CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model.

Millions of RNA sequencing samples have been deposited into public databases, providing a rich resource for biological research. These datasets encompass tens of thousands of experiments and offer comprehensive insights into human cellular regulation. However, a major challenge is how to integrate these experiments that acquired at different conditions. We propose a new statistical tool based on beta-binomial distributions that can construct robust gene co-regulation network (CoRegNet) across tens of thousands of experiments. Our analysis of over 12 000 experiments involving human tissues and cells shows that CoRegNet significantly outperforms existing gene co-expression-based methods. Although the majority of the genes are linearly co-regulated, we did discover an interesting set of genes that are non-linearly co-regulated; half of the time they change in the same direction and the other half they change in the opposite direction. Additionally, we identified a set of gene pairs that follows the Simpson's paradox. By utilizing public domain data, CoRegNet offers a powerful approach for identifying functionally related gene pairs, thereby revealing new biological insights.

A transient peak in marine sulfate after the 635-Ma snowball Earth.

SignificanceEarth system's response to major perturbations is of paramount interest. On the basis of multiple isotope compositions for pyrite, carbonate-associated sulfate, carbonates, and organics within, we inferred that the much-debated, enigmatic, extremely 13C-depleted calcite cements in the ∼635-Ma cap carbonates in South China preserve geochemical evidence for marine microbial sulfate reduction coupled to anaerobic oxidation of methane. This interpretation implies the existence of a brief interval of modern-level marine sulfate. We determined that this interval coincides with the earliest Ediacaran 17O-depletion episode, and both likely occurred within ∼50 ky since the onset of the 635-Ma meltdown, revealing an astonishing pace of transformation of the Earth system in the aftermath of Earth's latest snowball glaciation.

Allergenicity of alternative proteins: research hotspots, new findings, evaluation strategies, regulatory status, and future trends: a bibliometric analysis.

As the world population rises, the demand for protein increases, leading to a widening gap in protein supply. There is an unprecedented interest in the development of alternative proteins, but their allergenicity has raised consumer concerns. This review aims to highlight and correlate the current research status of allergenicity studies on alternative proteins based on previously published studies. Current research keywords, hotspots and trends in alternative protein sensitization were analyzed using a mixed-method approach that combined bibliometric analysis and literature review. According to the bibliometric analysis, current research is primarily focused on food science, agriculture, and immunology. There are significant variations in the type and amount of allergens found in alternative proteins. A significant amount of research has been focused on studying plant-based proteins and the cross-reactivity of insect proteins. The allergenicity of alternative proteins has not been studied extensively or in depth. The allergenicity of other alternative proteins and the underlying mechanisms warrant further study. In addition, the lack of a standardized allergy assessment strategy calls for additional efforts by international organizations and collaborations among different countries. This review provides new research and regulatory perspectives for the safe utilization of alternative proteins in human food systems.

Paired Electrolysis-Enabled Arylation of Quinoxalin-2(1H)-ones.

The first paired electrolysis-enabled arylation of quinoxalin-2(1H)-ones was achieved using cyanoarenes as the arylation reagents. A variety of 3-arylquinoxalin-2(1H)-ones with various important functional groups were obtained in moderate to good yields under metal- and chemical oxidant-free conditions. With a pair of reductive and oxidative processes occurring among the substrates and reaction intermediates, the power consumption can be dramatically reduced.

Macrophage MAPK7/AhR/STAT3 Signaling Mediates Mitochondrial ROS Burst and Enterohepatic Inflammatory Responses Induced by Deoxynivalenol Relevant to Low-Dose Exposure in Children.

Deoxynivalenol (DON) can induce endoplasmic reticulum (ER) stress, mitochondrial ROS burst, and macrophage polarization. Here, we investigated the mechanism linking the above three aspects with the dose range relevant to low-level exposure in children. At 0.5 µg/kg bw/day, we found remarkable liver and gut inflammatory responses after 6-week exposure in mice age comparable to humans 7-12 years old. Through antioxidant intervention, we found that ROS played a driver role in macrophage polarization and inflammatory responses induced by DON in the liver and gut. Further bioinformatics analysis uncovered that ER stress-associated protein MAPK7 (ERK5) may bind with AhR to initiate a mitochondrial ROS burst and macrophage M1 polarization. The downstream cellular events of MAPK7-AhR interaction may be mediated by the AhR/STAT3/p-STAT(Ser727) pathway. This mechanism was further supported by DON toxicity mitigation using cyanidin-3-glucoside (C-3-G), which docks to MAPK7 oligomerization region 200-400 aa and disrupts MAPK7-AhR interaction. Overall, our study provides novel evidence and mechanism for DON-induced inflammatory responses in the liver and gut system. Our findings call attention to the health risks associated with low-level DON exposure in the prepuberty children population.

