Gene expression analysis of diagnostic biopsies predicts pathological response to neoadjuvant chemoradiotherapy of esophageal cancer

OBJECTIVE: This study explored gene expression differences in predicting response to chemoradiotherapy in esophageal cancer. PURPOSE:: A major pathological response to neoadjuvant chemoradiation is observed in about 40% of esophageal cancer patients and is associated with favorable outcomes. However, patients with tumors of similar histology, differentiation, and stage can have vastly different responses to the same neoadjuvant therapy. This dichotomy may be due to differences in the molecular genetic environment of the tumor cells. BACKGROUND DATA: Diagnostic biopsies were obtained from a training cohort of esophageal cancer patients (13), and extracted RNA was hybridized to genome expression microarrays. The resulting gene expression data was verified by qRT-PCR. In a larger, independent validation cohort (27), we examined differential gene expression by qRT-PCR. The ability of differentially-regulated genes to predict response to therapy was assessed in a multivariate leave-one-out cross-validation model. RESULTS: Although 411 genes were differentially expressed between normal and tumor tissue, only 103 genes were altered between responder and non-responder tumor; and 67 genes differentially expressed >2-fold. These included genes previously reported in esophageal cancer and a number of novel genes. In the validation cohort, 8 of 12 selected genes were significantly different between the response groups. In the predictive model, 5 of 8 genes could predict response to therapy with 95% accuracy in a subset (74%) of patients. CONCLUSIONS: This study has identified a gene microarray pattern and a set of genes associated with response to neoadjuvant chemoradiation in esophageal cancer. The potential of these genes as biomarkers of response to treatment warrants further investigation. Copyright © 2009 by Lippincott Williams & Wilkins.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS)

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.

The acute effects of eccentrically-biased versus conventional weight training in older adults : a randomised controlled cross-over study

Background Whilst resistance training has been proven to convey considerable benefits to older people; immediately post-exercise there may be elevated transient risks for cardiac events and falls. Objectives and Measurements We assessed the acute effects of eccentrically-biased (EB) and conventional (CONV) resistance exercise on: platelet number, activation and granule exocytsosis; and mean velocity of centre of pressure displacement (Vm). Design, Setting, Participants and Intervention Ten older adults (7 males, 3 females; 69 ± 4 years) participated in this randomised controlled cross-over study in which they performed EB and CONV training sessions that were matched for total work and a control condition. Results Immediately post-exercise there was a statistically significant difference in platelet count between the control condition, in which it fell (pre 224 ± 35 109/L; post 211 ± 30 109/L: P < 0.05) and CONV in which it increased (pre 236 ± 55 109/L; post 242 ± 51 109/L: P > 0.05). There was no change in platelet activation and granule exocytsosis or Vm following EB and CONV. Conclusions Overall, while minor differences between regimens were observed, no major adverse effect on parameters of platelet function or centre of pressure displacement were observed acutely following either regimen. Eccentrically-biased and conventional resistance exercise training regimens do not appear to present an elevated acute risk in the context of changes to platelet function contributing to a cardiac event or postural stability increasing falls risk for apparently healthy older adults.

Cross-cultural learning experiences in architectural education

This qualitative study looks at the joint output of 20 architecture students from 2 different countries during their short respective Study Tours to each other’s country to discern the effect of cross-cultural experiences on their learning. This paper uses the students’ joint design efforts and reflective writings to investigate the outcome of this cross-cultural educational exchange. Their joint design efforts resulted in the making of small built structures, drawings and collaborative design proposals for an urban setting. In addition, a short questionnaire and personal interviews were also used as methods to gain insight into their experience and to use as a comparative study. The question is also raised in this paper of whether spontaneous friendship among students is integral to long term learning in a cross-cultural context in comparison to pre-designed learning objectives on the part of the educators. This paper also initiates the dialogue of the extent of cultural influences and universal ideas on collaborative architectural design. With increasing joint design ventures between architectural firms in different countries, there is interest in how collaborative design can be understood in a cross-cultural context. This paper examines short term cross cultural experiences and its contribution to architectural education.

Physical activity and health-related quality of life among physiotherapists : a cross sectional survey in an Australian hospital and health service

