multiMiAT: an optimal microbiome-based association test for multicategory phenotypes

Microbes can affect the metabolism and immunity of human body incessantly, and the dysbiosis of human microbiome drives not only the occurrence but also the progression of disease (i.e. multiple statuses of disease). Recently, microbiome-based association tests have been widely developed to detect the association between the microbiome and host phenotype. However, the existing methods have not achieved satisfactory performance in testing the association between the microbiome and ordinal/nominal multicategory phenotypes (e.g. disease severity and tumor subtype). In this paper, we propose an optimal microbiome-based association test for multicategory phenotypes, namely, multiMiAT. Specifically, under the multinomial logit model framework, we first introduce a microbiome regression-based kernel association test for multicategory phenotypes (multiMiRKAT). As a data-driven optimal test, multiMiAT then integrates multiMiRKAT, score test and MiRKAT-MC to maintain excellent performance in diverse association patterns. Massive simulation experiments prove the success of our method. Furthermore, multiMiAT is also applied to real microbiome data experiments to detect the association between the gut microbiome and clinical statuses of colorectal cancer as well as for diverse statuses of Clostridium difficile infections.

Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses

Spatial proteome reorganization in response to a changing environment represents a different layer of adaptation mechanism in addition to differential expression of a subset of stress responsive genes in photosynthetic organisms. Profiling such reorganization events is critically important to extend our understanding how photosynthetic organisms adapt to adverse environments. Thus, we treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis), with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble fractions using a quantitative proteomics approach. A number of proteins showing such a redistribution in response to a single or multiple types of abiotic stresses were identified. These include 12 ribosomal proteins displaying unanimous cold-induced redistribution to the membrane and the protein FurA, a master regulator of iron acquisition, displaying iron deficiency- and nitrogen starvation-induced redistribution to the membrane. Such findings shed light on a novel regulatory mechanism underlying the corresponding stress responses, and establish the results in the present study as an important resource for future studies intended to understand how photosynthetic organisms cope with adverse environments.

Network pharmacology, molecular docking, and experimental validation to explore the potential mechanism of Long Mu Qing Xin mixture for the treatment of attention deficit hyperactivity disorder

Background: Long Mu Qing Xin Mixture (LMQXM) has shown potentially positive effects in alleviating attention deficit hyperactivity disorder (ADHD); however, the action mechanism is still not fully understood. This study aimed to predict the potential mechanism of LMQXM for ADHD using network pharmacology and molecular docking, which were then validated using animal experiments.

Methods: Network pharmacology and molecular docking techniques were used to predict the core targets and potential pathways of LMQXMQ for ADHD, and KEGG pathway enrichment analysis revealed the potential significance of dopamine (DA) and cyclic adenosine monophosphate (cAMP) signaling pathways. To verify the hypothesis, we conducted an animal experiment. In the animal experiment, the young spontaneously hypertensive rats (SHRs) were randomly divided into the model group (SHR), the methylphenidate hydrochloride group (MPH, 4.22 mg/kg), and 3 LMQXM groups (low-dose (LD) group, 5.28 ml/kg; medium-dose (MD) group, 10.56 ml/kg; and high-dose (HD) group, 21.12 ml/kg), and administered by gavage for 4 weeks; the WKY rats were set as the control group. The open field test and Morris water maze test were used to evaluate the behavioral performance of rats, high performance liquid chromatography mass spectrometry (LC-MS) was used to analyze DA levels in the prefrontal cortex (PFC) and striatum of rats, ELISA was used to detect cAMP concentrations in the PFC and striatum, and immunohistochemistry and qPCR were used to analyze positive cell expression and mRNA expression for indicators related to DA and cAMP pathways.

