The Thalamocortical Mechanism Underlying the Generation and Regulation of the Auditory Steady-State Responses in Awake Mice.

The auditory steady-state response (ASSR) is a cortical oscillation induced by trains of 40 Hz acoustic stimuli. While the ASSR has been widely used in clinic measurement, the underlying neural mechanism remains poorly understood. In this study, we investigated the contribution of different stages of auditory thalamocortical pathway-medial geniculate body (MGB), thalamic reticular nucleus (TRN), and auditory cortex (AC)-to the generation and regulation of 40 Hz ASSR in C57BL/6 mice of both sexes. We found that the neural response synchronizing to 40 Hz sound stimuli was most prominent in the GABAergic neurons in the granular layer of AC and the ventral division of MGB (MGBv), which were regulated by optogenetic manipulation of TRN neurons. Behavioral experiments confirmed that disrupting TRN activity has a detrimental effect on the ability of mice to discriminate 40 Hz sounds. These findings revealed a thalamocortical mechanism helpful to interpret the results of clinical ASSR examinations.Significance Statement Our study contributes to clarifying the thalamocortical mechanisms underlying the generation and regulation of the auditory steady-state response (ASSR), which is commonly used in both clinical and neuroscience research to assess the integrity of auditory function. Combining a series of electrophysiological and optogenetic experiments, we demonstrate that the generation of cortical ASSR is dependent on the lemniscal thalamocortical projections originating from the ventral division of medial geniculate body to the GABAergic interneurons in the granule layer of the auditory cortex. Furthermore, the thalamocortical process for ASSR is strictly regulated by the activity of thalamic reticular nucleus (TRN) neurons. Behavioral experiments confirmed that dysfunction of TRN would cause a disruption of mice's behavioral performance in the auditory discrimination task.

The m6A methyltransferase RBM15 affects tumor cell stemness and progression of cervical cancer by regulating the stability of lncRNA HEIH.

Cervical cancer (CC), as a common female malignant tumor in the world, is an important risk factor endangering women's health worldwide. The purpose of this study was to investigate the role of RBM15 in CC. The TCGA database was used to screen differentially expressed m6A genes in normal and tumor tissues. QRT-PCR was used to quantify HEIH, miR-802, EGFR, cell stemness, and epithelial-mesenchymal transition (EMT)-related genes. The interaction between HEIH and miR-802 was verified by dual-luciferase reporter assay and RIP assay. The occurrence of tumor cells after different treatments was detected by CCK-8, transwell and EdU staining. BALB/c nude mice were used to examine the effects of different treatments on tumor growth and cell stemness in vivo. RBM15 was upregulated in tumor tissues and cells. M6A was highly enriched in HEIH and enhances its RNA stability. HEIH acts as an oncogenic lncRNA to promote CC cell proliferation, migration and tumor growth. Mechanistically, HEIH regulates tumor cell stemness and promotes the proliferation and migration of CC cells by competitively adsorbing miR-802 and up-regulating the expression of EGFR. In short, our data shown that the m6A methyltransferase RBM15 could affect tumor cell proliferation, metastasis and cell stemness by stabilizing HEIH expression.

Simultaneous Protonation and Metalation of a Porphyrin Covalent Organic Framework Enhance Photodynamic Therapy.

Covalent organic frameworks (COFs) have been explored for photodynamic therapy (PDT) of cancer, but their antitumor efficacy is limited by excited state quenching and low reactive oxygen species generation efficiency. Herein, we report a simultaneous protonation and metalation strategy to significantly enhance the PDT efficacy of a nanoscale two-dimensional imine-linked porphyrin-COF. The neutral and unmetalated porphyrin-COF (Ptp) and the protonated and metalated porphyrin-COF (Ptp-Fe) were synthesized via imine condensation between 5,10,15,20-tetrakis(4-aminophenyl)porphyrin and terephthalaldehyde in the absence and presence of ferric chloride, respectively. The presence of ferric chloride generated both doubly protonated and Fe3+-coordinated porphyrin units, which red-shifted and increased the Q-band absorption and disrupted exciton migration to prevent excited state quenching, respectively. Under light irradiation, rapid energy transfer from protonated porphyrins to Fe3+-coordinated porphyrins in Ptp-Fe enabled 1O2 and hydroxyl radical generation via type II and type I PDT processes. Ptp-Fe also catalyzed the conversion of hydrogen peroxide to hydroxy radical through a photoenhanced Fenton-like reaction under slightly acidic conditions and light illumination. As a result, Ptp-Fe-mediated PDT exhibited much higher cytotoxicity than Ptp-mediated PDT on CT26 and 4T1 cancer cells. Ptp-Fe-mediated PDT afforded potent antitumor efficacy in subcutaneous CT26 murine colon cancer and orthotopic 4T1 murine triple-negative breast tumors and prevented metastasis of 4T1 breast cancer to the lungs. This work underscores the role of fine-tuning the molecular structures of COFs in significantly enhancing their PDT efficacy.

