Spatial and temporal localization of cell wall associated pili in Enterococcus faecalis.

Enterococcus faecalis virulence requires cell wall-associated proteins, including the sortase-assembled endocarditis and biofilm associated pilus (Ebp), important for biofilm formation in vitro and in vivo. The current paradigm for sortase-assembled pilus biogenesis in Gram-positive bacteria is that sortases attach substrates to lipid II peptidoglycan (PG) precursors, prior to their incorporation into the growing cell wall. Contrary to prevailing dogma, by following the distribution of Ebp and PG throughout the E. faecalis cell cycle, we found that cell surface Ebp do not co-localize with newly synthesized PG. Instead, surface-exposed Ebp are localized to the older cell hemisphere and excluded from sites of new PG synthesis at the septum. Moreover, Ebp deposition on the younger hemisphere of the E. faecalis diplococcus appear as foci adjacent to the nascent septum. We propose a new model whereby sortase substrate deposition can occur on older PG rather than at sites of new cell wall synthesis. Consistent with this model, we demonstrate that sequestering lipid II to block PG synthesis via ramoplanin, does not impact new Ebp deposition at the cell surface. These data support an alternative paradigm for sortase substrate deposition in E. faecalis, in which Ebp are anchored directly onto uncrosslinked cell wall, independent of new PG synthesis.

Tidal Versus Intermittent Peritoneal Dialysis in Chronic Peritoneal Dialysis Patients: Randomized, Open-Label, Prospective Control Study.

BACKGROUND: Tidal peritoneal dialysis (TPD) provides better fluid flow mechanics and is more comfortable for the patient, owing to fewer alarms and less pain during inflow and outflow. The long-term characteristics of patients with TPD were not evident. In this randomized controlled follow-up study, we aimed to explore the characteristics of patients with TPD, compared to IPD. METHODS: A total of 85 patients were randomized to either IPD or 70% TPD between January 2019 and December 2020, and all patients were followed up on December 2021. The characteristics of patients between the two groups were analyzed using a t-test or chi-square as appropriate. The overall survival and technical survival were analyzed using Kaplan-Meier analysis. RESULTS: Forty-two patients were assigned to IPD, and 43 patients were assigned to TPD. The basal characteristics of patients were not different between the two groups. In an average of 16 months of follow-up, 19 patients died, and 25 patients dropped out of peritoneal dialysis. The two groups had no difference in overall survival and technical survival. TPD was associated with high urine volume (p = 0.001), lower blood urea nitrogen (p = 0.002), lower phosphorus (p = 0.004), and fewer cycler alarms (p < 0.001). The chance of patients reporting abdominal fullness was higher in patients with TPD (p = 0.001). CONCLUSION: In the randomized, controlled, follow-up study, TPD may preserve residual renal function and is associated with lower urea nitrogen and phosphorus in chronic peritoneal dialysis patients. TPD is associated with fewer cycler alarms but may increase the chance of patients reporting abdominal distension.

SGLT-2 inhibitors in chronic peritoneal dialysis patients: a follow-up study.

BACKGROUND: Sodium-glucose transporter-2 inhibitors (SGLT-2i) are recommended for use in patients with type 2 diabetes comorbid atherosclerotic cardiovascular disease, heart failure, or chronic kidney disease. Limited reports are currently available for their use in dialysis patients. In an observational, retrospective follow-up study, we reported the clinical characteristics of chronic peritoneal dialysis (PD) patients on SGLT-2i. METHODS: We enrolled 50 diabetic chronic PD patients, and 11 continued SGLT-2i after PD treatment. We reported the patients' ultrafiltration, HbA1c, urinary tract infection episodes, and venous CO2 during follow-up and compared the differences in these factors between patients with and without SGLT-2i. RESULTS: The mean age of the patients was 65 ± 15 years, and 16 (32%) patients were female. The age, gender, heart failure, and primary kidney disease were not different between patients with and without SGLT-2i at enrollment. In an average of 31 months follow-up, patients with SGLT-2i had higher ultrafiltration (1322 ± 200 ml/day vs. 985 ± 415 ml/day, p = 0.013), hemoglobin (11.2 ± 1.7 vs. 10.2 ± 1.7 g/dl), white blood cell count (9.2 ± 3.7 vs. 7.4 ± 2.1 109/L), and a lower venous CO2 (p = 0.036). The urine amount, the overall survival, the technical survival, and the chance of UTI were not different between patients with and without SGLT2i. CONCLUSION: SGLT-2i may increase ultrafiltration volume and hemoglobin levels in chronic PD patients. SGLT-2i did not increase urinary tract infection but was linked to subclinical metabolic acidosis. WHAT WAS KNOWN: The effect of SGLT-2i in chronic PD patients is not clear? THIS STUDY ADDS: SGLT-2i is associated with increased ultrafiltration, hemoglobin, white blood cell counts, and a decreased CO2 in PD patient. POTENTIAL IMPACT: SGLT-2i may increase ultrafiltration in PD patients.

