An unconventional approach for the efficient recovery of iron, cobalt, copper and silicon from copper slag.

High-grade heavy metal elements in copper slag (CS) are worth recovering. Unfortunately, the high viscosity of leaching solution, low leaching efficiency, difficult filtration and low separation efficiency of valuable components exist in the traditional sulfuric acid leaching process. In this study, the above problems are solved by sulfuric acid pretreatment + curing + water leaching. Moreover, iron, cobalt and copper ions in solution are separated by stepwise precipitation. The final iron, cobalt, copper and silicon recoveries are 99.01 %, 98.45 %, 93.13 % and 99.52 %, respectively. Thermodynamic calculations show that H4SiO4 can be converted to insoluble SiO2 to improve filtration properties under curing conditions of sulfur dioxide partial pressures of 10-20∼0 atm, oxygen partial pressures of 10-20∼0 atm and 400-600k. Simulation studies of the phase equilibria of the components of the leach solution by Visual MINTEQ showed that the oxidation of Fe2+ to Fe3+ is necessary for the removal of Fe2+ from the solution by precipitation. This study provides a new idea for the efficient utilization of CS.

Photovoltaic nanocells for high-performance large-scale-integrated organic phototransistors.

A high-performance large-scale-integrated organic phototransistor needs a semiconductor layer that maintains its photoelectric conversion ability well during high-resolution pixelization. However, lacking a precise design for the nanoscale structure, a trade-off between photoelectric performance and device miniaturization greatly limits the success in commercial application. Here we demonstrate a photovoltaic-nanocell enhancement strategy, which overcomes the trade-off and enables high-performance organic phototransistors at a level beyond large-scale integration. Embedding a core-shell photovoltaic nanocell based on perovskite quantum dots in a photocrosslinkable organic semiconductor, ultralarge-scale-integrated (>221 units) imaging chips are manufactured using photolithography. 27 million pixels are interconnected and the pixel density is 3.1 × 106 units cm-2, at least two orders of magnitude higher than in existing organic imaging chips and equivalent to the latest commercial full-frame complementary metal-oxide-semiconductor camera chips. The embedded photovoltaic nanocells induce an in situ photogating modulation and enable photoresponsivity and detectivity of 6.8 × 106 A W-1 and 1.1 × 1013 Jones (at 1 Hz), respectively, achieving the highest values of organic imaging chips at large-scale or higher integration. In addition, a very-large-scale-integrated (>216 units) stretchable biomimetic retina based on photovoltaic nanocells is manufactured for neuromorphic imaging recognition with not only resolution but also photoresponsivity and power consumption approaching those of the biological counterpart.

Expression of Tshb and Tshr in the ricefield eel Monopterus albus: Potential paracrine/autocrine roles in gonads.

Thyroid stimulating hormone (TSH), a glycoprotein synthesized and secreted from thyrotrophs of the pituitary gland, is composed of a glycoprotein hormone common alpha subunit (CGA) and a specific beta subunit (TSHB). The major biological function of TSH is to stimulate thyroidal follicles to synthesize and secrete thyroid hormones through activating its cognate receptor, the thyroid stimulating hormone receptor (TSHR). In the present study, polyclonal antisera against ricefield eel Tshb and Tshr were generated respectively, and the expression of Tshb and Tshr was examined at mRNA and protein levels. RT-PCR analysis showed that tshb mRNA was expressed mainly in the pituitary as well as in some extrapituitary tissues including the ovary and testis. Tshr mRNA was also expressed in a tissue-specific manner, with transcripts detected in tissues including the kidney, ovary, and testis. The immunoreactive Tshb signals in the pituitary were shown to be localized to the inner areas of adenohypophysis which are close to the neurohypophysis of adult ricefield eels. Tshb-immunoreatvie cells in the pituitary of ricefield eel larvae were firstly observed at hatching. The expression of immunoreactive Tshb and Cga was also detected in ricefield eel ovary and testis together with Tshr. In the ovary, immunoreactive Tshb, Cga, and Tshr were observed in oocytes and granulosa cells. In the testis, immunoreactive Tshb was mainly observed in Sertoli cells while immunoreactive Cga and Tshr were detected in germ cells as well as somatic cells. Results of the present study suggest that Tsh may be synthesized both in the ovary and testis locally, which may play paracrine and/or autocrine roles in gonadal development in ricefield eels.

