Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder.

Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder's adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub ( https://github.com/tjcadd2020/xMarkerFinder ), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server ( https://www.biosino.org/xmarkerfinder ).

Ligation of cervical lymphatic vessels decelerates blood clearance and worsens outcomes after experimental subarachnoid hemorrhage.

Subarachnoid hemorrhage (SAH) is characterized by the extravasation of blood into the subarachnoid space, in which erythrocyte lysis is the primary contributor to cell death and brain injuries. New evidence has indicated that meningeal lymphatic vessels (mLVs) are essential in guiding fluid and macromolecular waste from cerebrospinal fluid (CSF) into deep cervical lymph nodes (dCLNs). However, the role of mLVs in clearing erythrocytes after SAH has not been completely elucidated. Hence, we conducted a cross-species study. Autologous blood was injected into the subarachnoid space of rabbits and rats to induce SAH. Erythrocytes in the CSF were measured with/without deep cervical lymph vessels (dCLVs) ligation. Additionally, prior to inducing SAH, we administered rats with vascular endothelial growth factor C (VEGF-C), which is essential for meningeal lymphangiogenesis and maintaining integrity and survival of lymphatic vessels. The results showed that the blood clearance rate was significantly lower after dCLVs ligation in both the rat and rabbit models. DCLVs ligation aggravated neuroinflammation, neuronal damage, brain edema, and behavioral impairment after SAH. Conversely, the treatment of VEGF-C enhanced meningeal lymphatic drainage of erythrocytes and improved outcomes in SAH. In summary, our research highlights the indispensable role of the meningeal lymphatic pathway in the clearance of blood and mediating consequences after SAH.

The Planar Cell Polarity Protein Fat1 in Sertoli Cell Function.

Fat (FAT atypical cadherin) and Dchs (Dachsous cadherin-related protein) in adjacent Sertoli:Sertoli, Sertoli:spermatid, and spermatid:spermatid interfaces create an important intercellular bridge whose adhesive function is in turn supported by Fjx1, a nonreceptor Ser/Thr protein kinase. This concept is derived from earlier studies of Drosophila, which has been confirmed in this and earlier reports as well. Herein, we use the approach of knockdown of Fat1 by RNAi using primary cultures of Sertoli cells that mimicked the blood-testis barrier (BTB) in vivo, and a series of coherent experiments including functional assays to monitor the Sertoli cell tight junction (TJ) permeability barrier and a functional in vitro TJ integrity assay to assess the role of Fat1 in the testis. It was shown that planar cell polarity (PCP) protein Fat1 affected Sertoli cell function through its modulation of actin and microtubule cytoskeletal function, altering their polymerization activity through the Fat1/Fjx1 complex. Furthermore, Fat1 is intimately associated with ß-catenin and α-N-catenin, as well as with Prickle 1 of the Vangl1/Prickle 1 complex, another PCP core protein to support intercellular interactions to confer PCP. In summary, these findings support the notion that the Fat:Dchs and the Vangl2:Fzd PCP intercellular bridges are tightly associated with basal ES/TJ structural proteins to stabilize PCP function at the Sertoli:Sertoli, Sertoli:spermatid, and spermatid:spermatid interface to sustain spermatogenesis.

Efficacy and Predictive Factors of Oral Spironolactone Treatment in Chronic Central Serous Chorioretinopathy.