A double-conducting polymer nanowire-based electrochemical aptasensor for highly sensitive and low fouling detection of cortisol in saliva.

A cortisol biosensor was developed based on double-conducting polymer nanowires, which exhibits excellent conductivity, resistance to biological contamination, and outstanding sensing performance. The biosensor employs dual-mode electrochemical techniques, namely, differential pulse voltammetry (DPV) and chronoamperometry (CA), for the sensitive and low fouling detection of the glucocorticoid hormone cortisol. Experimental results demonstrated that the linear detection range of the biosensor in DPV mode was 1.0 × 10-14-1.0 × 10-8 M, with a detection limit of 0.131 × 10-14 M. In CA mode, the biosensor exhibited a detection range of 1.0 × 10-13-1.0 × 10-7 M and a detection limit of 0.313 × 10-13 M. The biosensor was successfully utilized for the rapid detection of cortisol in human saliva. The combination of a high-specificity cortisol aptamer and functionalized double-conducting polymer nanowires ensured the exceptional specificity and sensitivity of the biosensor in detecting real biological samples.

Real-world evidence of incidence and outcomes of aplastic anaemia following administration of immune checkpoint inhibitors.

Aplastic anaemia (AA) is a rare immune-related adverse events (irAEs) after immune checkpoint inhibitors (ICIs) administration with poorly understood incidence and outcomes. We analysed an electronic health record database of 52 303 ICI-treated patients and found 77 (0.15%) cases of AA, with a median onset of 126 days (interquartile range, 58-363 days). The most used treatment for AA was systemic glucocorticoids 60 (77.9%) and 32 (41.6%) patients were able to resume ICI within 1 year. Patients diagnosed with AA had a steep decline in overall survival (OS) within the first 120 days; when compared to propensity score-matched patients without AA, they had a significantly worse OS (hazard ratio 1.72, 95% confidence interval 1.19-2.50; p = 0.003).

A Simplified Amplification-Free Strategy with Lyophilized CRISPR-CcrRNA System for Drug-Resistant Salmonella Detection.

Drug resistance in pathogenic bacteria has become a major threat to global health. The misuse of antibiotics has increased the number of resistant bacteria in the absence of rapid, accurate, and cost-effective diagnostic tools. Here, an amplification-free CRISPR-Cas12a time-resolved fluorescence immunochromatographic assay (AFC-TRFIA) is used to detect drug-resistant Salmonella. Multi-locus targeting in combination crRNA (CcrRNA) is 27-fold more sensitive than a standalone crRNA system. The lyophilized CRISPR system further simplifies the operation and enables one-pot detection. Induction of nucleic acid fixation via differentially charged interactions reduced the time and cost required for flowmetric chromatography with enhanced stability. The induction of nucleic acid fixation via differentially charged interactions reduces the time and cost required for flowmetric chromatography with enhanced stability. The platform developed for the detection of drug-resistant Salmonella has an ultra-sensitive detection limit of 84 CFU mL-1 within 30 min, with good linearity in the range of 102 -106 CFU mL-1 . In real-world applications, spiked recoveries range from 76.22% to 145.91%, with a coefficient of variation less than 10.59%. AFC-TRFIA offers a cost-effective, sensitive, and virtually equipment-independent platform for preventing foodborne illnesses, screening for drug-resistant Salmonella, and guiding clinical use.

General Method to Synthesize Highly Stable Nanoclusters via Pickering-Stabilized Microemulsions.