Homozygous ACTL9 mutations cause irregular mitochondrial sheath arrangement and abnormal flagellum assembly in spermatozoa and male infertility.

PURPOSE: To identify novel variants in ACTL9 and new phenotypes responsible for male infertility. METHODS: Genomic DNA was extracted from peripheral blood samples for whole-exome sequencing (WES). Computer-assisted sperm analysis (CASA) was used to test the motility of spermatozoa. The ultrastructure of flagella and the mitochondrial sheath were assessed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Immunostaining was used to validate the localization and expression of ACTL9 and ACTL7A. An Actl9-mutated mouse model was used to validate the phenotypes by CASA and TEM. RESULTS: We identified novel homozygous variants in ACTL9 in two independent Chinese families. Spermatozoa with ACTL9 mutations showed decreased CASA parameters and a higher proportion of spermatozoa with abnormal morphology, exhibiting coiled flagella and a thickened midpiece. The spermatozoa were characterized by chaotic or irregular '9+2' structures and irregular mitochondrial sheath arrangements in the flagellum. Actl9 knock-in mice also showed abnormal CASA parameters and irregular '9+2' structures in flagella. CONCLUSIONS: Our study expands the mutation spectrum and phenotypic spectrum of ACTL9.

Variations in the oxidation potential of PM2.5 in an old industrial city in China from 2015 to 2018.

PM2.5 pollution in China has decreased dramatically, but how its health effects change is not clear. There are 120 old industrial cities in China, where the sources, composition, and health effects of PM2.5 may be significantly different with other cities. Huangshi, an old industrial city in central China, underwent intense green transformations from 2015 to 2018. In this study, we collected ambient PM2.5 samples in 2015 and 2018 at an urban site in Huangshi. The average PM2.5 concentration decreased from 83.44 ±â€¯48.04 µg/m3 in 2015 to 68.03 ±â€¯39.41 µg/m3 in 2018. However, the average volume-normalized dithiothreitol (DTTv) of PM2.5 increased from 1.38 ±â€¯0.45 nmol/min/m3 to 2.14 ±â€¯1.31 nmol/min/m3 and the DTT normalized by particulate mass (DTTm) increased from 20.6 ±â€¯10.1 pmol/min/µg to 40.07 ±â€¯21.9 pmol/min/µg, indicating increased exposure risk and inherent toxicity. The increased toxicity of PM2.5 might be related to the increased trace elements (TEs) concentrations. The positive matrix factorization and multiple linear regression methods were employed to quantify the contributions of emission sources to PM2.5 and DTTv. The results showed that the contribution of coal combustion, industry, and dust to PM2.5 decreased significantly from 2015 to 2018, while that of vehicle emission and secondary sources increased. Despite the decreased fraction of coal combustion and industry sources, their contribution to DTTv increased slightly, which was caused by the increased intrinsic toxicity. The increased intrinsic toxicity was possibly caused by increased TEs, such as Pb, Cu, and V. Besides, the contribution of vehicle emission to DTTv also increased. Overall, these results provide valuable insights into the effectiveness of controlling strategies in reducing particulate health impacts in old industrial cities, and stress the necessity of formulating toxicity-oriented controlling strategies, with special attention to TEs from coal combustion and industry sources as well as vehicle emissions.

SARS-CoV-2 brainstem encephalitis in human inherited DBR1 deficiency.

