BertTCR: a Bert-based deep learning framework for predicting cancer-related immune status based on T cell receptor repertoire.

The T cell receptor (TCR) repertoire is pivotal to the human immune system, and understanding its nuances can significantly enhance our ability to forecast cancer-related immune responses. However, existing methods often overlook the intra- and inter-sequence interactions of T cell receptors (TCRs), limiting the development of sequence-based cancer-related immune status predictions. To address this challenge, we propose BertTCR, an innovative deep learning framework designed to predict cancer-related immune status using TCRs. BertTCR combines a pre-trained protein large language model with deep learning architectures, enabling it to extract deeper contextual information from TCRs. Compared to three state-of-the-art sequence-based methods, BertTCR improves the AUC on an external validation set for thyroid cancer detection by 21 percentage points. Additionally, this model was trained on over 2000 publicly available TCR libraries covering 17 types of cancer and healthy samples, and it has been validated on multiple public external datasets for its ability to distinguish cancer patients from healthy individuals. Furthermore, BertTCR can accurately classify various cancer types and healthy individuals. Overall, BertTCR is the advancing method for cancer-related immune status forecasting based on TCRs, offering promising potential for a wide range of immune status prediction tasks.

Meta-DHGNN: method for CRS-related cytokines analysis in CAR-T therapy based on meta-learning directed heterogeneous graph neural network.

Chimeric antigen receptor T-cell (CAR-T) immunotherapy, a novel approach for treating blood cancer, is associated with the production of cytokine release syndrome (CRS), which poses significant safety concerns for patients. Currently, there is limited knowledge regarding CRS-related cytokines and the intricate relationship between cytokines and cells. Therefore, it is imperative to explore a reliable and efficient computational method to identify cytokines associated with CRS. In this study, we propose Meta-DHGNN, a directed and heterogeneous graph neural network analysis method based on meta-learning. The proposed method integrates both directed and heterogeneous algorithms, while the meta-learning module effectively addresses the issue of limited data availability. This approach enables comprehensive analysis of the cytokine network and accurate prediction of CRS-related cytokines. Firstly, to tackle the challenge posed by small datasets, a pre-training phase is conducted using the meta-learning module. Consequently, the directed algorithm constructs an adjacency matrix that accurately captures potential relationships in a more realistic manner. Ultimately, the heterogeneous algorithm employs meta-photographs and multi-head attention mechanisms to enhance the realism and accuracy of predicting cytokine information associated with positive labels. Our experimental verification on the dataset demonstrates that Meta-DHGNN achieves favorable outcomes. Furthermore, based on the predicted results, we have explored the multifaceted formation mechanism of CRS in CAR-T therapy from various perspectives and identified several cytokines, such as IFNG (IFN-γ), IFNA1, IFNB1, IFNA13, IFNA2, IFNAR1, IFNAR2, IFNGR1 and IFNGR2 that have been relatively overlooked in previous studies but potentially play pivotal roles. The significance of Meta-DHGNN lies in its ability to analyze directed and heterogeneous networks in biology effectively while also facilitating CRS risk prediction in CAR-T therapy.

PrCRS: a prediction model of severe CRS in CAR-T therapy based on transfer learning.

BACKGROUND: CAR-T cell therapy represents a novel approach for the treatment of hematologic malignancies and solid tumors. However, its implementation is accompanied by the emergence of potentially life-threatening adverse events known as cytokine release syndrome (CRS). Given the escalating number of patients undergoing CAR-T therapy, there is an urgent need to develop predictive models for severe CRS occurrence to prevent it in advance. Currently, all existing models are based on decision trees whose accuracy is far from meeting our expectations, and there is a lack of deep learning models to predict the occurrence of severe CRS more accurately. RESULTS: We propose PrCRS, a deep learning prediction model based on U-net and Transformer. Given the limited data available for CAR-T patients, we employ transfer learning using data from COVID-19 patients. The comprehensive evaluation demonstrates the superiority of the PrCRS model over other state-of-the-art methods for predicting CRS occurrence. We propose six models to forecast the probability of severe CRS for patients with one, two, and three days in advance. Additionally, we present a strategy to convert the model's output into actual probabilities of severe CRS and provide corresponding predictions. CONCLUSIONS: Based on our findings, PrCRS effectively predicts both the likelihood and timing of severe CRS in patients, thereby facilitating expedited and precise patient assessment, thus making a significant contribution to medical research. There is little research on applying deep learning algorithms to predict CRS, and our study fills this gap. This makes our research more novel and significant. Our code is publicly available at https://github.com/wzy38828201/PrCRS . The website of our prediction platform is: http://prediction.unicar-therapy.com/index-en.html .