Synergistic Interfacial Effect of Ru/Co3O4 Heterojunctions for Boosting Overall Water Splitting.

Low-cost bifunctional electrocatalysts capable of efficiently driving the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) are needed for the growth of a green hydrogen economy. Herein, a Ru/Co3O4 heterojunction catalyst rich in oxygen vacancies (VO) and supported on carbon cloth (RCO-VO@CC) is prepared via a solid phase reaction (SPR) strategy. A RuO2/Co9S8@CC precursor (ROC@CC) is first prepared by loading Co9S8 nanosheets onto CC, following the addition of RuO2 nanoparticles (NPs). After the SPR process in an Ar atmosphere, Ru/Co3O4 heterojunctions with abundant VO are formed on the CC. The compositionally optimized RCO-VO@CC electrocatalyst with a Ru content of 0.55 wt.% exhibits very low overpotential values of 11 and 253 mV at 10 mA cm-2 for HER and OER, respectively, in 1 m KOH. Further, a low cell voltage of only 1.49 V is required to achieve a current density of 10 mA cm-2. Density functional theoretical calculations verify that the outstanding bifunctional electrocatalytic performance originates from synergistic charge transfer between Ru metal and VO-rich Co3O4. This work reports a novel approach toward a high-efficiency HER/OER electrocatalyst for energy storage and conversion.

TS-1@MCM-48 Core-Shell Catalysts for Efficient Oxidation of p-Diethylbenzene to High Value-Added Derivatives.

To expand the market capacity of p-diethylbenzene (PDEB), core-shell zeolite (TS-1@MCM-48) is designed as a catalyst for PDEB oxidation. TS-1@MCM-48 catalyst is synthesized by in-situ crystallization method and characterized by X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS), N2 adsorption-desorption, in-situ electron paramagnetic resonance (EPR) and 29Si nuclear magnetic resonance (29Si MAS-NMR). Oxidation of PDEB by H2O2 was investigated systematically in liquid phase. The conversion of PDEB over TS-1@MCM-48 was 28.1 % and the total selectivity was 72.6 %, where the selectivity of EAP (p-ethylacetophenone) and EPEA (4-ethyl-α-methylbenzyl alcohol) was 28.6 % and 44.0 %, respectively. Compared with TS-1 and MCM-48 zeolite, the conversion rate of reactants and the selectivity of products have been significantly improved. The catalytic performance of TS-1@MCM-48 is derived from its well-crystallized microporous core and mesoporous shell with regular channels, which make active sites of TS-1 zeolite in the catalyst be fully utilized and mass transfer resistance be largely reduced. Further through theoretical calculation, we propose that the oxidation of PDEB is the result of the combination and mutual transformation of free radical process and carbocation process. Core-shell structure ensures the conversion rate of raw materials and improves the selectivity of products.

Green and efficient catalytic oxidation of ethylbenzene to acetophenone over cobalt oxide supported on a carbon material derived from sugar.