Inherited deficiency of the RNA lariat-debranching enzyme 1 (DBR1) is a rare etiology of brainstem viral encephalitis. The cellular basis of disease and the range of viral predisposition are unclear. We report inherited DBR1 deficiency in a 14-year-old boy who suffered from isolated SARS-CoV-2 brainstem encephalitis. The patient is homozygous for a previously reported hypomorphic and pathogenic DBR1 variant (I120T). Consistently, DBR1 I120T/I120T fibroblasts from affected individuals from this and another unrelated kindred have similarly low levels of DBR1 protein and high levels of RNA lariats. DBR1 I120T/I120T human pluripotent stem cell (hPSC)-derived hindbrain neurons are highly susceptible to SARS-CoV-2 infection. Exogenous WT DBR1 expression in DBR1 I120T/I120T fibroblasts and hindbrain neurons rescued the RNA lariat accumulation phenotype. Moreover, expression of exogenous RNA lariats, mimicking DBR1 deficiency, increased the susceptibility of WT hindbrain neurons to SARS-CoV-2 infection. Inborn errors of DBR1 impair hindbrain neuron-intrinsic antiviral immunity, predisposing to viral infections of the brainstem, including that by SARS-CoV-2.

Hypoxia-induced activation of HIF-1alpha/IL-1beta axis in microglia promotes glioma progression via NF-κB-mediated upregulation of heparanase expression.

BACKGROUND: Glioma is a common tumor that occurs in the brain and spinal cord. Hypoxia is a crucial feature of the tumor microenvironment. Tumor-associated macrophages/microglia play a crucial role in the advancement of glioma. This study aims to illuminate the detailed mechanisms by which hypoxia regulates microglia and, consequently, influences the progression of glioma. METHODS: The glioma cell viability and proliferation were analyzed by cell counting kit-8 assay and 5-ethynyl-2'-deoxyuridine assay. Wound healing assay and transwell assay were implemented to detect glioma cell migration and invasion, respectively. Enzyme-linked immunosorbent assay was conducted to detect protein levels in cell culture medium. The protein levels in glioma cells and tumor tissues were evaluated using western blot analysis. The histological morphology of tumor tissue was determined by hematoxylin-eosin staining. The protein expression in tumor tissues was determined using immunohistochemistry. Human glioma xenograft in nude mice was employed to test the influence of hypoxic microglia-derived interleukin-1beta (IL-1ß) and heparanase (HPSE) on glioma growth in vivo. RESULTS: Hypoxic HMC3 cells promoted proliferation, migration, and invasion abilities of U251 and U87 cells by secreting IL-1ß, which was upregulated by hypoxia-induced activation of hypoxia inducible factor-1alpha (HIF-1α). Besides, IL-1ß from HMC3 cells promoted glioma progression and caused activation of nuclear factor-κB (NF-κB) and upregulation of HPSE in vivo. We also confirmed that IL-1ß facilitated HPSE expression in U251 and U87 cells by activating NF-κB. Hypoxic HMC3 cells-secreted IL-1ß facilitated the proliferation, migration, and invasion of U251 and U87 cells via NF-κB-mediated upregulation of HPSE expression. Finally, we revealed that silencing HPSE curbed the proliferation and metastasis of glioma in mice. CONCLUSION: Hypoxia-induced activation of HIF-1α/IL-1ß axis in microglia promoted glioma progression via NF-κB-mediated upregulation of HPSE expression.

A novel integrated approach employing Desertifilum tharense BERC-3 for efficient wastewater valorization and recycling for developing peri-urban algae farming system.