Background Physiotherapists are a professional group with a high rate of attrition and at high risk of musculoskeletal disorders. The purpose of this investigation was to examine the physical activity levels and health-related quality of life of physiotherapists working in metropolitan clinical settings in an Australian hospital and health service. It was hypothesized that practicing physiotherapists would report excellent health-related quality of life and would already be physically active. Such a finding would add weight to a claim that general physical activity conditioning strategies may not be useful for preventing musculoskeletal disorders among active healthy physiotherapists, but rather, future investigations should focus on the development and evaluation of role specific conditioning strategies. Methods A questionnaire was completed by 44 physiotherapists from three inpatient units and three ambulatory clinics (63.7% response rate). Physical activity levels were reported using the Active Australia Survey. Health-related quality of life was examined using the EQ-5D instrument. Physical activity and EQ-5D data were examined using conventional descriptive statistics; with domain responses for the EQ-5D presented in a frequency histogram. Results The majority of physiotherapists in this sample were younger than 30 years of age (n = 25, 56.8%) consistent with the presence of a high attrition rate. Almost all respondents exceeded minimum recommended physical activity guidelines (n = 40, 90.9%). Overall the respondents engaged in more vigorous physical activity (median = 180 minutes) and walking (median = 135 minutes) than moderate exercise (median = 35 minutes) each week. Thirty-seven (84.1%) participants reported no pain or discomfort impacting their health-related quality of life, with most (n = 35,79.5%) being in full health. Conclusions Physical-conditioning based interventions for the prevention of musculoskeletal disorders among practicing physiotherapists may be better targeted to role or task specific conditioning rather than general physical conditioning among this physically active population. It is plausible that an inherent attrition of physiotherapists may occur among those not as active or healthy as therapists who cope with the physical demands of clinical practice. Extrapolation of findings from this study may be limited due to the sample characteristics. However, this investigation addressed the study objectives and has provided a foundation for larger scale longitudinal investigations in this field.

The impact of the built environment on health across the life course : design of a cross-sectional data linkage study

Introduction: The built environment is increasingly recognised as being associated with health outcomes. Relationships between the built environment and health differ among age groups, especially between children and adults, but also between younger, mid-age and older adults. Yet few address differences across life stage groups within a single population study. Moreover, existing research mostly focuses on physical activity behaviours, with few studying objective clinical and mental health outcomes. The Life Course Built Environment and Health (LCBEH) project explores the impact of the built environment on self-reported and objectively measured health outcomes in a random sample of people across the life course. Methods and analysis: This cross-sectional data linkage study involves 15 954 children (0–15 years), young adults (16–24 years), adults (25–64 years) and older adults (65+years) from the Perth metropolitan region who completed the Health and Wellbeing Surveillance System survey administered by the Department of Health of Western Australia from 2003 to 2009. Survey data were linked to Western Australia's (WA) Hospital Morbidity Database System (hospital admission) and Mental Health Information System (mental health system outpatient) data. Participants’ residential address was geocoded and features of their ‘neighbourhood’ were measured using Geographic Information Systems software. Associations between the built environment and self-reported and clinical health outcomes will be explored across varying geographic scales and life stages. Ethics and dissemination: The University of Western Australia's Human Research Ethics Committee and the Department of Health of Western Australia approved the study protocol (#2010/1). Findings will be published in peer-reviewed journals and presented at local, national and international conferences, thus contributing to the evidence base informing the design of healthy neighbourhoods for all residents.

Cross-cultural web user interface design for Indigenous internet users

This project investigated 1) Australian web designers’ cultural perceptions towards Australian Indigenous users and 2) Australian Indigenous cultural features in terms of user interface design. In doing so, it reviews the literature of cross-cultural user interface design by focusing on feasible models and arguments to articulate and integrate Australian Indigenous Internet users’ cultural needs of web user interface. The online survey results collected from 101 Indigenous users and 126 Web designers showed a distinctive difference between them on the integration of Indigenous users' cultural in Web sites. The interview data collected from 14 Indigenous users and 14 web designers suggested practical approaches to the design implications of Indigenous culture.

Cross-layer design for traffic management in wireless networked control systems

Wireless networked control systems (WNCSs) have been increasingly deployed in industrial applications. As they require timely data packet transmissions, it is difficult to make efficient use of the limited channel resources, particularly in contention based wireless networks in the layered network architecture. Aiming to maintain the WNCSs under critical real-time traffic condition at which the WNCSs marginally meet the real-time requirements, a cross-layer design (CLD) approach is presented in this paper to adaptively adjust the control period to achieve improved channel utilization while still maintaining effective and timely packet transmissions. The effectiveness of the proposed approach is demonstrated through simulation studies.

A finite volume method with linearisation in time for the solution of advection-reaction-diffusion systems

The numerical solution in one space dimension of advection--reaction--diffusion systems with nonlinear source terms may invoke a high computational cost when the presently available methods are used. Numerous examples of finite volume schemes with high order spatial discretisations together with various techniques for the approximation of the advection term can be found in the literature. Almost all such techniques result in a nonlinear system of equations as a consequence of the finite volume discretisation especially when there are nonlinear source terms in the associated partial differential equation models. This work introduces a new technique that avoids having such nonlinear systems of equations generated by the spatial discretisation process when nonlinear source terms in the model equations can be expanded in positive powers of the dependent function of interest. The basis of this method is a new linearisation technique for the temporal integration of the nonlinear source terms as a supplementation of a more typical finite volume method. The resulting linear system of equations is shown to be both accurate and significantly faster than methods that necessitate the use of solvers for nonlinear system of equations.

