-yl(3,5-dibromo-2-hy-droxy-benzoato-κO)tin(IV).

In the title compound, [Sn(C(6)H(11))(3)(C(7)H(3)Br(2)O(3))], the Sn atom is four-coordinate and possesses a distorted Sn(C(3)O) tetra-hedral geometry, with Sn-C bond lengths in the range 2.132 (6)-2.144 (6) Šand with Sn-O = 2.086 (4) Å. The uncoordinated carboxyl-ate O atom forms a weak contact with the Sn atom, with an Sn⋯O separation of 2.962 (2) Å.