Purpose: To evaluate the efficacy of spironolactone in the treatment of chronic central serous chorioretinopathy (CSC) and identify imaging characteristics that can predict the benefit of spironolactone treatment. Methods: Patients with chronic CSC were treated with spironolactone (20 mg/tid) and followed for 6 months. The primary outcome measure was complete resolution of the subretinal fluid (SRF), and the best-corrected visual acuity (BCVA), the SRF area, the central macular thickness (CMT), the subfoveal choroidal thickness (SFCT), and the density of the choriocapillaris vessel and adverse events were secondary outcome measures. Patients who presented complete resolution of SRF were included in the responder group and the other patients who had moderate or no resolution were included in the nonresponder group. Imaging characteristic comparisons between the responder and nonresponder groups were performed with regression analyses to identify factors that are predictive of a good response to treatment. Results: Forty-two eyes of 42 patients with a mean age of 46.06 ± 6.66 years were included. A total of 57.1% of the patients achieved a complete resolution of SRF. The mean SRF area, CMT, and SFCT decreased significantly (all P < 0.05) throughout the follow-up period and BCVA improved slightly (P > 0.05). The vascular density of the choriocapillaris of the fellow eyes did not vary significantly during treatment. Logistic regression analysis revealed that SFCT (P=0.002) and the intact ellipsoid zone (P=0.001) were correlated with disease resolution. A relatively higher baseline SFCT was a predictive factor associated with a good response to treatment according to multivariate analysis. Conclusions: This study suggested that oral spironolactone could be an effective and safe therapy for chronic CSC patients. Eyes with a higher baseline SFCT and intact ellipsoid zone could have a good response. These parameters are an important prognostic marker.

Surfactant-assisted preparation of all-gel-state flexible supercapacitor with remarkable electrochemical performance based on polyaniline-polyacrylamide/sodium alginate hydrogels.

The electrochemical performance of polyaniline-based all-gel-state supercapacitor (AGSSC) is significantly depended on the dispersity and mass loaded of polyaniline (PANI). In this manuscript, inspired by the properties of surfactant, sodium dodecylbenzene sulfonate (SDBS) was introduced to prepare various PANI-polyacrylamide/sodium alginate/SDBS (PANIy-PSSx) AGSSCs. With presence of SDBS, the electrochemical performance of PANIy-PSSx AGSSCs was greatly improved, displaying a trend of initial rise and then decrease with increasing concentration of SDBS from 0 to 0.75 wt%. As the content of SDBS was 0.5 wt%, the resulting PANI1.0-PSS0.5 AGSSC displayed the optimum electrochemical properties with area capacitance and energy density of 913.79 mF/cm2 and 81.23 µWh/cm2, respectively. The capacitance rate of PANI1.0-PSS0.5 AGSSC was still more than 93 % after 2000 cycles of sequential CV scans at the scan rate of 200 mV/s. These data were greatly higher than many reported PANI-based AGSSCs. Moreover, the resultant PANI1.0-PSS0.5 AGSSC could maintain high electrochemical performance even after various operations, such as compression, puncture, fluctuating temperature, bending situations and various voltage windows and series-parallel connections. The resultant PANI1.0-PSS0.5 AGSSC had the wide potentials to satisfy the real application requirements. This study offered a facile strategy for design and preparation of flexible supercapacitor with excellent electrochemical performance.

Challenges and opportunities in inflammatory bowel disease: from current therapeutic strategies to organoid-based models.

BACKGROUND: Inflammatory bowel disease (IBD) is an increasingly prevalent global health concern that has garnered substantial attention. However, the underlying mechanisms are still unclear and the current treatments have significant limitations. Intestinal organoids provide an in vitro model to explore the pathogenesis, test the therapeutic effects, and develop regenerative treatments as well as offer the potential to transform drug discovery of IBD. METHODS: To advance our understanding of the whole story of IBD spanning from the pathogenesis to the current therapeutic strategies and latest advancements, a comprehensive search of major databases including PubMed, Scopus, and Web of Science was conducted to retrieve original articles and reviews related to IBD, organoids, pathogenesis and therapy. RESULTS: This review deciphers the etiopathogenesis and the current therapeutic approaches in the treatment of IBD. Notably, critical aspects of intestinal organoids in IBD, such as their potential applications, viability, cell renewal ability, and barrier functionality are highlighted. We also discuss the advances, limitations, and prospects of intestinal organoids for precision medicine. CONCLUSION: The latest strides made in research about intestinal organoids help elucidate intricate aspects of IBD pathogenesis, and pave the prospective avenues for novel therapeutic interventions.