ILGBMSH: an interpretable classification model for the shRNA target prediction with ensemble learning algorithm.

Short hairpin RNA (shRNA)-mediated gene silencing is an important technology to achieve RNA interference, in which the design of potent and reliable shRNA molecules plays a crucial role. However, efficient shRNA target selection through biological technology is expensive and time consuming. Hence, it is crucial to develop a more precise and efficient computational method to design potent and reliable shRNA molecules. In this work, we present an interpretable classification model for the shRNA target prediction using the Light Gradient Boosting Machine algorithm called ILGBMSH. Rather than utilizing only the shRNA sequence feature, we extracted 554 biological and deep learning features, which were not considered in previous shRNA prediction research. We evaluated the performance of our model compared with the state-of-the-art shRNA target prediction models. Besides, we investigated the feature explanation from the model's parameters and interpretable method called Shapley Additive Explanations, which provided us with biological insights from the model. We used independent shRNA experiment data from other resources to prove the predictive ability and robustness of our model. Finally, we used our model to design the miR30-shRNA sequences and conducted a gene knockdown experiment. The experimental result was perfectly in correspondence with our expectation with a Pearson's coefficient correlation of 0.985. In summary, the ILGBMSH model can achieve state-of-the-art shRNA prediction performance and give biological insights from the machine learning model parameters.

Infectious Keratitis After Keratorefractive Surgery: Update and Review of the Literature.

OBJECTIVES: To summarize the clinical manifestations, microbiological profile, treatment, and prognosis of corneal infections after different keratorefractive surgery. METHODS: To obtain relevant studies, English-language databases, including PubMed, Ovid Embase, Web of Science, and CLNAHL, were searched from January 1979 to March 2022. The fundamentals of the literature, clinical characteristics, pathogens, and treatments were retrieved for each included article. RESULTS: Eighty-four studies involving 306 infectious eyes were included in this review. Risk factors of potential infection included a history of blepharitis, contact lens usage, and contaminated surgical instruments. The mean onset time was 22.9±38.7 days (range: 1 day to 3 years). The most common organism isolated from infectious keratitis after keratorefractive surgery were Staphylococcus aureus , followed by Mycobacterium and coagulase-negative Staphylococcus . Most of the infections after refractive procedures were sensitive to medical treatment alone, and the ultimate best-corrected visual acuity after medical treatment was as follows: 20/20 or better in 82 cases (37.0%), 20/40 or better in 170 cases (76.5%), and worse than 20/40 in 52 cases (23.5%). Surgical interventions including flap lift, flap amputation, ring removal, and keratoplasty were performed in 120 eyes (44.5%). CONCLUSIONS: Most infections after keratorefractive surgery occur within a week, whereas more than half of the cases after laser-assisted in situ keratomileusis happen after about a month. Gram-positive cocci and mycobacterium are the most common isolates. Infections after LASIK, intracorneal ring (ICR) implantation, and small incision lenticule extraction, which primarily occur between the cornea layers, require irrigation of the tunnels or pocket with antibiotics.

Sense of community improves community participation in Chinese residential communities: The mediating role of sense of community responsibility and prosocial tendencies.

Community participation is essential for community development and enhancing quality of life. Several studies have focused on the relationship between sense of community (SOC) and community participation in organizational settings. Guided by the community experiences framework, this study aims to examine how a SOC improves community participation in Chinese residential communities. Moreover, the study aims to assess the mediating role of SOC responsibility (SOC-R) and prosocial tendencies in that relationship. A sample of 433 residents completed questionnaires regarding their SOC, sense of community responsibility, prosocial tendencies, and community participation. Using a linear regression model, we found that a SOC can positively predict the level of community participation. Mediation effect analysis revealed that a SOC-R mediated the relationship between SOC and community participation. In addition, prosocial tendencies mediated the association between the SOC and community participation. Using multiple mediation analysis, we found that SOC-R and prosocial tendencies mediated the link between a SOC and community participation in a sequential manner. The findings of this study complement existing research by uncovering the mechanism underlying the relationship between a SOC and community participation.