The use of biomass as a carbon source to support metal oxides has significant advantages in environmental protection and reducing the cost of the catalyst. The critical point lies on the development of highly active and recyclable catalysts. In this study, sugar was used as a carbon source, and cobalt oxide was loaded via an in situ method and an impregnation method to prepare the catalyst, respectively. The catalysts were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR) spectroscopy, Raman, in situ electron paramagnetic resonance (in situ EPR) and N2 adsorption-desorption. The characterization results show that the macroporous carbon-supported cobalt oxide catalyst prepared by the in situ method contains CoOx nanoparticles on the support, but the dispersion of cobalt oxide on the support is more uniform compared with the catalyst prepared by the impregnation method. The catalytic performance of the prepared catalyst was evaluated through the oxidation of ethylbenzene (EB) to acetophenone (AP) as a probe reaction. Under the optimized reaction conditions, temperature (T) = 80 °C, m(catalyst) : m(EB) = 0.15, n(H2O2) : n(EB) : n(KBr) = 14.4 : 1 : 0.1, t = 8 h, and V(EB) : V(CH3COOH) = 1 : 10, the conversion of EB and the selectivity of AP were 84.1% and 81.3%, respectively. CoOx/SC-10-in situ exhibits improved reactivity of EB oxidation owing to cobalt ions on the carbon support that promote the free radical and acid catalytic reaction pathway. The cobalt oxide catalyst supported by biomass carbon has decent recycling and regeneration ability, which provides a new idea for the application of biomass.

Cortical and thalamic modulation of auditory gating in the posterior parietal cortex of awake mice.

Auditory gating (AG) is an adaptive mechanism for filtering out redundant acoustic stimuli to protect the brain against information overload. AG deficits have been found in many mental illnesses, including schizophrenia (SZ). However, the neural correlates of AG remain poorly understood. Here, we found that the posterior parietal cortex (PPC) shows an intermediate level of AG in auditory thalamocortical circuits, with a laminar profile in which the strongest AG is in the granular layer. Furthermore, AG of the PPC was decreased and increased by optogenetic inactivation of the medial dorsal thalamic nucleus (MD) and auditory cortex (AC), respectively. Optogenetically activating the axons from the MD and AC drove neural activities in the PPC without an obvious AG. These results indicated that AG in the PPC is determined by the integrated signal streams from the MD and AC in a bottom-up manner. We also found that a mouse model of SZ (postnatal administration of noncompetitive N-methyl-d-aspartate receptor antagonist) presented an AG deficit in the PPC, which may be inherited from the dysfunction of MD. Together, our findings reveal a neural circuit underlying the generation of AG in the PPC and its involvement in the AG deficit of SZ.

Neurophysiological evidence for goal-oriented modulation of speech perception.

Speech perception depends on the dynamic interplay of bottom-up and top-down information along a hierarchically organized cortical network. Here, we test, for the first time in the human brain, whether neural processing of attended speech is dynamically modulated by task demand using a context-free discrimination paradigm. Electroencephalographic signals were recorded during 3 parallel experiments that differed only in the phonological feature of discrimination (word, vowel, and lexical tone, respectively). The event-related potentials (ERPs) revealed the task modulation of speech processing at approximately 200 ms (P2) after stimulus onset, probably influencing what phonological information to retain in memory. For the phonological comparison of sequential words, task modulation occurred later at approximately 300 ms (N3 and P3), reflecting the engagement of task-specific cognitive processes. The ERP results were consistent with the changes in delta-theta neural oscillations, suggesting the involvement of cortical tracking of speech envelopes. The study thus provides neurophysiological evidence for goal-oriented modulation of attended speech and calls for speech perception models incorporating limited memory capacity and goal-oriented optimization mechanisms.

Peripheral biomarkers to differentiate bipolar depression from major depressive disorder: a real-world retrospective study.

BACKGROUND: Bipolar depression (BPD) is often misdiagnosed as a major depressive disorder (MDD) in clinical practice, which may be attributed to a lack of robust biomarkers indicative of differentiated diagnosis. This study analysed the differences in various hormones and inflammatory markers to explore peripheral biomarkers that differentiate BPD from MDD patients. METHODS: A total of 2,048 BPD and MDD patients were included. A panel of blood tests was performed to determine the levels of sex hormones, stress hormones, and immune-related indicators. Propensity score matching (PSM) was used to control for the effect of potential confounders between two groups and further a receiver operating characteristic (ROC) curve was used to analyse the potential biomarkers for differentiating BPD from MDD. RESULTS: Compared to patients with MDD, patients with BPD expressed a longer duration of illness, more hospitalisations within five years, and an earlier age of onset, along with fewer comorbid psychotic symptoms. In terms of biochemical parameters, MDD patients presented higher IgA and IgM levels, while BPD patients featured more elevated neutrophil and monocyte counts. ROC analysis suggested that combined biological indicators and clinical features could moderately distinguish between BPD and MDD. In addition, different biological features exist in BPD and MDD patients of different ages and sexes. CONCLUSIONS: Differential peripheral biological parameters were observed between BPD and MDD, which may be age-sex specific, and a combined diagnostic model that integrates clinical characteristics and biochemical indicators has a moderate accuracy in distinguishing BPD from MDD.

