bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning
Authors: Vokes Steven A. , Ji Hongkai , McCuine Scott , Tenzen Toyoaki , Giles Shane , Zhong Sheng , Longabaugh William J. R. , Davidson Eric H. , Wong Wing H. , McMahon Andrew P.
Published: April 2007

Sonic hedgehog (Shh) acts as a morphogen to mediate the specification of distinct cell identities in the ventral neural tube through a Gli-mediated(Gli1-3) transcriptional network. Identifying Gli targets in a systematic fashion is central to the understanding of the action of Shh. We examined this issue in differentiating neural progenitors in mouse. An epitope-tagged Gli-activator protein was used to directly isolate cis-regulatory sequences by chromatin immunoprecipitation (ChIP). ChIP products were then used to screen custom genomic tiling arrays of putative Hedgehog (Hh) targets predicted from transcriptional profiling studies, surveying 50-150 kb of non-transcribed sequence for each candidate. In addition to identifying expected Gli-target sites, the data predicted a number of unreported direct targets of Shh action. Transgenic analysis of binding regions in Nkx2.2, Nkx2.1 (Titf1) and Rab34 established these as direct Hh targets. These data also facilitated the generation of an algorithm that improved in silico predictions of Hh target genes. Together, these approaches provide significant new insights into both tissue-specific and general transcriptional targets in a crucial Shh-mediated patterning process.
A Dynein-dependent shortcut rapidly delivers axis determination transcripts into theDrosophilaoocyte
Authors: Clark Alejandra , Meignin Carine , Davis Ilan
Published: April 2007

The primary axes of Drosophila are set up by the localization of transcripts within the oocyte. These mRNAs originate in the nurse cells, but how they move into the oocyte remains poorly understood. Here, we study the path and mechanism of movement of gurken RNA within the nurse cells and towards and through ring canals connecting them to the oocyte. gurken transcripts, but not control transcripts, recruit the cytoplasmic Dynein-associated co-factors Bicaudal D (BicD) and Egalitarian in the nurse cells. gurken RNA requires BicD and Dynein for its transport towards the ring canals, where it accumulates before moving into the oocyte. Our results suggest that bicoid and oskartranscripts are also delivered to the oocyte by the same mechanism, which is distinct from cytoplasmic flow. We propose that Dynein-mediated transport of specific RNAs along specialized networks of microtubules increases the efficiency of their delivery, over the flow of general cytoplasmic components,into the oocyte.
The basis and management of metabolic abnormalities associated with cardiovascular risk in human immunodeficiency virus infection and its treatment
Authors: Crook Martin
Published: April 2007

The high global prevalence of human immunodeficiency virus (HIV) infection has been associated with high morbidity and mortality. The advent of highly active antiretroviral therapy (HAART) has, however, dramatically increased survival of patients infected with HIV. These patients now survive to develop metabolic complications of HIV infection and its treatment, including increased predisposition to atherosclerotic disease. HIV infection is normally associated with hypocholesterolaemia, hypertriglyceridaemia, low plasma HDL-cholesterol as well as alterations in other cardiovascular risk factors including inflammatory markers, clotting factors, homocysteine, apolipoproteins, lipoprotein (a), oxidative stress and non-esterified fatty acids. The use of HAART is, in particular, associated with dyslipidaemia and lipodystrophy with underlying insulin resistance and associated glucose intolerance. This article explores the metabolic abnormalities associated with increased cardiovascular risk that occur in HIV infection before and after antiretroviral therapy. The laboratory investigation and clinical management of HIV-associated dyslipidaemia and lipodystrophy will be discussed.
Newer cardiac troponin I assays have similar performance to troponin T in patients with end-stage renal disease
Authors: Hickman Peter E , Koerbin Gus , Southcott Emma , Tate Jill , Dimeski Goce , Carter Andrew , McGill Darryl , Talaulikar Girish , Potter Julia M
Published: April 2007

Background: Troponin T is present in the blood of a majority of patients with endstage renal disease (ESRD) undergoing regular dialysis and presence of troponin T is a predictor of adverse outcome in these patients. With several new formulations of troponin I assays available, this study was performed to see whether these newer assays were able to detect troponin I in these patients more effectively than the older assays.

