A high-performance broadband phototransistor array of a PdSe2/SOI Schottky junction.

There is great interest in the incorporation of novel two-dimensional materials into Si-based technologies to realize multifunctional optoelectronic devices via heterogeneous integration. Here, we demonstrate a gate-tunable, self-driven, high-performance broadband phototransistor array based on a PdSe2/Si Schottky junction, which is fabricated by pre-depositing a semi-metallic PdSe2 film on a SOI substrate. In addition, thanks to the zero bandgap of the PdSe2 material and the PdSe2/Si vertical heterostructure, the prepared phototransistor exhibits pronounced photovoltaic properties in a wide spectral range from ultraviolet to near-infrared. The responsivity, specific detectivity and response time of the device at the incident light wavelength of 808 nm are 1.15 A W-1, 9.39 × 1010 Jones, and 27.1/40.3 µs, respectively, which are better than those of previously reported PdSe2-based photodetectors. The photoelectric performance can be further improved by applying an appropriate gate voltage to the phototransistor and the responsivity of the device increases to 1.61 A W-1 at VG = 5 V. We demonstrate the excellent imaging capabilities of a 4 × 4 array image sensor using PdSe2/SOI phototransistors under 375 nm, 532 nm, and 808 nm laser sources.

Defining Porphyromonas gingivalis strains associated with periodontal disease.

Porphyromonas gingivalis, a Gram-negative anaerobic bacterium commonly found in human subgingival plaque, is a major etiologic agent for periodontitis and has been associated with multiple systemic pathologies. Many P. gingivalis strains have been identified and different strains possess different virulence factors. Current oral microbiome approaches (16S or shotgun) have been unable to differentiate P. gingivalis strains. This study presents a new approach that aims to improve the accuracy of strain identification, using a detection method based on sequencing of the intergenic spacer region (ISR) which is variable between P. gingivalis strains. Our approach uses two-step PCR to amplify only the P. gingivalis ISR region. Samples are then sequenced with an Illumina sequencer and mapped to specific strains. Our approach was validated by examining subgingival plaque from 153 participants with and without periodontal disease. We identified the avirulent strain ATCC33277/381 as the most abundant strain across all sample types. The W83/W50 strain was significantly enriched in periodontitis, with 13% of participants harboring that strain. Overall, this approach can have significant implications not only for the diagnosis and treatment of periodontal disease but also for other diseases where P. gingivalis or its toxins have been implicated, such as Alzheimer's disease.

Alcohol Consumption and the Diversity of the Oral Microbiome in Postmenopausal Women.

BACKGROUND: Alcohol reduces neutrophil function and decreases salivary flow, which could affect the composition of the oral microbiome. OBJECTIVE: We hypothesized that the α- and ß-diversity of the oral microbiome and the relative abundance of bacterial taxa would differ by frequency and type of alcohol consumption. METHODS: We used a food frequency questionnaire to assess the frequency of consumption of beer, wine, and liquor (drinks/week) in a sample of 1179 postmenopausal women in the Osteoporosis and Periodontal Disease Study. Women were categorized as nondrinkers, drinking <1 drink/wk, ≥1 to <7 drinks/wk, or ≥7 drinks/wk for total alcohol consumption and for beer, wine, and liquor consumption. The composition and diversity of the oral microbiome was assessed from subgingival plaque samples using 16S ribosomal RNA amplicon sequencing. Permutational multivariate analysis of variance (PERMANOVA) was used to examine ß-diversity (between-sample diversity) in the microbiome between alcohol consumption categories. Analysis of covariance was used to examine the mean α-diversity (within-sample diversity), assessed by the Shannon index (species evenness), Chao1 index (species richness), and observed operational taxonomic unit (OTU) count and the mean relative abundance of 245 bacterial taxa across alcohol consumption categories. RESULTS: Over half of the participants (67%) consumed alcohol, with 14% reporting ≥1 drink/d. The ß-diversity across categories of total alcohol consumption, but not categories of alcohol type, was statistically significantly different (P for PERMANOVA = 0.016). Mean α-diversity measures were statistically significantly higher (P < 0.05) in the highest category of total alcohol and wine consumption compared to nondrinkers; no significant associations were found for beer or liquor consumption. The relative abundance of 1 OTU, Selenomonassp._oral_taxon_133, was significantly lower in the highest level of total alcohol consumption compared to nondrinkers after adjustment for multiple comparisons. CONCLUSIONS: Alcohol consumption was associated with the diversity and composition of the subgingival microbiome.