Anti-phasic oscillatory development for speech and noise processing in cochlear implanted toddlers.

Human brain demonstrates amazing readiness for speech and language learning at birth, but the auditory development preceding such readiness remains unknown. Cochlear implanted (CI) children (n = 67; mean age 2.77 year ± 1.31 SD; 28 females) with prelingual deafness provide a unique opportunity to study this stage. Using functional near-infrared spectroscopy, it was revealed that the brain of CI children was irresponsive to sounds at CI hearing onset. With increasing CI experiences up to 32 months, the brain demonstrated function, region and hemisphere specific development. Most strikingly, the left anterior temporal lobe showed an oscillatory trajectory, changing in opposite phases for speech and noise. The study provides the first longitudinal brain imaging evidence for early auditory development preceding speech acquisition.

The Prognosis and Immunotherapy Prediction Model of Ovarian Serous Cystadenocarcinoma Patient was Constructed Based on Cuproptosis-Related LncRNA.

Cuproptosis can serve as potential prognostic predictors in patients with cancer. However, the role of this relationship in ovarian serous cystadenocarcinoma (OV) remains unclear. 376 OV tumor samples were obtained from the Cancer Genome Atlas (TCGA) database, and long non-coding RNAs (lncRNAs) related to cuproptosis were obtained through correlation analysis. The risk assessment model was further constructed by univariate Cox regression analysis and LASSO Cox regression. Bioinformatics was used to analyze the regulatory effect of relevant risk assessment models on tumor mutational burden (TMB) and immune microenvironment. We obtained 5 lncRNAs (AC025287.2, AC092718.4, AC112721.2, LINC00996, and LINC01639) and incorporated them into the Cox proportional hazards model. Kaplan-Meier (KM) curve analysis of the prognosis found that the high-risk group was associated with a poorer prognosis. The receiver operating characteristic (ROC) curve showed stronger predictive power compared to other clinicopathological features. Immune infiltration analysis showed that high-risk scores were inversely correlated with CD8+ T cells, CD4+ T cells, macrophages, NK cells, and B cells. Functional enrichment analysis found that they may act via the extracellular matrix (ECM)-interacting proteins and other pathways. We successfully constructed a reliable cuproptosis-related lncRNA model for the prognosis of OV.

Functional study of the soybean stamen-preferentially expressed gene GmFLA22a in regulating male fertility.

China has a high dependence on soybean imports, yield increase at a faster rate is an urgent problem that need to be solved at present. The application of heterosis is one of the effective ways to significantly increase crop yield. In recent years, the development of an intelligent male sterility system based on recessive nuclear sterile genes has provided a potential solution for rapidly harnessing the heterosis in soybean. However, research on male sterility genes in soybean has been lagged behind. Based on transcriptome data of soybean floral organs in our research group, a soybean stamen-preferentially expressed gene GmFLA22a was identified. It encodes a fasciclin-like arabinogalactan protein with the FAS1 domain, and subcellular localization studies revealed that it may play roles in the endoplasmic reticulum. Take advantage of the gene editing technology, the Gmfla22a mutant was generated in this study. However, there was a significant reduction in the seed-setting rate in the mutant plants at the reproductive growth stage. The pollen viability and germination rate of Gmfla22a mutant plants showed no apparent abnormalities. Histological staining demonstrated that the release of pollen grains in the mutant plants was delayed and incomplete, which may due to the locule wall thickening in the anther development. This could be the reason of the reduced seed-setting rate in Gmfla22a mutants. In summary, our study has preliminarily revealed that GmFLA22a may be involved in regulating soybean male fertility. It provides crucial genetic materials for further uncovering its molecular function and gene resources and theoretical basis for the utilization of heterosis in soybean.