The ability to not only control but also maintain the well-defined size of nanoclusters is key to a scientific understanding as well as their practical application. Here, we report a synthetic protocol to prepare and stabilize nanoclusters of different metals and even metal salts. The approach builds on a Pickering stabilization effect inside a microemulsion system. We prove that the emulsion interface plays a critical role in the formation of nanoclusters, which are encapsulated in situ into a silica matrix. The resulting nanocapsule is characterized by a central cavity and a porous shell composed of a matrix of both silica and nanoclusters. This structure endows the nanoclusters simultaneously with high thermal stability, good biocompatibility, and excellent photostability, making them well suited for fundamental studies and practical applications ranging from materials chemistry, catalysis, and optics to bioimaging.

Diagnostic Accuracy of the Proton Pump Inhibitor Test in Gastroesophageal Reflux Disease and Noncardiac Chest Pain: A Systematic Review and Meta-analysis.

BACKGROUND: Response to a trial of proton pump inhibitors (PPIs) is currently accepted as a first step in the management of gastroesophageal reflux disease (GERD). However, information on the diagnostic performance of the PPI test is limited. AIM: The aim of this study was to determine the diagnostic accuracy of the PPI test in GERD and noncardiac chest pain (NCCP) and to assess the test performance in erosive reflux disease (ERD) and nonerosive reflux disease (NERD). METHODS: Web of Science, Cochrane Controlled Register of Trials (CENTRAL), and MEDLINE were searched for studies reporting the diagnostic accuracy of the PPI test in adult patients with typical GERD and NCCP who underwent evaluation using an accepted reference standard, from January 1, 1950, through February 1, 2021. Subgroup analyses were performed, and the risk of bias was assessed with the Quality Assessment of Diagnostic Accuracy Studies-2 tool. RESULTS: Nineteen studies (GERD=11, NCCP=8) involving 1691 patients were included. In GERD, the PPI test had 79% pooled sensitivity [95% confidence interval (CI), 72%-84%], and 45% pooled specificity (95% CI, 40%-49%). In NCCP, pooled sensitivity and specificity were 79% (95% CI, 69%-86%) and 79% (95% CI, 69%-86%), respectively. In ERD, the PPI test had 76% pooled sensitivity (95% CI, 66%-84%) and 30% pooled specificity (95% CI, 8%-67%). In NERD, the PPI test had 79% pooled sensitivity (95% CI, 70%-86%) and 50% pooled specificity (95% CI, 39%-61%). CONCLUSIONS: The PPI test was sensitive in GERD but with suboptimal specificity. The test performed better in GERD-related NCCP. Diagnostic accuracy was comparable in ERD and NERD.

Assembly of Alloyed PdM (Ag, Cu, and Sn) Nanosheets and Their Electrocatalytic Oxidation of Ethanol and Methanol.

Direct alcohol fuel cells are popular due to their high energy density, abundant sources, and ease of transportation and storage. Palladium-based nanosheet self-assembled materials have emerged as an effective catalyst for alcohol oxidation reactions. In this work, nanosheets were synthesized with the same feeding ratio assembly of alloyed PdM (M = Ag, Cu, and Sn). The introduction of the second element was able to enhance the catalytic response of the catalysts to alcohol electrooxidation. Among them, the PdCu alloy exhibited the best performance in terms of catalytic activity, toxicity resistance, and stability to ethanol oxidation reaction (EOR) and methanol oxidation reaction (MOR). The catalytic current densities for EOR can reach 2226, 2518, and 1598 mA mg-1 for PdAg, PdCu, and PdSn nanosheet assemblies, respectively. These are mainly attributed to better electronic effects, altered atomic distances within the cell for the d-band centers of Pd, and a larger electrochemical active surface area (ECSA). The optimized d-band center is beneficial to promote the catalytic performance of EOR and MOR. Experimental data also demonstrated that higher electrocatalytic temperature, higher pH, and higher alcohol concentration can accelerate the rate of alcohol electrooxidation. These results have the potential to be extended to Pd-M (M = other metals) nanosheets and help for a wider range of catalytic applications.

Update on Small Molecule Targeted Therapies for Acute Myeloid Leukemia.