Endoscopic-Assisted Forehead Augmentation with Polyetheretherketone (PEEK) Patient-Specific Implant (PSI) for Aesthetic Considerations.

BACKGROUND: Forehead augmentation have become popular aesthetic procedures among Asians in recent years. However, the use of polyetheretherketone (PEEK) patient-specific implant (PSI) in the facial contouring surgery for aesthetic considerations is not well documented in the existing studies. The purpose of this study was to develop a novel method for forehead augmentation and assess the clinical outcomes and complications in patients who underwent forehead augmentation with PEEK PSI assisted by endoscopy. METHODS: The PEEK PSIs were fabricated using the virtual surgical planning (VSP) and the computer-aided manufacturing (CAM) for each patient, preoperatively. The implant pockets were dissected in the subperiosteal plane, and PEEK PSIs were placed in their designed position and fixed assisting by endoscopy via small incision within the hairline. All patients were asked to complete the FACE-Q questionnaire before and 6 months after the operation. Pre- and postoperative demographics, photographs, and other clinical data of patients were collected and analyzed. RESULTS: 11 patients underwent forehead augmentation were enrolled in this study. All procedures were completed successfully with the help of endoscope. The average patient age was 30.63 ± 2.54 years. The mean thickness and size of PEEK PSI were 4.44 ± 1.77 mm and 38.43 ± 22.66 cm2, respectively. The mean operative time was 83.00 ± 29.44 min, and the mean postoperative follow-up period was 11.00 ± 6.50 months. No implant exposure, extrusion or removal were reported. The FACE-Q scores of patients in satisfaction with the forehead increased from 47.64 ± 7.15 to 78.81 ± 6.35. CONCLUSIONS: PEEK PSIs can be prefabricated to achieve accurate remodeling of the frontal contour with good esthetic outcomes. The endoscope provides direct and magnified vision, which allow easy access to the supraorbital rim and lateral edge of the eyebrow arch and confirming the position of the implants without damaging nerves and vessels. Endoscopic-assisted forehead augmentation with PEEK PSI is safe and effective. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these evidence-based medicine ratings, please refer to the Table of contents or the online Instructions to Authors www.springer.com/00266 .

Demixing microwave signals using system-on-chip photonic processor.

The integrated photonic processor, co-packaged with electronic peripherals, is proposed for blind source separation of microwave signals, which separates signal-of-interest from dynamic interference with real-time adaptability.

Modulation of Interleukin-23 Signaling With Guselkumab in Biologic-Naive Patients Versus Tumor Necrosis Factor Inhibitor-Inadequate Responders With Active Psoriatic Arthritis.

OBJECTIVE: We assessed and compared immunologic differences and associations with clinical response to guselkumab, a fully human interleukin (IL)-23p19 subunit inhibitor, in participants with active psoriatic arthritis (PsA) who were biologic-naive or had inadequate response to tumor necrosis factor inhibitors (TNFi-IR). METHODS: Serum biomarker levels at baseline and after treatment with guselkumab 100 mg every 8 weeks were compared between biologic-naive (n = 251) and TNFi-IR (n = 93) subgroups identified in the pooled DISCOVER-1/DISCOVER-2/COSMOS data set. Baseline biomarker levels determined by achievement of week 24 clinical responses (≥75%/90% improvement in Psoriasis Area and Severity Index [PASI 75/90], Investigator's Global Assessment [IGA] of psoriasis score 0/1 and ≥2-point improvement], ≥20% improvement in American College of Rheumatology criteria [ACR20]) were compared between prior treatment subgroups. RESULTS: Baseline IL-22, TNFα, and beta defensin-2 (BD-2) levels were significantly lower in biologic-naive than in TNFi-IR participants. With guselkumab, week 24 IL-17A, IL-17F, IL-22, serum amyloid A, C-reactive protein, IL-6, and BD-2 levels were significantly reduced from baseline in biologic-naive and TNFi-IR participants (≥1.4-fold difference, nominal P < 0.05). Clinical responders to guselkumab exhibited significantly higher baseline levels of several biomarkers than nonresponders (IL-17A, IL-17F, BD-2 in biologic-naive PASI 90 responders; IL-17A, BD-2 in TNFi-IR IGA 0/1 responders; IL-22, BD-2 in TNFi-IR PASI 90 responders [nominal P < 0.05]) and trended higher in TNFi-IR ACR20 responders. CONCLUSION: Guselkumab modulates IL-23 signaling and provides consistent pharmacodynamic effects in both biologic-naive and TNFi-IR PsA patients. Significantly elevated baseline IL-22, TNFα, and BD-2 levels and associations between baseline IL-22, IL-17A, and BD-2 levels and skin responses to guselkumab suggest greater dysregulation of IL-23/Th17 signaling in patients with TNFi-IR.

