Novel Implementation of Conditional Co-Regulation by Graph Theory to Derive Co-Expressed Genes from Microarray Data

BackgroundMost existing transcriptional databases like Comprehensive Systems-Biology Database (CSB.DB) and Arabidopsis Microarray Database and Analysis Toolbox (GENEVESTIGATOR) help to seek a shared biological role (similar pathways and biosynthetic cycles) based on correlation. These utilize conventional methods like Pearson correlation and Spearman rank correlation to calculate correlation among genes. However, not all are genes expressed in all the conditions and this leads to their exclusion in these transcriptional databases that consist of experiments performed in varied conditions. This leads to incomplete studies of co-regulation among groups of genes that might be linked to the same or related biosynthetic pathway. ResultsWe have implemented an alternate method based on graph theory that takes into consideration the biological assumption – conditional co-regulation is needed to mine a large transcriptional data bank and properties of microarray data. The algorithm calculates relationships among genes by converting discretized signals from the time series microarray data (AtGenExpress) to output strings. A \u27score\u27 is generated by using a similarity index against all the other genes by matching stored strings for any gene queried against our database. Taking carbohydrate metabolism as a test case, we observed that those genes known to be involved in similar functions and pathways generate a high \u27score\u27 with the queried gene. We were also able to recognize most of the randomly selected correlated pairs from Pearson correlation in CSB.DB and generate a higher number of relationships that might be biologically important. One advantage of our method over previously described approaches is that it includes all genes regardless of its expression values thereby highlighting important relationships absent in other contemporary databases. ConclusionBased on promising results, we understand that incorporating conditional co-regulation to study large expression data helps us identify novel relationships among genes. The other advantage of our approach is that mining expression data from various experiments, the genes that do not express in all the conditions or have low expression values are not excluded, thereby giving a better overall picture. This results in addressing known limitations of clustering methods in which genes that are expressed in only a subset of conditions are omitted. Based on further scope to extract information, ASIDB implementing above described approach has been initiated as a model database. ASIDB is available at http://www.asidb.co

Impact of Meditation–Based Lifestyle Modification on HRV in Outpatients With Mild to Moderate Depression: An Exploratory Study

Background: The scientific evaluation of mind-body-interventions (MBI), including yoga and meditation, has increased significantly in recent decades. However, evidence of MBI's efficacy on biological parameters is still insufficient. Objectives: In this study, we used HRV analysis to evaluate a novel MBI as a treatment of outpatients with mild to moderate depressive disorder. The Meditation-Based Lifestyle Modification (MBLM) program incorporates all major elements of classical yoga, including ethical principles of yoga philosophy, breathing exercises, postural yoga, and meditation. Methods: In this exploratory randomized controlled trial, we compared the changes in HRV indices of a MBLM group (N = 22) and a minimal treatment group (MINIMAL, drugs only, N = 17) with those of a multimodal treatment-as-usual group (TAU, according to best clinical practice, N = 22). Electrocardiogram (ECG) recordings were derived from a Holter monitoring device, and HRV indices have been extracted from nearly stationary 20-min periods. Results: Short-term HRV analysis revealed statistically significant differences in the pre-to-post changes between MBLM and TAU. In particular, the vagal tone mediating RMSSD and the Renyi entropy of symbolic dynamics indicated HRV gains in MBLM participants compared with TAU. Almost no alterations were observed in the MINIMAL group. Conclusions: Our results suggest a benefit in selected HRV parameters for outpatients with mild to moderate depression participating in the MBLM program. For further investigations, we propose analysis of complete 24-h HRV recordings and additional continuous pulse wave or blood pressure analysis to assess long-term modulations and cardiovascular effects