OPINION STATEMENT: The search for effective therapies for the highly heterogenous disease acute myeloid leukemia (AML) has remained elusive. While cytotoxic therapies can induce complete remission and even, at times, long-term survival, this approach is associated with significant toxic effects to visceral organs and worsening of immune dysfunction and marrow suppression leading to death. Sophisticated molecular studies have revealed defects within the AML cell that can be exploited by utilizing small molecule agents to target these defects, often dubbed "target therapy." Several medications have already established new standards of care for many patients with AML, including FDA-approved agents that inhibitor IDH1, IDH2, FLT3, and BCL-2. Emerging small molecules hold additional to add to the armamentarium of AML treatment options including MCL-1 inhibitors, TP53 inhibitors, menin inhibitors, and E-selectin antagonists. Moreover, the increasing options also mean that future combinations of these agents need to be explored, including with cytotoxic drugs and other newer emerging strategies such as immunotherapies for AML. Recent investigations continue to show that overcoming many of the challenges of treating AML finally is on the horizon.

Homochiral organic molecular cage RCC3-R-modified silica as a new multimodal and multifunctional stationary phase for high-performance liquid chromatography.

In this work, homochiral reduced imine cage was covalently bonded to the surface of the silica to prepare a novel high-performance liquid chromatography stationary phase, which was applied for the multiple separation modes such as normal phase, reversed-phase, ion exchange, and hydrophilic interaction chromatography. The successful preparation of the homochiral reduced imine cage bonded silica stationary phase was confirmed by performing a series of methods including X-ray photoelectron spectroscopy, thermogravimetric analysis, and infrared spectroscopy. From the extracted results of the chiral resolution in normal phase and reversed-phase modes, it was demonstrated that seven chiral compounds were successfully separated, among which the resolution of 1-phenylethanol reached the value of 3.97. Moreover, the multifunctional chromatographic performance of the new molecular cage stationary phase was systematically investigated in the modes of reversed-phase, ion exchange, and hydrophilic interaction chromatography for the separation and analysis of a total of 59 compounds in eight classes. This work demonstrated that the homochiral reduced imine cage not only achieved multiseparation modes and multiseparation functions performance with high stability, but also expanded the application of the organic molecular cage in the field of liquid chromatography.

Efficacy of Transcranial Direct Current Stimulation Combined with Conventional Swallowing Rehabilitation Training on Post-stroke Dysphagia.

To observe the clinical effects of transcranial direct current stimulation (tDCS) combined with conventional swallowing rehabilitation training on post-stroke dysphagia and explore its long-term efficacy. A total of 40 patients with dysphagia after the first stroke were randomly divided into a treatment group (n = 20) and a conventional group (n = 20). The treatment group received tDCS combined with conventional swallowing rehabilitation training, while the conventional group only received conventional swallowing rehabilitation training. The Standardized Swallowing Assessment (SSA) Scale and the Penetration-Aspiration Scale (PAS) were used to assess dysphagia before and after treatment, at the end of 10 treatments, and at the 3-month follow-up. The changes in infection indicators [the white blood cell (WBC), C-reactive protein (CRP) and procalcitonin (PCT)], the oxygenation indicator [arterial partial pressure of oxygen (PaO2)] and nutrition-related indicators [hemoglobin (Hb) and serum prealbumin (PAB)] were compared before and after treatment. The SSA and PAS scores were lower in both groups after treatment than before treatment, and the difference was statistically significant (P < 0.01). The SSA and PAS scores of the treatment group were lower than those of the conventional group before and after treatment and during follow-up, and the difference was statistically significant (P < 0.05, P < 0.01). A within-group comparison showed that WBC, CRP and PCT after treatment were lower than those before treatment, and the difference was statistically significant (P < 0.05). The PaO2, Hb and serum PAB were higher after treatment than before treatment, with a statistically significant difference (P < 0.05). The WBC, CRP and PCT of the tDCS group were lower than those of the conventional group, and PaO2, Hb and serum PAB were higher in the treatment group than in the conventional group, with a statistically significant difference (P < 0.01). The tDCS combined with conventional swallowing rehabilitation training can improve dysphagia with a better effect than conventional swallowing rehabilitation training and has a certain long-term efficacy. In addition, tDCS combined with conventional swallowing rehabilitation training can improve nutrition and oxygenation and reduce infection levels.

An antifouling electrochemical biosensor based on chondroitin sulfate-functionalized polyaniline and DNA-peptide conjugates for cortisol determination in body fluids.

