Early Prediction of Mortality for Septic Patients Visiting Emergency Room Based on Explainable Machine Learning: A Real-World Multicenter Study

BACKGROUND

Worldwide, sepsis is the leading cause of death in hospitals. If mortality rates in patients with sepsis can be predicted early, medical resources can be allocated efficiently. We constructed machine learning (ML) models to predict the mortality of patients with sepsis in a hospital emergency department.

METHODS

This study prospectively collected nationwide data from an ongoing multicenter cohort of patients with sepsis identified in the emergency department. Patients were enrolled from 19 hospitals between September 2019 and December 2020. For acquired data from 3,657 survivors and 1,455 deaths, six ML models (logistic regression, support vector machine, random forest, extreme gradient boosting [XGBoost], light gradient boosting machine, and categorical boosting [CatBoost]) were constructed using fivefold cross-validation to predict mortality. Through these models, 44 clinical variables measured on the day of admission were compared with six sequential organ failure assessment (SOFA) components (PaO2/FIO2 [PF], platelets (PLT), bilirubin, cardiovascular, Glasgow Coma Scale score, and creatinine). The confidence interval (CI) was obtained by performing 10,000 repeated measurements via random sampling of the test dataset. All results were explained and interpreted using Shapley's additive explanations (SHAP).

RESULTS

Of the 5,112 participants, CatBoost exhibited the highest area under the curve (AUC) of 0.800 (95% CI, 0.756-0.840) using clinical variables. Using the SOFA components for the same patient, XGBoost exhibited the highest AUC of 0.678 (95% CI, 0.626-0.730). As interpreted by SHAP, albumin, lactate, blood urea nitrogen, and international normalization ratio were determined to significantly affect the results. Additionally, PF and PLTs in the SOFA component significantly influenced the prediction results.

CONCLUSION

Newly established ML-based models achieved good prediction of mortality in patients with sepsis. Using several clinical variables acquired at the baseline can provide more accurate results for early predictions than using SOFA components. Additionally, the impact of each variable was identified.

In-Advance Prediction of Pressure Ulcers via Deep-Learning-Based Robust Missing Value Imputation on Real-Time Intensive Care Variables

Pressure ulcers (PUs) are a prevalent skin disease affecting patients with impaired mobility and in high-risk groups. These ulcers increase patients' suffering, medical expenses, and burden on medical staff. This study introduces a clinical decision support system and verifies it for predicting real-time PU occurrences within the intensive care unit (ICU) by using MIMIC-IV and in-house ICU data. We develop various machine learning (ML) and deep learning (DL) models for predicting PU occurrences in real time using the MIMIC-IV and validate using the MIMIC-IV and Kangwon National University Hospital (KNUH) dataset. To address the challenge of missing values in time series, we propose a novel recurrent neural network model, GRU-D++. This model outperformed other experimental models by achieving the area under the receiver operating characteristic curve (AUROC) of 0.945 for the on-time prediction and AUROC of 0.912 for 48h in-advance prediction. Furthermore, in the external validation with the KNUH dataset, the fine-tuned GRU-D++ model demonstrated superior performances, achieving an AUROC of 0.898 for on-time prediction and an AUROC of 0.897 for 48h in-advance prediction. The proposed GRU-D++, designed to consider temporal information and missing values, stands out for its predictive accuracy. Our findings suggest that this model can significantly alleviate the workload of medical staff and prevent the worsening of patient conditions by enabling timely interventions for PUs in the ICU.

Factors influencing organised faecal occult blood test screening participation in culturally and linguistically diverse populations: a scoping review

OBJECTIVE

This review aims to provide a comprehensive overview of the literature examining factors influencing participation in organised faecal occult blood test (FOBT) screening programmes in culturally and linguistically diverse populations. This article addresses gaps in the literature by providing a mixed methods review of the multilevel influences on FOBT screening in culturally and linguistically diverse (CALD) populations. This review was guided by the question "What are the factors influencing participation in organised FOBT screening programs in CALD populations?"

STUDY DESIGN

Scoping review.

METHODS

A scoping review methodology was used to summarise the available evidence. A thematic analysis of the included studies was undertaken to identify factors influencing organised FOBT screening participation in CALD populations from the literature.

RESULTS

FOBT screening participation was lower by ethnicity, religion, birthplace and language spoken. Barriers to screening included, faecal aversion, fatalism, fear of cancer, language and literacy barriers, difficulty accessing translated materials and low colorectal screening knowledge and awareness. CALD populations also had lower perceived benefits, susceptibility and cues to action, higher perceived barriers and greater perceived external health locus control than non-CALD populations. Facilitators of screening included positive attitudes to screening, general practitioner recommendations and social support. Group education sessions and narrative-based screening information were found to increase screening participation.

CONCLUSION

This review highlights the range of interrelated factors influencing participation in organised FOBT screening programmes in CALD populations and proposes multicomponent interventions to address low screening uptake. Features of successful community-level interventions should be explored further. Narratives show promise for engaging CALD populations. Accessibility of screening information should be addressed at the system level. Leveraging the general practitioner relationship in promoting FOBT screening programmes may also be an effective strategy to target 'hard-to-reach' populations.