Bifunctional Metal-Organic Framework Synergistically Enhances Radiotherapy and Activates STING for Potent Cancer Radio-Immunotherapy.

The activation of the stimulator of interferon genes (STING) protein by cyclic dinucleotide metabolites plays a critical role in antitumor immunity. However, synthetic STING agonists like 4-(5,6-dimethoxybenzo[b]thiophen-2-yl)-4-oxobutanoic acid (MSA-2) exhibit suboptimal pharmacokinetics and fail to sustain STING activation in tumors for effective antitumor responses. Here, we report the design of MOF/MSA-2, a bifunctional MSA-2 conjugated nanoscale metal-organic framework (MOF) based on Hf6 secondary building units (SBUs) and hexakis(4'-carboxy[1,1'-biphenyl]-4-yl)benzene bridging ligands, for potent cancer radio-immunotherapy. By leveraging the high-Z properties of the Hf6 SBUs, the MOF enhances the therapeutic effect of X-ray radiation and elicits potent immune stimulation in the tumor microenvironment. MOF/MSA-2 further enhances radiotherapeutic effects of X-rays by enabling sustained STING activation and promoting the infiltration and activation of immune cells in the tumors. MOF/MSA-2 plus low-dose X-ray irradiation elicits strong STING activation and potent tumor regression, and when combined with an immune checkpoint inhibitor, effectively suppresses both primary and distant tumors through systemic immune activation.

Phosphate Coordination to Metal-Organic Layer Secondary Building Units Prolongs Drug Retention for Synergistic Chemoradiotherapy.

Chemoradiotherapy combines radiotherapy with concurrent chemotherapy to potentiate antitumor activity but exacerbates toxicities and causes debilitating side effects in cancer patients. Herein, we report the use of a nanoscale metal-organic layer (MOL) as a 2D nanoradiosensitizer and a reservoir for the slow release of chemotherapeutics to amplify the antitumor effects of radiotherapy. Coordination of phosphate-containing drugs to MOL secondary building units prolongs their intratumoral retention, allowing for continuous release of gemcitabine monophosphate (GMP) for effective localized chemotherapy. In the meantime, the MOL sensitizes cancer cells to X-ray irradiation and provides potent radiotherapeutic effects. GMP-loaded MOL (GMP/MOL) enhances cytotoxicity by 2-fold and improves radiotherapeutic effects over free GMP in vitro. In a colon cancer model, GMP/MOL retains GMP in tumors for more than four days and, when combined with low-dose radiotherapy, inhibits tumor growth by 98 %. The synergistic chemoradiotherapy enabled by GMP/MOL shows a cure rate of 50 %, improves survival, and ameliorates cancer-proliferation histological biomarkers.

Follistatin-like 1 (FSTL1) interacts with Wnt ligands and Frizzled receptors to enhance Wnt/ß-catenin signaling in obstructed kidneys in vivo.

Follistatin (FS)-like 1 (FSTL1) is a member of the FS-SPARC (secreted protein, acidic and rich in cysteine) family of secreted and extracellular matrix proteins. The functions of FSTL1 have been studied in heart and lung injury as well as in wound healing; however, the role of FSTL1 in the kidney is largely unknown. Here, we show using single-cell RNA-Seq that Fstl1 was enriched in stromal cells in obstructed mouse kidneys. In addition, immunofluorescence demonstrated that FSTL1 expression was induced in fibroblasts during kidney fibrogenesis in mice and human patients. We demonstrate that FSTL1 overexpression increased renal fibrosis and activated the Wnt/ß-catenin signaling pathway, known to promote kidney fibrosis, but not the transforming growth factor ß (TGF-ß), Notch, Hedgehog, or Yes-associated protein (YAP) signaling pathways in obstructed mouse kidneys, whereas inhibition of FSTL1 lowered Wnt/ß-catenin signaling. Importantly, we show that FSTL1 interacted with Wnt ligands and the Frizzled (FZD) receptors but not the coreceptor lipoprotein receptor-related protein 6 (LRP6). Specifically, we found FSTL1 interacted with Wnt3a through its extracellular calcium-binding (EC) domain and von Willebrand factor type C-like (VWC) domain, and with FZD4 through its EC domain. Furthermore, we show that FSTL1 increased the association of Wnt3a with FZD4 and promoted Wnt/ß-catenin signaling and fibrogenesis. The EC domain interacting with both Wnt3a and FZD4 also enhanced Wnt3a signaling. Therefore, we conclude that FSTL1 is a novel extracellular enhancer of the Wnt/ß-catenin pathway.