Higher return to sport and lower revision rates when performing arthroscopic Bankart repair with remplissage for anterior shoulder instability with a Hill-Sachs lesion: a meta-analysis.

BACKGROUND: Recurrent anterior shoulder instability remains the most common complication from a prior shoulder dislocation, especially among young and active individuals who engage in athletic activities. This instability can lead to repeated subluxation or dislocations of the humeral head from the glenoid fossa. The purpose of this study is to compare postoperative recurrence rates, instability-related revision and return to sport (RTS) rates between isolated arthroscopic Bankart repair (ABR) and ABR with remplissage (ABR + R) for anterior shoulder instability with subcritical glenoid bone loss (GBL) and a Hill-Sachs lesion (HSL). METHODS: PubMed, Embase, and Web of Science were searched on June 2022. Studies sought were those comparing postoperative outcomes of ABR + R versus isolated ABR for subcritical GBL and an HSL. Study quality was evaluated using the revised Cochrane tool. Redislocations, instability-related revisions, and RTS rates were extracted and pooled estimates were calculated using the random-effect model. RESULTS: Twelve studies were included with a mean follow-up of 48.2 months for isolated ABR and 43.2 months for ABR + R. The meta-analytic comparison demonstrated that ABR + R resulted in statistically significant improvement in Rowe and American Shoulder and Elbow Surgeons scores by 6.5 and 2.2 points, respectively; however, the improvements in patient-reported outcomes were not clinically meaningful. ABR + R resulted in reduced external rotation at the side by 1° which was not clinically meaningful and there was no significant difference in terms of forward elevation. ABR + R resulted in a statistically significant reduction of overall postoperative recurrences (odds ratio [OR]: 9.36), postoperative dislocations (OR: 6.28), instability-related revision (OR: 3.46), and RTS to any level (OR: 2.85). CONCLUSION: The addition of remplissage to ABR for recurrent anterior shoulder instability with subcritical GBL and HSL results in significantly lower postoperative instability recurrence, lower instability-related revisions, and higher RTS to any level.

A Stem-like Patient-Derived Ovarian Cancer Model of Platinum Resistance Reveals Dissociation of Stemness and Resistance.

To understand chemoresistance in the context of cancer stem cells (CSC), a cisplatin resistance model was developed using a high-grade serous ovarian cancer patient-derived, cisplatin-sensitive sample, PDX4. As a molecular subtype-specific stem-like cell line, PDX4 was selected for its representative features, including its histopathological and BRCA2 mutation status, and exposed to cisplatin in vitro. In the cisplatin-resistant cells, transcriptomics were carried out, and cell morphology, protein expression, and functional status were characterized. Additionally, potential signaling pathways involved in cisplatin resistance were explored. Our findings reveal the presence of distinct molecular signatures and phenotypic changes in cisplatin-resistant PDX4 compared to their sensitive counterparts. Surprisingly, we observed that chemoresistance was not inherently linked with increased stemness. In fact, although resistant cells expressed a combination of EMT and stemness markers, functional assays revealed that they were less proliferative, migratory, and clonogenic-features indicative of an underlying complex mechanism for cell survival. Furthermore, DNA damage tolerance and cellular stress management pathways were enriched. This novel, syngeneic model provides a valuable platform for investigating the underlying mechanisms of cisplatin resistance in a clinically relevant context, contributing to the development of targeted therapies tailored to combat resistance in stem-like ovarian cancer.

Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of the BDF2 mRNA.

The expression of bromodomain-containing proteins that regulate chromatin structure and accessibility must be tightly controlled to ensure the appropriate regulation of gene expression. In the yeast S. cerevisiae, Bromodomain Factor 2 (BDF2) expression is extensively regulated post-transcriptionally during stress by RNase III-mediated decay (RMD), which is triggered by cleavage of the BDF2 mRNA in the nucleus by the RNase III homolog Rnt1p. Previous studies have shown that RMD-mediated down-regulation of BDF2 is hyperactivated in osmotic stress conditions, yet the mechanisms driving the enhanced nuclear cleavage of BDF2 RNA under these conditions remain unknown. Here, we show that RMD hyperactivation can be detected in multiple stress conditions that inhibit mRNA export, and that Rnt1p remains primarily localized in the nucleus during salt stress. We show that globally inhibiting mRNA nuclear export by anchoring away mRNA biogenesis or export factors out of the nucleus can recapitulate RMD hyperactivation in the absence of stress. RMD hyperactivation requires Rnt1p nuclear localization but does not depend on the BDF2 gene endogenous promoter, and its efficiency is affected by the structure of the stem-loop cleaved by Rnt1p. Because multiple stress conditions have been shown to mediate global inhibition of mRNA export, our results suggest that the hyperactivation of RMD is primarily the result of the increased nuclear retention of the BDF2 mRNA during stress.

Flexible, high-resolution cortical arrays with large coverage capture microscale high-frequency oscillations in patients with epilepsy.

OBJECTIVE: Effective surgical treatment of drug-resistant epilepsy depends on accurate localization of the epileptogenic zone (EZ). High-frequency oscillations (HFOs) are potential biomarkers of the EZ. Previous research has shown that HFOs often occur within submillimeter areas of brain tissue and that the coarse spatial sampling of clinical intracranial electrode arrays may limit the accurate capture of HFO activity. In this study, we sought to characterize microscale HFO activity captured on thin, flexible microelectrocorticographic (µECoG) arrays, which provide high spatial resolution over large cortical surface areas. METHODS: We used novel liquid crystal polymer thin-film µECoG arrays (.76-1.72-mm intercontact spacing) to capture HFOs in eight intraoperative recordings from seven patients with epilepsy. We identified ripple (80-250 Hz) and fast ripple (250-600 Hz) HFOs using a common energy thresholding detection algorithm along with two stages of artifact rejection. We visualized microscale subregions of HFO activity using spatial maps of HFO rate, signal-to-noise ratio, and mean peak frequency. We quantified the spatial extent of HFO events by measuring covariance between detected HFOs and surrounding activity. We also compared HFO detection rates on microcontacts to simulated macrocontacts by spatially averaging data. RESULTS: We found visually delineable subregions of elevated HFO activity within each µECoG recording. Forty-seven percent of HFOs occurred on single 200-µm-diameter recording contacts, with minimal high-frequency activity on surrounding contacts. Other HFO events occurred across multiple contacts simultaneously, with covarying activity most often limited to a .95-mm radius. Through spatial averaging, we estimated that macrocontacts with 2-3-mm diameter would only capture 44% of the HFOs detected in our µECoG recordings. SIGNIFICANCE: These results demonstrate that thin-film microcontact surface arrays with both highresolution and large coverage accurately capture microscale HFO activity and may improve the utility of HFOs to localize the EZ for treatment of drug-resistant epilepsy.

Editorial Commentary: Fascia Lata Allograft for Shoulder Superior Capsular Reconstruction: In the Fight Over Optimal Graft Choice for Irreparable Rotator Cuff Tears, Superior Capsular Reconstruction Proponents May Be Changing Their Gloves.