Peri-urban environments are significant reservoirs of wastewater, and releasing this untreated wastewater from these resources poses severe environmental and ecological threats. Wastewater mitigation through sustainable approaches is an emerging area of interest. Algae offers a promising strategy for carbon-neutral valorization and recycling of urban wastewater. Aiming to provide a proof-of-concept for complete valorization and recycling of urban wastewater in a peri-urban environment in a closed loop system, a newly isolated biocrust-forming cyanobacterium Desertifilum tharense BERC-3 was evaluated. Here, the highest growth and lipids productivity were achieved in urban wastewater compared to BG11 and synthetic wastewater. D. tharense BERC-3 showed 60-95% resource recovery efficiency and decreased total dissolved solids, chemical oxygen demand, biological oxygen demand, nitrate nitrogen, ammonia nitrogen and total phosphorus contents of the water by 60.37%, 81.11%, 82.75%, 87.91%, 85.13%, 85.41%, 95.87%, respectively, making it fit for agriculture as per WHO's safety limits. Soil supplementation with 2% wastewater-cultivated algae as a soil amender, along with its irrigation with post-treated wastewater, improved the nitrogen content and microbial activity of the soil by 0.3-2.0-fold and 0.5-fold, respectively. Besides, the availability of phosphorus was also improved by 1.66-fold. The complete bioprocessing pipeline offered a complete biomass utilization. This study demonstrated the first proof-of-concept of integrating resource recovery and resource recycling using cyanobacteria to develop a peri-urban algae farming system. This can lead to establishing wastewater-driven algae cultivation systems as novel enterprises for rural migrants moving to urban areas.

Two MADS-box proteins, AGL9 and AGL15, recruit the FIS-PRC2 complex to trigger the phase transition from endosperm proliferation to embryo development in Arabidopsis.

Spatiotemporal regulation of gene expression by polycomb repressive complex 2 (PRC2) is critical for animal and plant development. The Arabidopsis fertilization independent seed (FIS)-PRC2 complex functions specifically during plant reproduction from gametogenesis to seed development. After a double fertilization event, triploid endosperm proliferates early, followed by the growth of a diploid embryo, which replaces the endosperm in Arabidopsis and many dicots. Key genes critical for endosperm proliferation such as IKU2 and MINI3 are activated after fertilization. Here we report that two MADS-box AGAMOUS-LIKE (AGL) proteins associate with the key endosperm proliferation loci and recruit the FIS-PRC2 repressive complex at 4-5 days after pollination (DAP). Interestingly, AGL9 and AGL15 only accumulate toward the end of endosperm proliferation at 4-5 DAP and promote the deposition of H3K27me3 marks at key endosperm proliferation loci. Disruption of AGL9 and AGL15 or overexpression of AGL9 or AGL15 significantly influence endosperm proliferation and cellularization. Genome-wide analysis with cleavage Under Targets and tagmentation (CUT&Tag) sequencing and RNA sequencing revealed the landscape of endosperm H3K27me3 marks and gene expression profiles in Col-0 and agl9 agl15. CUT&Tag qPCR also demonstrated the occupancy of the two MADS-box proteins and FIS-PRC2 on a few representative target loci. Our studies suggest that MADS-box proteins could potentially recruit PRC2 to regulate many other developmental processes in plants or even in fungi and animals.

Diagnostic value of carbohydrate antigen 50 in biliary tract cancer: A large-scale multicenter study.

BACKGROUND: To date, carbohydrate antigen 19-9 (CA19-9) and carcinoembryonic antigen (CEA) have been widely used for the screening, diagnosis and prediction of biliary tract cancer (BTC) patients. However, few studies with large sample sizes of carbohydrate antigen 50 (CA50) were reported in BTC patients. METHODS: A total of 1121 patients from the Liver Cancer Clin-Bio Databank of Anhui Hepatobiliary Surgery Union between January 2017 and December 2022 were included in this study (673 in the training cohort and 448 in the validation cohort): among them, 458 with BTC, 178 with hepatocellular carcinoma (HCC), 23 with combined hepatocellular-cholangiocarcinoma, and 462 with nontumor patients. Receiver operating characteristic (ROC) curves and decision curve analysis (DCA) were used to evaluate the diagnostic efficacy and clinical usefulness. RESULTS: ROC curves obtained by combining CA50, CA19-9, and AFP showed that the AUC value of the diagnostic MODEL 1 was 0.885 (95% CI 0.856-0.885, specificity 70.3%, and sensitivity 84.0%) in the training cohort and 0.879 (0.841-0.917, 76.7%, and 84.3%) in the validation cohort. In addition, comparing iCCA and HCC (235 in the training cohort, 157 in the validation cohort), the AUC values of the diagnostic MODEL 2 were 0.893 (95% CI 0.853-0.933, specificity 96%, and sensitivity 68.6%) in the training cohort and 0.872 (95% CI 0.818-0.927, 94.2%, and 64.6%) in the validation cohort. CONCLUSION: The model combining CA50, CA19-9, and AFP not only has good diagnostic value for BTC but also has good diagnostic value for distinguishing iCCA and HCC.