Methods: One hundred and forty-three patients undergoing regular haemodialysis or peritoneal dialysis had plasma collected and troponin T and troponin I measured by a variety of assays.

Results: The newer troponin I assays (Abbott Architect, Bayer Centaur and Beckman Accu-TnI) were able to detect troponin I (>75% of samples) as effectively as the Roche assay was able to detect troponin T, while other troponin I assays had a much lower rate of detection of troponin - DPC Immulite 2000 16% and Abbott AxSYM 35%. However, the troponin T assay had more samples detected at concentrations corresponding to an assay CV of 10% (59% of samples) than did the newer troponin I assays (highest on the Bayer Centaur at 37%).

Conclusions: Newer assays demonstrate that troponin I is present in a similar number of samples as is troponin T, in the blood of patients with dialysis-dependent renal failure, and these newer troponin I assays identify patients at risk of experiencing a cardiac event.
Quartz renal calculi: were we being led up the garden path?
Authors: Sies C W , Cadwallader J , Florkowski C M , Woods S H , George P M
Published: April 2007

Quartz stones are often considered to be of non-human origin or factitious, although in some cases, they may have a biological aetiology. X-ray diffraction (XRD) spectroscopy was used to analyse fragmented renal stones from a 61-year-old lady who presented with bilateral nephrocalcinosis. Analysis of the calculi from the left kidney showed a mixed composition: 50% calcium oxalate monohydrate and 50% quartz. This case highlights the usefulness of XRD in the differentiation of authentic from possibly factitious renal calculi.
Overview on robotics in the laboratory
Authors: Wheeler M J
Published: April 2007

This review provides a short history of the development of robotic systems in Clinical Chemistry and discusses the early expectations for these systems. The systems currently available are discussed and every attempt has been made to keep this section up-to-date, but this is a constantly changing field. Much of the review is taken up looking at the impact resulting from the introduction of robotic systems in the laboratory and whether they have met the expectations of the laboratory. It is difficult to get hard data since laboratories are most concerned with getting their instrumentation up and running and there is little time, or thought given, to pre- and post-introduction studies. Therefore, the literature is sparse but much of the data for the UK has come from a Medicines and Healthcare products Regulatory Agency (MHRA) review of pre-analytical systems. Finally thought has been given to future developments and their possible impact on the functioning of the laboratory.
Hypokalaemic rhabdomyolysis
Authors: Kishore Bhuvan , Thurlow Vanessa , Kessel Belinda
Published: April 2007

Hypokalaemic rhabdomyolysis is unusual, but the association between hypokalaemia and rhabdomyolysis can be overlooked if intracellular potassium leakage normalizes serum potassium by the time of presentation. This report describes a patient who presented with severe pain due to non-traumatic rhabdomyolysis and was found to have serum potassium of 1.4 mmol/L; magnesium 0.40 mmol/L; phosphate 1.40 mmol/L; adjusted calcium 1.87 mmol/L and creatine kinase 6421 U/L. In this case, intervention occurred before rhabdomyolysis could progress to the stage at which serum potassium may have self-corrected. This patient's hypokalaemia was at first refractory to treatment with potassium chloride, possibly due to coexisting magnesium deficiency. Initially, the patient denied alcohol abuse, but later admitted alcohol misuse prior to withdrawal three days before presentation. Hypokalaemia is associated with alcohol misuse, but abrupt withdrawal may exacerbate hypokalaemia and hypomagnesaemia. Acute or chronic myopathy is common in alcoholics due to alcohol toxicity and paradoxically the risk of rhabdomyolysis may be increased during periods of abrupt alcohol withdrawal.
Osteopontin and C-reactive protein in Egyptian patients affected with tuberculous and malignant pleural effusion
Authors: Elsammak M Mohamed Y , Morsi Tamer S , Khamis Hend I , Ragab Mahmoud S , Zaki Moyassar A , Abdel-Hadi Mona , Hassan Hoda A
Published: April 2007