Modeling perceived influences on journalism : evidence from a cross-national survey of journalists

Surveying 1,700 journalists from seventeen countries, this study investigates perceived influences on news work. Analysis reveals a dimensional structure of six distinct domains—political, economic, organizational, professional, and procedural influences, as well as reference groups. Across countries, these six dimensions build up a hierarchical structure where organizational, professional, and procedural influences are perceived as more powerful limits to journalists' work than political and economic influences.

Does gender determine journalists' professional views? A reassessment based on cross-national evidence

Research into journalism and gender to date has found somewhat contradictory evidence as to the ways in which women and men practice journalism. While some scholars claim that women have inherently different concepts and practices of journalism and that this has led to a feminization of journalism, others have found little evidence to suggest that men and women differ significantly in terms of their role conceptions. While numerous studies have been conducted into this issue around the world, few have taken a truly comparative approach. This paper presents results from a large-scale comparative survey into gender differences in journalists’ professional views in 18 diverse countries around the world. Results suggest that women and men do not differ in any meaningful ways in their role conceptions on neither the individual level, in newsrooms dominated by women, nor in socio-cultural contexts where women have achieved a certain level of empowerment.

Reaction of Aromatic Peroxyl Radicals with Alkynes: A Mass Spectrometric and Computational Study Using the Distonic Radical Ion Approach

The reaction of the aromatic distonic peroxyl radical cations N-methyl pyridinium-4-peroxyl (PyrOO center dot+) and 4-(N,N,N-trimethyl ammonium)-phenyl peroxyl (AnOO center dot+), with symmetrical dialkyl alkynes 10?ac was studied in the gas phase by mass spectrometry. PyrOO center dot+ and AnOO center dot+ were produced through reaction of the respective distonic aryl radical cations Pyr center dot+ and An center dot+ with oxygen, O2. For the reaction of Pyr center dot+ with O2 an absolute rate coefficient of k1=7.1X10-12 cm3 molecule-1 s-1 and a collision efficiency of 1.2?% was determined at 298 K. The strongly electrophilic PyrOO center dot+ reacts with 3-hexyne and 4-octyne with absolute rate coefficients of khexyne=1.5X10-10 cm3 molecule-1 s-1 and koctyne=2.8X10-10 cm3 molecule-1 s-1, respectively, at 298 K. The reaction of both PyrOO center dot+ and AnOO center dot+ proceeds by radical addition to the alkyne, whereas propargylic hydrogen abstraction was observed as a very minor pathway only in the reactions involving PyrOO center dot+. A major reaction pathway of the vinyl radicals 11 formed upon PyrOO center dot+ addition to the alkynes involves gamma-fragmentation of the peroxy O?O bond and formation of PyrO center dot+. The PyrO center dot+ is rapidly trapped by intermolecular hydrogen abstraction, presumably from a propargylic methylene group in the alkyne. The reaction of the less electrophilic AnOO center dot+ with alkynes is considerably slower and resulted in formation of AnO center dot+ as the only charged product. These findings suggest that electrophilic aromatic peroxyl radicals act as oxygen atom donors, which can be used to generate alpha-oxo carbenes 13 (or isomeric species) from alkynes in a single step. Besides gamma-fragmentation, a number of competing unimolecular dissociative reactions also occur in vinyl radicals 11. The potential energy diagrams of these reactions were explored with density functional theory and ab initio methods, which enabled identification of the chemical structures of the most important products.

Ozone-induced dissociation of conjugated lipids reveals significant reaction rate enhancements and characteristic odd-electron product ions

Ozone-induced dissociation (OzID) is an alternative ion activation method that relies on the gas phase ion-molecule reaction between a mass-selected target ion and ozone in an ion trap mass spectrometer. Herein, we evaluated the performance of OzID for both the structural elucidation and selective detection of conjugated carbon-carbon double bond motifs within lipids. The relative reactivity trends for \[M + X](+) ions (where X = Li, Na, K) formed via electrospray ionization (ESI) of conjugated versus nonconjugated fatty acid methyl esters (FAMEs) were examined using two different OzID-enabled linear ion-trap mass spectrometers. Compared with nonconjugated analogues, FAMEs derived from conjugated linoleic acids were found to react up to 200 times faster and to yield characteristic radical cations. The significantly enhanced reactivity of conjugated isomers means that OzID product ions can be observed without invoking a reaction delay in the experimental sequence (i.e., trapping of ions in the presence of ozone is not required). This possibility has been exploited to undertake neutral-loss scans on a triple quadrupole mass spectrometer targeting characteristic OzID transitions. Such analyses reveal the presence of conjugated double bonds in lipids extracted from selected foodstuffs. Finally, by benchmarking of the absolute ozone concentration inside the ion trap, second order rate constants for the gas phase reactions between unsaturated organic ions and ozone were obtained. These results demonstrate a significant influence of the adducting metal on reaction rate constants in the fashion Li > Na > K.