Sulfadiazine detection in aquatic products using upconversion nanosensor based on photo-induced electron transfer with imidazole ligands and copper ions.

Contamination of aquatic products with sulfonamide antibiotics poses a threat to consumer health and can lead to the emergence of drug-resistant bacteria. Common methods to detect such compounds are slow and require expensive instruments. We developed a sensitive sulfadiazine (SDZ) detection method based on the photoinduced electron transfer between UCNPs and Cu2+. The surface-modified upconversion nanoparticles bind to Cu2+ by electrostatic adsorption, causing fluorescence quenching. The quenched fluorescence was subsequently recovered by the addition of imidazole and SDZ to the detection system, which formed a complex with Cu2+. The sensor showed excellent linearity over a wide concentration range (0.05-1000 ng/mL), had a low limit of detection (0.04 ng/mL), was selective, and was not affected by common substances present in aquatic media. This indicates that the sensor has great potential for application in the detection of SDZ residues in aquatic products.

Evaluation of Radiation Dose Effect on Lung Function Using Iodine Maps Derived From Dual-Energy Computed Tomography.

PURPOSE: There is interest in using dual-energy computed tomography (DECT) to evaluate organ function before and after radiation therapy (RT). The purpose of this study (trial identifier: NCT04863027) is to assess longitudinal changes in lung perfusion using iodine maps derived from DECT in patients with lung cancer treated with conventional or stereotactic RT. METHODS AND MATERIALS: For 48 prospectively enrolled patients with lung cancer, a contrast-enhanced DECT using a dual-source CT simulator was acquired pretreatment and at 6 and 12 months posttreatment. Pulmonary functions tests (PFT) were obtained at baseline and at 6 and 12 months posttreatment. Iodine maps were extracted from the DECT images using a previously described 2-material decomposition framework. Longitudinal iodine maps were normalized using a reference region defined as all voxels with perfusion in the top 10% outside of the 5 Gy isodose volume. Normalized functional responses (NFR) were calculated for 3 dose ranges: <5, 5 to 20, and >20 Gy. Mixed model analysis was used to assess the correlation between dose metrics and NFR. Pearson correlation was used to assess if NFRs were correlated with PFT changes. RESULTS: Out of the 48 patients, 21 (44%) were treated with stereotactic body RT and 27 (56%) were treated with conventionally fractionated intensity-modulated RT. Thirty-one out of these 48 patients were ultimately included in data analysis. It was found that NFR is linearly correlated with dose (P < .001) for both groups. The number of months elapsed post-RT was also found to correlate with NFR (P = .029), although this correlation was not observed for the stereotactic body RT subgroup. The NFR was not found to correlate with PFT changes. CONCLUSIONS: DECT-derived iodine maps are a promising method for detailed anatomic evaluation of radiation effect on lung function, including potentially subclinical changes.

Chronic endometritis and the endometrial microbiota: implications for reproductive success in patients with recurrent implantation failure.