Polycrystalline Lead-Free Perovskite Direct X-Ray Detectors with High Durability and Low Limit of Detection via Low-Temperature Coating.

Direct X-ray detectors represent a transformative technology in the realm of radiography and imaging. The double halide-based perovskite cesium silver bismuth bromide (Cs2AgBiBr6) has emerged as a promising material for use in direct X-ray imaging, owing to its nontoxic composition, strong X-ray absorption, decent charge mobility lifetime product (µτ), and low-cost preparation. However, formidable issues related to scalability and ion migration, stemming from intrinsic factors such as halogen vacancies and grain boundaries, have presented significant impediments. These issues have been associated with substantial noise, baseline instability, and a curtailment of detection performance. In response to these multifaceted challenges, we propose a slurry-based in situ treatment technique for fabricating robust Cs2AgBiBr6 thick films. This novel approach adeptly mitigates halogen vacancies, actively passivates grain boundaries, and concurrently elevates the ion migration activation energy, thus effectively suppressing ion migration. Consequently, the obtained X-ray detector exhibits excellent operating stability with minimal signal drift of 8.5 × 10-9 nA cm-1 s-1 V-1 and achieves a remarkable 385% increase in sensitivity with a limit of detection as low as 7.8 nGyair s-1. These results mark a significant step toward the development of high-performance and long-lasting lead-free perovskite direct X-ray detectors.

OXCT1 regulates hippocampal neurogenesis and alleviates cognitive impairment via the Akt/GSK-3ß/ß-catenin pathway after subarachnoid hemorrhage.

BACKGROUND: Subarachnoid hemorrhage (SAH) is a life-threatening neurological disease that usually has a poor prognosis. Neurogenesis is a potential therapeutic target for brain injury. Ketone metabolism also plays neuroprotective roles in many neurological disorders. OXCT1 (3-Oxoacid CoA-Transferase 1) is the rate-limiting enzyme of ketone body oxidation. In this study, we explored whether increasing ketone oxidation by upregulating OXCT1 in neurons could promote neurogenesis after SAH, and evaluated the potential mechanism involved in this process. METHODS: The ß-hydroxybutyrate content was measured using an enzymatic colorimetric assay. Adeno-associated virus targeting neurons was injected to overexpress OXCT1, and the expression and localization of proteins were evaluated by western blotting and immunofluorescence staining. Adult hippocampal neurogenesis was evaluated by dual staining with doublecortin and 5-Ethynyl-2'-Deoxyuridine. LY294002 was intracerebroventricularly administered to inhibit Akt activity. The Morris water maze and Y-maze tests were employed to assess cognitive function after SAH. RESULTS: The results showed that OXCT1 expression and hippocampal neurogenesis significantly decreased in the early stage of SAH. Overexpression of OXCT1 successfully increased hippocampal neurogenesis via activation of Akt/GSK-3ß/ß-catenin signaling and improved cognitive function, both of which were reversed by administration of LY294002. CONCLUSIONS: OXCT1 regulated hippocampal ketone body metabolism and increased neurogenesis through mechanisms mediated by the Akt/GSK-3ß/ß-catenin pathway, improving cognitive impairment after SAH.

Long-read single-cell sequencing reveals the transcriptional landscape of spermatogenesis in obstructive azoospermia and sertoli cell-only patients.