Background: The first step in the evaluation of patients with pleural effusion is to determine whether the effusion is a transudate or an exudate. Osteopontin (OPN) is a pleiotropic integrin-binding protein with many functions. We assessed pleural effusion and serum concentrations of OPN and C-reactive protein (CRP) in patients with different types of pleural effusions.

Methods: The current study comprised three groups: 20 patients with transudative effusion, 30 patients with malignant effusion and 30 patients with tuberculous effusion. OPN was analysed using a commercially available enzyme-linked immunosorbent assay kit.

Results: OPN effusion values were significantly higher in exudates (both malignant and tuberculous effusion cases) compared with transudative effusion. Also when compared separately, patients with tuberculous effusion and those with malignant effusion had a significantly higher fluid and OPN effusion/serum ratio than those with transudative effusion. Patients with tuberculous effusion had a significantly higher serum CRP effusion and effusion/serum ratio of CRP than those with malignant or transudative effusion.

Conclusion: OPN is significantly increased in exudative effusion compared with transudative ones. However, serum OPN and effusion/serum OPN ratio were not significantly different in patients with malignant from those with tuberculous effusions. The lack of difference in serum OPN and effusion/serum OPN ratio between patients with malignant and those with tuberculous effusion may be attributed to the heterogeneity of the malignant effusion group. Receiver-operating characteristic (ROC) curve analysis has shown that effusion/serum CRP ratio outperformed effusion/serum OPN ratio as a diagnostic marker for tuberculous pleural effusion.
Metabolic syndrome and cardiovascular disease
Authors: Qiao Qing , Gao Weiguo , Zhang Lei , Nyamdorj Regzedmaa , Tuomilehto Jaakko
Published: April 2007

The clustering of metabolic and pathophysiological cardiovascular risk factors has long been recognized but it was Reaven who popularized the syndrome in the Banting lecture of 1988. Since 1999, several major international or national organizations proposed their own definitions for the syndrome, named the metabolic syndrome. The prevalence of the metabolic syndrome varies according to definition, ethnicity and gender. The prevalence is under 20% among Chinese and Korean people but over 50% among Maori and Pacific Islanders in New Zealand. People with the metabolic syndrome have 50-60% higher cardiovascular risk than those without. The absolute cardiovascular risk of the metabolic syndrome, however, is not necessarily higher than those of its individual components. The pathogenesis underlying the clustering of cardiovascular risk factors remains unclear. Factors including genetic disposition, obesity, insulin resistance and inflammation have been suggested as being involved. Since the metabolic syndrome is multifactorial in origin, strategies for reducing cardiovascular risk in individuals with the metabolic syndrome involve the management of multiple risks. Lifestyle changes are an effective first-line management; pharmacological interventions for hypertension, diabetes and dyslipidaemia are in accordance with established guidelines. Pharmacological and surgical therapies for obesity are effective in selected patients. In this article we discuss the definitions, prevalence, pathogenesis and management of the metabolic syndrome in relation to cardiovascular risk.
Rotten apple or rotten barrel? Social identity and children's responses to bullying
Authors: Jones Sian E. , Haslam S. Alexander. , York Lucy. , Ryan Michelle K.
Published: April 2007