Yoga, Meditation and Mindfulness in pediatric oncology − A review of literature

Purpose: Children and adolescents undergoing treatment for cancer are exposed to a wide variety of stressors both physical and mental. Not only adults but also children and adolescents increasingly practice yoga in a health-promoting manner and to cope with stressful situations. Methods: A review of literature was conducted to present the current outcomes on yoga, meditation and mindfulness for children and adolescents who are affected by an oncological disease. Results: Eight studies were identified that examined yoga treatment for children and adolescents with oncological diseases. Three studies were found on mindfulness in pediatric oncology. The studies summarized here suggest that yoga and mindfulness could help to improve quality of life, reduce fatigue, improve activity and fitness levels, improve sleep quality, increase appetite and decrease anxiety in various stages of the disease and its treatment. The reviewed studies showed that yoga and mindfulness-based interventions for children and adolescents with oncological illnesses are feasible in different settings and are well received. Conclusions: The results of the studies suggest that yoga and mindfulness may help to support children and adolescents during and after oncological treatment. Based on the current body of evidence it is not possible to draw conclusions about the efficacy of yoga and mindfulness-based interventions in pediatric oncology patients. Research must meet this challenge to develop suitable designs to further and better investigate the effects of yoga and mindfulness in children and adolescents with oncological diseases

Use of Homeopathy in Pediatric Oncology in Germany

Homeopathy is a frequently used complementary and alternative medicine (CAM) treatment. We present results comparing responses of homeopathy users (HUs) and users of other forms of CAM (NHUs) in pediatric oncology (PO) in Germany. Differences between these two groups (usage, associated demographic characteristics, previous experience with CAM) are investigated. 186 (45.2%) of the 367 CAM users were exposed to homeopathy. The treatment duration amounted to a median of 601 days for HUs and 282 days for NHUs. Parents with p (127; 76.5%) also used homeopathy for their child's cancer. Nonmedical practitioners played a considerably greater role as source of information than did treating physician. In the majority HUs received their prescriptions from nonmedical practitioners (56%; 29.4% of NHUs). HUs communicate more frequently with their physicians about the CAM-use (77.7% versus 65.2%) and recommend CAM more often than NHUs (94% versus 85.6%). Homeopathy is the most frequently used CAM treatment in PO in Germany. HUs sustain treatment and therapies considerably longer than NHUs. Most families who had used homeopathy before their child was diagnosed with cancer also used homeopathy for the treatment of their child's cancer. Compared to other CAM treatments, patient satisfaction with homeopathy appears to be very high

Evaluation of an Integrative Care Program in Pediatric Oncology

Purpose: This article discusses the results of an evaluation of the one-year implementation period of an integrative care program at a pediatric oncology ward, which consists of integrative care treatments offered three times a week to the patients. The guiding questions are how the model was implemented, which factors have to be considered for successful implementation, and which factors showed to be obstacles during implementation. Methods: A mixed-methods approach was applied for data saturation. Qualitative data consist of participant observations and informal conversations during the implementation phase. All observational records were filed in the data program MAXQDA. For the quantitative data, all integrative care treatments applied on the intensive care unit were documented and subsequently filed in an Excel sheet. Both sets of data were analyzed for the evaluation. Results: Four main thematic clusters influenced the implementation: (1) the organization and structure of the intensive care unit; (2) mood and atmosphere; (3) feedback on treatment; and (4) time and experience. All factors are interlinked and cannot be looked at independently. Results of the quantitative data show that the most frequent used treatments were those with calming and relaxing effects, followed by treatments for stomachache, nausea, and obstipation. Conclusions: The implementation of an integrative model of care is a process that demands thorough understanding of the complex setting of the ward, ongoing adaptation to the structures and organization of the ward, and the integration of factors like feedback, time, atmosphere, and the mood of parents, patients, and nurses

Impact of Mistletoe Triterpene Acids on the Uptake of Mistletoe Lectin by Cultured Tumor Cells