Transverse bunch-by-bunch feedback system for time-resolved experiments at PLS-II

A description of the upgraded bunch-by-bunch feedback system for time-resolved experiments at Pohang Light Source II (PLS-II) is provided. The bunch-by-bunch feedback system has been upgraded to increase the single-bunch current in the hybrid fill pattern of the PLS-II facility. The project is part of the SPring-8 and PLS-II collaboration. The main features of the upgrade are to employ a single 500 MHz analog-to-digital converter (ADC) instead of the previous four 125 MHz interleaved ADCs for 500 MHz rate, to replace a single-loop two-dimensional feedback with two independent one-dimensional feedback loops, to implement the tune measurement function with a single bunch, and mainly to implement single-bunch and stretcher control. The realization of a 400 mA hybrid fill pattern including a 10 mA single bunch demonstrates the precision of the upgraded bunch-by-bunch feedback system.

Hybrid team based learning-personalised education for teaching epidemiology in public health degrees

Background

University education in Australia and internationally involves teaching diverse students: in terms of age, life experience, previous degrees completed, and level of English competency. In Australia the Bachelors of Public Health (BPH) at The University of Wollongong, epidemiology is a core subject. It aims to equip students with the knowledge and skills needed to design, critique and interpret studies that investigate why different populations experience different health outcomes. A student-centred learning strategy; Hybrid Team Based Learning and Personalised Education teaching strategy (HTBL-PE) was created to maximise academic success. Each phase has a distinct purpose based on learning theories (e.g. TBL, Bloom's taxonomy and Vygotsky). HTBL-PE aims to systematically build students abilities; strengthen self-confidence and belief, by teaching the way students learn and harnessing the capabilities of the team to strengthen the individual.

Objectives

HTBL-PE was evaluated in spring 2019 in the BPH, where their experiences at the beginning and end of semester were measured.

Results

In total 73 out of 84 enrolled students provided data at both time-points (87%). At the end of the semester, the vast majority of students indicated their interest in epidemiology had increased (93%), critical thinking had improved (92%), and confidence as independent learners had increased (86%). Outcomes did not differ significantly by gender or across learning styles. More than two thirds of students had already applied learnings from this subject in other settings (67%). Students' final mark for this subject was significantly higher than their Weighted Average Mark (WAM) prior to the semester (+17.4, p < 0.001). Average scores for the subject were > 84/100 with a < 0.5% failure rate.

Conclusions

HTBL-PE has positive learning outcomes; low failure rates, increased confidence in learning and themselves, increased interest in epidemiology and high overall scores in the subject.

Key messages

An effective new innovative teaching strategy resulted in a subject average score > 84/100 and <0.5% failure rate. The vast majority of students reported increased confidence as independent lifelong learners, critical thinking, confidence in epidemiology (knowledge, skills, and attitudes) and themselves.

Differences in Colorectal Cancer (CRC) patients who did and did not undergo screening

Background

The Australian National Bowel Cancer Screening Program (NBSCP) is a free population-based screening program which aims to identify precancerous lesions and early colorectal cancer (CRC) using an immunochemical faecal occult blood test in average risk Australians. Formally commencing in 2006, NBCSP participation rate in eligible 50-74-year-old people was 42% in 2018. The barriers and facilitators of participation in the NBCSP have been explored for the general, at-risk population but not in a population of CRC patients. This is the first study to assess a population of CRC patients, post diagnosis, who would have been eligible for CRC screening to determine the barriers and facilitators to screening.

Methods

A cross sectional study nested within a cohort study. Data from CRC patients who participated in the 45 and Up Study; the largest cohort study in Australia and southern hemisphere, were analysed to compare those who had and had not participated in CRC screening. Logistic regression analyses were conducted using RStudio (version 3.5.2, Boston, Massachusetts, USA.). Multiple Imputation (MI), was used to handle missing values assumed to be missing at random.

Results

A total of 339 CRC patients were included. Patients who were female, overweight (≥25kg/m2), consumed less than the recommended five servings of vegetables per day, consumed less than or equal to fourteen standard drinks per week (compared to non-drinkers) or did not meet physical activity guidelines were significantly less likely to have participated in screening.

Conclusions

Our study has taken a unique approach to identifying a high-risk group by exploring factors to screening participation in CRC patients. CRC patients with less healthy lifestyles were less likely to participate in screening. In contrast to previous studies, female patients were less likely to participate in screening than males were. This was an unexpected finding and should be replicated.

Key messages

Not surprising that those with less healthy lifestyle practices also reflected less than ideal screening practices. Surprising that female patients participated less in screening than males. Future interventions to improve CRC screening participation rates should consider specialised messaging for average-risk females who are overweight not meeting dietary or physical activity guidelines.

Percentage volume of delayed kinetics in computer-aided diagnosis of MRI of the breast to reduce false-positive results and unnecessary biopsies

AIM

To investigate the best cut-off percentage volume of delayed kinetics using magnetic resonance imaging (MRI) with computer-aided diagnosis (CAD) to reduce unnecessary biopsies in patients with newly diagnosed breast cancer.