Recent research has suggested that bullying behaviour may be understood as a group process, where those involved act in ways predicted by social identity theory (Ojala & Nesdale, 2004). One relevant phenomenon is the black sheep effect, whereby individuals evaluate deviant members of their in‐group more negatively than that of an out‐group. To examine this process, a study was conducted (N = 60) in which 10‐ and 11‐year‐old children were randomly assigned to a high‐status, peripheral or irrelevant group. They were then read a scenario in which a member of the high‐status group bullied a person outside the group and was supported by other high‐status group members. It was found that assigned group membership affected judgements of the acceptability of the bullying behaviour and the likeability of both (a) the high‐status group and (b) the high‐status group member. Specifically, evidence of a black sheep effect meant that high‐status group members showed less liking for the high‐status group member than for the high‐status group, and believed that this member deserved greater punishment than the high‐status group as a whole. Peripheral group members differentiated between the high‐status group member and the high‐status group in terms of liking but not punishment, while members of the irrelevant group did not make a distinction on either measure. Implications for the conceptualization of bullying are discussed.
Are modern health worries, personality and attitudes to science associated with the use of complementary and alternative medicine?
Authors: Furnham Adrian
Published: April 2007

Objectives. To investigate whether personality traits, modern health worries (MHWs) and attitudes to science predict attitudes to, and beliefs about, complementary and alternative medicine (CAM). This study set out to test whether belief in, and use of CAM was significantly associated with high levels of MHWs, a high level of neuroticism and sceptical attitudes towards science.

Methods. Two hundred and forty‐three British adults completed a four part questionnaire that measured MHWs, the Big Five personality traits and beliefs about science and medicine and attitudes to CAM.

Results. There were many gender differences in MHWs (females expressed more), though results were similar to previous studies. Contrary to prediction, personality traits were not related to MHWs, CAM usage or beliefs about CAM. Regular and occasional users of CAM did have higher MHWs than those non or infrequent users. Those with high totalled MHWs also tended to believe in the importance of psychological factors in health and illness, as well as the potential harmful effects of modern medicine. Young males who had positive attitudes to science were least likely to be CAM users. Further, positive attitudes to science were associated with increased scepticism about CAM.

Conclusion. Concern about health, belief about modern medicine and CAM are logically inter‐related. Those who have high MHWs tend to be more sceptical about modern medicine and more convinced of the possible role of psychological factors in personal health and illness.
Daily patterns of symptom reporting in families with adolescent children
Authors: Michel Gisela
Published: April 2007

Objectives. This study was designed to investigate how symptom reporting varies by time of day, day of the week, gender and generation.

Design. Concurrent symptom reporting was assessed prospectively using a computer‐assisted self‐report method.

Methods. A computer‐assisted self‐observation method was used to assess concurrent somatic complaints six times a day for 7 consecutive days. Parents and adolescents from 173 families (568 individuals) filled in questionnaires during a normal workweek. A generalized linear model approach for multi‐level models was used to analyse the multiple daily observations.

Results. Results show a curvilinear within‐day pattern for the reporting of somatic complaints, such that complaints were reported most in the morning and evening and least in the middle of the day. On weekends, participants reported fewer complaints in the evening. Women reported more symptoms throughout the day. Adolescents show an earlier and more pronounced increase in symptom reporting towards the evening. In addition, a slight decline in symptom reporting over the observation period was observed.

Conclusion. Symptom reporting changes throughout the day, and is influenced by gender, generation and day of the week.
‘How do you explain a pain that can't be seen?’: The narratives of women with chronic pelvic pain and their disengagement with the diagnostic cycle
Authors: McGowan Linda , Luker Karen , Creed Francis , Chew‐Graham Carolyn A.
Published: April 2007

Objectives. Chronic pelvic pain (CPP) has an adverse effect on women's quality of life. Research has suggested that many women become dissatisfied with their care and withdraw from seeking help despite continuing symptoms. The aim of this study was to explore the processes which lead to disengagement and to understand the psychosocial processes that affect this group of women.

Design. A qualitative narrative approach was used, guided by phenomenological‐hermeneutic tradition, and informed by the philosophy of Paul Ricoeur.