Results: The results showed that beta-sitosterol, stigmasterol, rhynchophylline, baicalein, and formononetin might be key components of LMQXM for ADHD and that these components bind well to the core targets, DA receptors (DRD1 and DRD2). Furthermore, LMQXM might act through the DA and cAMP signaling pathways. In the animal experiment, we found that MPH and LMQXM-MD controlled hyperactivity and improved learning and memory in SHRs, while LMQXM-HD only controlled hyperactivity in SHRs; meanwhile, MPH and LMQXM-MD upregulated DA and cAMP levels, mean optical density (MOD) of cAMP, and MOD and mRNA expression of DRD1 and PKA in the prefrontal cortex (PFC) and striatum of SHRs, while LMQXM-LD and LMQXM-HD upregulated DA and cAMP levels in the striatum, MOD of cAMP in the PFC, and mRNA expression of PKA in the PFC. However, we did not find a significant regulatory effect of LMQXM on DRD2.

Conclusion: To sum up, this study demonstrated that LMQXM may increase DA levels mainly by activating the cAMP/PKA signaling pathway through DRD1, thereby controlling the behavioral disorders of SHRs, which is most effective at moderate doses, and this may be a key mechanism for LMQXM in the treatment of ADHD.

Active Ingredients of Reduning Injection Maintain High Potency against SARS-CoV-2 Variants

OBJECTIVE

To investigate the anti-coronavirus potential and the corresponding mechanisms of the two ingredients of Reduning Injection: quercetin and luteolin.

METHODS

A pseudovirus system was designed to test the efficacy of quercetin and luteolin to inhibit SARS-CoV-2 infection and the corresponding cellular toxicity. Luteolin was tested for its activities against the pseudoviruses of SARS-CoV-2 and its variants. Virtual screening was performed to predict the binding sites by Autodock Vina 1.1.230 and PyMol. To validate docking results, surface plasmon resonance (SPR) was used to measure the binding affinity of the compounds with various proteins of the coronaviruses. Quercetin and luteolin were further tested for their inhibitory effects on other coronaviruses by indirect immunofluorescence assay on rhabdomyosarcoma cells infected with HCoV-OC43.

RESULTS

The inhibition of SARS-CoV-2 pseudovirus by luteolin and quercetin were strongly dose-dependent, with concentration for 50% of maximal effect (EC₅₀) of 8.817 and 52.98 µmol/L, respectively. Their cytotoxicity to BHK21-hACE2 were 177.6 and 405.1 µmol/L, respectively. In addition, luetolin significantly blocked the entry of 4 pseudoviruses of SARS-CoV-2 variants, with EC₅₀ lower than 7 µmol/L. Virtual screening and SPR confirmed that luteolin binds to the S-proteins and quercetin binds to the active center of the 3CLpro, PLpro, and helicase proteins. Quercetin and luteolin showed over 99% inhibition against HCoV-OC43.

CONCLUSIONS

The mechanisms were revealed of quercetin and luteolin inhibiting the infection of SARS-CoV-2 and its variants. Reduning Injection is a promising drug for COVID-19.

The Joint Effect of Body Mass Index and Serum Lipid Levels on Incident Dementia among Community-Dwelling Older Adults

OBJECTIVES

This study aimed to explore the joint effect of body mass index (BMI) and serum lipids levels on incident dementia.

METHODS

We prospectively followed up with 1,627 dementia-free community residents aged ≥60 for 5.7 years on average. At baseline, weight, and height were measured, and total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) were detected in serum. Demographic characteristics were collected through questionnaires. Dementia was based on consensus diagnosis of neurologists and neuropsychologists using DSM-IV criteria. Additive Cox proportional model was used to assess the exposure-response relationship between BMI and serum lipid levels and dementia risk. Interactions and further classifications of BMI and serum lipid levels were further presented by bivariate surface models and decision-tree models.