MATERIALS AND METHODS

Between January 2017 and December 2018, 94 malignant and 56 benign masses were analysed using MRI CAD. All malignant and benign masses measured <2 cm and were confirmed histopathologically. The optimal cut-off values for washout, plateau, and persistent components were determined using the maximum Youden Index. The positive predictive value (PPV) was analysed using morphological descriptors and combining the percentage volume of delayed kinetics.

RESULTS

The area under the curve (AUC) was highest at ≤73% persistent component (AUC=0.759). In the subgroup analyses of masses <1 cm, the AUC was highest a plateau of >26% (AUC=0.697). When the persistent ≤73% criterion was applied to the lesions of C4a, the positive predictive value (PPV) increased from 61.9% to 72.44% with reduced false-negative cases and when applied to the lesions of C4a and C4b, the PPV increased from 61.9% to 78.1% with slightly increased false-negative cases. For subcentimetre lesions, the PPV increased from 46.77% to 54.72% with the same number of false-negative cases, when a plateau of >26% was applied to C4a, and the PPV increased from 46.77% to 61.36% with five false-negative cases when applied to C4a and C4b.

CONCLUSION

The percentage volume of delayed kinetics has the potential to improve the PPV of breast MRI. When suspicious masses <2 cm do not show ≤73% persistence, follow-up rather than biopsy could be considered; however, to avoid increasing false-negative cases, delayed kinetic information should be used with caution and accurate margin assessment is essential.

Equivalence of Assurance® Gold Enzyme Immunoassay for Visual or Instrumental Detection of Motile and Nonmotile Salmonella in All Foods to AOAC Culture Method: Collaborative Study

Six foods representative of a wide variety of processed, dried powder processed, and raw food types were analyzed by the Assurance® Gold Salmonella Enzyme Immunoassay (EIA) and AOAC INTERNATIONAL culture method. Paired samples of each food type were simultaneously analyzed; one sample by the Assurance method and one by the AOAC culture method. The results for Assurance method were read visually and instrumentally with a microplate reader. A total of 24 laboratories representing federal government agencies and private industry, in the United States and Canada, participated in this collaborative study. Food types were inoculated with species of Salmonella with the exception of raw ground chicken, which was naturally contaminated. No statistical differences (p &lt; 0.05) were observed between Assurance Gold Salmonella EIA with either visual or instrumental interpretation and the AOAC culture method for any inoculation level of any food type or naturally contaminated food. The Assurance visual and instrumental options of reading sample reactions produced the same results for 1277 of the 1296 sample and controls analyzed.

Real-Time Computed Tomography Volume Visualization with Ambient Occlusion of Hand-Drawn Transfer Function Using Local Vicinity Statistic

Objectives

In this paper, we present an efficient method to visualize computed tomography (CT) datasets using ambient occlusion, which is a global illumination technique that adds depth cues to the output image. We can change the transfer function (TF) for volume rendering and generate output images in real time.

Methods

In preprocessing, the mean and standard deviation of each local vicinity are calculated. During rendering, the ambient light intensity is calculated. The calculation is accelerated on the assumption that the CT value of the local vicinity of each point follows the normal distribution. We approximate complex TF forms with a smaller number of connected line segments to achieve additional acceleration. Ambient occlusion is combined with the existing local illumination technique to produce images with depth in real time.

Results

We tested the proposed method on various CT datasets using hand-drawn TFs. The proposed method enabled real-time rendering that was approximately 40 times faster than the previous method. As a result of comparing the output image quality with that of the conventional method, the average signal-to-noise ratio was approximately 40 dB, and the image quality did not significantly deteriorate.

Conclusions

When rendering CT images with various TFs, the proposed method generated depth-sensing images in real time.

Self-care educational intervention to reduce hospitalisations in heart failure: A randomised controlled trial

Background:

A variety of educational interventions have been implemented to assist patients with heart failure to maintain their own health, develop self-care behaviours and decrease readmissions.

Aims:

The purpose of this study was to determine the effectiveness of a multimedia educational intervention for patients with heart failure in reducing unplanned hospital readmissions.

Methods:

The study, a randomised controlled trial in a large tertiary referral hospital in Australia, recruited 200 patients. Patients diagnosed with heart failure were randomly allocated 1:1 to usual education or a multimedia educational intervention. The multimedia approach began with an individual needs assessment to develop an educational plan. The educational intervention included viewing a DVD, and verbal discussion supported by a written manual with a teach-back evaluation strategy. The primary outcome was all-cause unplanned hospital readmission at 28 days, three months and 12 months post-recruitment. The secondary outcomes were changes in knowledge and self-care behaviours at three months and 12 months post-recruitment.

Results:

At 12 months, data on 171 participants were analysed. There were 24 participants who had an unplanned hospital readmission in the intervention group compared to 44 participants in the control group ( p=0.005). The self-care educational intervention reduced the risk of readmission at 12 months by 30% (relative risk: 0.703; 95% confidence interval: 0.548–0.903).

Conclusion:

A targeted multimedia educational intervention can be effective in reducing all-cause unplanned readmissions for people with heart failure.