Method. Thirty‐two women with CPP were asked to write their stories about their illness trajectories. These written stories served as data which were analysed thematically according to narrative theory.

Results. In the search for validation and recognition women engaged in the diagnostic cycle. Many women do not complete this cycle, become stuck at a certain point, or re‐enter the cycle repeatedly. They can only opt out if the problem is resolved or by choosing to disengage with medical care.

Conclusion. While the medical consultation was a dominant theme, a complex interaction of factors was required to initiate disengagement. The dualistic nature of the diagnostic process prohibits women from telling their stories. Women were left feeling disempowered and in limbo, and they were at a loss as to how to manage their pain.
Literacy not intelligence moderates the relationships between economic development, income inequality and health
Authors: Marks David F.
Published: April 2007

Objectives.Kanazawa (2006)presented data allegedly supporting a racist version of evolutionary psychology that claims that the populations of wealthier and more egalitarian societies live longer and stay healthier, not because they are wealthier and more egalitarian, but because they are more intelligent. The objectives of this study are: (i) to determine the relationship between IQ and literacy in Kanazawa's sample of countries and (ii) to reanalyse Kanazawa's dataset using measures of literacy in lieu of national IQ test scores.

Method.Correlation and regression were employed.

Results.National literacy scores across the countries in the sample are highly skewed. In spite of this, the literacy measures are highly correlated with alleged differences in national IQ (r= .83–.86). The measure of literacy together with economic development (GDPpc) and income inequality (Gini coefficient) control at least 59–64% of the variance in national life expectancy at birth.

Conclusion.There is no scientific justification for believing that alleged intelligence differences play any role in explaining international differences in health status. Measures of alleged national IQ scores are highly confounded with differences in literacy. Literacy is a key factor in the health of any community and policies designed to enhance the literacy of a population are expected to lead to significant improvements in health status.
A commentary on Satoshi Kanazawa's study of intelligence and health
Authors: Alemayehu Demissie , Sineshaw Tilahun
Published: April 2007

We provide an exposition of the major conceptual, methodological and statistical shortcomings of the paper byKanazawa (2006), concerning the relationship between intelligence and life expectancy. It is argued that the validity and robustness of the conclusions of the paper are compromised by fundamental problems, including failure to present competing views with fair balance, use of samples of convenience to draw conclusions about populations, performing tests of significance when there is no theoretical basis to do so and confusing association with causation. Given the far‐reaching socio‐economic implications of the conclusions, it is suggested that the messages of the paper be critically evaluated in relation to the major limitations of the research.
From Curdlan Powder to the Triple Helix Gel Structure: An Attenuated Total Reflection—Infrared Study of the Gelation Process
Authors: Gagnon Marc-André , Lafleur Michel
Published: April 2007

Infrared spectroscopy was used to probe the hydration and gelation of curdlan, a linear polysaccharide built from repeating units of (1→3)-β-D-glucose. The spectra have been recorded using a temperature-controlled attenuated total reflection (ATR) device. Thermal gelation of curdlan could therefore be followed in situ and in real time. The transformation of the low-set gel, mainly formed with single helices, into a high-set gel, associated with a triple helix structure, could be directly observed. The relative intensities and positions of characteristic absorption bands in the C–O region (1200–850 cm−1) were found to be representative of the gel structure, as they are believed to be sensitive to the helical conformation of the polymer chains. Infrared (IR) spectroscopy is shown to be a useful tool for rapid and efficient characterization of curdlan gels.
Bayesian Maximum Entropy (Two-Dimensional) Lifetime Distribution Reconstruction from Time-Resolved Spectroscopic Data
Authors: Lórenz-Fonfría Victor A. , Kandori Hideki
Published: April 2007

