A High-Precision Micropipette Sensor for Cellular-Level Real-Time Thermal Characterization

We report herein development of a novel glass micropipette thermal sensor fabricated in a cost-effective manner, which is capable of measuring steady thermal fluctuation at spatial resolution of similar to 2 mu m with an accuracy of +/- 0.01 degrees C. We produced and tested various micrometer-sized sensors, ranging from 2 mu m to 30 mu m. The sensor comprises unleaded low-melting-point solder alloy (Sn-based) as a core metal inside a pulled borosilicate glass pipette and a thin film of nickel coating outside, creating a thermocouple junction at the tip. The sensor was calibrated using a thermally insulated calibration chamber, the temperature of which can be controlled with an accuracy of +/- 0.01 degrees C, and the thermoelectric power (Seebeck coefficient) of the sensor was recorded from 8.46 to 8.86 mu V/degrees C. We have demonstrated the capability of measuring temperatures at a cellular level by inserting our temperature sensor into the membrane of a live retinal pigment epithelium cell subjected to a laser beam with a focal spot of 6 mu m. We measured transient temperature profiles and the maximum temperatures were in the range of 38-55 +/- 0.5 degrees C.open111212sciescopu

Plasma membrane cholesterol homeostasis is essential for preventing oxidative damage in wild-type Chinese hamster ovary cells

published_or_final_versio

Efficacy of Functional Magnetic Stimulation in Neurogenic Bowel Dysfunction after Spinal Cord Injury

[[abstract]]Objective: The aims of this study were to assess the usefulness of functional magnetic stimulation in controlling neurogenic bowel dysfunction in spinal cord injured patients with supraconal and conal/caudal lesions, and to investigate the efficacy of this regimen with a 3-month follow-up. Design: A longitudinal, prospective before-after trial. Subjects: A total of 22 patients with chronic spinal cord injured and intractable neurogenic bowel dysfunction. They were divided into group 1 (supraconal lesion) and group 2 (conal/caudal lesion). Methods: The colonic transit time assessment and Knowles-Eccersley-Scott Symptom Questionnaire were carried out for each patient before they received a 3-week functional magnetic stimulation protocol and on the day following the treatment. Results and conclusion: Following functional magnetic stimulation, the mean colonic transit time for all patients decreased from 62.6 to 50.4 h (p < 0.001). The patients’ Knowles-Eccersley-Scott Symptom scores decreased from 24.5 to 19.2 points (p < 0.001). The colonic transit time decrement in both group 1 (p = 0.003) and group 2 (p = 0.043) showed significant differences, as did the Knowles-Eccersley-Scott Symptom score in both groups following stimulation and in the 3-month follow-up results (p < 0.01). The improvements in bowel function indicate that functional magnetic stimulation, featuring broad-spectrum application, can be incorporated successfully into other therapies as an optimal adjuvant treatment for neurogenic bowel dysfunction resulting from spinal cord injury.[[journaltype]]國外[[incitationindex]]SCI[[booktype]]紙本[[countrycodes]]SW

Discovering monotonic stemness marker genes from time-series stem cell microarray data

© 2015 Wang et al.; licensee BioMed Central Ltd. Background: Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Monotonic Feature Selector (MFSelector) based on a concept of total discriminating error (DEtotal) to identify monotonic genes. MFSelector considers various time stages in stage order (i.e., Stage One vs. other stages, Stages One and Two vs. remaining stages and so on) and computes DEtotal of each gene. MFSelector can successfully identify genes with monotonic characteristics.Results: We have demonstrated the effectiveness of MFSelector on two synthetic data sets and two stem cell differentiation data sets: embryonic stem cell neurogenesis (ESCN) and embryonic stem cell vasculogenesis (ESCV) data sets. We have also performed extensive quantitative comparisons of the three monotonic gene selection approaches. Some of the monotonic marker genes such as OCT4, NANOG, BLBP, discovered from the ESCN dataset exhibit consistent behavior with that reported in other studies. The role of monotonic genes found by MFSelector in either stemness or differentiation is validated using information obtained from Gene Ontology analysis and other literature. We justify and demonstrate that descending genes are involved in the proliferation or self-renewal activity of stem cells, while ascending genes are involved in differentiation of stem cells into variant cell lineages.Conclusions: We have developed a novel system, easy to use even with no pre-existing knowledge, to identify gene sets with monotonic expression patterns in multi-stage as well as in time-series genomics matrices. The case studies on ESCN and ESCV have helped to get a better understanding of stemness and differentiation. The novel monotonic marker genes discovered from a data set are found to exhibit consistent behavior in another independent data set, demonstrating the utility of the proposed method. The MFSelector R function and data sets can be downloaded from: http://microarray.ym.edu.tw/tools/MFSelector/