Direct Visualization of Helicase Dynamics Using Fluorescence Localization and Optical Trapping

Helicases control the accessibility of single-stranded (ss) nucleic acid (NA) generated as a transient intermediate during almost every step in cells related to nucleic acid metabolisms. For subsequent processing, however, helicases need to adjust the pace of unwinding adequately to avoid ssNA exposure to nucleases. Therefore, understanding how the unwinding process of helicases is regulated is crucial to address genome integrity and repair mechanisms. Using single-molecule fluorescence-force spectroscopy with fluorescence localization, we recently observed the stoichiometry of UvrD helicase, which determines the functions of UvrD: translocation and unwinding. For the first time, we provide direct evidence that a UvrD dimer is required to initiate the unwinding pathway. Moreover, with subpixel precision of fluorescence localization, the dynamic parameters of helicases can be obtained directly. Here, we present detailed single-molecule assays for observing the biochemical activities of helicases in real time and revealing how mechanical forces are involved in protein-nucleic acid interactions. These single-molecule approaches are generally applicable to many other protein-nucleic acid systems.

Experimental demonstration of energy-chirp control in relativistic electron bunches using a corrugated pipe

The first experimental study is presented of a corrugated wall device that uses wakefields to remove a linear energy correlation in a relativistic electron beam (a "dechirper"). Time-resolved measurements of both longitudinal and transverse wakefields of the device are presented and compared with simulations. This study demonstrates the feasibility to employ a dechirper for precise control of the beam phase space in the next generation of free-electron-lasers.

Abstract P3-05-06: Automated analysis of Her2 FISH using combined Immunofluorescence and FISH signals

Introduction: Qualifying patients for Her2 targeted therapy is currently done by detecting Her2 protein overexpression or gene amplification using immunohistochemistry and/or FISH. We have recently developed a method for detecting both signals on the same tissue section allowing direct correlation of protein expression and gene copy number on a cell by cell basis. Accurate assessment of Her2 gene copy number is critical and can pose a challenge due to tumor heterogeneity. This paper reports the accuracy of a proprietary FISH dot counting algorithm on a cell-by-cell basis, potentially allowing analysis of thousands instead of dozens of tumor cells.

Method: Automatic FISH signal counts were compared to manual counts of 888 cells selected from 19 invasive ductal breast carcinoma samples exhibiting varying degrees of Her2 expression collected between June 2011 and March 2012. Tissue sections (4 µm) were mounted on positively charged slides, baked and processed through deparaffinization, rehydration and antigen retrieval, then stained for immunofluorescence (IF) using Cy5 labeled Her2 and Cy3 labeled cytokeratin antibodies, counterstained with DAPI, and imaged using InCell 2000 analyzer with GE-proprietary acquisition and processing software. Images were collected at 10x magnification and digitally stitched to span the entire tissue section. A pathologist then selected separate tumor and adjacent normal epithelium regions for subsequent imaging at 40x magnification. Slides were subsequently processed for FISH by pepsin digestion and then subjected to FISH by using PathVysion kit (Abbott Molecular, Des Plaines, IL). After hybridization and subsequent high stringency washes, samples were DAPI stained and mounted for microscopy. Samples were imaged at 40x at the same regions recorded for 40x IF acquisition, using filtersets appropriate for FISH fluorophores and DAPI.

A proprietary automated processing algorithm was used to analyze combined IF and FISH signals and derive case specific Her2 score from the tumor and/or adjacent normal epithelium. Cell-level dot counting accuracy was assessed using two metrics comparing automated counts to manual counts: cell classification agreement, where a normal cell was defined as having 3 or less Her2 and Cep17 dots; and dot-counting match, where a difference of more than 20% in absolute counts was considered an error.

Result: Our automatic results gave an overall cell-by-cell classification agreement of 88% (range 71% to 98% by case). Combining classification agreement and counting match, our algorithm gave an overall accuracy of 81% (range 63% to 97% by case). Restricting to tumor tissues (as judged by pathologist review of IF) classification agreement and accuracy were 84% and 72%, respectively.

Conclusion: The observed variability in algorithm performance between the different cases was due to the fact that error root causes were case dependent. For instance, the main cause of over-counting errors was image noise and artifacts. On the other hand, the main cause of under-counting was low image contrast, especially in highly amplified cases. These results are an early indication of the promise of automatic dot counting applied to breast cancer slides multiplexed for Her2 IF and FISH.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-05-06.

Abstract P3-05-05: HER2 Expression and Gene copy analysis by Immunofluorescence and Fluorescence in situ Hybridization, on a Single formalin-fixed paraffin-embedded tissue section

Introduction: Breast cancer is the most common cancer for women worldwide. HER2 expression and gene copy number are important when determining eligibility for adjuvant therapy and/or chemotherapy medications. One challenging issue for breast cancer testing is intratumoral heterogeneity of HER2 gene amplification. Intratumoral heterogeneity can make it difficult to localize target cells of interest. Serial tissue sections used for independent H&E, IHC and FISH stains also increase the difficulty to localize targets due to cellular truncation. We have developed a system to assess both HER2 expression and gene copy number on the same cell.