Optimal treatment of irreparable rotator cuff tears is still debated. Proponents of the superior capsule reconstruction (SCR) have previously used fascia lata autograft and acellular dermal allograft. Interest is growing in using fascia lata allograft as a new graft material. Well-designed biomechanical studies are important to understand the mechanical properties of the superior capsular tissue and fascia lata allograft. Recent biomechanical research shows that fascia lata allograft has similar initial stiffness (over the first 2 mm) and ultimate load compared to the native superior capsule. That said, ultimate load is the load at which a construct fails, whereas the yield point is the load on the stress-strain curve at which a material transitions from elastic to plastic deformation. In the shoulder where the SCR, for example, is going to be repetitively loaded, it is potentially more meaningful to talk about the yield point in order to stay within the elastic range. Using this framework, the yield point for fascia lata allograft is approximately one third the yield point of native capsular tissue. Additionally, "initial" stiffness is not the entire story. At greater loads, fascia lata allograft has higher displacement compared to native tissue. Of importance, fascia lata allograft failed by sutures slowly cutting through the allograft tissue; this may represent a limitation of the construct that could be addressed using stitch configurations resistant to cut through. Fascia lata allograft is a promising solution for SCR. Biomechanical studies require nuanced interpretation, and most of all, do not evaluate clinical healing.

Association Between Physical Activity and Sedentary Behavior With Depressive Symptoms Among US High School Students, 2019.

INTRODUCTION: The prevalence of depression among US adolescents has increased during the past decade. Previous studies found relationships among physical activity, sedentary behavior, and depression, but more recent information is needed to inform research and practice. We used national surveillance data to assess the association of physical activity and sedentary behavior with depressive symptoms among US high school students. METHODS: This study included 13,526 high school students from the 2019 Youth Risk Behavior Survey. The dependent variable was the presence of depressive symptoms in the past year that lasted almost every day for at least 2 weeks in a row and interfered with usual activities. The independent variables were physical activity (overall activity, muscle-strengthening exercises, participation on sports teams) and sedentary behavior (watching television, using a computer or digital device). We used weighted multivariable logistic regression to evaluate the association of physical activity and sedentary behavior variables with depressive symptoms, while controlling for demographic characteristics and other health behaviors. RESULTS: The prevalence of depressive symptoms was 36.7%. Participating in physical activity 5 or more days in the past 7 days (adjusted odds ratio [aOR], 0.81; 95% CI, 0.68-0.97) and participating on 1 or more sports teams in the past year (aOR, 0.66; 95% CI, 0.55-0.78) were associated with reduced odds of depressive symptoms. Using a computer or digital device for 3 or more hours per school night was associated with higher odds of reporting depressive symptoms (aOR, 1.61; 95% CI, 1.41-1.85). CONCLUSION: Inadequate physical activity and excessive sedentary behavior are associated with depressive symptoms among US high school students. Interventions targeting physical activity and sedentary behavior may be a public health strategy to reduce depressive symptoms in this population.

Machine learning-based triage to identify low-severity patients with a short discharge length of stay in emergency department.

BACKGROUND: Overcrowding in emergency departments (ED) is a critical problem worldwide, and streaming can alleviate crowding to improve patient flows. Among triage scales, patients labeled as "triage level 3" or "urgent" generally comprise the majority, but there is no uniform criterion for classifying low-severity patients in this diverse population. Our aim is to establish a machine learning model for prediction of low-severity patients with short discharge length of stay (DLOS) in ED. METHODS: This was a retrospective study in the ED of China Medical University Hospital (CMUH) and Asia University Hospital (AUH) in Taiwan. Adult patients (aged over 20 years) with Taiwan Triage Acuity Scale level 3 were enrolled between 2018 and 2019. We used available information during triage to establish a machine learning model that can predict low-severity patients with short DLOS. To achieve this goal, we trained five models-CatBoost, XGBoost, decision tree, random forest, and logistic regression-by using large ED visit data and examined their performance in internal and external validation. RESULTS: For internal validation in CMUH, 33,986 patients (75.9%) had a short DLOS (shorter than 4 h), and for external validation in AUH, there were 13,269 (82.7%) patients with short DLOS. The best prediction model was CatBoost in internal validation, and area under the receiver operating cha racteristic curve (AUC) was 0.755 (95% confidence interval (CI): 0.743-0.767). Under the same threshold, XGBoost yielded the best performance, with an AUC value of 0.761 (95% CI: 0.742- 0.765) in external validation. CONCLUSIONS: This is the first study to establish a machine learning model by applying triage information alone for prediction of short DLOS in ED with both internal and external validation. In future work, the models could be developed as an assisting tool in real-time triage to identify low-severity patients as fast track candidates.