BACKGROUND: Chronic endometritis (CE) is associated with poor reproductive outcomes, yet the role of endometrial microbiota in patients with recurrent implantation failure (RIF) and CE remains unclear. This study aims to characterize endometrial microbiota in RIF patients with CE and assess its implications for reproductive outcomes. METHODS: In this prospective study, we enrolled RIF patients both with and without CE. Endometrial and cervical samples were collected for 16 S rRNA gene sequencing. Microbiota composition was compared between groups using diversity indices, phylum, and genus-level analysis. Canonical correlation analysis (CCA) and Spearman's correlation coefficients were used to assess relationships between CE, reproductive outcomes, and microbiota. Predictive functional profiling was performed to evaluate metabolic pathways associated with CE. RESULTS: Endometrial microbiota in CE patients exhibited greater diversity and evenness compared to non-CE patients. Principal coordinates analysis (PCoA) revealed distinct clustering between CE and non-CE groups. Linear discriminant analysis (LDA) identified Proteobacteria, Aminicenantales, and Chloroflexaceae as characteristic of CE, while Lactobacillus, Acinetobacter, Herbaspirillum, Ralstonia, Shewanela, and Micrococcaceae were associated with non-CE. CCA demonstrated associations between CE, adverse reproductive outcomes, and specific bacterial taxa. Microbial metabolic pathways significantly differed between CE and non-CE groups, with enrichment in pathways related to cofactors, vitamins, secondary metabolites, and the immune system in CE patients. CONCLUSION: RIF patients with CE exhibit distinct endometrial microbiota compositions associated with adverse reproductive outcomes. The increased microbial diversity and altered metabolic pathways in CE suggest a potential correlation with reproductive outcomes, although further studies are necessary to elucidate the causal relationship between microbiota alterations and fertility. Modulating the endometrial microbiome may represent a novel therapeutic strategy to improve IVF outcomes in patients with CE.

In search of a function for human type III interferons: insights from inherited and acquired deficits.

The essential and redundant functions of human type I and II interferons (IFNs) have been delineated over the last three decades by studies of patients with inborn errors of immunity or their autoimmune phenocopies, but much less is known about type III IFNs. Patients with cells that do not respond to type III IFNs due to inherited IL10RB deficiency display no overt viral disease, and their inflammatory disease phenotypes can be explained by defective signaling via other interleukine10RB-dependent pathways. Moreover, patients with inherited deficiencies of interferon-stimulated gene factor 3 (ISGF-3) (STAT1, STAT2, IRF9) present viral diseases also seen in patients with inherited deficiencies of the type I IFN receptor (IFNAR1/2). Finally, patients with autoantibodies neutralizing type III IFNs have no obvious predisposition to viral disease. Current findings thus suggest that type III IFNs are largely redundant in humans. The essential functions of human type III IFNs, particularly in antiviral defenses, remain to be discovered.

Sea Anemone-Inspired Slippery Liquid-Infused Porous Surface (SLIPS) with Bionic Cilia for Responsive 4D Antifouling.

The formation process of biofouling is actually a 4D process with both spatial and temporal dimensions. However, most traditional antifouling coatings, including slippery liquid-infused porous surface (SLIPS), are limited to performing antifouling process in the 2D coating plane. Herein, inspired by the defensive behavior of sea anemones' wielding toxic tentacles, a "4D SLIPS" (FSLIPS) is constructed with biomimetic cilia via a magnetic field self-assembly method for antifouling. The bionic cilia move in 3D space driven by an external magnetic field, thereby preventing the attachment of microorganisms. The FSLIPS releases the gaseous antifoulant (nitric oxide) at 1D time in response to light, thereby achieving a controllable biocide effect on microorganisms. The FSLIPS regulates the movement of cilia via the external magnetic field, and controls the release of NO overtime via the light response, so as to adjust the antifouling modes on demand during the day or night. The light/magnetic response mechanism endow the FSLIPS with the ability to adjust the antifouling effect in the 4D dimension of 1D time and 3D space, effectively realizing the intelligence, multi-dimensionality and precision of the antifouling process.

Photosynthetic Bacteria-Hitchhiking 2D iMXene-mRNA Vaccine to Enable Photo-Immunogene Cancer Therapy.