Method: Immunofluorescence (IF) and Fluorescence in situ Hybridization (FISH) were performed on tissue sections from 19 patients with invasive ductal breast carcinoma. Cases were selected based on prior HER2 FISH results (HER2:Chromosome 17 = ratio) representing unamplified (&lt;2.0), amplified (≥2.0) and equivocal (1.8–2.2). Samples were collected from June 2011 – February 2012. Tissue sections were cut at 4uM from formalin-fixed paraffin-embedded tissue blocks. Slides were stained with antibodies for HER2 (Clone #D8F12, Cell Signaling, Danvers, MA), cytokeratin (Clone #AE1, eBioscience, San Diego, CA) and Pan cytokeratin (Clone #PCK-26, Sigma-Aldrich, St. Louis, MO). The whole tissue imaging was performed on the In-Cell (GE Healthcare, Chalfont St. Giles, UK) at 10X. Proprietary software developed by GRC (GE Global Research, Niskayuna, NY) controlled the hardware and performed numerous algorithmic functions. Regions of Interest (ROI) were selected by a pathologist on a whole tissue image and coordinates were recorded by the software. The slides were then imaged at 40x using the previously recorded ROI's. The same slides were stained with the PathVysion HER2/CEP17 FISH kit (Abbott Molecular, Des Plaines, IL). Slides were registered to the previous IF scan using recorded coordinates and tissue morphology recognition algorithms. The sections were imaged for FISH at 40X using the previous ROI selections. Cases were assessed for successful protein and genetic expression using proprietary visualization tools for combined analysis.

Results: We evaluated a total of 22 breast cancer cases with 19 cases detecting both protein and gene expression. Of the three cases that could not be evaluated the rationale is as follows: tissue damage incurred during imaging, insufficient focus during the FISH imaging portion, and poor signal to noise of the FISH dots.

Conclusion: The reported incidence of intratumoral HER2 amplification heterogeneity is as high as 30%. The challenges associated with tumor heterogeneity may benefit from a standardize analysis method. Using integrated images generated by this system, pathologist is able to select the appropriate cells for HER2 copy number enumeration based on the expression level of HER2 protein, in the same cell, allowing rapid identification of intratumoral heterogeneity.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-05-05.

Stm Studies of GMR Spin Valves

We have investigated the surface roughness and the grain size in giant magnetoresistance (GMR) spin valve multilayers of the general type: FeMn/Ni80Fe20Co/Cu/Co/Ni80Fe20 on glass and aluminum oxide substrates by scanning tunneling microscopy (STM). The two substrates give very similar results. These polycrystalline GMR multilayers have a tendency to exhibit larger grain size and increased roughness with increasing thickness of the metal layers. Samples deposited at a low substrate temperature (150 K) exhibit smaller grains and less roughness. Valleys between the dome-shaped individual grainsare the dominant form of roughness. This roughness contributes to the ferromagnetic, magnetostatic coupling in these films, an effect termed “orange peel” coupling by Néel. We have calculated the strength of this coupling, based on our STM images, and obtain values generally within about 20% of the experimental values. It appears likely that the ferromagnetic coupling generally attributed to so-called “pinholes” in the Cu when the Cu film thickness is too small is actually “orange peel” coupling caused by these valleys.

Protective effects of Glycyrrhiza uralensis Fisch. on the cognitive deficits caused by beta-amyloid peptide 25-35 in young mice

Amyloid beta protein (Abeta) may be involved in the progression of Alzheimer's disease (AD), by acting as a neurotoxin and eliciting oxidative stress. This study was designed to determine the effects of Glycyrrhiza uralensis Fisch. water extract (GWE) on the cognitive deficits and oxidative stress induced by the administration of Abeta(25-35) in mice. Mice in two of the four animal groups were fed an experimental diet containing either 0.5 or 1% GWE for the entire 6-week experimental period. Control mice and a further experimental group were fed a non-GWE diet. Abeta(25-35) was administered to the three experimental groups by intracerebroventricular (i.c.v.) injection (10 microg/10 microl/mouse) once per week in weeks 5 and 6 of the experimental period. Behavioral changes were assessed using both a passive avoidance (after the injection of Abeta(25-35) in week 5) and the Morris water-maze tests (after the injection of Abeta(25-35) in week 6). Control animals were administered vehicle alone. The prolonged consumption of a diet containing GWE ameliorated the cognitive deficits caused by the i.c.v. injections of Abeta(25-35). Treatment with Abeta(25-35) led to higher concentrations of thiobarbituric acid reactive substances in the brain, and GWE attenuated this response. There was a decrease in catalase activity in the group provided with 1% GWE. Acetylcholinesterase activity was significantly reduced in the brains of all GWE-treated animals compared to that in the non-GWE-fed experimental group. These results suggest that GWE exerts a protective effect against the cognitive impairments often observed in AD, and that in mice this effect is mediated by antioxidant actions against oxidative stress.

Folding and catalysis of the hairpin ribozyme

The active form of the hairpin ribozyme is brought about by the interaction of two formally unpaired loops. In a natural molecule, these are present on two adjacent arms of a four-way junction. Although activity can be obtained in molecules lacking this junction, the junction is important in the promotion of the folded state of the ribozyme under physiological conditions, at a rate that is faster than the chemical reaction. Single-molecule fluorescence resonance energy transfer studies show that the junction introduces a discrete intermediate into the folding process, which repeatedly juxtaposes the two loops and thus promotes their docking. Using single-molecule enzymology, the cleavage and ligation rates have been measured directly. The pH dependence of the rates is consistent with a role for nucleobases acting in general acid-base catalysis.

