In silico experiment system for testing hypothesis on gene functions using three condition specific biological networks

Determining functions of a gene requires time consuming, expensive biological experiments. Scientists can speed up this experimental process if the literature information and biological networks can be adequately provided. In this paper, we present a web-based information system that can perform in silico experiments of computationally testing hypothesis on the function of a gene. A hypothesis that is specified in English by the user is converted to genes using a literature and knowledge mining system called BEST. Condition-specific TF, miRNA and PPI (protein-protein interaction) networks are automatically generated by projecting gene and miRNA expression data to template networks. Then, an in silico experiment is to test how well the target genes are connected from the knockout gene through the condition-specific networks. The test result visualizes path from the knockout gene to the target genes in the three networks. Statistical and information-theoretic scores are provided on the resulting web page to help scientists either accept or reject the hypothesis being tested. Our web-based system was extensively tested using three data sets, such as E2f1, Lrrk2, and Dicer1 knockout data sets. We were able to re-produce gene functions reported in the original research papers. In addition, we comprehensively tested with all disease names in MalaCards as hypothesis to show the effectiveness of our system. Our in silico experiment system can be very useful in suggesting biological mechanisms which can be further tested in vivo or in vitro.

AVAILABILITY

http://biohealth.snu.ac.kr/software/insilico/.

Pool Boiling of Low-GWP Replacements for R134a on a Reentrant Cavity Surface

This paper quantifies the pool boiling performance of R134a, R1234yf, R513A, and R450A on a flattened, horizontal reentrant cavity surface. The study showed that the boiling performance of R134a on the Turbo-ESP exceeded that of the replacement refrigerants for heat fluxes greater than 20 kWm^-2. On average, the heat flux for R1234yf and R513A was 16 % and 19 % less than that for R134a, respectively, for R134a heat fluxes between 20 kWm^-2 and 110 kWm^-2. The heat flux for R450A was on average 57 % less than that of R134a for heat fluxes between 30 kWm^-2 and 110 kWm^-2. A model was developed to predict both single-component and multi-component pool boiling of the test refrigerants on the Turbo-ESP surface. The model accounts for viscosity effects on bubble population and uses the Fritz (1935) equation to account for increased vapor production with increasing superheat. Both loss of available superheat and mass transfer resistance effects were modeled for the refrigerant mixtures. For most heat fluxes, the model predicted the measured superheat to within ± 0.31 K.

Horizontal convective boiling of R1234yf, R134a, and R450A within a micro-fin tube

This paper presents local convective boiling heat transfer and Fanning friction factor measurements in a micro-fin tube for R134a and two possible low global warming potential (GWP) refrigerant replacements for R134a, namely R1234yf and R450A. Test section heating was achieved with water in either counterflow or in parallel flow with the test refrigerant to provide for a range of heat fluxes for each thermodynamic quality. An existing correlation from the literature for single and multi-component mixtures was shown to not satisfactorily predict the convective boiling measurements for flow qualities greater than 40%. Accordingly, a new correlation was developed specifically for the test fluids of this study so that a fair comparison of the heat transfer performance of the low GWP refrigerants to that of R134a could be made. The new correlation was used to compare the heat transfer coefficient of the three test fluids at the same heat flux, saturated refrigerant temperature, and refrigerant mass flux. The resulting example comparison, for the same operating conditions, showed that the heat transfer coefficient of the multi-component R450A and the single-component R1234yf were, on average, 15% less and 5% less, respectively, than that of the single-component R134a. Friction factor measurements were also compared to predictions from an existing correlation. A new correlation for the friction factor was developed to provide a more accurate prediction. The measurements and the new models are important for the evaluation of potential low-GWP refrigerants replacements for R134a.

Tests of the SIBYLL 2.3 high-energy hadronic interaction model using the KASCADE-Grande muon data

The KASCADE-Grande observatory was a ground-based air shower array dedicated to study the energy and composition of cosmic rays in the energy interval E = 1 PeV –1 EeV. The experiment consisted of different detector systems which allowed the simultaneous measurement of distinct components of air showers (EAS), such as the muon content. In this contribution, we study the total muon number and the lateral density distribution of muons in EAS detected by KASCADE-Grande as a function of the zenith angle and the total number of charged particles. The attenuation length of the muon content of EAS is also measured. The results are compared with the predictions of the SIBYLL 2.3 high-energy hadronic interaction model.