Thickness effect of 2D PdSe2film on performance of PdSe2/Si heterostructure photodetectors.

Two-dimensional (2D) PdSe2film has the characteristics of adjustable bandgap, high carrier mobility, and high stability. Photodetector (PD) based on 2D PdSe2exhibits wide spectral self-driving features, demonstrating enormous potential in the field of optical detection. Here, we design and fabricate PdSe2/Si heterojunction PDs with various thicknesses of the PdSe2films from 10 to 35 nm. Due to the enhancement of light absorption capacity and built-in electric field of heterojunction, the photodetector with thicker PdSe2film can generate more photo-generated carriers and effectively separate them to form a large photocurrent, thus showing more excellent photodetection performance. The responsivity and specific detectivity of the PdSe2/Si PDs with 10 nm, 20 nm, and 35 nm PdSe2films are 2.12 A W-1and 6.72 × 109Jones, 6.17 A W-1and 1.95 × 1010Jones, and 8.02 A W-1and 2.54 × 1010Jones, respectively (808 nm illumination). The PD with 35 nm PdSe2film exhibits better performance than the other two PDs, with the rise/fall times of 15.8µs/138.9µs atf= 1 kHz and the cut-off frequency of 8.6 kHz. Furthermore, we demonstrate that the properties of PdSe2/Si PD array have excellent uniformity and stability at room temperature and shows potential for image sensing in the UV-vis-NIR wavelength range.

Identifying Significantly Perturbed Subnetworks in Cancer Using Multiple Protein-Protein Interaction Networks.

BACKGROUND: The identification of cancer driver genes and key molecular pathways has been the focus of large-scale cancer genome studies. Network-based methods detect significantly perturbed subnetworks as putative cancer pathways by incorporating genomics data with the topological information of PPI networks. However, commonly used PPI networks have distinct topological structures, making the results of the same method vary widely when applied to different networks. Furthermore, emerging context-specific PPI networks often have incomplete topological structures, which pose serious challenges for existing subnetwork detection algorithms. METHODS: In this paper, we propose a novel method, referred to as MultiFDRnet, to address the above issues. The basic idea is to model a set of PPI networks as a multiplex network to preserve the topological structure of individual networks, while introducing dependencies among them, and, then, to detect significantly perturbed subnetworks on the modeled multiplex network using all the structural information simultaneously. RESULTS: To illustrate the effectiveness of the proposed approach, an extensive benchmark analysis was conducted on both simulated and real cancer data. The experimental results showed that the proposed method is able to detect significantly perturbed subnetworks jointly supported by multiple PPI networks and to identify novel modular structures in context-specific PPI networks.

Design, synthesis and evaluation of dihydro-1H-indene derivatives as novel tubulin polymerisation inhibitors with anti-angiogenic and antitumor potency.

Angiogenesis plays an important role in tumour generation and progression, which is used to supply nutrients and metastasis. Herein, a series of novel dihydro-1H-indene derivatives were designed and evaluated as tubulin polymerisation inhibitors by binding to colchicine site, exhibiting anti-angiogenic activities against new vessel forming. Through structure-activity relationships study, compound 12d was found to be the most potent derivative possessing the antiproliferative activity against four cancer lines with IC50 values among 0.028-0.087 µM. Compound 12d bound to colchicine site on tubulin and inhibited tubulin polymerisation in vitro. In addition, compound 12d induced cell cycle arrest at G2/M phase, stimulated cell apoptosis, inhibited tumour metastasis and angiogenesis. Finally, the results of in vivo assay suggested that compound 12d could prevent tumour generation, inhibit tumour proliferation and angiogenesis without obvious toxicity. Collectively, all these findings suggested that compound 12d is a novel tubulin polymerisation inhibitor deserving further research.