Investigation of CRS-associated cytokines in CAR-T therapy with meta-GNN and pathway crosstalk.

BACKGROUND: Chimeric antigen receptor T-cell (CAR-T) therapy is a new and efficient cellular immunotherapy. The therapy shows significant efficacy, but also has serious side effects, collectively known as cytokine release syndrome (CRS). At present, some CRS-related cytokines and their roles in CAR-T therapy have been confirmed by experimental studies. However, the mechanism of CRS remains to be fully understood. METHODS: Based on big data for human protein interactions and meta-learning graph neural network, we employed known CRS-related cytokines to comprehensively investigate the CRS associated cytokines in CAR-T therapy through protein interactions. Subsequently, the clinical data for 119 patients who received CAR-T therapy were examined to validate our prediction results. Finally, we systematically explored the roles of the predicted cytokines in CRS occurrence by protein interaction network analysis, functional enrichment analysis, and pathway crosstalk analysis. RESULTS: We identified some novel cytokines that would play important roles in biological process of CRS, and investigated the biological mechanism of CRS from the perspective of functional analysis. CONCLUSIONS: 128 cytokines and related molecules had been found to be closely related to CRS in CAR-T therapy, where several important ones such as IL6, IFN-γ, TNF-α, ICAM-1, VCAM-1 and VEGFA were highlighted, which can be the key factors to predict CRS.

Effect of artificial tears on dynamic optical quality in patients with dry eye disease.

BACKGROUND: In clinical practice, fluctuating vision or decreased quality of vision is a common complaint in DED patients. Our study was designed to investigate the change in dynamic optical quality in dry eye patients after the use of artificial tears. METHODS: Fifty-nine patients with dry eye disease (DED) and 31 control subjects were included in this prospective case-control study. There was no significant difference in age and sex between these two groups (P = 0.342, P = 0.847, respectively). Clinical evaluation of the ocular surface included Ocular Surface Disease Index (OSDI), tear film break-up time (TBUT), lipid layer thickness (LLT), and Schirmer I test. DED patients were divided into two groups, mild (31 patients) and severe (28 patients). The optical quality of the tear film was measured with the Optical Quality Analysis System (OQAS) using the mean objective scatter index (mean OSI), standard deviation of objective scatter index (SD-OSI) and modulation transfer function cut-off (MTF cut-off). After baseline examinations, one drop of artificial tears (ATs, carboxymethylcellulose ophthalmic solution, 0.5%) was instilled in both eyes, and optical quality parameters were measured again at 5 and 30 min following application of ATs. RESULTS: At baseline, the mean OSI was higher in the DED group (0.95 ± 0.54) than in controls (0.54 ± 0.23, P < 0.001). The SD-OSI was also significantly increased in DED patients (0.44 ± 0.71) compared to control subjects (0.12 ± 0.06, P = 0.003). Five minutes after AT instillation, mean OSI and SD-OSI decreased significantly in severe DED patients (P = 0.044; P = 0.018), remained unchanged in mild DED patients, and increased in the control group (P = 0.019; P < 0.001). Thirty minutes after AT instillation, no significant difference in optical quality parameters was observed among the three groups. CONCLUSION: The effect of ATs on optical quality in patients with DED may differ according to the severity of the disease. Measurement of optical quality might be a promising tool to evaluate the effects of various ATs and possibly individualize treatment in DED patients.

Lipoid Proteinosis presenting as beaded papules of the eyelid: report of three cases.