VEGF165 and angiopoietin-1 decreased myocardium infarct size through phosphatidylinositol-3 kinase and Bcl-2 pathways

Angiogenic growth factors, vascular endothelial growth factor (VEGF) and angiopoietin-1 (Ang1) could decrease myocardial infarct size, which was assumed to be related with newly formed capillaries. We doubted that these capillaries could do this solely and the potential protective mechanisms of VEGF and Ang1 on myocardium need to be evaluated. Three types of adenoviruses encoding human VEGF(165) (Ad-VEGF(165)), human angiopoietin-1 (Ad-Ang1) and green fluorescent protein (Ad-GFP, as a parallel control) were constructed. Experiments were taken both in vitro and in vivo. As in vitro, the antiapoptosis effect of VEGF(165), Ang1 and VEGF(165)+Ang1 on cardiac myoblasts was observed, which seemed to be related with the activation of phosphatidylinositol-3 kinase and Bcl-2 pathways. As in vivo, adenoviruses were intramyocardially injected immediately after the ligation of the left anterior descending coronay arteries in rats. The results showed positive effect of VEGF(165), Ang1 and VEGF(165)+Ang1 on decreasing the myocardial infarct size at the 7th day. Myocardial PI-3K activity and Bcl-2 expression were elevated relatively at the 3rd day. The protective effect of VEGF(165) and Ang1 on the myocardium may broaden their functional research and contribute to their clinical use in the future.

Single-molecule studies of DNA and RNA four-way junctions

Branched helical junctions are common in nucleic acids. In DNA, the four-way junction (Holliday junction) is an essential intermediate in homologous recombination and is a highly dynamic structure, capable of stacking conformer transitions and branch migration. Our single-molecule fluorescence studies provide unique insight into the energy landscape of Holliday junctions by visualizing these processes directly. In the hairpin ribozyme, an RNA four-way junction is an important structural element that enhances active-site formation by several orders of magnitude. Our single-molecule studies suggest a plausible mechanism for how the junction achieves this remarkable feat; the structural dynamics of the four-way junction bring about frequent contacts between the loops that are needed to form the active site. The most definitive evidence for this is the observation of three-state folding in single-hairpin ribozymes, the intermediate state of which is populated due to the intrinsic properties of the junction.

Withdrawal of cerivastatin induces monocyte chemoattractant protein 1 and tissue factor expression in cultured vascular smooth muscle cells

OBJECTIVE

The withdrawal of 3-hydroxy-3-methylglutaryl-coenzyme A-reductase inhibitors (statins) deteriorates endothelial function. We determined in vascular smooth muscle cells whether statin withdrawal leads to the expression of proinflammatory genes involved in the development and progression of arteriosclerosis.

METHODS AND RESULTS

The withdrawal of cerivastatin from pretreated vascular smooth muscle cells induced an increase in monocyte chemoattractant protein 1 (MCP-1) and tissue factor (TF) mRNA expression and enhanced MCP-1 secretion as well as cell surface TF activity. In the presence of cerivastatin, this effect was mimicked by geranylgeranyl pyrophosphate or mevalonate. Withdrawal-induced MCP-1 expression was sensitive to PD98059, SB203580, and diphenylene iodonium, suggesting an involvement of extracellular signal-regulated kinase 1/2, p38 mitogen-activated protein kinase, and the NADPH oxidase. Withdrawal increased the activity of extracellular signal-regulated kinase 1/2 and p38 mitogen-activated protein kinase and enhanced radical generation. Because the latter effect may result from an Rac-mediated activation of the NADPH oxidase, the effect of withdrawal on Rac translocation was studied. Statin treatment induced an increase in Rac-1 content in the cytoplasm. On withdrawal, however, an "overshoot" translocation of Rac to the plasma membrane occurred.

CONCLUSIONS

These observations suggest that statin withdrawal results in the activation of Rac and enhanced oxidative stress. The subsequent activation of redox-activated signal-transduction cascades results in the expression of MCP-1 and TF.

Defining the quantitative contribution of the melanocortin 1 receptor (MC1R) to variation in pigmentary phenotype

The melanocortin 1 receptor (MC1R) is a key determinant of pigmentary phenotype. Several sequence variants of the MC1R have been described, many of which are associated with red hair and cutaneous sensitivity to ultraviolet radiation even in the absence of red hair. Red hair approximates to an autosomal recessive trait, and most people with red hair are compound heterozygote or homozygous for limited numbers of mutations that show impaired function in in vitro assays. There is a clear heterozygote effect on sun sensitivity (even in those without red hair) and with susceptibility to the most common forms of skin cancer.

Single-molecule fluorescence resonance energy transfer

Fluorescent resonance energy transfer (FRET) is a powerful technique for studying conformational distribution and dynamics of biological molecules. Some conformational changes are difficult to synchronize or too rare to detect using ensemble FRET. FRET, detected at the single-molecule level, opens up new opportunities to probe the detailed kinetics of structural changes without the need for synchronization. Here, we discuss practical considerations for its implementation including experimental apparatus, fluorescent probe selection, surface immobilization, single-molecule FRET analysis schemes, and interpretation.