A systematic review and bibliometric study of Bertolotti's syndrome: clinical characteristics and global trends.

PURPOSE: Bertolotti's syndrome is a prevalent congenital deformity. However, many physicians fail to include it in their differential diagnosis for low back pain (LBP), which results in missed diagnosis or misdiagnosis. There is still a lack of standardized treatment and management strategies for Bertolotti's syndrome. This study aimed to review the clinical characteristics and management of Bertolotti's syndrome and reports bibliometric insights in advancements in Bertolotti's syndrome research. METHODS: Studies published until 30 September 2022 were systematically reviewed according to the PRISMA guidelines. Three independent reviewers extracted the data and assessed the quality and risk of bias of the studies based on the methodological index of non-randomized studies (MINORS). SPSS, VOS viewer, and the Citespace software were used for the systematic review, visual analysis, data mining, mapping, and clustering of the retrieved articles, which presented clear and visual presentations of the structural patterns of published research in graphs. RESULT: A total of 118 articles, describing a total of 419 patients with Bertolotti's syndrome, were included. There was an upward trend with a steady increase in the number of publications. The world map distribution showed that most publications were predominantly from North America and Asia. The most cited articles were published in the following journals: Spine, J Bone Joint Surg, and Radiology. The mean age of the patients was 47.7 years, and 49.6% of them were male. A total of 159 (96.4%) patients had LBP symptoms. The mean symptom duration was 41.4 months (74.8%), and most of the patients had Castellvi type II. Disc degeneration was the most reported comorbid spinal diseases. The mean methodological index of non-randomized studies score was 4.16±3.95 points (range, 1-21). A total of 265 (68.3%) patients underwent surgical treatments. Minimally invasive surgical techniques, prevalence, image classification, and disc degeneration were the current main research areas of Bertolotti's syndrome. CONCLUSIONS: The steady increase in the number of publications demonstrated the increased attention of researchers on this topic. Our results showed a significant prevalence of Bertolotti's syndrome in patients with LBP and a long symptom duration before the initiation of treatment. Surgical treatments were commonly used to treat patients with Bertolotti's syndrome after a non-effective conservative treatment. Minimally invasive surgical techniques, prevalence, image classification, and disc degeneration are the major research areas of Bertolotti's syndrome.

KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing.

Mitochondrial U-indel RNA editing in kinetoplastid protozoa is directed by trans-acting gRNAs and mediated by a holoenzyme with associated factors. Here, we examine the function of the holoenzyme-associated KREH1 RNA helicase in U-indel editing. We show that KREH1 knockout (KO) impairs editing of a small subset of mRNAs. Overexpression of helicase-dead mutants results in expanded impairment of editing across multiple transcripts, suggesting the existence of enzymes that can compensate for KREH1 in KO cells. In depth analysis of editing defects using quantitative RT-PCR and high-throughput sequencing reveals compromised editing initiation and progression in both KREH1-KO and mutant-expressing cells. In addition, these cells exhibit a distinct defect in the earliest stages of editing in which the initiator gRNA is bypassed, and a small number of editing events takes place just outside this region. Wild type KREH1 and a helicase-dead KREH1 mutant interact similarly with RNA and holoenzyme, and overexpression of both similarly disorders holoenzyme homeostasis. Thus, our data support a model in which KREH1 RNA helicase activity facilitates remodeling of initiator gRNA-mRNA duplexes to permit accurate utilization of initiating gRNAs on multiple transcripts.

[Analysis of continuous polysomnography in children with recurrent vertigo].