Time-resolved spectroscopy is often used to monitor the relaxation processes (or reactions) of physical, chemical, and biochemical systems after some fast physical or chemical perturbation. Time-resolved spectra contain information about the relaxation kinetics, in the form of macroscopic time constants of decay and their decay associated spectra. In the present paper we show how the Bayesian maximum entropy inversion of the Laplace transform (MaxEnt-iLT) can provide a lifetime distribution without sign-restrictions (or two-dimensional (2D)-lifetime distribution), representing the most probable inference given the data. From the reconstructed (2D) lifetime distribution it is possible to obtain the number of exponentials decays, macroscopic rate constants, and exponential amplitudes (or their decay associated spectra) present in the data. More importantly, the obtained (2D) lifetime distribution is obtained free from pre-conditioned ideas about the number of exponential decays present in the data. In contrast to the standard regularized maximum entropy method, the Bayesian MaxEnt approach automatically estimates the regularization parameter, providing an unsupervised and more objective analysis. We also show that the regularization parameter can be automatically determined by the L-curve and generalized cross-validation methods, providing (2D) lifetime reconstructions relatively close to the Bayesian best inference. Finally, we propose the use of MaxEnt-iLT for a more objective discrimination between data-supported and data-unsupported quantitative kinetic models, which takes both the data and the analysis limitations into account. All these aspects are illustrated with realistic time-resolved Fourier transform infrared (FT-IR) synthetic spectra of the bacteriorhodopsin photocycle.
Transfer of Near-Infrared Calibration Model for Determining Fiber Content in Flax: Effects of Transfer Samples and Standardization Procedure
Authors: Sohn Miryeong , Barton Franklin E. , Himmelsbach David S.
Published: April 2007

The transfer of a calibration model for determining fiber content in flax stem was accomplished between two near-infrared spectrometers, which are the same brand but which require a standardization. In this paper, three factors, including transfer sample set, spectral type, and standardization method, were investigated to obtain the best standardization result. Twelve standardization files were produced from two sets of the transfer sample (sealed reference standards and a subset of the prediction set), two types of the transfer sample spectra (raw and preprocessed spectra), and three standardization methods (direct standardization (DS), piecewise direct standardization (PDS), and double window piecewise direct standardization (DWPDS)). The efficacy of the model transfer was evaluated based on the root mean square error of prediction, calculated using the independent prediction samples. Results indicated that the standardization using the sealed reference standards was unacceptable, but the standardization using the prediction subset was adequate. The use of the preprocessed spectra of the transfer samples led to the calibration transfers that were successful, especially for the PDS and the DWPDS correction. Finally, standardization using the prediction subset and their preprocessed spectra with DWPDS correction proved to be the best method for transferring the model.
Variations in Predicted Values from Near-Infrared Spectra of Samples in Vials by Using a Calibration Model Developed from Spectra of Samples in Vials: Causes of the Variations and Compensation Methods
Authors: Watari Masahiro , Du Yiping , Ozaki Yukihiro
Published: April 2007

The causes and compensation methods of variations in the predicted values from near-infrared (NIR) spectra of samples in vials by using a calibration model developed from spectra of samples in vials were studied. From the viewpoint of the path length and the peak height of spectra in the NIR region, vials with 1 mL volume (external diameter: 8 mm, inside diameter: about 6 mm, length: 40 mm) were selected as disposable vials for the samples. To investigate the causes of the variations in the predicted values, the optical path lengths and transmittance spectra of empty vials in five lots produced during the last four years were examined. The results showed that there were some differences in the path lengths of the vials and in the intensities of peaks near 7130 and 4515 cm−1, which were attributed to the hydroxyl groups in the spectra of the vials among the five lots. The calibration models for the concentration of isopropyl alcohol (IPA) in toluene contained in vials of the same lot were developed. To search the pretreatment methods for the best calibration model with small variations in the predictive values of the samples in the vials, six kinds of pretreatments (no pretreatment, baseline correction, first derivative, second derivative, multiplicative scattering correction (MSC), and standard normal variate (SNV)) were compared. The results indicated that MSC is a very effective method with small variation in the predicted values from the spectra of samples in vials. It was found that the variations in the predicted values are caused mainly by variations in the path lengths of vials. In real quality control, the NIR-chemometrics method is requested for long-term traceability and good reproducibility of the predictive value. Therefore, it is crucial to watch changes in the path length under a fixed path length as a reference. From this standpoint, modified MSC, which uses a particular spectrum as a reference instead of the average spectrum of a sample set, was proposed in the present study, and it was demonstrated that the variations due to the individual differences in the vials can not only be compensated, but the path lengths of vials could also be estimated by the modified MSC. Moreover, a calibration model for the toluene concentration in silicone oil was developed to confirm the effects of modified MSC by using another sample set. The results showed that the compensation of vial path lengths using the modified MSC is also useful for other samples, similar to the case of the sample of IPA in toluene.
Portable Radiometer: A Novel Technique for in Situ Band Gap Measurements
Authors: Ravi Jyotsna , Lee S. Thomas , Paulraj M. , Hernandez Rolando
Published: April 2007

