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An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets
(2018)
Schmidt, Florian ; List, Markus ; Cukuroglu, Engin ; Köhler, Sebastian ; Göke, Jonathan ; Schulz, Marcel Holger
Motivation: International consortia such as the Genotype-Tissue Expression (GTEx) project, The Cancer Genome Atlas (TCGA) or the International Human Epigenetics Consortium (IHEC) have produced a wealth of genomic datasets with the goal of advancing our understanding of cell differentiation and disease mechanisms. However, utilizing all of these data effectively through integrative analysis is hampered by batch effects, large cell type heterogeneity and low replicate numbers. To study if batch effects across datasets can be observed and adjusted for, we analyze RNA-seq data of 215 samples from ENCODE, Roadmap, BLUEPRINT and DEEP as well as 1336 samples from GTEx and TCGA. While batch effects are a considerable issue, it is non-trivial to determine if batch adjustment leads to an improvement in data quality, especially in cases of low replicate numbers.
Results: We present a novel method for assessing the performance of batch effect adjustment methods on heterogeneous data. Our method borrows information from the Cell Ontology to establish if batch adjustment leads to a better agreement between observed pairwise similarity and similarity of cell types inferred from the ontology. A comparison of state-of-the art batch effect adjustment methods suggests that batch effects in heterogeneous datasets with low replicate numbers cannot be adequately adjusted. Better methods need to be developed, which can be assessed objectively in the framework presented here.
The formulation of the Partial Information Decomposition (PID) framework by Williams and Beer in 2010 attracted a significant amount of attention to the problem of defining redundant (or shared), unique and synergistic (or complementary) components of mutual information that a set of source variables provides about a target. This attention resulted in a number of measures proposed to capture these concepts, theoretical investigations into such measures, and applications to empirical data (in particular to datasets from neuroscience). In this Special Issue on “Information Decomposition of Target Effects from Multi-Source Interactions” at Entropy, we have gathered current work on such information decomposition approaches from many of the leading research groups in the field. We begin our editorial by providing the reader with a review of previous information decomposition research, including an overview of the variety of measures proposed, how they have been interpreted and applied to empirical investigations. We then introduce the articles included in the special issue one by one, providing a similar categorisation of these articles into: i. proposals of new measures; ii. theoretical investigations into properties and interpretations of such approaches, and iii. applications of these measures in empirical studies. We finish by providing an outlook on the future of the field.
Kozaki, Ryohei ; Vogler, Meike ; Walter, Harriet S. ; Jayne, Sandrine ; Dinsdale, David ; Siebert, Reiner ; Dyer, Martin J. S. ; Yoshizawa, Toshio
Bruton’s tyrosine kinase (BTK) is a key regulator of the B-cell receptor signaling pathway, and aberrant B-cell receptor (BCR) signaling has been implicated in the survival of malignant B-cells. However, responses of the diffuse large B-cell lymphoma (DLBCL) to inhibitors of BTK (BTKi) are infrequent, highlighting the need to identify mechanisms of resistance to BTKi as well as predictive biomarkers. We investigated the response to the selective BTKi, tirabrutinib, in a panel of 64 hematopoietic cell lines. Notably, only six cell lines were found to be sensitive. Although activated B-cell type DLBCL cells were most sensitive amongst all cell types studied, sensitivity to BTKi did not correlate with the presence of activating mutations in the BCR pathway. To improve efficacy of tirabrutinib, we investigated combination strategies with 43 drugs inhibiting 34 targets in six DLBCL cell lines. Based on the results, an activated B-cell-like (ABC)-DLBCL cell line, TMD8, was the most sensitive cell line to those combinations, as well as tirabrutinib monotherapy. Furthermore, tirabrutinib in combination with idelalisib, palbociclib, or trametinib was more effective in TMD8 with acquired resistance to tirabrutinib than in the parental cells. These targeted agents might be usefully combined with tirabrutinib in the treatment of ABC-DLBCL.