An antifouling electrochemical biosensor was constructed based on chondroitin sulfate (CS)-functionalized polyaniline (CS/PANI) and DNA-peptide conjugates that is capable of assaying cortisol directly in human fluids. First, a CS-doped PANI nanocomposite (sensing substrate) was electrodeposited onto a bare glassy carbon electrode to promote electron transport, providing the sensing signal from high peak currents of PANI to improve the sensitivity of the biosensor. Dendritic DNA-peptide conjugates were assembled onto the CS/PANI by exploiting the highly specific and strong interactions between biotin and streptavidin, which amplified the sensing signals toward cortisol. The integration of the DNA-peptide conjugates into the CS/PANI nanocomposite ensured that the biosensor had a synergistic antifouling effect and was capable of detecting cortisol directly in body fluids (sweat, saliva, and tears). When assaying cortisol levels, the biosensor exhibited a linear range over the cortisol concentrations of 1 × 10-12-1 × 10-7 M and a low limit of detection (0.333 × 10-12 M). In the detection of cortisol in real samples, the relative standard deviation (RSD) of the biological samples ranged from 2.94 to 4.23%, and the recovery were calculated to be in the range 95.2-103.2%.

A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics.

Mutations in MeCP2 result in a crippling neurological disease, but we lack a lucid picture of MeCP2's molecular role. Individual transcriptomic studies yield inconsistent differentially expressed genes. To overcome these issues, we demonstrate a methodology to analyze all modern public data. We obtained relevant raw public transcriptomic data from GEO and ENA, then homogeneously processed it (QC, alignment to reference, differential expression analysis). We present a web portal to interactively access the mouse data, and we discovered a commonly perturbed core set of genes that transcends the limitations of any individual study. We then found functionally distinct, consistently up- and downregulated subsets within these genes and some bias to their location. We present this common core of genes as well as focused cores for up, down, cell fraction models, and some tissues. We observed enrichment for this mouse core in other species MeCP2 models and observed overlap with ASD models. By integrating and examining transcriptomic data at scale, we have uncovered the true picture of this dysregulation. The vast scale of these data enables us to analyze signal-to-noise, evaluate a molecular signature in an unbiased manner, and demonstrate a framework for future disease focused informatics work.

Pd-Enriched-Core/Pt-Enriched-Shell High-Entropy Alloy with Face-Centred Cubic Structure for C1 and C2 Alcohol Oxidation.

High-entropy alloy nanoparticles (HEA NPs) have aroused great interest globally with their unique electrochemical, catalytic, and mechanical properties, as well as diverse activity and multielement tunability for multi-step reactions. Herein, a facile low-temperature synthesis method at atmospheric pressure is employed to synthesize Pd-enriched-HEA-core and Pt-enriched-HEA-shell NPs with a single phase of face-centred cubic structure. Interestingly, the lattice of both Pd-enriched-HEA-core and Pt-enriched-HEA-shell enlarge during the formation process of HEA, with tensile strains included in the core and shell of HEA. The as-obtained PdAgSn/PtBi HEA NPs show excellent electrocatalytic activity and durability for methanol oxidation reaction (MOR) and ethanol oxidation reaction (EOR). The specific (mass) activity of PdAgSn/PtBi HEA NPs for MOR is 4.7 mA cm-2 (2874 mA mg(Pd+Pt) -1 ), about 1.7 (5.9) and 1.5 (4.8) times higher than that of commercial Pd/C and Pt/C catalysts, respectively. Additional to high-entropy effect, Pt sites and Pd sites on the interface of the HEA act synergistically to facilitate the multi-step process towards EOR. This study offers a promising way to find a feasible route for scalable HEA manufacturing with promising applications.

Occurrence, transformation, and toxicity of fumonisins and their covert products during food processing.

Fumonisins comprise structurally related metabolites mainly produced by Fusarium verticillioides and Fusarium proliferatum. Contamination with fumonisins causes incalculable damage to the economy and poses a great risk to animal and human health. Fumonisins and their covert products are found in cereals and cereal products. Food processing significantly affects the degradation of toxins and the formation of covert toxins. However, studies on fumonisins and their covert mycotoxins remain inadequate. This review aims to summarize changes in fumonisins and the generation of covert fumonisins during processing. It also investigates the toxicity and determination methods of fumonisins and covert fumonisins, and elucidates the factors affecting fumonisins and their covert forms during processing. In addition to the metabolic production by plants and fungi, covert fumonisins are mainly produced by covalent or noncovalent binding, complexation, or physical entrapment of fumonisins with other substances. The toxicity of covert fumonisins is similar to that of free fumonisins and is a non-negligible hazard. Covert fumonisins are commonly found in food matrices, and methods to analyze them have yet to be improved. Food processing significantly affects the conversion of fumonisins to their covert toxins.