Nail plate combination in the upper extremity: surgical technique and clinical application.

Nail plate constructs (NPC) have shown promising results in complex lower extremity peri-articular fractures as well as in peri-prosthetic fractures. The combination of both implants allows for improved mechanical stability and immediate weight bearing. The use of NPC has not been described in the upper extremity in the literature. We herein describe potential indications and surgical technique for NPC usage for complex upper extremity trauma and reconstruction.

Association of diabetes, education level, and care dependency with use of temporary vascular access in patients with chronic kidney disease.

OBJECTIVE: Temporary vascular access (TVA) is frequently used during the first dialysis in patients with chronic kidney disease (CKD), and it is associated with an increased risk of infection, central vein stenosis, and mortality. Here, factors associated with TVA in patients with CKD were explored. METHODS: This study included patients in a single-center CKD care program who initiated long-term renal replacement therapy. The primary outcome was TVA use at first dialysis. Factors possibly associated with TVA use were analyzed using Cox regression. RESULTS: Temporary vascular access was used in 53.2% of the patients at first dialysis. In total, 73.2% (n = 865) and 26.8% (n = 317) of the patients were on hemodialysis and peritoneal dialysis, respectively. Multivariate Cox regression analysis showed that TVA use in patients with CKD was associated with diabetes (hazard ratio [HR] 1.52, 95% confidence interval [CI] 1.28-1.81, p < 0.001), lower albumin (HR 0.82, 95% CI 0.75-0.91, p < 0.001), lower education level (HR 0.75, 95% CI 0.56-1.00, p = 0.055), and total care dependency (HR 1.92, CI 1.44-3.43, p = 0.003). CONCLUSION: Diabetes, education level, and care dependency are associated with TVA at dialysis initiation in patients with CKD.

ABC transporter content diversity in Streptococcus pneumoniae impacts competence regulation and bacteriocin production.

The opportunistic pathogen Streptococcus pneumoniae (pneumococcus) uses natural genetic competence to increase its adaptability through horizontal gene transfer. One method of acquiring DNA is through predation of neighboring strains with antimicrobial peptides called "bacteriocins." Competence and production of the major family of pneumococcal bacteriocins, pneumocins, are regulated by the quorum-sensing systems com and blp, respectively. In the classical paradigm, the ABC transporters ComAB and BlpAB each secretes its own system's signaling pheromone and in the case of BlpAB also secretes the pneumocins. While ComAB is found in all pneumococci, only 25% of strains encode an intact version of BlpAB [BlpAB(+)] while the rest do not [BlpAB(-)]. Contrary to the classical paradigm, it was previously shown that BlpAB(-) strains can activate blp through ComAB-mediated secretion of the blp pheromone during brief periods of competence. To better understand the full extent of com-blp crosstalk, we examined the contribution of each transporter to competence development and pneumocin secretion. We found that BlpAB(+) strains have a greater capacity for competence activation through BlpAB-mediated secretion of the com pheromone. Similarly, we show that ComAB and BlpAB are promiscuous and both can secrete pneumocins. Consequently, differences in pneumocin secretion between BlpAB(+) and BlpAB(-) strains derive from the regulation and kinetics of transporter expression rather than substrate specificity. We speculate that BlpAB(-) strains (opportunists) use pneumocins mainly in a narrowly tailored role for DNA acquisition and defense during competence while BlpAB(+) strains (aggressors) expand their use for the general inhibition of rival strains.

Conductively coupled flexible silicon electronic systems for chronic neural electrophysiology.