YAP promotes AP-1 expression in tubular epithelial cells in the kidney.

Chronic kidney disease (CKD) is a major health problem. Kidney fibrosis is a hallmark and final common pathway of CKD. The Hippo/yes-associated protein (YAP) pathway regulates organ size, inflammation, and tumorigenesis. Our previous study demonstrated tubular YAP activation by tubule-specific double knockout of mammalian STE20-like protein kinase 1/2 (Mst1/2) induced CKD in mice, but the underlying mechanisms remain to be fully elucidated. Activator protein (AP)-1 activation was found to promote tubular atrophy and tubulointerstitial fibrosis. Therefore, we studied whether YAP regulates AP-1 expression in the kidney. We found that expression of various AP-1 components was induced in kidneys subjected to unilateral ureteric obstruction and in Mst1/2 double knockout kidneys, and these inductions were blocked by deletion of Yap in tubular cells, with Fosl1 being most affected compared with other AP-1 genes. Inhibition of Yap also most highly suppressed Fosl1 expression among AP-1 genes in HK-2 and IMCD3 renal tubular cells. YAP bound to the Fosl1 promoter and promoted Fosl1 promoter-luciferase activity. Our results suggest that YAP controls AP-1 expression and that Fosl1 is the primary target of YAP in renal tubular cells.NEW & NOTEWORTHY Yes-associated protein (YAP) activation leads to tubular injury, renal inflammation, and fibrosis, but the underlying mechanisms are not fully understood. We now provide genetic evidence that YAP promotes activator protein-1 expression and that Fosl1 is the primary target of YAP in renal tubular cells.

Kidney tubular transcription co-activator, Yes-associated protein 1 (YAP), controls the expression of collecting duct aquaporins and water homeostasis.

Final urine volume and concentration are defined by water reabsorption through the water channel proteins aquaporin (AQP)-2, -3 and -4 in the collecting duct. However, the transcriptional regulation of these AQPs is not well understood. The Hippo/Yes-associated protein 1 (YAP) pathway plays an important role in organ size control and tissue homeostasis. When the Hippo pathway including the Mst1/Mst2 kinases is inhibited, YAP is activated and functions as a transcription co-activator. Our previous work revealed a pathological role of tubular YAP activation in chronic kidney disease, but the physiological role of YAP in the kidney remains to be established. Here, we found that tubule-specific Yap knockout mice showed increased urine output and decreased urinary osmolality. Decreases in Aqp2, -3 and -4 mRNA and protein abundance in the kidney were evident in Yap knockout mice. Analysis of Mst1/Mst2 double knockout and Mst1/Mst2/Yap triple knockout mice showed that expression of Aqp2 and Aqp4 but not Aqp3 was dependent on YAP. Furthermore, YAP was recruited to the promoters of the Aqp2 and Aqp4 genes and stimulated their transcription. Interestingly, YAP was found to interact with transcription factors GATA2, GATA3 and NFATc1. These three factors promoted Aqp2 transcription in a YAP dependent manner in collecting duct cells. These three factors also promoted Aqp4 transcription whereas only GATA2 and GATA3 enhanced Aqp3 transcription. Thus, our results suggest that YAP promotes Aqp2 and Aqp4 transcription, interacts with GATA2, GATA3 and NFATc1 to control Aqp2 expression, while Aqp-2, -3 and -4 exploit overlapping mechanisms for their baseline transcriptional regulation.

LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro.