BACKGROUND: Lipoid proteinosis (LP) is a rare multisystem inherited disease. We report here in three LP cases with beaded papules of the eyelid. Their clinical presentations, histological characteristics, and genetic findings are described and discussed. CASE PRESENTATION: A 12-year-old boy reported to our hospital with a complaint of ocular irritation, redness, and tearing for two years. He had a history of hoarseness since childhood. His younger brother (5 years old) also complained of hoarseness. Another patient, a 26-year-old woman, described many beaded papules on the edge of her eyelids since age 11 years. She additionally reported hoarseness since 4 years of age. Careful slit-lamp examination in these cases revealed waxy beaded papules on the margins of both eyelids and mild conjunctival congestion. Physical examination showed irregular, rugged scars on their facial skin. Genetic analysis showed the mutation located in exon 6 of the ECM1 gene. CONCLUSIONS: Three LP cases first diagnosed by ophthalmologists are presented. The presence of eyelid papules should prompt the ophthalmologist to pay close attention to the patient's voice. If there is a definite history of hoarseness, these patients should undergo gene sequence analysis. If necessary, otorhinolaryngology and dermatology consults may help confirm the diagnosis. Treatment is primarily symptomatic to improve patients' quality of life.

Fabrication and Characterization of Flexible Capacitive Humidity Sensors Based on Graphene Oxide on Porous PTFE Substrates.

Porous polytetrafluoroethylene (PTFE) is physically flexible, thermally and chemically stable, relatively inexpensive, and commercially available. It is attractive for various flexible sensors. This paper has studied flexible capacitive humidity sensors fabricated on porous PTFE substrates. Graphene oxide (GO) was used as a sensing material, both hydrophobic and hydrophilic porous PTFE as the substrates, and interdigitated electrodes on the PTFE substrates were screen-printed. SEM and Raman spectrum were utilized to characterize GO and PTFE. An ethanol soak process is developed to increase the yield of the humidity sensors based on hydrophobic porous PTFE substrates. Static and dynamic properties of these sensors are tested and analyzed. It demonstrates that the flexible capacitive humidity sensors fabricated on the ethanol-treated hydrophobic PTFE exhibit high sensitivity, small hysteresis, and fast response/recovery time.

A Novel High-Q Dual-Mass MEMS Tuning Fork Gyroscope Based on 3D Wafer-Level Packaging.

Tuning fork gyroscopes (TFGs) are promising for potential high-precision applications. This work proposes and experimentally demonstrates a novel high-Q dual-mass tuning fork microelectromechanical system (MEMS) gyroscope utilizing three-dimensional (3D) packaging techniques. Except for two symmetrically decoupled proof masses (PM) with synchronization structures, a symmetrically decoupled lever structure is designed to force the antiparallel, antiphase drive mode motion and eliminate low frequency spurious modes. Thermoelastic damping (TED) and anchor loss are greatly reduced by the linearly coupled, momentum- and torque-balanced antiphase sense mode. Moreover, a novel 3D packaging technique is used to realize high Q-factors. A composite substrate encapsulation cap, fabricated by through-silicon-via (TSV) and glass-in-silicon (GIS) reflow processes, is anodically bonded to the wafer-scale sensing structures. A self-developed control circuit is adopted to realize loop control and characterize gyroscope performances. It is shown that a high-reliability electrical connection, together with a high air impermeability package, can be fulfilled with this 3D packaging technique. Furthermore, the Q-factors of the drive and sense modes reach up to 51,947 and 49,249, respectively. This TFG realizes a wide measurement range of ±1800 °/s and a high resolution of 0.1°/s with a scale factor nonlinearity of 720 ppm after automatic mode matching. In addition, long-term zero-rate output (ZRO) drift can be effectively suppressed by temperature compensation, inducing a small angle random walk (ARW) of 0.923°/√h and a low bias instability (BI) of 9.270°/h.