RESULTS

The joint effects of TC with BMI, TG with BMI, and LDL-C with BMI on the risk of incident dementia shared a similar pattern, different from their independent exposure-response curves. The joint effect of HDL-C with BMI showed an S-surface but without statistical significance. Participants with TC<5.4 mmol/L and BMI<21 kg/m2 (Hazard Ratio(HR) 1.93, 95% Confidence Interval (CI) 1.05-3.53), TC<5.4 mmol/L and BMI≥21 kg/m2 (HR 1.73, 95% CI 1.09-2.72), and TC≥5.4 mmol/L and BMI<21 kg/m2 (HR 4.02, 95% CI 2.10-7.71) were identified to have the increased risk of incident dementia compared to those with TC≥5.4 mmol/L and BMI≥21 kg/m2. Participants with TG<1.7 mmol/L and BMI<21 kg/m2 had an increased risk of incident dementia compared to those with TG≥1.7 mmol/L and BMI≥21 kg/m2 (HR 1.98, 95%CI 1.17-3.3). Participants with LDL-C≥3.3 mmol/L and BMI<21 kg/m2 were identified to have an increased risk of incident dementia compared to those with LDL-C≥3.3 mmol/L and BMI≥21 kg/m2 (HR 3.33, 95%CI 1.64-6.78).

CONCLUSIONS

Our study showed that low BMI combined with low or high levels of serum lipids may increase the risk of dementia among older adults. This finding suggests the potential impacts of these two metabolic indexes on the risk of dementia.

Diagnostic value of serum LDH in children with refractory Mycoplasma pneumoniae pneumoniae: A systematic review and meta-analysis

Background

To investigate the relationship between serum Lactate dehydrogenase (LDH) and refractory Mycoplasma pneumoniae pneumonia (RMPP) in juvenile individuals.

Methods

Search Chinese databases and English databases. The retrieval time limit is from the establishment of the database to 2022-04-27. And screening and inclusion of relevant diagnostic test literature. The QUADAS-2 method was used to evaluate the quality of the included literature. The random effects model was used to combine sensitivity, specificity, likelihood ratio, diagnostic odds ratio, summary receiver operating characteristic curve, and area under summary receiver operating characteristic curve to evaluate the prediction value of LDH for RMPP. Subgroup analyses were used to explore sources of heterogeneity.

Results

① A total of 29 literatures that met the criteria were included in the study, and the quality of the literature was medium and high, with a total of 702,2 patients. ② The combined sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the curve of the studies were: 0.75 (95% CI = 0.73-0.76), 0.73 (95% CI = 0.72-0.74), 3.61 (95% CI = 2.86-4.56), 0.30 (95% CI = 0.23-0.39), 13.04 (95% CI = 8.24-20.63), and 0.85(95% CI = 0.82-0.88). ③ The results of subgroup analysis showed that Compared with the subgroup with LDH threshold ≤400 IU/L, the AUC increased from 0.84 (95% CI = 0.80-0.87) to 0.89 (95% CI = 0.86-0.91).

Conclusions

The serum LDH has good accuracy for the diagnosis of RMPP and can serve as a diagnostic marker for RMPP.

Term breech presentation vaginal births in Tibet: A retrospective analysis of 451 cases

Background

In high altitude areas, like Tibet, most fetuses in breech presentation at term are delivered vaginally owing to a variety of reasons, but this has not been published.

Objective

This study aimed to provide references and evidence for the delivery of breach presentation term fetuses in high altitude areas, through comparing and analyzing the data of full-term singleton fetuses with breech or cephalic presentation in Naqu People's Hospital, Tibet.

Study design

We retrospectively analyzed the clinical data of 451 breech presentation fetuses mentioned above over a period of 5  years (2016-2020). A total of 526 cephalic presentation fetuses' data within 3  months (1 June to 1 September 2020) of the same period were collected too. Statistics were compared and assembled on fetal mortality, Apgar scores, and severe neonatal complications for both planned cesarean section (CS) and vaginal delivery. In addition, we also analyzed the types of breech presentation, the second stage of labor, and damage to the maternal perineum during vaginal delivery.

Results

Among the 451 cases of breech presentation fetuses, 22 cases (4.9%) elected for CS and 429 cases (95.1%) elected for vaginal delivery. Of the women who chose vaginal trial labor, 17 cases underwent emergency CSs. The perinatal and neonatal mortality rate was 4.2% in the planned vaginal delivery group and the incidence of severe neonatal complications was 11.7% in the transvaginal group, no deaths were detected in the CS group. Among the 526 cephalic control groups with planned vaginal delivery, the perinatal and neonatal mortality was 1.5% (p = 0.012), and the incidence of severe neonatal complications was 1.9%. Among vaginal breech deliveries, most of them were complete breech presentation (61.17%). Among the 364 cases, the proportion of intact perinea was 45.1%, and first degree lacerations accounted for 40.7%.

