Techniques for clustering gene expression data

Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered

Ethical Accountability of Licensed Professional Counselors: A Comparative Study of State Regulations and the Effects on Ethical Behavior

Accountability is an integral aspect of occupational regulation and professional licensure and helps to promote ethical behavior within professional occupations. States have the autonomy to implement laws and enact sanctions against professionals who are in violation of the regulations and professional norms of the field. This research explores accountability and ethical behavior in the licensed professional counselor occupation. The purpose is twofold, it examines how states vary in their approach to setting legal and professional accountability measures as defined by minimum requirements for education and practice and it explores the relationship between ethical outcomes as defined by disciplinary violations and disciplinary actions taken by the state board of counseling. Based on accountability and ethics literature, using a state comparative study, state licensure experience and practice requirements are examined, including how states vary in their approach to setting accountability measures including education and practice standards, and how state licensing board regulations affect the ethical behavior of licensed professional counselors. Data utilized for the study comes from pre-existing sources, including the American Counseling Association, the Center for Public Integrity, and government databases of the 50 states. States were ranked according to how they score overall on the education and experience requirements and grouped according to similarities and differences. The results of the study indicated that most of the identified educational and experience requirements were not significantly associated with lower levels of discipline violations and discipline actions. However, one statistically significant association was indicated, but it was in the opposite direction as expected. CACREP accreditation of graduate degree counseling programs was found to be positively associated with discipline violations and discipline actions, suggesting states that require CACREP accreditation of counseling programs report more incidents of discipline violations and discipline actions taken against professional counselors. This study indicates that there may be unidentified contributing factors affecting the ethical behaviors of professional counselors as well as raises the question if the rules and regulations currently in place are adequate to ensure proper oversite. Further exploration in this topic area is needed to fully understand how licensure board regulations can be improved to provide oversite and guidance to professionals in the field

Any Time? Any Place? The impact on student learning of an on-line learning environment.

Original paper can be found at: http://www.actapress.com/Content_of_Proceeding.aspx?proceedingID=292#pages Copyright ACTA Press [Full text of this paper is not available in the UHRA]An increasing number of HE institutions are adopting virtual and managed learning environments (VLEs and MLEs), which offer flexible access to on-line learning materials all day and every day. There are multiple claims about e-learning enhancing learning and teaching (eg. [1] Britain and Liber, 1999; [2]Conole, 2002; [4]Allen, 2003; [5]Littlejohn and Higginson, 2003) such as supporting active learning, facilitative rather than didactic teaching and increased student motivation but these are not pre determined outcomes. Much depends on how lecturers use the available technology and how students respond to that use. This paper reports on a research project which has evaluated the students' own experience of on-line learning at the University of Hertfordshire. Using its own institution-wide MLE (StudyNet) academic staff at the university have been able to offer students on-line access to their study material from September 2001. Activities available for students using StudyNet include participating in discussion forums, using formative assessment materials and accessing journal articles as well as viewing and downloading courseware for each of their courses. Students were invited to participate in a questionnaire and focus groups to identify the characteristics of the on-line learning environment which benefited their learning

Secondary organizing pneumonia (bronchiolitis obliterans with organizing pneumonia) associated with adalimumab for treatment of chronic plaque psoriasis

Organizing pneumonia is defined histopathologically by intra-alveolar buds of granulation tissue, consisting of intermixed myofibroblasts and connective tissue. The pathological pattern of organizing pneumonia may be idiopathic or related to a determined cause, termed secondary organizing pneumonia. We report a 68-year-old woman with a longstanding history of chronic plaque psoriasis, treated with the tumor necrosis factor (TNF) inhibitor, adalimumab. After 8 years of treatment, she developed a gradual-onset, non-productive cough with associated generalized fatigue and mild dyspnea. Radiological investigations demonstrated ground-glass opacities in the left lower lobe and bronchoscopy revealed a fibroinflammatory process consistent with organizing pneumonia. Her biologic treatment was ceased and corticosteroid treatment commenced, with resolution of both her symptoms and the radiological findings. Given the increasing incidence of biologic treatment in the management of dermatological conditions, clinicians should be aware of secondary organizing pneumonia as a possible side effect of TNF inhibitor therapy

Evaluation and Validity of a Predictive Equation for Measuring Core Temperature during Exercise in Heat Stress

Exercising in the heat is very common yet can pose significant health risks such as heat exhaustion and heat stroke when core temperature exceeds 38°C and 40°C, respectively. However, current methods of core temperature measurement are invasive and impractical. Recent research indicates that core temperature can be predicted with two non-invasive inputs, heart rate (HR) and skin temperature. PURPOSE: The objective of this study was to assess the validity and reliability of this predictive equation against the direct measurement of core temperature. METHODS: Participants (n = 11) cycled in an environmental chamber (40°C, 40% humidity) at 75% of maximal HR for 45 minutes. Measurements included HR, scapular skin and core temperature, blood pressure, and rating of perceived exertion. Exercise stopped if core temperature exceeded 38.5°C for two consecutive measurements or volitional fatigue. Agreement between predicted and actual core temperature was assessed with Bland–Altman analysis. RESULTS: There was a low correlation (r2 = 0.2) between the direct measure and predicted core temperatures. The Bland–Altman analysis for core minus predicted temperatures showed a bias of 0.14°C and limits of agreement ranging from 0.72°C to −0.45°C. In addition, a large proportion of measurements (40.5%) of the total scores had a difference in temperature greater than ±0.3°C. The predictive equation overpredicted as mean temperature increased from the average core temperature (37°C). CONCLUSION: Based on the narrow temperature range the human body must stay within to prevent heat-related issues, we’ve concluded that the predictive equation lacks sufficient validity and reliability