Autologous Serum Eye Drops versus Artificial Tear Drops for Dry Eye Disease: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

OBJECTIVE: To compare the efficacy of autologous serum (AS) eye drops and artificial tears (AT) in dry eye disease (DED). METHODS: Five databases (PubMed, Science Direct, the Cochrane Library, the Chinese National Knowledge Infrastructure, and the Wanfang Database) were searched for randomized controlled trials (RCTs). Efficacy was evaluated in terms of the Ocular Surface Disease Index (OSDI), Schirmer I test, tear break-up time (TBUT), and fluorescein and rose bengal staining of ocular surface. The estimated effects of AS or AT were expressed as a proportion with the 95% confidence interval and plotted on a forest plot. RESULTS: Seven RCTs with 267 subjects were included in the meta-analysis. For most of the studies, subjects' age was around 50 years old, and the mostly treatment duration was within 8 weeks. The follow-up results showed that the OSDI after AS treatment was lower than that after the AT treatment: the mean difference (MD) was -10.75 (95% CI, -18.12; -3.39) points. There was no difference on the Schirmer I test after treatment between the two groups: the MD was 1.68 (95% CI, -0.65; 4.00) mm. The TBUT of the AS group was longer than that of the AT group, with an MD of 4.53 (95% CI, 2.02; 7.05) s. There was no statistically significant difference on fluorescein staining score of the ocular surface between the AS group and the AT group, the MD was -2.53 (95% CI, -6.08; 1.03) points. The rose bengal staining score of the AS group was slightly lower than that of the AT group after treatment: the MD was -0.78 (95% CI, -1.34; -0.22) points. CONCLUSION: AS could be an effective treatment for DED, improving OSDI, TBUT, and rose bengal staining score. Further RCTs with large samples and long-term follow-up are still needed to determine the exact role of AS in the management of DED.

Down-regulation of the long noncoding RNA-HOX transcript antisense intergenic RNA inhibits the occurrence and progression of glioma.

This study aims to explore the role of long noncoding RNA (lncRNA)-HOX transcript antisense intergenic RNA (HOTAIR) in the occurrence and progression of glioma. Fresh glioma and normal brain tissues were classified into a glioma group (n = 67) and a normal group (n = 64) respectively. U87 cells were assigned into the blank, sh-NC, and sh-HOTAIR groups. Quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to determine HOTAIR expression. Cell proliferation, cell cycle and cell apoptosis rates were detected by cell counting kit-8 (CCK-8) and flow cytometry (FCM). Scratch test and transwell assay were conducted for cell migration and invasion. Orthotopic glioma tumor model in nude mice was established by inoculating tumor cell suspension. Hematoxylin-Eosin (HE) staining was used to observe the growth and invasion of orthotopic glioma tumors. The expression of HOTAIR and cell viability was found to be lowest in the sh-HOTAIR group among the three groups. The sh-HOTAIR group exhibited a higher apoptotic rate and lower number of cell migration compared with the blank and sh-NC groups. Additionally, the speed of wound healing was slower, the migration distance decreased and the survival time of nude mice was extended in the sh-HOTAIR compared to the other groups. Moreover, the sh-HOTAIR group demonstrated reduced lesion sizes and inflammation, no convulsions or hemiplegia and lesser number of satellite metastases. Our findings support that down-regulation of HOTAIR could inhibit cell proliferation, promote cell apoptosis as well as suppress cell invasion and migration in the progression of glioma.

Serum S-100ß and NSE levels after off-pump versus on-pump coronary artery bypass graft surgery.

BACKGROUND: We aimed to evaluate serum levels of S-100 beta (S-100ß) and neuron specific enolase (NSE) in patients with coronary heart disease (CHD) after off-pump versus on-pump coronary artery bypass graft (CABG) surgery. METHODS: The PubMed (~2013) and the Chinese Biomedical Database (CBM) (1982 ~ 2013) were searched without language restrictions. After extraction of relevant data from selected studies, meta-analyses were conducted using STATA software (Version 12.0, Stata Corporation, College Station, Texas USA). Possible sources of heterogeneity were examined through univariate and multivariate meta-regression analyses and verified by Monte Carlo Simulation. RESULTS: Eleven studies with a total of 411 CHD patients met the inclusion criteria. Our meta-analysis showed no significant difference in serum S-100ß and NSE levels between the on-pump group and the off-pump group before surgery. In the on-pump group, there was a significant difference in serum S-100ß levels of CHD patients between before and after surgery, especially within the first 24 h after surgery. Furthermore, in the on-pump group, there was a significant difference in serum NSE levels of CHD patients between before and after surgery, particularly at 0 h after surgery. In the off-pump group, there was an obvious difference in serum S-100ß levels between before and after surgery, especially within 24 h after surgery. Our results also demonstrated that serum S-100ß and NSE levels of CHD patients in the on-pump group were significantly higher than those of patients in the off-pump group, especially within 24 h after surgery. CONCLUSIONS: Our findings provide empirical evidence that off-pump and on-pump CABG surgeries may increase serum S-100ß and NSE levels in CHD patients, which was most prominent within 24 h after on-pump CABG surgery.