Carbon tetrachloride (CCl4) is an efficient but highly toxic solvent, used in households and commercially in the industry under regulatory surveillance to ensure safety at the working place and to protect the workers’ health. However, acute unintentional or intentional intoxications by CCl4 may rarely occur and are potentially life-threatening. In this review article, therapy options are discussed that are based on a literature review of traditional poisoning cases and the clinical experience with 16 patients with acute poisoning by CCl4. Among various therapy options, the CO2-induced hyperventilation therapy will be considered in detail as the most promising approach. This special therapy was developed because only around 1% of the intoxicating CCl4 is responsible for the liver injury after conversion to toxic radicals via microsomal cytochrome P450 2E1 whereas 99% of the solvent will leave the body unchanged by exhalation. Therefore, to enhance CCl4 elimination through the lungs, CO2 is added to the inspiration air at a flow rate of 2–3 L min−1 in order to achieve hyperventilation with a respiratory volume of 25–30 L min−1. Under this therapy, the clinical course was favorable in 15/16 patients, corresponding to 93.8%. In essence, patients with acute CCl4 intoxication should be treated by forced ventilation.
Ney, Julia ; Heyland, Daren K. ; Amrein, Karin ; Marx, Gernot ; Grottke, Oliver ; Choudrakis, Michael ; Autschbach, Teresa ; Hill, Aileen ; Meybohm, Patrick ; Benstöm, Carina ; Goetzenich, Andreas ; Fitzner, Christina ; Stoppe, Christian
Background & aims: Recent studies indicate that vitamin D deficiency is associated with increased morbidity and mortality in critically ill patients. Knowledge about the functional role and clinical relevance of vitamin D for patients undergoing cardiac surgery is sparse. Therefore, we investigated the clinical significance of vitamin D levels on outcome of cardiac surgery patients.
Methods: 92 patients undergoing elective cardiac surgery with cardiopulmonary arrest were included in this prospective observational pilot study. 25-hydroxyvitamin D (25OHD) and 1,25-dihydroxyvitamin D (1,25(OH)2D) levels were measured prior to surgery, immediately postoperatively as well as 6, 12 and 24 h after surgery. We assessed postoperative organ dysfunctions, infections and death until hospital discharge.
Results: The serum concentration of 1,25(OH)2D significantly decreased intraoperatively by 29.3% (p < 0.001) and was significantly lower at any postoperative time point compared to baseline values, whereas 25OHD levels did not show significant changes during the observation period. Coronary artery bypass graft (CABG) patients had significant higher baseline 1,25(OH)2D values than patients with valve surgery (39.7 ± 13.9 ng/l vs. 30.1 ± 14.1 ng/l, p = 0.010) or CABG + valve surgery (39.7 ± 13.9 ng/l vs. 32.6 ± 11.8 ng/l, p = 0.044).
Our data showed a significant odds ratio to develop postoperative organ dysfunction (OR 0.95; p = 0.009) and PCT levels ≥5 μg/l (OR 0.94; p = 0.046) for every ng/l increment in 1,25(OH)2D, when performing multivariable analysis and after adjusting for preoperative illness and demographics. In addition, multivariable-adjusted statistical analyses revealed that patients stayed significantly shorter on ICU (−0.21 h; p = 0.001) and in hospital (−2.6 days; p = 0.009) for every ng/l increment in 1,25(OH)2D.
Conclusion: Our data highlight important evidence about the clinical significance of 1,25(OH)2D levels in cardiac surgery patients. Higher levels were associated with significantly less postoperative organ dysfunctions, elevated PCT levels, death and prolonged hospital stay. 1,25(OH)2D levels decreased significantly intra- and postoperatively, while serum levels of 25OHD did not.
Trial registration: clinicaltrials.gov (NCT 02488876), registered May 1, 2015.