Conclusion

In the Tibetan Plateau region, vaginal delivery was less safe than cephalic presentation fetuses for full-term breech presentation fetuses delivered in the lithotomy position. However, if dystocia or fetal distress can be identified in time and then encouraged to convert to cesarean, its safety will be greatly improved.

Increasing the antioxidant capacity of ceria nanoparticles with catechol-grafted poly(ethylene glycol)

Ceria nanoparticles are remarkable antioxidants due to their large cerium(III) content and the possibility of recovering cerium(III) from cerium(IV) after reaction. Here we increase the cerium(III) content of colloidally stable nanoparticles (e.g., nanocrystals) using a reactive polymeric surface coating. Catechol-grafted poly(ethylene glycols) (PEG) polymers of varying lengths and architectures yield materials that are non-aggregating in a variety of aqueous media. Cerium(IV) on the ceria surface both binds and oxidizes the catechol functionality, generating a dark-red colour emblematic of surface-oxidized catechols with a concomitant increase in cerium(III) revealed by X-ray photoemission spectroscopy (XPS). The extent of ceria reduction depends sensitively on the architecture of the coating polymer; small and compact polymer chains pack with high density at the nanoparticle surface yielding the most cerium(III). Nanoparticles with increased surface reduction, quantified by the intensity of their optical absorption and thermogravimetric measures of polymer grafting densities, were more potent antioxidants as measured by a standard TEAC antioxidant assay. For the same core composition nanoparticle antioxidant capacities could be increased over an order of magnitude by tailoring the length and architecture of the reactive surface coatings.

Wettability, Self-Cleaning Property, and Mechanical Durability of A390 Aluminum Alloy with the Major Effect of Si Phases

Si phases with specific shapes, including primary and eutectic Si phases, were etched on the surface of A390 Al alloy by chemical etching. Meanwhile, their effects on the wettability, self-cleaning properties, and mechanical durability of etched A390 aluminum alloy surfaces were investigated. The results showed that the surface etched for 5 min and modified by 1H,1H,2H,2H-perfluorodecyltrimethoxysilane (FAS-17) demonstrated a contact angle of 153.2 ± 1.4° and a sliding angle of 11.2 ± 1.6°. The theoretical contact angle calculated by constructing a wetting model of Si phases approximates the actual contact angle. Further experiments indicated that the etched surface acquired excellent self-cleaning properties. In addition, the exposed Si phases formed a strong support skeleton, which greatly improved the wear resistance of the hydrophobic surface.

Multifunctional Magnetic Nanoclusters Can Induce Immunogenic Cell Death and Suppress Tumor Recurrence and Metastasis

Metastasis is the predominant cause of cancer deaths due to solid organ malignancies; however, anticancer drugs are not effective in treating metastatic cancer. Here we report a nanotherapeutic approach that combines magnetic nanocluster-based hyperthermia and free radical generation with an immune checkpoint blockade (ICB) for effective suppression of both primary and secondary tumors. We attached 2,2'-azobis(2-midinopropane) dihydrochloride (AAPH) molecules to magnetic iron oxide nanoclusters (IONCs) to form an IONC-AAPH nanoplatform. The IONC can generate a high level of localized heat under an alternating magnetic field (AMF), which decomposes the AAPH on the cluster surface and produces a large number of carbon-centered free radicals. A combination of localized heating and free radicals can effectively kill tumor cells under both normoxic and hypoxic conditions. The tumor cell death caused by the combination of magnetic heating and free radicals led to the release or exposure of various damage-associated molecule patterns, which promoted the maturation of dendritic cells. Treating the tumor-bearing mice with IONC-AAPH under AMF not only eradicated the tumors but also generated systemic antitumor immune responses. The combination of IONC-AAPH under AMF with anti-PD-1 ICB dramatically suppressed the growth of untreated distant tumors and induced long-term immune memory. This IONC-AAPH based magneto-immunotherapy has the potential to effectively combat metastasis and control cancer recurrence.