Predictors of early neurological deterioration in patients with acute ischemic stroke.

Background: The present study aimed to develop a reliable and straightforward Nomogram by integrating various parameters to accurately predict the likelihood of early neurological deterioration (END) in patients with acute ischemic stroke (AIS). Methods: Acute ischemic stroke patients from Shaoxing People's Hospital, Shanghai Yangpu District Shidong Hospital, and Shanghai Fifth People's Hospital were recruited based on specific inclusion and exclusion criteria. The primary outcome was END. Using the LASSO logistic model, a predictive Nomogram was generated. The performance of the Nomogram was evaluated using the ROC curve, the Hosmer-Lemeshow test, and a calibration plot. Additionally, the decision curve analysis was conducted to assess the effectiveness of the Nomogram. Results: It was found that the Nomogram generated in the present study showed strong discriminatory performance in both the training and the internal validation cohorts when their ROC-AUC values were 0.715 (95% CI 0.648-0.782) and 0.725 (95% CI 0.631-0.820), respectively. Similar results were observed in two external validation cohorts when their ROC-AUC values were 0.685 (95% CI 0.541-0.829) and 0.673 (95% CI 0.545-0.800), respectively. In addition, CAD, SBP, neutrophils, TBil, and LDL were found to be positively correlated with the occurrence of END post-stroke, while lymphocytes and UA were negatively correlated. Conclusion: Our study developed a novel Nomogram that includes CAD, SBP, neutrophils, lymphocytes, TBil, UA, and LDL and it demonstrated strong discriminatory performance in identifying AIS patients who are likely to develop END.

Corneal Epithelial Dendritic Cells: An Objective Indicator for Ocular Surface Inflammation in Patients with Obstructive Meibomian Gland Dysfunction?

PURPOSE: To examine whether corneal epithelial dendritic cells (CEDC) could serve as an indicator to distinguish obstructive meibomian gland dysfunction (MGD) with or without ocular surface inflammation (OSI). METHODS: We performed a case-control study on patients with diagnosed obstructive MGD between August 2017 and November 2019. RESULTS: 30 MGD cases and 25 healthy controls were recruited. The classification of MGD patients with and without OSI was based on the tear pro-inflammatory cytokine levels. Compared with the MGD without OSI and the control group, a higher CEDC density was detected in the MGD with OSI subgroup. The presence of >15.6 cells/mm2 CEDC had a sensitivity of 73% and specificity of 75% for the diagnosis of MGD with OSI. CONCLUSIONS: OSI is not present in all patients with obstructive MGD. Evaluation of CEDC density in the central cornea may help identify whether MGD is concomitant with OSI.

Whole Genome Sequencing Highlights the Pathogenic Profile in Nocardia Keratitis.

Purpose: Nocardia keratitis is a serious and sight-threatening condition. This study aims to reveal the virulence and antimicrobial resistance gene profile of Nocardia strains using whole genome sequencing. Methods: Whole-genome sequencing was performed on 23 cornea-derived Nocardia strains. Together with genomic data from the respiratory tract and the environment, 141 genomes were then utilized for phylogenetic and pan-genome analyses, followed by virulence and antibiotic resistance analysis. The correlations between virulence genes and pathogenicity were experimentally validated, including the characteristics of Nocardia colonies and clinical and histopathological evaluations of Nocardia keratitis mice models. Results: Whole-genome sequencing of 141 Nocardia strains revealed a mean of 220 virulence genes contributed to bacterial pathogenesis. The mce gene family analysis led to the categorization of strains from the cornea into groups A, B, and C. The colonies of group C had the largest diameter, height, and fastest growth rate. The size of corneal ulcers and the clinical scores showed a significant increase in mouse models induced by group C. The relative expression levels of pro-inflammatory cytokines (CD4, IFN-γ, IL-6Rα, and TNF-α) in the lesion area exhibited an increasing trend from group A to group C. Antibiotic resistance genes (ARGs) spanned nine distinct drug classes, four resistance mechanisms, and seven primary antimicrobial resistance gene families. Conclusions: Whole genome sequencing highlights the pathogenic role of mce gene family in Nocardia keratitis. Its distribution pattern may contribute to the distinct characteristics of the growth of Nocardia colonies and the clinical severity of the mice models.