A novel adoptive synthetic TCR and antigen receptor (STAR) T-Cell therapy for B-Cell acute lymphoblastic leukemia.

We developed a T-cell-receptor (TCR) complex-based chimeric antigen receptor (CAR) named Synthetic TCR and Antigen Receptor (STAR). Here, we report pre-clinical and phase I clinical trial data (NCT03953599) of this T-cell therapy for refractory and relapsed (R/R) B-cell acute lymphoblastic leukemia (B-ALL) patients. STAR consists of two protein modules each containing an antibody light or heavy chain variable region and TCR α or ß chain constant region fused to the co-stimulatory domain of OX40. T-cells were transduced with a STAR-OX40 lentiviral vector. A leukemia xenograft mouse model was used to assess the STAR/STAR-OX40 T cell antitumor activity. Eighteen patients with R/R B-ALL were enrolled into the clinical trial. In a xenograft mouse model, STAR-T-cells exhibited superior tumor-specific cytotoxicity compared with conventional CAR-T cells. Incorporating OX40 into STAR further improved the proliferation and persistence of tumor-targeting T-cells. In our clinical trial, 100% of patients achieved complete remission 4 weeks post-STAR-OX40 T-cell infusion and 16/18 (88.9%) patients pursued consolidative allogeneic hematopoietic stem cell transplantation (allo-HSCT). Twelve of 16 patients (75%) remained leukemia-free after a median follow-up of 545 (433-665) days. The two patients without consolidative allo-HSCT relapsed on Day 58 and Day 186. Mild cytokine release syndrome occurred in 10/18 (55.6%) patients, and 2 patients experienced grade III neurotoxicity. Our preclinical studies demonstrate super anti-tumor potency of STAR-OX40 T-cells compared with conventional CAR-T cells. The first-in-human clinical trial shows that STAR-OX40 T-cells are tolerable and an effective therapeutic platform for treating R/R B-ALL.

Osteal Tissue Macrophages Are Involved in Endplate Osteosclerosis through the OSM-STAT3/YAP1 Signaling Axis in Modic Changes.

Modic changes (MCs) are radiographic manifestations of lumbar degenerative diseases. Various types of MCs are often associated with endplate osteosclerosis. Osteal tissue macrophages (Osteomacs) were reported to be crucial for bone homeostasis and bone repair, but whether osteomacs participate in the endplate osteosclerosis in MCs remained unclear. In this study, we tried to explore the critical role of osteomacs in regulating osteogenesis in MCs. We collected MCs from patient samples and developed a Propionibacterium acnes-induced rat MCs model, using microcomputed tomography and immunohistochemistry to detect the endplate bone mass and distribution of osteomacs. In patients' MCs, osteomacs increased in endplate subchondral bone, especially in Modic type II. Endplate in Modic type III presented a stable osteosclerosis. In rat MCs model, osteomacs increased in the bone hyperplasia area but not in the inflammation area of the endplate region, whereas the distribution of osteomacs was consistent with the area of osteosclerosis. To further explore the functions of osteomacs in vitro, we isolated osteomacs using MACS technology and found osteomacs secreted oncostatin M (OSM) and strongly promoted osteoblast differentiation rather than osteoclast through the mechanism of OSM-mediated tyrosine phosphorylation and interaction of STAT3 and Yes-associated protein 1 (YAP1). STAT3 phosphorylation inhibition or YAP1 knockdown attenuated OSM-mediated osteoblast differentiation. Finally, we confirmed that blockade of OSM in vivo using anti-OSM-neutralizing Ab prevented endplate osteosclerosis in rat MCs model. Taken together, these findings confirmed that endplate osteosclerosis in MCs was accompanied by an increased number of osteomacs, which regulated osteogenesis via the OSM-STAT3/YAP1 signaling axis.