A (1-->3)-beta-D-linked heptasaccharide is the unit ligand for glucan pattern recognition receptors on human monocytes

Glucans are fungal cell wall polysaccharides which stimulate innate immune responses. We determined the minimum unit ligand that would bind to glucan receptors on human U937 cells using laminarin-derived pentaose, hexaose, and heptaose glucan polymers. When U937 membranes were pretreated with the oligosaccharides and passed over a glucan surface, only the heptasaccharide inhibited the interaction of glucan with membrane receptors at a K(d) of 31 microM (95% CI 20-48 microM) and 100% inhibition. However, the glucan heptasaccharide did not stimulate U937 monocyte NFkappaB signaling, nor did it increase survival in a murine model of polymicrobial sepsis. Laminarin, a larger and more complex glucan polymer (M(w) = 7700 g/mol), only partially inhibited binding (61 +/- 4%) at a K(d) of 2.6 microM (99% CI 1.7-4.2 microM) with characteristics of a single binding site. These results indicate that a heptasaccharide is the smallest unit ligand recognized by macrophage glucan receptors. The data also indicate the presence of at least two glucan-binding sites on U937 cells and that the binding sites on human monocyte/macrophages can discriminate between glucan polymers. The heptasaccharide and laminarin were receptor antagonists, but they were not receptor agonists with respect to activation of NFkappaB-dependent signaling pathways or protection against experimental sepsis.

Single-molecule fluorescence methods for the study of nucleic acids

Single-molecule fluorescence methods and biomechanical tools provide exciting new opportunities to probe biochemical processes in unprecedented detail. The detection and spectroscopy of single fluorophores have recently been used to observe conformational changes and biochemical events involving nucleic acids. A number of fluorescence observables, including localization, quenching, polarization response and fluorescence resonance energy transfer, have been utilized. An exciting new opportunity of combining fluorescence methods and biomechanical tools to study the structural changes and functions of enzymes that participate in nucleic acid metabolism has also arisen.

Physical activity-antidepressant treatment combination: impact on brain-derived neurotrophic factor and behavior in an animal model

The mechanism of antidepressant action, at the cellular level, is not clearly understood. It has been reported that chronic antidepressant treatment leads to an up-regulation of brain-derived neurotrophic factor (BDNF) mRNA levels in the hippocampus, and that physical activity (voluntary running) enhances this effect. We wished to investigate whether BDNF expression brought about by these interventions may overcome deficits caused by acute stress, and might impact behavior in an animal model. In this report, we have tested the hypothesis that the combination of the antidepressant, tranylcypromine, and physical exercise could lead to decreased neurotrophin deficits and enhanced swimming time in animals that have been forced to swim in an inescapable water tank. Rats were either treated with tranylcypromine, engaged in voluntary running, or both for one week. After these treatments, the animals underwent a two-day forced swimming procedure. BDNF mRNA levels were significantly depressed in untreated animals subjected to forced swimming. Animals that either underwent prior activity or received antidepressant showed BDNF mRNA levels restored to baseline. Animals receiving the combined intervention showed an increase in hippocampal BDNF mRNA well above baseline. Swimming time during a five-minute test was significantly enhanced in animals receiving the combined intervention over untreated animals. Swimming time was not significantly enhanced over that of animals receiving antidepressant alone, however. Enhanced swimming time correlated with increased levels of BDNF mRNA in one hippocampal sub-region (CA4-hilus). These results suggest that the combination of exercise and antidepressant treatment may have significant neurochemical, and possibly behavioral, effects. In addition, these results support the possibility that the enhancement of BDNF expression may be an important element in the clinical response to antidepressant treatment. The induction of BDNF expression by activity/pharmacological treatment combinations could represent an important intervention for further study, to potentially improve depression treatment and management.

Early activation of IKKbeta during in vivo myocardial ischemia

We have demonstrated that in vitro brief ischemia activates nuclear factor (NF)-kappaB in rat myocardium. We report in vivo ischemia-reperfusion (I/R)-induced NF-kappaB activation, IkappaB kinase -beta (IKKbeta) activity, and IkappaBalpha phosphorylation and degradation in rat myocardium. Rat hearts were subjected to occlusion of the coronary artery for up to 45 min or occlusion for 15 min followed by reperfusion for up to 3 h. Cytoplasmic and nuclear proteins were isolated from ischemic and nonischemic areas of each heart. NF-kappaB activation was increased in the ischemic area (680%) after 10 min of ischemia and in the nonischemic area (350%) after 15 min of ischemia and remained elevated during prolonged ischemia and reperfusion. IKKbeta activity was markedly increased in ischemic (1,800%) and nonischemic (860%) areas, and phosphorylated IkappaBalpha levels were significantly elevated in ischemic (180%) and nonischemic (280%) areas at 5 min of ischemia and further increased after reperfusion. IkappaBalpha levels were decreased in the ischemic (45%) and nonischemic (36%) areas after 10 min of ischemia and remained low in the ischemic area during prolonged ischemia and reperfusion. The results suggest that in vivo I/R rapidly induces IKKbeta activity and increases IkappaBalpha phosphorylation and degradation, resulting in NF-kappaB activation in the myocardium.