Statistical estimation of trailing edge noise from finite wall-mounted airfoils

The 2016 Joint Conference of The Australian Acoustical Society and The Acoustical Society of New Zealand. Acoustics2016 - The Second Australasian Acoustical Societies ConferenceIt is important to be able to accurately model the flow and noise generated by finite wall-mounted airfoil flows because of the many engineering applications in which these flows occur. One method for predicting turbulent trailing edge noise is the Reynolds-averaged Navier-Stokes based statistical noise model (RSNM) of Doolan et al. (Proceedings of 20th International Congress on Acoustics, ICA 2010). The RSNM method has previously been used successfully on a range of two-dimensional geometry-flow cases. In this paper a new turbulent velocity cross-spectrum model and improved implementation are proposed to allow the RSNM method to be used to effectively and efficiently predict turbulent trailing edge noise from more complex three-dimensional cases. Reynolds-averaged Navier-Stokes (RANS) simulations of a series of wing-in-junction cases are used in combination with the developed acoustic model to predict the far-field noise and compared against experimental noise measurements.Jesse Coombs, Con Doolan, Anthony Zander, Danielle Moreau and Laura Brook

A high-throughput screening RT-qPCR assay for quantifying surrogate markers of immunity from PBMCs

Immunoassays that quantitate cytokines and other surrogate markers of immunity from peripheral blood mononuclear cells (PBMCs), such as flow cytometry or Enzyme-Linked Immunosorbent Spot (ELIspot), allow highly sensitive measurements of immune effector function. However, those assays consume relatively high numbers of cells and expensive reagents, precluding comprehensive analyses and high-throughput screening (HTS). To address this issue, we developed a sensitive and specific reverse transcription-quantitative PCR (RT-qPCR)-based HTS assay, specifically designed to quantify surrogate markers of immunity from very low numbers of PBMCs. We systematically evaluated the volumes and concentrations of critical reagents within the RT-qPCR protocol, miniaturizing the assay and ultimately reducing the cost by almost 90% compared to current standard practice. We assessed the suitability of this cost-optimized RT-qPCR protocol as an HTS tool and determined the assay exceeds HTS uniformity and signal variance testing standards. Furthermore, we demonstrate this technique can effectively delineate a hierarchy of responses from as little as 50,000 PBMCs stimulated with CD4+ or CD8+ T cell peptide epitopes. Finally, we establish that this HTS-optimized protocol has single-cell analytical sensitivity and a diagnostic sensitivity equivalent to detecting 1:10,000 responding cells (i.e., 100 Spot Forming Cells/106 PBMCs by ELIspot) with over 90% accuracy. We anticipate this assay will have widespread applicability in preclinical and clinical studies, especially when samples are limited, and cost is an important consideration

An analytically and diagnostically sensitive RNA extraction and RT-qPCR protocol for peripheral blood mononuclear cells

Reliable extraction and sensitive detection of RNA from human peripheral blood mononuclear cells (PBMCs) is critical for a broad spectrum of immunology research and clinical diagnostics. RNA analysis platforms are dependent upon high-quality and high-quantity RNA; however, sensitive detection of specific responses associated with high-quality RNA extractions from human samples with limited PBMCs can be challenging. Furthermore, the comparative sensitivity between RNA quantification and best-practice protein quantification is poorly defined. Therefore, we provide herein a critical evaluation of the wide variety of current generation of RNA-based kits for PBMCs, representative of several strategies designed to maximize sensitivity. We assess these kits with a reverse transcription quantitative PCR (RT-qPCR) assay optimized for both analytically and diagnostically sensitive cell-based RNA-based applications. Specifically, three RNA extraction kits, one post-extraction RNA purification/concentration kit, four SYBR master-mix kits, and four reverse transcription kits were tested. RNA extraction and RT-qPCR reaction efficiency were evaluated with commonly used reference and cytokine genes. Significant variation in RNA expression of reference genes was apparent, and absolute quantification based on cell number was established as an effective RT-qPCR normalization strategy. We defined an optimized RNA extraction and RT-qPCR protocol with an analytical sensitivity capable of single cell RNA detection. The diagnostic sensitivity of this assay was sufficient to show a CD8+ T cell peptide epitope hierarchy with as few as 1 × 104 cells. Finally, we compared our optimized RNA extraction and RT-qPCR protocol with current best-practice immune assays and demonstrated that our assay is a sensitive alternative to protein-based assays for peptide-specific responses, especially with limited PBMCs number. This protocol with high analytical and diagnostic sensitivity has broad applicability for both primary research and clinical practice

Inter-comparison of relative stopping power estimation models for proton therapy

Theoretical stopping power values were inter-compared for the Bichsel, Janni, ICRU and Schneider relative stopping power (RSP) estimation models, for a variety of tissues and tissue substitute materials taken from the literature. The RSPs of eleven plastic tissue substitutes were measured using Bragg peak shift measurements in water in order to establish a gold standard of RSP values specific to our centre's proton beam characteristics. The theoretical tissue substitute RSP values were computed based on literature compositions to assess the four different computation approaches. The Bichsel/Janni/ICRU approaches led to mean errors in the RSP of  −0.1/+0.7/−0.8%, respectively. Errors when using the Schneider approach, with I-values from the Bichsel, Janni and ICRU sources, followed the same pattern but were generally larger. Following this, the mean elemental ionisation energies were optimized until the differences between theoretical RSP values matched measurements. Failing to use optimized I-values when applying the Schneider technique to 72 human tissues could introduce errors in the RSP of up to  −1.7/+1.1/−0.4% when using Bichsel/Janni/ICRU I-values, respectively. As such, it may be necessary to introduce an additional step in the current stoichiometric calibration procedure in which tissue insert RSPs are measured in a proton beam. Elemental I-values can then optimized to match these measurements, reducing the uncertainty when calculating human tissue RSPs