Brinker, Titus Josef ; Alfitian, Jonas ; Seeger, Werner ; Groneberg, Jan David Alexander ; Kalle, Christof von ; Enk, Alexander ; Herth, Felix ; Kreuter, Michael ; Bauer, Claudia M. ; Gatzka, Martina ; Suhre, Janina Leonie
The Education Against Tobacco (EAT) network delivers smoking prevention advice in secondary schools, typically using the mirroring approach (i.e., a "selfie" altered with a face-aging app and shared with a class). In November 2017, however, the German assembly of EAT opted to expand its remit to include nursing students. To assess the transferability of the existing approach, we implemented it with the self-developed face-aging app "Smokerface" (=mixed − methods approach) in six nursing schools. Anonymous questionnaires were used to assess the perceptions of 197 students (age 18–40 years; 83.8% female; 26.4% smokers; 23.3% daily smokers) collecting qualitative and quantitative data for our cross-sectional study. Most students perceived the intervention to be fun (73.3%), but a minority disagreed that their own animated selfie (25.9%) or the reaction of their peers (29.5%) had motivated them to stop smoking. The impact on motivation not to smoke was considerably lower than experienced with seventh graders (63.2% vs. 42.0%; notably, more smokers also disagreed (45.1%) than agreed (23.5%) with this statement. Agreement rates on the motivation not to smoke item were higher in females than in males and in year 2–3 than in year 1 students. Potential improvements included greater focus on pathology (29%) and discussing external factors (26%). Overall, the intervention seemed to be appealing for nursing students
Minh, Truong Ngoc ; Xuan, Tran Dang ; Ahmad, Ateeque ; Elzaawely, Abdelnaser Abdelghany ; Teschke, Rolf ; Van, Truong Mai
Momilactones A and B (MA and MB, respectively) are phytoalexins and plant growth inhibitors available in rice husks. However, to date, the isolation and purification of the two compounds have been complicated, laborious, and less effective. The present study was conducted to establish a protocol to simplify and optimize quantities of MA and MB by combinations of ethyl acetate (EtOAc), distilled water, methanol (MeOH), temperature, and pressure for extractions. At a temperature of 100 °C, combined with EtOAc and MeOH 100%, MA and MB were enriched in greater quantities than non-treated rice husks, of which MB was much augmented than MA. The EtOAc extract obtained from samples dried at 100 °C for 1 h, then placed in MeOH 100% for 1 week, provided maximum yields of MA [58.76 µg/g dry weight (DW)] and MB (104.43 µg/g DW). The use of pressure effectively enhanced yields of MA (17.90–26.26 µg/g DW) and MB (40.78–71.0 µg/g DW). The actual purified amounts of MA and MB increased by 5 and 15 folds, respectively. The use of either sole distilled water or MeOH ≤ 50% at any temperature did not successfully isolate both MA and MB. The yield optimization aids to easier and more productive purification of the two compounds, and thus extends researches on biological activities of MA and MB, including pharmaceutical and medicinal properties.