SUMMARY: Emerging evidences have suggested that liquid-liquid phase separation (LLPS) of proteins plays a vital role both in a wide range of biological processes and in related diseases. Whether a protein undergoes phase separation not only is determined by the chemical and physical properties of biomolecule themselves, but also is regulated by environmental conditions such as temperature, ionic strength, pH, as well as volume excluded by other macromolecules. A web accessible database LLPSDB was developed recently by our group, in which all the proteins involved in LLPS in vitro as well as corresponding experimental conditions were curated comprehensively from published literatures. With the rapid increase of investigations in biomolecular LLPS and growing popularity of LLPSDB, we updated the database, and developed a new version LLPSDB v2.0. In comparison of the previously released version, more than double contents of data are curated, and a new class 'Ambiguous system' is added. In addition, the web interface is improved, such as that users can search the database by selecting option 'phase separation status' alone or combined with other options. We anticipate that this updated database will serve as a more comprehensive and helpful resource for users. AVAILABILITY AND IMPLEMENTATION: LLPSDB v2.0 is freely available at: http://bio-comp.org.cn/llpsdbv2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Screening of immune-related secretory proteins linking chronic kidney disease with calcific aortic valve disease based on comprehensive bioinformatics analysis and machine learning.

BACKGROUND: Chronic kidney disease (CKD) is one of the most significant cardiovascular risk factors, playing vital roles in various cardiovascular diseases such as calcific aortic valve disease (CAVD). We aim to explore the CKD-associated genes potentially involving CAVD pathogenesis, and to discover candidate biomarkers for the diagnosis of CKD with CAVD. METHODS: Three CAVD, one CKD-PBMC and one CKD-Kidney datasets of expression profiles were obtained from the GEO database. Firstly, to detect CAVD key genes and CKD-associated secretory proteins, differentially expressed analysis and WGCNA were carried out. Protein-protein interaction (PPI), functional enrichment and cMAP analyses were employed to reveal CKD-related pathogenic genes and underlying mechanisms in CKD-related CAVD as well as the potential drugs for CAVD treatment. Then, machine learning algorithms including LASSO regression and random forest were adopted for screening candidate biomarkers and constructing diagnostic nomogram for predicting CKD-related CAVD. Moreover, ROC curve, calibration curve and decision curve analyses were applied to evaluate the diagnostic performance of nomogram. Finally, the CIBERSORT algorithm was used to explore immune cell infiltration in CAVD. RESULTS: The integrated CAVD dataset identified 124 CAVD key genes by intersecting differential expression and WGCNA analyses. Totally 983 CKD-associated secretory proteins were screened by differential expression analysis of CKD-PBMC/Kidney datasets. PPI analysis identified two key modules containing 76 nodes, regarded as CKD-related pathogenic genes in CAVD, which were mostly enriched in inflammatory and immune regulation by enrichment analysis. The cMAP analysis exposed metyrapone as a more potential drug for CAVD treatment. 17 genes were overlapped between CAVD key genes and CKD-associated secretory proteins, and two hub genes were chosen as candidate biomarkers for developing nomogram with ideal diagnostic performance through machine learning. Furthermore, SLPI/MMP9 expression patterns were confirmed in our external cohort and the nomogram could serve as novel diagnosis models for distinguishing CAVD. Finally, immune cell infiltration results uncovered immune dysregulation in CAVD, and SLPI/MMP9 were significantly associated with invasive immune cells. CONCLUSIONS: We revealed the inflammatory-immune pathways underlying CKD-related CAVD, and developed SLPI/MMP9-based CAVD diagnostic nomogram, which offered novel insights into future serum-based diagnosis and therapeutic intervention of CKD with CAVD.

Spin-orbit interactions of a circularly polarized vortex beam in paraxial propagation.

Spin-orbit interactions (SOIs) of circularly polarized beam and circularly polarized vortex beam during paraxial propagation in a radial gradient-index (GRIN) fiber are analyzed using the generalized Huygens-Fresnel principle and the GRIN fiber's ABCD matrix. SAM is only associated with polarized light helicity and OAM is only associated with topological charge m. SAM and OAM do not crosstalk or convert between each other; SOIs did not occur at the GRIN fiber's focal plane. SOIs of partially coherent circularly polarized beam and partially coherent circularly polarized vortex beam in the GRIN fiber are also studied and show the same characteristics as the perfectly polarized beam.