Objective:To explore the relationship between sleep status and the disease in children with recurrent vertigo（RVC） by analyzing the objective sleep condition of children with recurrent vertigo. Methods:According to the diagnostic criteria of RVC, 50 children with RVC and 20 normal controls without RVC were selected. According to the vertigo questionnaire score, the RVC group was divided into mild, moderate and severe groups according to severity. Continuous polysomnography（PSG） was performed for all participants, and SPSS 25.0 statistical software was used to analyze the monitoring results. Results:①There were significant differences in sleep time of each period, total sleep time and sleep efficiency between RVC group and control group（P<0.05）, but there was no significant difference in sleep latency（P>0.05）. The specific manifestations were that the proportion of sleep time in N1 and N2 phases increased, the proportion of sleep time in N3 and REM phases decreased, the total sleep time and sleep efficiency decreased in RVC group. ②The abnormal rate of sleep apnea hypopnea index, that is, the proportion of AHI≥5 times/h and the abnormal rate of lowest blood oxygen saturation in RVC group were higher than those in normal control group. There was significant difference between the two groups（P<0.05）. ③There were significant differences in the proportion of AHI≥5 times/h and lowest SpO2 among mild group, moderate group and severe group（P<0.05）. ④There was no significant correlation between the degree of vertigo and the abnormal rate of AHI in children with RVC, but there was a negative correlation between the degree of vertigo and the abnormal rate of lowest SpO2 in children with RVC. Conclusion:Children with RVC are often accompanied by sleep disorders, clinicians should pay attention to both the symptoms of vertigo and sleep condition in children. Polysomnography is non-invasive and operable, providing a new idea to the auxiliary examination of RVC in children. It is of certain clinical significance for the comprehensive treatment of children with RVC to actively improve vertigo symptoms and pay attention to improving sleep quality.

Dose titration of sacubitril/valsartan for heart failure with reduced ejection fraction: a real-world study.

AIMS: The study aims to explore the real-world titration patterns of sacubitril/valsartan in a chronic heart failure (HF) follow-up management system and the effect on the recovery of ventricular remodelling and cardiac function in China. METHODS AND RESULTS: This is a single-centre, observational study of 153 adult outpatients with HF and reduced ejection fraction who were managed in the chronic HF follow-up management system and prescribed with sacubitril/valsartan from August 2017 to August 2021 in China. All patients tried to titrated sacubitril/valsartan to the tolerant dose during follow-up. The primary outcome was the proportion of patients who reached and maintained the target dose of sacubitril/valsartan. The main secondary outcomes were the changes in left atrium diameter, left ventricular end-diastolic diameter (LVEDD), and left ventricular ejection fraction (LVEF) from baseline to 12 months. Among the patients, 69.3% were male, with a median age of 49 years. The baseline systolic blood pressure (SBP) was 117.6 ± 18.3 mmHg before starting the treatment of sacubitril/valsartan. Benefiting from the management system, 117 (76.5%) patients achieved the target dose of sacubitril/valsartan, and the median time to reach the target dose was 3 (IQR 1-5) months. Advanced age and lower SBP may be predictors of failure to reach the target dose. Compared with baseline, standard treatment resulted in a pronounced improvement in left ventricular geometry and cardiac function. The patients showed a significant increase in LVEF [28 (IQR 21-34) % vs. 42 (IQR 37.0-54.3) %, P < 0.001], with a great reduction in left atrium diameter [45 (IQR 40.3-51.0) mm vs. 41 (IQR 37.0-45.3) mm, P < 0.001] and LVEDD [65 (IQR 60.0-70.3) mm vs. 55 (IQR 52-62) mm, P < 0.001] during 12 month follow-up. Of patients, 36.5% had a LVEF ≥50%, 54.1% had LVEF >40%, and 81.1% experienced an increase in LVEF of ≥10%. After 12 month follow-up, the proportion of patients with New York Heart Association classification I or II increased from 41.8% to 96.4%. Additionally, there was a significant improvement in N-terminal pro-B-type natriuretic peptide (P < 0.001). At Month 12, 50% of patients achieved the target dose of beta-blockers. No serious adverse events caused by sacubitril/valsartan were observed during the follow-up. CONCLUSIONS: Optimising HF follow-up management was essential and effective in a real-world clinical setting; the majority could reach the target dose of sacubitril/valsartan within the management system and achieve a remarkable improvement in cardiac function and ventricular remodelling.

Periodontal disease is associated with increased gut colonization of pathogenic Haemophilus parainfluenzae in patients with Crohn's disease.