Complementary treatment possibilities for the therapy of cancer are increasing in demand due to the severe side effects of the standard cytostatics used in the first-line therapy. A common approach as a complementary treatment is the use of aqueous extracts of Viscum album L. (Santalaceace). The therapeutic activity of these extracts is attributed to Mistletoe lectins which are Ribosome-inactivating proteins type II. Besides these main constituents the extract of Viscum album L. comprises also a mixture of lipophilic ingredients like triterpene acids of the oleanane, lupane and ursane type. However, these constituents are not contained in commercially available aqueous extracts due to their high lipophilicity and insolubility in aqueous extraction media. To understand the impact of the extract ingredients in cancer therapy, the intracellular uptake of the mistletoe lectin I (ML) by cultured tumor cells was investigated in relation to the mistletoe triterpene acids, mainly oleanolic acid. Firstly, these hydrophobic triterpene acids were solubilized using cyclodextrins ("TT" extract). Afterwards, the uptake of either single compounds (isolated ML and the aqueous "viscum" extract) or in combination with the TT extract (ML+TT, viscumTT), was analyzed. The uptake of ML was studied inTHP-1-, HL-60-, 143B- and Ewing TC-71-cells and determined after 30, 60 and 120 minutes by an enzyme linked immunosorbent assay which quantifies the A-chain of the hololectin. It could be shown that the intracellular uptake after 120 minutes amounted to 20 % in all cell lines after incubation with viscumTT. The studies further revealed that the uptake in THP-1-, HL-60- and Ewing TC-71-cells was independent of the addition of TT extract. Interestingly, the uptake of ML by 143B-cells could only be measured after addition of triterpenes pointing to resistance to mistletoe lectin

Mindfulness-Based Student Training Improves Vascular Variability Associated With Sustained Reductions in Physiological Stress Response

In today's fast-paced society, chronic stress has become an increasing problem, as it can lead to psycho-physiological health problems. University students are also faced with stress due to the demands of many courses and exams. The positive effects of mindfulness-based stress reduction (MBSR) on stress management and self-regulation have already been studied. We have developed a new mindfulness intervention tailored for students—the Mindfulness-Based Student Training (MBST). In this study, we present longitudinal results of the MBST evaluation. Biosignal analysis methods, including pulse wave variability (PWV), heart rate variability, and respiratory activity, were used to assess participants' state of autonomic regulation during the 12-week intervention and at follow-up. The progress of the intervention group (IGR, N = 31) up to 3 months after the end of MBST was compared with that of a control group (CON , N = 34). In addition, the long-term effect for IGR up to 1 year after intervention was examined. The analysis showed significant positive changes in PWV exclusively for IGR. This positive effect, particularly on vascular function, persists 1 year after the end of MBST. These results suggest a physiologically reduced stress level in MBST participants and a beneficial preventive health care program for University students

Interplay of itinerant magnetism and reentrant spin-glass behavior in Fex_{x}Cr1−x_{1-x}

When suppressing the itinerant antiferromagnetism in chromium by doping with the isostructual itinerant ferromagnet iron, a dome of spin-glass behavior emerges around a putative quantum critical point at an iron concentration $x \approx 0.15$. Here, we report a comprehensive investigation of polycrystalline samples of Fe$_{x}$Cr$_{1-x}$ in the range $0.05 \leq x \leq 0.30$ using x-ray powder diffraction, magnetization, ac susceptibility, and neutron depolarization measurements, complemented by specific heat and electrical resistivity data for $x = 0.15$. Besides antiferromagnetic ($x < 0.15$) and ferromagnetic regimes ($0.15 \leq x$), we identify a dome of reentrant spin-glass behavior at low temperatures for $0.10 \leq x \leq 0.25$ that is preceded by a precursor phenomenon. Neutron depolarization indicates an increase of the size of ferromagnetic clusters with increasing $x$ and the Mydosh parameter $\phi$, inferred from the ac susceptibility, implies a crossover from cluster-glass to superparamagnetic behavior. Taken together, these findings consistently identify Fe$_{x}$Cr$_{1-x}$ as an itinerant-electron system that permits to study the evolution of spin-glass behavior of gradually varying character in unchanged crystalline environment

Modulating the polarization of broadband terahertz pulses from a spintronic emitter at rates up to 10 kHz

eliable modulation of terahertz electromagnetic waveforms is important for many applications. Here, we rapidly modulate the direction of the electric field of linearly polarized terahertz electromagnetic pulses with 1–30 THz bandwidth by applying time-dependent magnetic fields to a spintronic terahertz emitter. Polarity modulation of the terahertz field with more than 99% contrast at a rate of 10 kHz is achieved using a harmonic magnetic field. By adding a static magnetic field, we modulate the direction of the terahertz field between angles of, for instance, −53° and 53° at kilohertz rates. We believe our approach makes spintronic terahertz emitters a promising source for low-noise modulation spectroscopy and polarization-sensitive techniques such as ellipsometry at 1–30 THz