BACKGROUND：: High-throughput single-cell RNA sequencing (scRNA-seq) is widely used in spermatogenesis. However, it only reveals short reads in germ and somatic cells, limiting the discovery of novel transcripts and genes. AIM: This study shows the long-read transcriptional landscape of spermatogenesis in obstructive azoospermia (OA) and Sertoli cell-only (SCO) patients. DESIGN: Single cells were isolated from testicular biopsies of OA and NOA patients. Cell culture was identified by comparing Pacbio long-read single-cell sequencing (OA n = 3, NOA n = 3) with short-read scRNA-seq (OA n = 6, NOA n = 6). Ten germ cell types and eight somatic cell types were classified based on known markers. METHODS: Pacbio long read single-cell sequencing, short-read scRNA-seq, Polymerase Chain Reaction. RESULTS: A total of 130,426 long-read transcripts (100,517 novel transcripts and 29,909 known transcripts) and 49,508 long-read transcripts (26,002 novel transcripts, and 23,506 known transcripts) have been detected in OA and NOA patients, respectively. Moreover, 36,373 and 1642 new genes are identified in OA and NOA patients, respectively. Importantly, specific expressions of long-read transcripts were detected in germ and stomatic cells during normal spermatogenesis. CONCLUSION: We have identified total full-length transcripts in OA and NOA, and new genes were found. Furthermore, specific expressed full-length transcripts were detected, and the genomic structure of transcripts was mapped in different cell types. These findings may provide valuable information on human spermatogenesis and the treatment of male infertility.

JS-K activates G2/M checkpoints through the DNA damage response and induces autophagy via CAMKKß/AMPKα/mTOR pathway in bladder cancer cells.

The aim of this study was to investigate the effects of JS-K, a nitric oxide donor prodrug, on DNA damage and autophagy in bladder cancer (BCa) cells and to explore the potential related mechanisms. Through detecting proliferation viability, cell morphology observation and colony formation assay low concentrations of JS-K significantly inhibited BCa growth while having no effect on normal cells. JS-K induced an increase in the level of DNA damage protein γH2AX and a decrease in the level of DNA damage repair-related proteins PCNA and RAD51 in BCa cells, indicating that JS-K can induce DNA damage in BCa cells and inhibit DNA damage repair. JS-K induced G2/M phase block and calcium overload using flow cytometry analysis. Moreover, we also investigated the levels of cell G2/M cycle checkpoint-related protein and autophagy-associated protein by western blot. The results of our study demonstrated that JS-K induced BCa cells G2/M phase arrest due to upregulating proteins related to DNA damage-related G2/M checkpoint activation (p-ATM, p-ATR, p-Chk1, p-Chk2, and p-Cdc2) and down-regulation of Cyclin B1 protein. In addition, our study demonstrated that JS-K-induced autophagy in BCa cells was related to the CAMKKß/AMPKα/mTOR pathway.

Relationship Between Serum Uric Acid and Carotid Plaque in Patients With Coronary Artery Disease by Sex and Blood Pressure Status.

The purpose of this study was to explore the sex difference and effects of blood pressure (BP) on the relationship between serum uric acid (SUA) and carotid plaque in patients with coronary heart disease (CHD). This large multicenter retrospective study included 12099 patients with CHD (aged 35-75 years) between January 1, 2014 and September 30, 2020. Patients were divided into three groups according to systolic BP (SBP) and diastolic BP (DBP), and the SUA levels in males and females were converted into three groups. Logistic regression was used to analyze the influence of sex and BP on the relationship between SUA levels and carotid plaque in patients with CHD. In the model of male BP subgroups, using the BP of group A (normal with SBP <120 mmHg and DBP <80 mmHg) as a reference, SUA levels were significantly correlated with the occurrence of carotid plaque under different BP states (P < .001). In contrast, in the model of female BP subgroups, most of these correlations were not statistically significant. Our study showed that SUA levels were significantly associated with carotid plaque occurrence in males with CHD, which remained significant across different BP states.

NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease.

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with a broad spectrum of histologic manifestations. The rapidly growing prevalence and the complex pathologic mechanisms of NAFLD pose great challenges for treatment development. Despite tremendous efforts devoted to drug development, there are no FDA-approved medicines yet. Here, we present NAFLDkb, a specialized knowledge base and platform for computer-aided drug design against NAFLD. With multiperspective information curated from diverse source materials and public databases, NAFLDkb presents the associations of drug-related entities as individual knowledge graphs. Practical drug discovery tools that facilitate the utilization and expansion of NAFLDkb have also been implemented in the web interface, including chemical structure search, drug-likeness screening, knowledge-based repositioning, and research article annotation. Moreover, case studies of a knowledge graph repositioning model and a generative neural network model are presented herein, where three repositioning drug candidates and 137 novel lead-like compounds were newly established as NAFLD pharmacotherapy options reusing data records and machine learning tools in NAFLDkb, suggesting its clinical reliability and great potential in identifying novel drug-disease associations of NAFLD and generating new insights to accelerate NAFLD drug development. NAFLDkb is freely accessible at https://www.biosino.org/nafldkb and will be updated periodically with the latest findings.

Insights into the complex interactions between Rab22a and extracellular vesicles in cancers.

INTRODUCTION: Oncogenic Ras-related GTP-binding proteins, referred to as Rabs, are characterized by their intricate interactions with upstream, downstream molecules, and notably, extracellular vesicles (EVs). While the expansive family of Rabs and their associated signaling pathways have been exhaustively dissected, Rab22a emerges as an entity of outstanding interest, owing to its potent influence in many biological processes and its conspicuous correlation with cancer metastasis and migration. A burgeoning interest in the interactions between Rab22a and EVs in the field of oncology underscores the necessity for more in-depth reviews and scholarly discourses. METHODS: We performed a review based on published original and review articles related to Rab22a, tumor, microRNA, exosome, microvesicles, EVs, CD147, lysosome, degradation, endosomal recycling, etc. from PubMed, Web of Science and Google Scholar databases. RESULTS AND CONCLUSIONS: We summarize the regulatory processes governing the expression of Rab22a and the mutants of Rab22a. Notably, the present understanding of complex interactions between Rab22a and EVs are highlighted, encompassing both the impact of Rab22a on the genesis of EVs and the role of EVs that are affected by Rab22a mutants in propelling tumor advancement. The dynamic interaction between Rab22a and EVs plays a significant role in the progression of tumors, and it can provide novel insights into the pathogenesis of cancers and the development of new therapeutic targets.

Astrocyte-derived hepcidin aggravates neuronal iron accumulation after subarachnoid hemorrhage by decreasing neuronal ferroportin1.

Iron accumulation is one of the most essential pathological events after subarachnoid hemorrhage (SAH). Ferroportin1 (FPN1) is the only transmembrane protein responsible for exporting iron. Hepcidin, as the major regulator of FPN1, is responsible for its degradation. Our study investigated how the interaction between FPN1 and hepcidin contributes to iron accumulation after SAH. We found that iron accumulation aggravated after SAH, along with decreased FPN1 in neurons and increased hepcidin in astrocytes. After knocking down hepcidin in astrocytes, the neuronal FPN1 significantly elevated, thus attenuating iron accumulation. After SAH, p-Smad1/5 and Smad4 tended to translocate into the nucleus. Moreover, Smad4 combined more fragments of the promoter region of Hamp after OxyHb stimulation. By knocking down Smad1/5 or Smad4 in astrocytes, FPN1 level restored and iron overload attenuated, leading to alleviated neuronal cell death and improved neurological function. However, the protective role disappeared after recombinant hepcidin administration. Therefore, our study suggests that owing to the nuclear translocation of transcription factors p-Smad1/5 and Smad4, astrocyte-derived hepcidin increased significantly after SAH, leading to a decreased level of neuronal FPN1, aggravation of iron accumulation, and worse neurological outcome.