Abstract P6-09-50: Impact of young age on recurrence and mortality after surgery in breast cancer: 15 years active surveillance

Introduction:Substantial efforts have been made to find factors associated with breast cancer (BC) recurrence and mortality after BC treatment. So far TNM stage, ER, PR, and HER2 status are considered as the major predictive markers of BC recurrence and used for treatment decision. However, most of these factors were evaluated independent from other important confounders such as age, stage, and various anti-cancer treatments because they were mostly derived from clinical trials. In Korea, up to 50% of BC patients are premenopausal women, it is not clear how age at diagnosis affect the progression and outcomes of the disease considering all known prognostic factors including TNM stage, ER, PR, and HER2 status. We aim to evaluate the impact of young age on recurrence and mortality after surgery among Korean women with BC.

Methods: This is a retrospective cohort study conducted using the data from BC registry from 2000 to 2016 at Samsung Medical Cancer, Seoul, Korea. Patients who received curative BC surgery and who had histologically-confirmed invasive BC between 2000 to 2011 were included in the study. Patients who second primary cancer or double primary cancer were excluded. Information local, regional, or distant recurrence and death until May 2016 was collected using electronic medical records and National Health Statistics. Cumulative incidence rates of distant recurrence and morality at 3-years, 5-years and 10-years were calculated using a competing-risk model. Cox proportional hazards analysis were conducted with 3 different models to take into account for potential confounding factors including age, body mass index (BMI), stage and subtype at breast cancer diagnosis, chemotherapy, radiotherapy and hormone therapy.

Results:There were 7360 BC patients with curative BC surgery between 2000 and 2011, and the average follow up duration was 75.4 months. The mean age at diagnosis was 48.4 years old (Standard deviation (SD)=±10), and 6.2% (n=459) was diagnosed younger than 35. Of total, 13.3% were stage III BC and 73.4% of patients had hormone receptor positive BC. The cumulative incidence (95%CI) of recurrence at 3, 5, and 10 years was 4.4% (3.9-4.9), 7.5% (6.8-8.2), and 14.8% (12.9-16.7) respectively. The incidence of mortality at 3, 5, and 10 years was 1.8% (1.5-2.1), 3.8% (3.3-4.3), and 10.2% (9.1-11.5) respectively. Patients who were diagnosed BC under 35 years of age had 2.14 (95% confidence interval (CI):1.74-3.10) and 1.62 (95% CI:1.02-2.56) times higher risk of distant recurrence and mortality compared to patients whose age at diagnosis were between 50 to 60 after adjusting all well-known prognostic factors including stage, subtype, and BMI at diagnosis, chemotherapy, radiotherapy and hormone therapy.

Conclusions: Young age at diagnosis (<35) was the most significant predictor on BC recurrence and mortality independently from BC stage and subtype. Further study is warranted to explain biologic background for the differences in outcomes in young women with BC.

Citation Format: Kim J-Y, Cho J, Kim H, Kang D, Jung HA, Lee S-H, Bae S, Yu JH, Lee SK, Kim SW, Lee JE, Nam SJ, Ahn JS, Im Y-H, Guallar E, Park YH. Impact of young age on recurrence and mortality after surgery in breast cancer: 15 years active surveillance [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-09-50.

Serum CXCR3 ligands as biomarkers for the diagnosis and treatment monitoring of tuberculosis

SETTING

Tertiary care academic medical centre.

OBJECTIVE

To evaluate the clinical utility of CXC chemokine receptor 3 (CXCR3) ligands in the diagnosis and monitoring of tuberculosis (TB).

DESIGN

Presumptive TB patients (active TB, 256; non-TB disease, 52) and 201 healthy controls were enrolled. The serum levels of interferon-gamma (IFN-γ) and CXCR3 ligands (CXCL9, a monokine induced by IFN-γ [MIG] and CXCL11, an IFN-inducible T-cell α chemoattractant [I-TAC]) were measured using enzyme-linked immunosorbent assay. An IFN-γ release assay (IGRA) was also performed. Serial samplings were performed in 19 TB patients at baseline and at 1, 2, 3, 6 and 12 months after treatment initiation.

RESULTS

All marker levels were higher in TB patients than in controls and non-TB patients. The area under the curve (AUC) for differentiating between all TB patients and controls was 0.96 (95%CI 0.94-0.98) for CXCL9, 0.84 (95%CI 0.80-0.87) for CXCL11 and 0.61 (95%CI 0.57-0.66) for IFN-γ. CXCL9 levels afforded particularly high discriminatory power between TB patients and IGRA-positive controls (AUC = 0.95, 95%CI 0.92-0.97). The levels of CXCR3 ligands decreased significantly during follow-up, and these changes were correlated with treatment response.

CONCLUSION

CXCR3 ligands CXCL9 and CXCL11 may be useful surrogate markers for the diagnosis and follow-up of TB.