Nucleotide excision repair gene XPD polymorphisms and genetic predisposition to melanoma

The nucleotide excision repair pathway has evolved to deal with UV light-induced DNA damage. Individuals with the rare inherited nucleotide excision repair deficiency disease xeroderma pigmentosum have a 1000-fold increased incidence of skin cancer. We are interested in the possibility that more subtle changes in nucleotide excision repair genes, resulting in either a reduced capacity for repair or in altered interactions between repair proteins and components of the cell cycle control machinery, might constitute important genetic risk factors for the development of skin cancer in the general population. To investigate this hypothesis we have compared the frequency of polymorphisms in exons 6, 22 and 23 of the XPD gene in melanoma patients and a control group. For each of these two allele polymorphisms one of the alleles was over-represented in the melanoma group and there was a significant association with melanoma. Importantly, this association did not extend to markers immediately flanking the XPD gene, thus providing evidence that XPD gene polymorphisms might predispose to melanoma in the general population. There is a report that one of the polymorphic XPD alleles (exon 23 Lys), which is over-represented in the melanoma group, has reduced repair proficiency and we discuss the possibility that this is the causal change to the XPD gene that predisposes to melanoma.

[A study on the mechanism of the biological roles of danshensu on fibroblast]

OBJECTIVE

To explore the effects of danshensu on fibroblast apoptosis and the expression of procollagen gene.

METHODS

Danshensu was added to in vitro culture of human cutaneous fibroblasts, and the nuclear proteins and total RNA were harvested from the cells. Electrophoretic mobility shift assay (EMSA) was adopted to determine the combining activity of nuclear transcription factors NF-kB and NF-1. Cell apoptosis was analyzed by DNA ladder fragmentation. The procollagen gene expression was analyzed by RT-PCR.

RESULTS

Eight hours after the action of danshensu on the culture fibroblasts, the NF-kB combining activity was almost inhibited completely and the NF-1 combining activity decreased by about 50%. In addition, ladder-like DNA fragments were revealed clearly by sepharose electrophoresis. The mRNA levels of type I procollagen alpha1 and alpha2 decreased by 56% and 59%, respectively.

CONCLUSION

Danshensu could inhibit the nuclear transcription factor NF-kB activity of fibroblast and induce the occurrence of its apoptosis. Furthermore, danshensu could also inhibit the nuclear transcription factor NF-1 activity of fibroblast and modulate the synthesis and secretion of collagen.

Fluorescence quenching: A tool for single-molecule protein-folding study

By using titin as a model system, we have demonstrated that fluorescence quenching can be used to study protein folding at the single molecule level. The unfolded titin molecules with multiple dye molecules attached are able to fold to the native state. In the native folded state, the fluorescence from dye molecules is quenched due to the close proximity between the dye molecules. Unfolding of the titin leads to a dramatic increase in the fluorescence intensity. Such a change makes the folded and unfolded states of a single titin molecule clearly distinguishable and allows us to measure the folding dynamics of individual titin molecules in real time. We have also shown that fluorescence quenching can signal folding and unfolding of a small protein with only one immunoglobulin domain.

Nuclear factor kappaB activation in acute appendicitis: a molecular marker for extent of disease?

Nuclear factor-kappaB (NF-kappaB) has been demonstrated to regulate the transcription of target genes and stimulate inflammatory cytokine responses in a variety of inflammatory diseases. Preliminary studies have demonstrated that NF-kappaB is activated early in acute inflammation and sepsis and may serve as an indicator of clinical severity. The present study was designed to evaluate the degree of activation of NF-kappaB in patients with acute appendicitis and correlate activation with clinical extent of disease. Ten patients with acute appendicitis and five control patients (elective inguinal hernia repair) were evaluated by assaying NF-kappaB activity preoperatively and 12 to 18 hours postoperatively. Assaying of NF-kappaB was determined by binding activity for consensus probes in nuclear extracts from peripheral mixed white blood cells obtained by venous puncture. The bands of NF-kappaB activity from gel electrophoresis were quantified with a phosphor imager and reported as units of integrated intensity. The preoperative NF-kappaB activity was increased in all patients with appendicitis versus the controls [mean 151 (range 97-189) vs mean 50.3 (range 13.7-77); P < 0.0001]. The increased NF-kappaB activity also correlated with length of time of symptoms before operation. The patients who were symptomatic for less than 24 hours had an average NF-kappaB value of 103 (range 97-105) versus 171.4 (range 152-189) (P < 0.0001) in those who were symptomatic 24 or more hours. The NF-kappaB activity did not correlate with the white blood cell count. Postoperative NF-kappaB binding activity in the appendicitis patients dropped to minimal levels (mean 50.3), even lower than the control patients' baseline values (mean 55.6). Control patients demonstrated low baseline values preoperatively and a slight rise postoperatively [mean 50.3 (range 13.7-77) vs mean 100 (range 45-186)]. We conclude the following: (1) NF-kappaB binding activity is elevated in patients with acute appendicitis and correlates with symptoms longer than 24 hours. (2) This increased activity returns to baseline values within 18 hours after appendectomy. (3) Molecular indicators of inflammation may have a role in both staging surgical inflammatory conditions and predicting ultimate outcome.