Novel exploration of Raman microscopy and non-linear optical imaging in adenomyosis

Background

Adenomyosis is a common gynecological disease in women. A relevant literature search found that approximately 82% of patients with adenomyosis chose to undergo hysterectomy. However, women of childbearing age are more likely to undergo surgery to preserve the uterus. Because it is difficult to determine the extent of adenomyosis, it is almost impossible to resect adenomyotic tissue and retain the uterus at the same time.

Materials and methods

Following ethics approval and patient consent, tissue samples were resected and prepared to create frozen slices for analysis. One slice was subjected to H&E staining while the remaining slices were photographed with Coherent Anti-Stokes Raman Scattering (CARS), Second-Harmonic Generation (SHG) microscopy, and Raman spectroscopy. Comparative observations and analyses at the same positions were carried out to explore the diagnostic ability of CARS, SHG, and Raman spectroscopy for adenomyosis.

Results

In adenomyotic tissue, we found two characteristic peaks at 1,155 and 1,519 cm^–1 in the Raman spectrum, which were significantly different from normal tissue. The substances shown in the CARS spectrum were represented by peaks of 1,519 cm^–1. SHG microscopy showed a distribution of collagen at the focus of the adenomyosis.

Conclusion

This study represents a novel analysis of Raman microscopy, CARS, and SHG in the analysis of adenomyotic lesions. We found the diffraction spectrum useful in determining the focal boundary and the diagnosis of adenomyosis in the tested samples.

Insights into the binding mode of AS1411 aptamer to nucleolin

AS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin overexpressed in cancer cells, however, little is known about their binding process. This study proposed a feasible binding mode for the first time and provided atomic-level descriptions for the high affinity and specific binding of AS1411. The binding pose predicted by docking was screened using knowledge-based criteria, and a microsecond molecular dynamics (MD) simulation showed the stable existence of the predicted structure in the solution. Structural analysis shows that the unique capping of the 5′ end of AS1411 provides the specific binding with RBD1, and the interactions of hydrogen bond, salt bridge, and water-mediated network between AS1411 and RBD1,2 stabilize the binding. The calculation of per-residue decomposition emphasizes the dominant contribution of van der Waals energy and critical residues are screened. Our study provides the molecular basis of this specific binding and can guide rational AS1411-based aptamers design. Further insights require tight collaborations between the experiments and in silico studies.

The adipocyte-enriched secretory protein tetranectin exacerbates type 2 diabetes by inhibiting insulin secretion from β cells

Pancreatic β cell failure is a hallmark of diabetes. However, the causes of β cell failure remain incomplete. Here, we report the identification of tetranectin (TN), an adipose tissue-enriched secretory molecule, as a negative regulator of insulin secretion in β cells in diabetes. TN expression is stimulated by high glucose in adipocytes via the p38 MAPK/TXNIP/thioredoxin/OCT4 signaling pathway, and elevated serum TN levels are associated with diabetes. TN treatment greatly exacerbates hyperglycemia in mice and suppresses glucose-stimulated insulin secretion in islets. Conversely, knockout of TN or neutralization of TN function notably improves insulin secretion and glucose tolerance in high-fat diet-fed mice. Mechanistically, TN binds with high selectivity to β cells and inhibits insulin secretion by blocking L-type Ca²⁺ channels. Our study uncovers an adipocyte-β cell cross-talk that contributes to β cell dysfunction in diabetes and suggests that neutralization of TN levels may provide a new treatment strategy for type 2 diabetes.

Nontargeted metabolomics to characterize the effects of isotretinoin on skin metabolism in rabbit with acne

Background: Acne vulgaris is a chronic inflammatory disease of the pilosebaceous unit. This study aimed to explore the pathogenesis of acne and the therapeutic mechanism of isotretinoin from the metabolic perspective in coal tar-induced acne in rabbits.