Chronic periodontitis can affect the levels of potential oral cancer salivary mRNA biomarkers

BACKGROUND AND OBJECTIVE

More than 100 salivary constituents have been found to show levels significantly different in patients with oral squamous cell carcinoma (OSCC) from those found in healthy controls, and therefore have been suggested to be potential salivary biomarkers for OSCC detection. However, many of these potential OSCC salivary biomarkers are also involved in chronic inflammation, and whether the levels of these biomarkers could be affected by the presence of chronic periodontitis was not known. The objective of this pilot study was therefore to measure the levels of seven previously reported potential OSCC salivary mRNA biomarkers in patients with chronic periodontitis and compare them to levels found in patients with OSCC and healthy controls. The seven salivary mRNAs were interleukin (IL)-8, IL-1β, dual specificity phosphatase 1, H3 histone family 3A, ornithine decarboxylase antizyme 1, S100 calcium-binding protein P (S100P) and spermidine/spermine N1-acetyltransferase 1.

MATERIAL AND METHODS

Unstimulated whole saliva samples were collected from a total of 105 human subjects from the following four study groups: OSCC; CPNS (chronic periodontitis, moderate to severe degree, non-smokers); CPS (chronic periodontitis, moderate to severe degree, smokers); and healthy controls. Levels of each mRNA in patient groups (OSCC or chronic periodontitis) relative to the healthy controls were determined by a pre-amplification reverse transcription-quantitative polymerase chain reaction approach with nested gene-specific primers. Results were recorded and analyzed by the Bio-Rad CFX96 Real-Time System. Mean fold changes between each pair of patient vs. control groups were analyzed by the Mann-Whitney U-test with Bonferroni corrections.

RESULTS

Only S100P showed significantly higher levels in patients with OSCC compared to both patients with CPNS (p = 0.003) and CPS (p = 0.007). The difference in S100P levels between patients with OSCC and healthy controls was also marginally significant (p = 0.009). There was no significant difference in the levels of salivary IL-8, IL-1β and dual specificity phosphatase 1 mRNAs between patients with OSCC and patients with CPNS (p = 0.510, 0.058 and 0.078, respectively); no significant difference in levels of salivary ornithine decarboxylase antizyme 1 and spermine N1-acetyltransferase mRNAs between patients with OSCC and patients with CPS (p = 0.318 and 0.764, respectively); and no significant difference in levels of the H3 histone family 3A mRNA between patients with OSCC and either CPS (p = 0.449) or healthy controls (p = 0.107).

CONCLUSIONS

Salivary S100P mRNA could be a reliable biomarker for OSCC detection, regardless of the presence of chronic periodontitis. The presence of chronic periodontitis could significantly affect the levels of the other six mRNAs, and negatively influence reliability for using them as biomarkers for oral cancer detection.

Forward and inverse dynamic study during pedaling: Comparison between the young and the elderly

BACKGROUND

As it is not easy to investigate various variables that affect exercise efficacies and cause injuries while pedaling in the actual experiment, especially for the elderly, the musculoskeletal model simulation with a comparison of measured electromyography (EMG) data could be used to minimize experimental trials.

OBJECTIVE

The measured EMG data were compared with the muscle activities from the musculoskeletal model through forward (FD) and inverse dynamic (ID) analysis.

METHODS

EMG was measured from eight young adult (20's) and eight elderly (70's) in three minutes pedaling with a constant load and 40 revolutions per minute (RPM) cadence. The muscles used for the analysis were the VastusLateralis, Tibialis Anterior, Bicep Femoris, and Gastrocnemius Medial. Pearson's correlation coefficients of the muscle activity patterns, on-off set, and peak timing at the maximum muscle activity were calculated and compared. BIKE3D and GaitLowerExtremity model were used for the FD and ID simulation.

RESULTS

There are significant correlations in the muscle activity patterns except in the case of Biceps Femoris muscle by ID. Thus, it can be concluded that muscle activities of model & EMG showed similar results.

CONCLUSION

The result shows that it could be possible to use the musculoskeletal model for various pedaling simulations.

Abstract P1-10-31: Impact of increased physical activities after diagnosis on fatigue and overall pain during cancer treatment: A prospective cohort study

Background

Existing evidence strongly suggests that exercise is not only safe but also feasible during cancer treatment. Physical activity is recommended for improving multiple post-treatment adverse effects on bone health, muscle strength, and other quality-of-life measures. Yet, limited evidence exists regarding effect of increased physical activity after diagnosis on symptoms management of breast cancer patients.