Therapeutic mRNA vaccines have become powerful therapeutic tools for severe diseases, including infectious diseases and malignant neoplasms. mRNA vaccines encoding tumor-associated antigens provide unprecedented hope for many immunotherapies that have hit the bottleneck. However, the application of mRNA vaccines is limited because of biological instability, innate immunogenicity, and ineffective delivery in vivo. This study aims to construct a novel mRNA vaccine delivery nanosystem to successfully co-deliver a tumor-associated antigen (TAA) encoded by the Wilms' tumor 1 (WT1) mRNA. In this system, named PSB@Nb1.33C/mRNA, photosynthetic bacteria (PSB) efficiently delivers the iMXene-WT1 mRNA to the core tumor region using photo-driven and hypoxia-driven properties. The excellent photothermal therapeutic (PTT) properties of PSB and 2D iMxene (Nb1.33C) trigger tumor immunogenic cell death, which boosts the release of the WT1 mRNA. The released WT1 mRNA is translated, presenting the TAA and amplifying immune effect in vivo. The designed therapeutic strategy demonstrates an excellent ability to inhibit distant tumors and counteract postsurgical lung metastasis. Thus, this study provides an innovative and effective paradigm for tumor immunotherapy, i.e., photo-immunogene cancer therapy, and establishes an efficient delivery platform for mRNA vaccines, thereby opening a new path for the wide application of mRNA vaccines.

fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data.

MOTIVATION: The composition and structure of microbial communities on the body surface are closely related to human health. The interaction relationship among microbes can help us understand the formation of the microecological environment and the biological mechanism by which microorganisms influence host health. With the help of high-throughput sequencing technologies, microbial abundances in a natural environment can be directly measured without the isolation of microorganisms in culture. Sequencing experiments in microbiome studies can measure the relative abundance of microbes, which is called compositional data. Although there are already many methods for correlation analysis for compositional data, the computation time or accuracy still needs to be improved for current microbiome studies. RESULTS: We develop a fast and efficient algorithm, called fastCCLasso, based on a penalized weighted least squares for inferring the correlation structure of microbes from compositional data in microbiome studies. We perform a large number of numerical experiments and the simulation results show that fastCCLasso outperforms its competitors in edge detection for inferring the correlation network. We also apply fastCCLasso for estimating microbial networks in microbiome studies and fastCCLasso provides a conservative network with comparable false discovery counts that are derived from shuffled data. AVAILABILITY AND IMPLEMENTATION: FastCCLasso is open source and freely available from https://github.com/ShenZhang-Statistics/fastCCLasso under GNU LGPL v3.

In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium(IV)-Grafted Mesoporous Silica Enrichment.

Detection of endogenous peptides, especially those with modifications (such as phosphorylation) in biofluids, can serve as an indicator of intracellular pathophysiology. Although great progress has been made in phosphoproteomics in recent years, endogenous phosphopeptidomics has largely lagged behind. One main hurdle in endogenous phosphopeptidomics analysis is the coexistence of proteins and highly abundant nonmodified peptides in complex matrices. In this study, we developed an approach using zirconium(IV)-grafted mesoporous beads to enrich phosphopeptides, followed by analysis with a high resolution nanoRPLC-MS/MS system. The bifunctional material was first tested with digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. Given the size exclusion nature, the beads were directly applied for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphopeptide data set cataloged to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies of serum and other biofluid samples.

Upconversion fluorescence nanosensor based on enzymatic inhibited and copper-triggered o-phenylenediamine oxidation for the detection of dimethoate pesticides.

Pesticide residues in agricultural products pose a significant threat to human health. Herein, a sensitive fluorescence method employing upconversion nanoparticles was developed for detecting organophosphorus pesticides (OPs) based on the principle of enzyme inhibition and copper-triggered o-phenylenediamine (OPD) oxidation. Copper ions (Cu2+) oxidized the colorless OPD to a yellow 2,3-diaminophenazine (oxOPD). The yellow solution oxOPD quenched the fluorescence of upconversion nanoparticles due to the fluorescence resonance energy transfer. The high affinity of Cu2+ for thiocholine reduced the level of oxOPD, resulting in almost no fluorescence quenching. The addition of dimethoate led to the inhibition of acetylcholinesterase activity and thus prevented the formation of thiocholine. Subsequently, Cu2+ oxidized OPD to form oxOPD, which attenuated the fluorescence signal of the system. The detection system has a good linear range of 0.01 ng/mL to 50 ng/mL with a detection limit of 0.008 ng/mL, providing promising applications for rapid detection of dimethoate.

Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection.

Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.