A potential risk of overestimating apparent diffusion coefficient in parotid glands

Objectives: To investigate transient signal loss on diffusion weighted images (DWI) and overestimation of apparent diffusion coefficient (ADC) in parotid glands using single shot echoplanar DWI (EPDWI). Materials and Methods: This study enrolled 6 healthy subjects and 7 patients receiving radiotherapy. All participants received dynamic EPDWI with a total of 8 repetitions. Imaging quality of DWI was evaluated. Probability of severe overestimation of ADC (soADC), defined by an ADC ratio more than 1.2, was calculated. Error on T2WI, DWI, and ADC was computed. Statistical analysis included paired Student t testing and Mann-Whitney U test. A P value less than 0.05 was considered statistically significant. Results: Transient signal loss was visually detected on some excitations of DWI but not on T2WI or mean DWI. soADC occurred randomly among 8 excitations and 3 directions of diffusion encoding gradients. Probability of soADC was significantly higher in radiotherapy group (42.86%) than in healthy group (24.39%). The mean error percentage decreased as the number of excitations increased on all images, and, it was smallest on T2WI, followed by DWI and ADC in an increasing order. Conclusions: Transient signal loss on DWI was successfully detected by dynamic EPDWI. The signal loss on DWI and overestimation of ADC could be partially remedied by increasing the number of excitations. © 2015 Liu et al.published_or_final_versio

μ-CS: An extension of the TM4 platform to manage Affymetrix binary data

<p>Abstract</p> <p>Background</p> <p>A main goal in understanding cell mechanisms is to explain the relationship among genes and related molecular processes through the combined use of technological platforms and bioinformatics analysis. High throughput platforms, such as microarrays, enable the investigation of the whole genome in a single experiment. There exist different kind of microarray platforms, that produce different types of binary data (images and raw data). Moreover, also considering a single vendor, different chips are available. The analysis of microarray data requires an initial preprocessing phase (i.e. normalization and summarization) of raw data that makes them suitable for use on existing platforms, such as the TIGR M4 Suite. Nevertheless, the annotations of data with additional information such as gene function, is needed to perform more powerful analysis. Raw data preprocessing and annotation is often performed in a manual and error prone way. Moreover, many available preprocessing tools do not support annotation. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of microarray data are needed.</p> <p>Results</p> <p>The paper presents <it>μ</it>-CS (Microarray Cel file Summarizer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix binary data. <it>μ</it>-CS is based on a client-server architecture. The <it>μ</it>-CS client is provided both as a plug-in of the TIGR M4 platform and as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data, avoiding the manual invocation of external tools (e.g. the Affymetrix Power Tools), the manual loading of preprocessing libraries, and the management of intermediate files. The <it>μ</it>-CS server automatically updates the references to the summarization and annotation libraries that are provided to the <it>μ</it>-CS client before the preprocessing. The <it>μ</it>-CS server is based on the web services technology and can be easily extended to support more microarray vendors (e.g. Illumina).</p> <p>Conclusions</p> <p>Thus <it>μ</it>-CS users can directly manage binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the <it>μ</it>-CS plugin for TM4 can manage Affymetrix binary files without using external tools, such as APT (Affymetrix Power Tools) and related libraries. Consequently, <it>μ</it>-CS offers four main advantages: (i) it avoids to waste time for searching the correct libraries, (ii) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or the use of old libraries, (iii) it implements the annotation of preprocessed data, and finally, (iv) it may enhance the quality of further analysis since it provides the most updated annotation libraries. The <it>μ</it>-CS client is freely available as a plugin of the TM4 platform as well as a standalone application at the project web site (<url>http://bioingegneria.unicz.it/M-CS</url>).</p