Methods

A total of 422 patients were recruited from July 2010 to July 2011 at two cancer hospitals in Seoul, Korea. Physical activity in sports (PAS) was assessed using Minnesota Leisure Time Physical Activity Questionnaire before and 2 weeks, 3-, 6-, 12-, 24- and 36-months after diagnosis. Physical symptoms including fatigue, pain, arm symptom, and insomnia were measured using EORTC-C30 and BR23. Growth mixture models were used to identify trajectory classes of physical activity patterns. Multivariate analysis was used to find impact of PAS on symptom management using SAS.

Results

Three distinct PAS groups were identified according to 3-year change patterns: moderate to moderate (MM): 40.8%, none to moderate (NM): 31.1% and moderate to high (MH): 28.1%. The LM and MH group increased PAS from diagnosis but it began to decrease from 1 year after diagnosis. Compared to the MM, the NM and MH reported significantly lower level of fatigue (MM:40.7, NM:32.2, MH:33.7), pain(MM:28.0, NM:25.6, MH:20.6), systemic therapy side effects (MM:26.9, NM:22.6, MH:21.8), and breast symptoms (MM:25.4, NM:21.7, MH:20.2) during active treatment (6 months after diagnosis).

Change patterns of quality of life according to trajectory groups At diagnosis2 weeks3 months6 months12 months24 months36 monthsFatigueMM31.3±1.930.2±1.935.3±2.0140.7±2.1137.8±2.1138.5±2.1141.0±2.21NM30.2±1.928.2±1.931.9±2.132.2±2.2233.6±2.135.6±2.2137.8±2.31MH28.8±2.327.4±2.233.0±2.433.7±2.51233.9±2.4136.2±2.5137.1±2.51PainMM15.1±1.531.3±1.9123.2±2.0128.0±2.0123.5±2.0122.0±2.0121.2±1.91NM15.4±1.532.4±2.023.3±2.0125.6±2.122.7±2.021.1±2.123.8±2.01MH17.2±1.828.4±2.3121.2±2.320.6±2.4219.7±2.321.1±2.318.6±2.2Systemic therapy side effectsMM16.8±1.114.3±1.2133.2±1.7126.9±1.5125.4±1.5126.2±1.6128.6±1.71NM15.0±1.114.5±1.235.2±1.7122.6±1.61222.0±1.6124.5±1.7127.7±1.81MH15.6±1.412.9±1.4134.4±2.0121.8±1.81221.8±1.7122.1±1.9124.7±2.01Breast symptomsMM13.8±1.226.4±1.6120.8±1.5125.4±1.6123.6±1.6119.2±1.7119.6±1.71NM13.0±1.224.7±1.6119.6±1.5121.7±1.61222.3±1.7119.9±1.8119.1±1.81MH16.0±1.424.1±1.8119.4±1.820.2±1.81217.8±1.8217.4±2.014.0±1.92*adjusted with age, stage, and radiotherapy 1 p<0.05 (differences from baseline within group), 2 p<0.05 (differences from MM group within time)

Conclusion

The results of the study confirmed that increased physical activity after diagnosis, even with patients who did not exercise at all before diagnosis, helps to control fatigue, pain, systemic side effects, and breast symptoms during treatment. It is necessary to find ways to promote physical activity after diagnosis and help patients to stay active during treatment.

Citation Format: Lee JK, Kang D, Choi E-K, Kong S, Lee S-K, Lee JE, Han W, Park YH, Ahn JS, Im YH, Noh D-Y, Nam S-J, Cho J. Impact of increased physical activities after diagnosis on fatigue and overall pain during cancer treatment: A prospective cohort study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-10-31.

Theta-rhythmic drive between medial septum and hippocampus in slow-wave sleep and microarousal: a Granger causality analysis

Medial septum (MS) plays a critical role in controlling the electrical activity of the hippocampus (HIPP). In particular, theta-rhythmic burst firing of MS neurons is thought to drive lasting HIPP theta oscillations in rats during waking motor activity and REM sleep. Less is known about MS-HIPP interactions in nontheta states such as non-REM sleep, in which HIPP theta oscillations are absent but theta-rhythmic burst firing in subsets of MS neurons is preserved. The present study used Granger causality (GC) to examine the interaction patterns between MS and HIPP in slow-wave sleep (SWS, a nontheta state) and during its short interruptions called microarousals (a transient theta state). We found that during SWS, while GC revealed a unidirectional MS→HIPP influence over a wide frequency band (2-12 Hz, maximum: ∼8 Hz), there was no theta peak in the hippocampal power spectra, indicating a lack of theta activity in HIPP. In contrast, during microarousals, theta peaks were seen in both MS and HIPP power spectra and were accompanied by bidirectional GC with MS→HIPP and HIPP→MS theta drives being of equal magnitude. Thus GC in a nontheta state (SWS) vs. a theta state (microarousal) primarily differed in the level of HIPP→MS. The present findings suggest a modification of our understanding of the role of MS as the theta generator in two regards. First, a MS→HIPP theta drive does not necessarily induce theta field oscillations in the hippocampus, as found in SWS. Second, HIPP theta oscillations entail bidirectional theta-rhythmic interactions between MS and HIPP.