Methods: Ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UHPLC-qTOF-MS) based metabolomics was used to identify skin metabolites in groups C (blank control), M (model group) and T (isotretinoin group). Multivariate statistical analysis was used to process the metabolomics data.

Results: 98 differential metabolites in group C and group M were identified. The highest proportion of differential metabolites were organic acids and derivatives, lipid metabolites, organic heterocyclic compounds, and nucleoside metabolites. The most significant metabolic pathways included protein digestion and absorption, central carbon metabolism in cancer, ABC transporters, aminoacyl-tRNA biosynthesis, biosynthesis of amino acids, and sphingolipid signaling pathway. Isotretinoin treatment normalized eight of these metabolites.

Conclusions: Our study will help to further elucidate the pathogenesis of acne, the mechanism of isotretinoin at the metabolite level, and identify new therapeutic targets for treating acne.

Cervical cancer screening in high-altitude areas in China: A large cross-section study of 25,173 women in northern Tibet

Background

Cervical cancer has become a worldwide concern owing to its high incidence and mortality rates. To date, high-altitude areas of Tibet have not benefited from any large-scale cervical cancer screening programs. Therefore, we initiated a screening program to investigate the prevalence of human papilloma virus (HPV) and HPV genotype distribution to reveal cervical cancer and its precursor which lead to morbidity among women in the city of Nagqu in northern Tib3et.

Methods

A total of 25,173 women were recruited to undergo HPV genotype tests between June and December 2019. Women infected with HPV 16 and/or 18 underwent colposcopy and histological examination. Women with other high-risk HPV type (hr-HPV) underwent cytological tests to determine whether to conduct further colposcopy and histological examination for diagnosis. HPV prevalence was calculated in the total population and further stratified according to various parameters, such as age group, area location (altitude level), and single or mixed infection status. The HPV genotype distribution was also investigated accordingly. Cervical lesions revealed by further colposcopic findings were also analyzed; high-grade and malignant lesion morbidities were calculated in total and in each county. Most data were collected and analyzed using descriptive and consistency check statistical methods, and a risk factor investigation for HPV infection was performed using logistic regression models.

Results

The total HPV infection rate among women in Nagqu was 13.42%. Of the 25,173 women in the study, 999 (3.97%) were HPV 16/18 positive, 2,379 (9.45%) were other hr-HPV-positive, and 21,795 (86.58%) were HPV-negative. The five most common HPV genotypes, accounting for more than 60% of all HPV infections in Nagqu people, were HPV 16, 58, 31, 18, and 52. Tibetan women younger than 20 years and older than 60 years were the two age groups with the highest rates of HPV infection, 26.7% and 19.8%, respectively. Among the HPV-positive women, 2,656 (78.33%) were infected with a single strain and 732 (21.67%) were infected with multiple strains (more than two genotypes). HPV prevalence increased in high-altitude areas (positive rate highest in Nyima with an altitude of 5,000 m, 23.9%) and decreased in relatively low-altitude areas (positive rate lowest in Lhari with an altitude of 4,000 m, 6.6%). Multiple analyses showed that age, parity, age at first delivery, and altitude of residence were independent factors facilitating HPV infection in Tibetan women. High-grade and malignant cervical lesions revealed by histological findings were different among living locations, with the highest rates in Xainza, Baingoin, and Nyainrong, these being 2.019%, 1.820%, and 1.116%, respectively, among women in these areas.

Conclusion

Our survey provides an overall perspective on HPV genotype infection and cervical lesions in women in northern Tibet. The data not only provide useful information for the treatment of cervical lesions but also has great value in terms of the primary and secondary prevention measures that can be taken for women living in these regions.

Clinical Trial Registration

www.chictr.org.cn, indentifier ChiCTR2000035061.

A new POLH mutation in a consanguineous Chinese family with xeroderma pigmentosum variant type

We report a Chinese consanguineous family with a variant type of xeroderma pigmentosum (XPV), and identified one novel mutation in the patient. Our study expands the mutational spectrum of XPV.