Corrigendum: Prediction of severe CRS and determination of biomarkers in B cell-acute lymphoblastic leukemia treated with CAR-T cells.

[This corrects the article DOI: 10.3389/fimmu.2023.1273507.].

Acanthamoeba Keratitis in China: Genotypic and Clinical Correlations.

Purpose: To investigate the relationship between Acanthamoeba genotypes, clinical manifestations, and outcomes in Acanthamoeba keratitis (AK) patients. Methods: This retrospective study included 159 culture-confirmed AK patients. Patients' data were collected, including demographics, initial diagnosis, treatments, and clinical features. The genotype of Acanthamoeba was identified through sequencing the Diagnostic Fragment 3 (DF3) region in the small ribosomal subunit RNA genes. The phylogenetic tree was constructed using the ClustalW model and maximum likelihood method. Cases with "poor outcome" were defined based on specific clinical criteria, including corneal perforation, keratoplasty, other eye surgery, duration of anti-amoebic therapy ≥8.0 months, and final visual acuity ≤20/80. "Better outcome" cases were the remainder. The correlation between T4 subtypes, clinical phenotypes, and clinical prognosis were further analyzed. Results: In this study, AK was primarily attributed to the T4A genotype, with a positive correlation between geographical and genetic distances. The primary clinical associated with T4 subtypes was deep stromal infiltration. Results was also showed a significant association between T4 subtypes and clinical outcomes (P = 0.021). Further analysis revealed that T4C was closely associated with a better prognosis (P = 0.040) and T4D with worse outcomes (P = 0.013). Conclusions: In China, AK was predominantly caused by the T4A subtype. Geographical distance positively correlated with genetic distance. Clinical prognosis varied among different subtypes, notably in T4C and T4D. Translational Relevance: This study demonstrated the association between T4 subtypes and clinical phenotypes, as well as the effects of T4 subtypes on clinical prognosis.

A suitable and efficient optimization system for the culture of chlamydia trachomatis in adult inclusion conjunctivitis.

The prevalence of Chlamydia trachomatis infection in the genitourinary tract is increasing, with an annual rise of 9 million cases. Individuals afflicted with these infections are at a heightened risk of developing adult inclusive conjunctivitis (AIC), which is commonly recognized as the ocular manifestation of this sexually transmitted infection. Despite its significant clinical implications, the lack of distinctive symptoms and the overlap with other ocular conditions often lead to underdiagnosis or misdiagnosis of AIC associated with C. trachomatis infection. Here, we established six distinct C. trachomatis culture cell lines, specifically highlighting the MA104 N*V cell line that exhibited diminished expression of IRF3 and STAT1, resulting in reduced interferons. Infected MA104 N*V cells displayed the highest count of intracytoplasmic inclusions detected through immunofluorescence staining, peaking at 48 hours post-infection. Subsequently, MA104 N*V cells were employed for clinical screening in adult patients diagnosed with AIC. Among the evaluated cohort of 20 patients, qPCR testing revealed positive results in seven individuals, indicating the presence of C. trachomatis infection. Furthermore, the MA104 N*V cell cultures derived from these infected patients demonstrated successful cultivation and replication of the pathogen, confirming its viability and infectivity. Molecular genotyping identified four distinct urogenital serovars, with serovar D being the most prevalent (4/7), followed by E (1/7), F (1/7), and Ia (1/7). This novel cellular model contributes to studies on C. trachomatis pathogenesis, molecular mechanisms, and host-pathogen interactions both in vitro and in vivo. It also aids in acquiring clinically relevant strains critical for advancing diagnostics, treatments, and vaccines against C. trachomatis.