Potentiation of tonic GABAergic inhibition by activation of postsynaptic kainate receptors

Presynaptic kainate-type glutamate ionotropic receptors (KARs) that mediate either the depression or the facilitation of GABA release have been intensively studied. Little attention has been given to the modulation of GABAA receptors (GABAARs) by postsynaptic KARs. Recent studies suggest that two GABAAR populations, synaptic (sGABAAR) and extrasynaptic (eGABAAR) GABAARs, mediate phasic and tonic forms of inhibition, respectively. Tonic inhibition plays an important role in the excitability of neuronal circuits and the occurrence of epileptic seizures. For this study, we are the first to report that the activation of postsynaptic KARs by the KAR agonist, Kainic acid (KA, 5 μM), enhanced tonic inhibition by potentiating eGABAARs. KA enhanced THIP-induced eGABAAR currents and prolonged the rise and decay time of muscimol-induced sGABAAR/eGABAAR currents, but also depressed the amplitude of evoked inhibitory postsynaptic currents (IPSCs), unitary IPSCs (uIPSCs), and muscimol-induced sGABAAR/eGABAAR currents. The PKC inhibitor, staurosporine (1 μM), in the patch pipette solution fully blocked the KA-induced potentiation of tonic inhibition, suggesting the involvement of an intracellular PKC pathway. Our study suggests that the activation of postsynaptic KARs potentiates eGABAARs but depresses sGABAARs. By activating postsynaptic KARs, synaptically released glutamate depresses phasic inhibition to facilitate neuronal plasticity, but potentiates tonic inhibition to protect neurons from over-excitation.

First Experimental Characterization of Microwave Emission from Cosmic Ray Air Showers

We report the first direct measurement of the overall characteristics of microwave radio emission from extensive air showers. Using a trigger provided by the KASCADE-Grande air shower array, the signals of the microwave antennas of the Cosmic-Ray Observation via Microwave Emission experiment have been read out and searched for signatures of radio emission by high-energy air showers in the GHz frequency range. Microwave signals have been detected for more than 30 showers with energies above 3×10^{16}  eV. The observations presented in this Letter are consistent with a mainly forward-directed and polarized emission process in the GHz frequency range. The measurements show that microwave radiation offers a new means of studying air showers at E≥10^{17}  eV.

Metabolic syndrome and sex-specific socio-economic disparities in childhood and adulthood: the Korea National Health and Nutrition Examination Surveys

AIMS

To examine whether adulthood and/or childhood sex-specific socio-economic disparities are associated with metabolic syndrome and its components in a developed non-Western setting.

METHODS

Based on the Fourth Korea National Health and Nutrition Examination Surveys, 14 888 people aged ≥ 20 years were analysed to evaluate the effect of adult and childhood socio-economic status on metabolic syndrome. Metabolic syndrome was defined according to the National Cholesterol Education Program Adult Treatment Panel III guidelines. Logistic regression analyses were conducted to calculate the odds ratios for metabolic syndrome and each component of metabolic syndrome in later life.

RESULTS

The age-standardized prevalence of metabolic syndrome was 26.6% for men and 21.3% for women. Compared with the highest level of education, men with the lowest education level were significantly less likely to have metabolic syndrome (odds ratio 0.76, 95% CI 0.60-0.96), whereas the opposite association was found in women (odds ratio 3.29, 95% CI 2.45-4.42). Men who were manual labourers and economically inactive had a lower prevalence of metabolic syndrome compared with those with non-manual jobs (odds ratio 0.82, 95% CI 0.69-0.98 and odds ratio 0.79, 95% CI 0.64-0.99, respectively), but the reverse association was observed in women (odds ratio 1.34, 95% CI 1.04-1.73 and odds ratio 1.40, 95% CI 1.09-1.81, respectively). A significant interaction between combined adulthood and childhood socio-economic status on the presence of metabolic syndrome was observed (P < 0.05).

CONCLUSIONS

Our findings suggest that sex-specific socio-economic disparities in childhood and adulthood have differential effects on the prevalence of metabolic syndrome and its individual components in Korea.