Efficacy from different extractions for chemical profile and biological activities of rice husk
(2018)
Minh, Truong Ngoc ; Xuan, Tran Dang ; Ahmad, Ateeque ; Elzaawely, Abdelnaser Abdelghany ; Teschke, Rolf ; Van, Truong Mai
Rice husk is a by-product produced abundantly in rice production but it has low commercial value and causes environmental pollution. This study was conducted to examine different extracting solvents and conditions to optimize the efficacy of antioxidant and antimicrobial potentials, and chemical components in rice husk. By the use of distilled water at 100 °C, the ethyl acetate (EtOAc) extract was potent in both total phenolic content (TPC), total flavonoid content (TFC), and DPPH scavenging activity. The treatment of either ethyl acetate (100 °C, 1 h), combined with MeOH 100%, showed the highest percent of lipid peroxidation inhibition (LPI) (86%), meaning that the strongest antioxidant activity was by the β-carotene bleaching method. The treatment of distilled water at room temperature possessed the strongest antioxidant activity in the assay of the reducing power. The use of dried samples at 100 °C for 2 h, combined with methanol (MeOH) 10%, provided the most potent antimicrobial activities against Escherichia coli, Klebsiella pneumoniae, Listeria monocytogenes, Bacillus subtilis, and Proteus mirabilis. The results suggested that the EtOAc extract from rice husk could be a potential source of natural antioxidants. In general, the use of temperature 100 °C for 2 h, combined with either EtOAc or 10% MeOH, can optimize chemical components and antioxidant and antimicrobial capacities in rice husk. Principal constituents putatively identified by gas chromatography–mass spectrometry (GC–MS) revealed the presence of momilactones A and B (MA and MB, respectively), phenols, phenolic acids, and long-chain fatty acids, although yields of these compounds varied among extracts. The bioactive MA and MB were found in most of the extracts, except distilled water and MeOH ≤ 50%, at any temperature. Findings of this study provided optimal conditions for future production at an industrial scale for rice husk to exploit its potent biological properties. It thus helps to increase the economic value and reduce the disposal burden and environmental troubles caused by rice husk.
De Sousa Fernandes Perna, Elizabeth B. ; Theunissen, Eef L. ; Dolder, Patrick ; Mason, Natasha L. ; Hutten, Nadia R. P. W. ; Tönnes, Stefan W. ; Kuypers, Kim P. C. ; Ramaekers, Johannes G.
Availability of novel psychoactive substances (NPS) exponentially increased over the last years. Risk evaluations of NPS are hampered by the lack of pharmacological studies in humans on health parameters. The aim of the present study was to evaluate safety and neurocognitive function of healthy volunteers (N = 12) who received single doses of 100 and 150 mg 4-fluoroamphetamine (4-FA), a phenethylamine that has been associated with severe cardiovascular and cerebrovascular complications. The study was set-up as a placebo controlled, within subject, phase 1 trial as it was the first to administer 4-FA to humans under controlled conditions. Overall, 4-FA produced a strong elevation in blood pressure up until 4-5 h after administration that was followed by a sustained increase in heart rate. After an interim review of safety data from five participants, a decision was taken to cancel administration of 150 mg. We subsequently obtained complete datasets for placebo and 100 mg 4-FA treatments only. Effects of 4-FA on mood and neurocognitive function were most distinct at 1 h post drug and included significant elevations of vigor, friendliness, elation, arousal, positive mood, as well as improvements in attention and motor performance. Negative affect was also reported as time progressed in the acute phase and even more so during the subacute phase. Overall, the influence of 4-FA on vital signs, mood, and neurocognition was similar to that observed with other stimulants. Present findings confirm clinical observations of acute toxicity among 4-FA users and warrant warnings about potential health risks associated with 4-FA use.
Wörtge, Dennis ; Moll, Jochen ; Krozer, Viktor ; Bazrafshan, Babak ; Hübner, Frank ; Park, Clara ; Vogl, Thomas J.
Hemispherical and cylindrical antenna arrays are widely used in radar-based and tomography-based microwave breast imaging systems. Based on the dielectric contrast between healthy and malignant tissue, a three-dimensional image could be formed to locate the tumor. However, conventional X-ray mammography as the golden standard in breast cancer screening produces two-dimensional breast images so that a comparison between the 3D microwave image and the 2D mammogram could be difficult. In this paper, we present the design and realisation of a UWB breast imaging prototype for the frequency band from 1 to 9 GHz. We present a refined system design in light of the clinical usage by means of a planar scanning and compare microwave images with those obtained by X-ray mammography. Microwave transmission measurements were processed to create a two-dimensional image of the breast that can be compared directly with a two-dimensional mammogram. Preliminary results from a patient study are presented and discussed showing the ability of the proposed system to locate the tumor.