Intestinal colonization of the oral bacterium Haemophilus parainfluenzae has been associated with Crohn's disease (CD) severity and progression. This study examines the role of periodontal disease (PD) as a modifier for colonization of H. parainfluenzae in patients with CD and explores the mechanisms behind H. parainfluenzae-mediated intestinal inflammation. Fifty subjects with and without CD were evaluated for the presence of PD, and their oral and fecal microbiomes were characterized. PD is associated with increased levels of H. parainfluenzae strains in subjects with CD. Oral inoculation of H. parainfluenzae elicits strain-dependent intestinal inflammation in murine models of inflammatory bowel disease, which is associated with increased intestinal interferon-γ (IFN-γ)+ CD4+ T cells and disruption of the host hypusination pathway. In summary, this study establishes a strain-specific pathogenic role of H. parainfluenzae in intestinal inflammation and highlights the potential effect of PD on intestinal colonization by pathogenic H. parainfluenzae strains in patients with CD.

Climate change and infectious disease: A prologue on multidisciplinary cooperation and predictive analytics.

Climate change impacts global ecosystems at the interface of infectious disease agents and hosts and vectors for animals, humans, and plants. The climate is changing, and the impacts are complex, with multifaceted effects. In addition to connecting climate change and infectious diseases, we aim to draw attention to the challenges of working across multiple disciplines. Doing this requires concentrated efforts in a variety of areas to advance the technological state of the art and at the same time implement ideas and explain to the everyday citizen what is happening. The world's experience with COVID-19 has revealed many gaps in our past approaches to anticipating emerging infectious diseases. Most approaches to predicting outbreaks and identifying emerging microbes of major consequence have been with those causing high morbidity and mortality in humans and animals. These lagging indicators offer limited ability to prevent disease spillover and amplifications in new hosts. Leading indicators and novel approaches are more valuable and now feasible, with multidisciplinary approaches also within our grasp to provide links to disease predictions through holistic monitoring of micro and macro ecological changes. In this commentary, we describe niches for climate change and infectious diseases as well as overarching themes for the important role of collaborative team science, predictive analytics, and biosecurity. With a multidisciplinary cooperative "all call," we can enhance our ability to engage and resolve current and emerging problems.

WITHDRAWN: Characteristics, Treatment and Research Development of Bertolotti's Syndrome: A Bibliometric Analysis and Systematic Review.

This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause.

Association between visceral adiposity index and heart failure: A cross-sectional study.

BACKGROUND: Obesity is an important risk factor for heart failure (HF). HYPOTHESIS: Visceral adiposity index (VAI) is a simple metric for assessing obesity; however, the association between VAI and risk for HF has not been studied. METHODS: A cross-sectional study involving 28 764 participants ≥18 years of age from the National Health and Nutrition Examination Survey (NHANES), 2009-2018, in the United States was performed. VAI was calculated using body mass index (BMI), waist circumference (WC), triglycerides (TG), and high-density lipoprotein cholesterol. VAI was analyzed as a continuous and categorical variable to examine its association with HF. Subgroup analysis was also performed. RESULTS: The highest VAI (fourth quartile [Q4]) was found among males, BMI, systolic and diastolic blood pressure, WC, hypertension, diabetes, liver disease, coronary heart disease, smoking, total cholesterol, and TG. More participants in Q4 took ß-receptor blockers, angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers/angiotensin receptor-neprilysin inhibitor, calcium channel blockers, and antidiabetic and antihyperlipidemic medications. Participants with HF exhibited greater VAI. A per-unit increase in VAI resulted in a 4% increased risk for HF (odds ratio [OR] 1.04 [95% confidence interval (CI) 1.02-1.05]). After multivariable adjustment, compared with the lowest quartile, the OR for Q3 was 1.55 (95% CI 1.24-1.94). Subgroup analysis revealed no significant interactions between VAI and specific subgroups. CONCLUSION: VAI was independently associated with the risk for HF. As a noninvasive index of visceral adiposity, VAI could be used for a "one shot" assessment of HF risk and may serve as a novel marker.

[The value of high intensity stimulation training of semicircular canal of SRM-â £ vertigo diagnosis and treatment system in the rehabilitation of vestibular neuritis].