Materials and structures that enable long-term, intimate coupling of flexible electronic devices to biological systems are critically important to the development of advanced biomedical implants for biological research and for clinical medicine. By comparison with simple interfaces based on arrays of passive electrodes, the active electronics in such systems provide powerful and sometimes essential levels of functionality; they also demand long-lived, perfect biofluid barriers to prevent corrosive degradation of the active materials and electrical damage to the adjacent tissues. Recent reports describe strategies that enable relevant capabilities in flexible electronic systems, but only for capacitively coupled interfaces. Here, we introduce schemes that exploit patterns of highly doped silicon nanomembranes chemically bonded to thin, thermally grown layers of SiO2 as leakage-free, chronically stable, conductively coupled interfaces. The results can naturally support high-performance, flexible silicon electronic systems capable of amplified sensing and active matrix multiplexing in biopotential recording and in stimulation via Faradaic charge injection. Systematic in vitro studies highlight key considerations in the materials science and the electrical designs for high-fidelity, chronic operation. The results provide a versatile route to biointegrated forms of flexible electronics that can incorporate the most advanced silicon device technologies with broad applications in electrical interfaces to the brain and to other organ systems.

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.

Complementing genome sequence with deep transcriptome and proteome data could enable more accurate assembly and annotation of newly sequenced genomes. Here, we provide a proof-of-concept of an integrated approach for analysis of the genome and proteome of Anopheles stephensi, which is one of the most important vectors of the malaria parasite. To achieve broad coverage of genes, we carried out transcriptome sequencing and deep proteome profiling of multiple anatomically distinct sites. Based on transcriptomic data alone, we identified and corrected 535 events of incomplete genome assembly involving 1196 scaffolds and 868 protein-coding gene models. This proteogenomic approach enabled us to add 365 genes that were missed during genome annotation and identify 917 gene correction events through discovery of 151 novel exons, 297 protein extensions, 231 exon extensions, 192 novel protein start sites, 19 novel translational frames, 28 events of joining of exons, and 76 events of joining of adjacent genes as a single gene. Incorporation of proteomic evidence allowed us to change the designation of more than 87 predicted "noncoding RNAs" to conventional mRNAs coded by protein-coding genes. Importantly, extension of the newly corrected genome assemblies and gene models to 15 other newly assembled Anopheline genomes led to the discovery of a large number of apparent discrepancies in assembly and annotation of these genomes. Our data provide a framework for how future genome sequencing efforts should incorporate transcriptomic and proteomic analysis in combination with simultaneous manual curation to achieve near complete assembly and accurate annotation of genomes.

Repeated centrifuging and washing concentrates bacterial samples in peritoneal dialysis for optimal culture: an original article.

BACKGROUND: Bacterial cultures allow the identification of infectious disease pathogens. However, obtaining the results of conventional culture methods is time-consuming, taking at least two days. A more efficient alternative is the use of concentrated bacterial samples to accelerate culture growth. Our study focuses on the development of a high-yield sample concentrating technique. RESULTS: A total of 71 paired samples were obtained from patients on peritoneal dialysis (PD). The peritoneal dialysates were repeat-centrifuged and then washed with saline, namely the centrifuging and washing method (C&W method). The concentrated samples were Gram-stained and inoculated into culture plates. The equivalent unprocessed dialysates were cultured as the reference method. The times until culture results for the two methods were compared. The reference method yielded no positive Gram stain results, but the C&W method immediately gave positive Gram stain results for 28 samples (p < 0.001). The culture-negative rate was lower in the C&W method (5/71) than in the reference method (13/71) (p = 0.044). The average time for bacterial identification achieved with the C&W method (22.0 h) was shorter compared to using the reference method (72.5 h) (p < 0.001). CONCLUSIONS: The C&W method successfully concentrated bacterial samples and superseded blood culture bottles for developing adequate bacterial cultures. The C&W method may decrease the culture report time, thus improving the treatment of infectious diseases.

Text mining in a literature review of urothelial cancer using topic model.

BACKGROUND: Urothelial cancer (UC) includes carcinomas of the bladder, ureters, and renal pelvis. New treatments and biomarkers of UC emerged in this decade. To identify the key information in a vast amount of literature can be challenging. In this study, we use text mining to explore UC publications to identify important information that may lead to new research directions. METHOD: We used topic modeling to analyze the titles and abstracts of 29,883 articles of UC from Pubmed, Web of Science, and Embase in Mar 2020. We applied latent Dirichlet allocation modeling to extract 15 topics and conducted trend analysis. Gene ontology term enrichment analysis and Kyoto encyclopedia of genes and genomes pathway analysis were performed to identify UC related pathways. RESULTS: There was a growing trend regarding UC treatment especially immune checkpoint therapy but not the staging of UC. The risk factors of UC carried in different countries such as cigarette smoking in the United State and aristolochic acid in Taiwan and China. GMCSF, IL-5, Syndecan-1, ErbB receptor, integrin, c-Met, and TRAIL signaling pathways are the most relevant biological pathway associated with UC. CONCLUSIONS: The risk factors of UC may be dependent on the countries and GMCSF, IL-5, Syndecan-1, ErbB receptor, integrin, c-Met, and TRAIL signaling pathways are the most relevant biological pathway associated with UC. These findings may provide further UC research directions.

Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina.

The website and database https://snengs.nichd.nih.gov provides RNA sequencing data from multi-species analysis of the pineal glands from zebrafish (Danio rerio), chicken (White Leghorn), rat (Rattus novegicus), mouse (Mus musculus), rhesus macaque (Macaca mulatta), and human (Homo sapiens); in most cases, retinal data are also included along with results of the analysis of a mixture of RNA from tissues. Studies cover day and night conditions; in addition, a time series over multiple hours, a developmental time series and pharmacological experiments on rats are included. The data have been uniformly re-processed using the latest methods and assemblies to allow for comparisons between experiments and to reduce processing differences. The website presents search functionality, graphical representations, Excel tables, and track hubs of all data for detailed visualization in the UCSC Genome Browser. As more data are collected from investigators and improved genomes become available in the future, the website will be updated. This database is in the public domain and elements can be reproduced by citing the URL and this report. This effort makes the results of 21st century transcriptome profiling widely available in a user-friendly format that is expected to broadly influence pineal research.

Optimizing the electronic medical record to improve patient care and conduct quality improvement initiatives in a concussion specialty clinic.

Objective: To use the electronic medical record (EMR) to optimize patient care, facilitate documentation, and support quality improvement and practice-based research in a concussion (mild traumatic brain injury; mTBI) clinic.Methods: We built a customized structured clinical documentation support (SCDS) toolkit for patients in a concussion specialty clinic. The toolkit collected hundreds of fields of discrete, standardized data. Autoscored and interpreted score tests include the Generalized Anxiety Disorder 7-item scale, Center for Epidemiology Studies Depression scale, Insomnia Severity Index, and Glasgow Coma Scale. Additionally, quantitative score measures are related to immediate memory, concentration, and delayed recall. All of this data collection occurred in a standard appointment length.Results: To date, we evaluated 619 patients at an initial office visit after an mTBI. We provided a description of our toolkit development process, and a summary of the data electronically captured using the toolkit.Conclusions: The electronic medical record can be used to effectively structure and standardize care in a concussion clinic. The toolkit supports the delivery of care consistent with Best Practices, provides opportunities for point of care decision support, and writes comprehensive progress notes that can be communicated to other providers.

Identification of most influential co-occurring gene suites for gastrointestinal cancer using biomedical literature mining and graph-based influence maximization.

BACKGROUND: Gastrointestinal (GI) cancer including colorectal cancer, gastric cancer, pancreatic cancer, etc., are among the most frequent malignancies diagnosed annually and represent a major public health problem worldwide. METHODS: This paper reports an aided curation pipeline to identify potential influential genes for gastrointestinal cancer. The curation pipeline integrates biomedical literature to identify named entities by Bi-LSTM-CNN-CRF methods. The entities and their associations can be used to construct a graph, and from which we can compute the sets of co-occurring genes that are the most influential based on an influence maximization algorithm. RESULTS: The sets of co-occurring genes that are the most influential that we discover include RARA - CRBP1, CASP3 - BCL2, BCL2 - CASP3 - CRBP1, RARA - CASP3 - CRBP1, FOXJ1 - RASSF3 - ESR1, FOXJ1 - RASSF1A - ESR1, FOXJ1 - RASSF1A - TNFAIP8 - ESR1. With TCGA and functional and pathway enrichment analysis, we prove the proposed approach works well in the context of gastrointestinal cancer. CONCLUSIONS: Our pipeline that uses text mining to identify objects and relationships to construct a graph and uses graph-based influence maximization to discover the most influential co-occurring genes presents a viable direction to assist knowledge discovery for clinical applications.