Objective:To evaluate the value of high intensity stimulation training of semicircular canal of SRM-Ⅳ vertigo diagnosis and treatment system in the rehabilitation of vestibular neuritis. Methods:To analyze 68 patients with vestibular neuritis treated in Department of Otorhinolaryngology Head and Neck Surgery, Shijiazhuang People's Hospital from January 2020 to January 2021, conduct spontaneous nystagmus and head toss test, and perform spontaneous nystagmus and rotation test of SRM-Ⅳvertigo system, compare the positive rate of the side of disease was between the two. To randomly divide 68 patients into treatment group 1, 2 and control group, the control group with drugs, treatment group 1 with drugs and vestibular rehabilitation training exercise, treatment group 2 with additional high intensity stimulation training of semicircular canal at one week after onset, on the basis of drug therapy and vestibular rehabilitation training exercise. At 2 weeks and 1 month, through swivel chair test negative rate, DHI score, compare the efficacy of the three groups. Results:Spontaneous nystagmus combined with head toss test confirmed 80.9% of the side of the disease, spontaneous nystagmus and rotation test of SRM-Ⅳ vertigo system confirmed 100%, the difference is statistically significant（P<0.05）. Compared with the control group and the treatment group 1, the negative conversion rate of the rotation test in the treatment group 2 at the second week and the first month of treatment, the difference is statistically significant（P<0.05, the second week χ²=6.474, the first month χ²=6.245）; the DHI score of treatment group 2 was statistically significant compared with that of control group and treatment group 1 at the second week and first month of treatment（P<0.05, the second week F=13.578, the first month F=28.599）. Conclusion:SRM-Ⅳ vertigo diagnosis and treatment system semicircular canal high intensity stimulation training has a certain role in the rehabilitation treatment of vestibular neuritis. It is simple to operate, patient tolerance and compliance are good, and it is worth promoting.

Alignment-free comparison of metagenomics sequences via approximate string matching.

Summary: Quantifying pairwise sequence similarities is a key step in metagenomics studies. Alignment-free methods provide a computationally efficient alternative to alignment-based methods for large-scale sequence analysis. Several neural network-based methods have recently been developed for this purpose. However, existing methods do not perform well on sequences of varying lengths and are sensitive to the presence of insertions and deletions. In this article, we describe the development of a new method, referred to as AsMac that addresses the aforementioned issues. We proposed a novel neural network structure for approximate string matching for the extraction of pertinent information from biological sequences and developed an efficient gradient computation algorithm for training the constructed neural network. We performed a large-scale benchmark study using real-world data that demonstrated the effectiveness and potential utility of the proposed method. Availability and implementation: The open-source software for the proposed method and trained neural-network models for some commonly used metagenomics marker genes were developed and are freely available at www.acsu.buffalo.edu/~yijunsun/lab/AsMac.html. Supplementary information: Supplementary data are available at Bioinformatics online.

Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing.

Uridine insertion/deletion RNA editing is an extensive post-transcriptional modification of mitochondrial mRNAs in kinetoplastid organisms, including Trypanosoma brucei This process is carried out using trans-acting gRNAs and complex protein machinery. The essential RNA editing substrate binding complex (RESC) serves as the scaffold that modulates protein and RNA interactions during editing, and contains the guide RNA binding complex (GRBC), the RNA editing mediator complexes (REMCs), and organizer proteins. Despite the importance of RESC in editing, the functions of each protein comprising this complex are not completely understood. Here, we further define the roles of a REMC protein, RESC13, and a RESC organizer, RESC14, using high-throughput sequencing on two large pan-edited mRNAs, A6 and COIII. When comparing our analyses to that of a previously published small pan-edited mRNA, RPS12, we find that RESC13 has conserved functions across the three transcripts with regard to editing initiation, gRNA utilization, gRNA exchange, and restricting the formation of long misedited junctions that likely arise from its ability to modulate RNA structure. However, RESC13 does have transcript-specific effects on the types of long junctions whose formation it restricts. RESC14 has a conserved effect on gRNA utilization across the three transcripts analyzed, but has transcript-specific effects on editing initiation, gRNA exchange, and junction formation. Our data suggest that transcript-specific effects of both proteins are due to differences in transcript length and sequences as well as transcript-specific protein interactions. These findings highlight the importance of studying multiple transcripts to determine the function of editing factors.

Computational approach to modeling microbiome landscapes associated with chronic human disease progression.

A microbial community is a dynamic system undergoing constant change in response to internal and external stimuli. These changes can have significant implications for human health. However, due to the difficulty in obtaining longitudinal samples, the study of the dynamic relationship between the microbiome and human health remains a challenge. Here, we introduce a novel computational strategy that uses massive cross-sectional sample data to model microbiome landscapes associated with chronic disease development. The strategy is based on the rationale that each static sample provides a snapshot of the disease process, and if the number of samples is sufficiently large, the footprints of individual samples populate progression trajectories, which enables us to recover disease progression paths along a microbiome landscape by using computational approaches. To demonstrate the validity of the proposed strategy, we developed a bioinformatics pipeline and applied it to a gut microbiome dataset available from a Crohn's disease study. Our analysis resulted in one of the first working models of microbial progression for Crohn's disease. We performed a series of interrogations to validate the constructed model. Our analysis suggested that the model recapitulated the longitudinal progression of microbial dysbiosis during the known clinical trajectory of Crohn's disease. By overcoming restrictions associated with complex longitudinal sampling, the proposed strategy can provide valuable insights into the role of the microbiome in the pathogenesis of chronic disease and facilitate the shift of the field from descriptive research to mechanistic studies.

PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity.

The extracellular activity of Plasminogen activator inhibitor-1 (PAI-1) is well described, acting as an inhibitor of tissue plasminogen activator and urokinase-type plasminogen activator, impacting fibrinolysis. Recent studies have revealed a pro-tumorigenic role of PAI-1 in human cancers, via the regulation of angiogenesis and tumor cell survival. In this study, immunohistochemical staining of 939 human bladder cancer specimens showed that PAI-1 expression levels correlated with tumor grade, tumor stage and overall survival. The typical subcellular localization of PAI-1 is cytoplasmic, but in approximately a quarter of the cases, PAI-1 was observed to be localized to both the tumor cell cytoplasm and the nucleus. To investigate the potential function of nuclear PAI-1 in tumor biology we applied chromatin immunoprecipitation (ChIP)-sequencing, gene expression profiling, and rapid immunoprecipitation mass spectrometry to a pair of bladder cancer cell lines. ChIP-sequencing revealed that PAI-1 can bind DNA at distal intergenic regions, suggesting a role as a transcriptional coregulator. The downregulation of PAI-1 in bladder cancer cell lines caused the upregulation of numerous genes, and the integration of ChIP-sequence and RNA-sequence data identified 57 candidate genes subject to PAI-1 regulation. Taken together, the data suggest that nuclear PAI-1 can influence gene expression programs and support malignancy.

A Diagnostic Gene Expression Signature for Bladder Cancer Can Stratify Cases into Prescribed Molecular Subtypes and Predict Outcome.

Bladder cancer is a biologically heterogeneous disease with variable clinical presentations, outcomes and responses to therapy. Thus, the clinical utility of single biomarkers for the detection and prediction of biological behavior of bladder cancer is limited. We have previously identified and validated a bladder cancer diagnostic signature composed of 10 biomarkers, which has been incorporated into a multiplex immunoassay bladder cancer test, Oncuria™. In this study, we evaluate whether these 10 biomarkers can assist in the prediction of bladder cancer clinical outcomes. Tumor gene expression and patient survival data from bladder cancer cases from The Cancer Genome Atlas (TCGA) were analyzed. Alignment between the mRNA expression of 10 biomarkers and the TCGA 2017 subtype classification was assessed. Kaplan-Meier analysis of multiple gene expression datasets indicated that high expression of the combined 10 biomarkers correlated with a significant reduction in overall survival. The analysis of three independent, publicly available gene expression datasets confirmed that multiplex prognostic models outperformed single biomarkers. In total, 8 of the 10 biomarkers from the Oncuria™ test were significantly associated with either luminal or basal molecular subtypes, and thus, the test has the potential to assist in the prediction of clinical outcome.