Portable radiometers are commonly used in remote sensing applications for studying vegetation, soil, minerals, etc. However, we propose and demonstrate, for the first time, the applicability of this radiometer for high-resolution in situ band gap measurements of materials. The excitation source can be any white light source such as sun or tungsten halogen lamp. The flexibility in sample size and relative ease of varying temperature during measurements add to the advantages of using a portable radiometer for investigating new materials. Accurate measurements were made on standard samples of silicon, germanium, and gallium antimonide to demonstrate the feasibility of this technique.
Spectral Simulation Methodology for Calibration Transfer of Near-Infrared Spectra
Authors: Sulub Yusuf , Small Gary W.
Published: April 2007

A spectrum simulation method is described for use in the development and transfer of multivariate calibration models from near-infrared spectra. By use of previously measured molar absorptivities and solvent displacement factors, synthetic calibration spectra are computed using only background spectra collected with the spectrometer for which a calibration model is desired. The resulting synthetic calibration set is used with partial least squares regression to form the calibration model. This methodology is demonstrated for use in the analysis of physiological levels of glucose (1–30 mM) in an aqueous matrix containing variable levels of alanine, ascorbate, lactate, urea, and triacetin. Experimentally measured data from two different Fourier transform spectrometers with different noise levels and stabilities are used to evaluate the simulation method. With the more stable instrument (A), well-performing calibration models are obtained, producing a standard error of prediction (SEP) of 0.70 mM. With the less stable instrument (B), the calibration based solely on synthetic spectra is less successful, producing an SEP value of 1.58 mM. For cases in which the synthetic spectra do not describe enough spectral variance, an augmentation protocol is evaluated in which the synthetic calibration spectra are augmented with the spectra of a small number of experimentally measured calibration samples. For instruments A and B, respectively, augmentation with measured spectra of nine samples lowers the SEP values to 0.64 and 0.85 mM.
Detection of Trace Water Vapor in High-Purity Phosphine Using Cavity Ring-Down Spectroscopy
Authors: Funke Hans H. , Raynor Mark W. , Bertness Kris A. , Chen Yu
Published: April 2007

The presence of trace water vapor in process gases such as phosphine, used for compound semiconductor epitaxial growth, can negatively affect the optical and electrical properties of the final device. Therefore, sensitive H2O measurement techniques are required to monitor precursor purity and detect unacceptable contamination levels. A commercial cavity ring-down spectrometer that monitors an H2O absorption line at a wavelength of 1392.53 nm was investigated for service in high purity PH3. Spectral parameters such as the line shape of water vapor in the presence of PH3 as well as background features due to PH3 were measured at different pressures and incorporated into the data analysis software for accurate moisture readings. Test concentrations generated with a diffusion vial-based H2O source and dilution manifold were used to verify instrument accuracy, sensitivity, linearity, and response time. H2O readings at 13.2 kPa corresponded well to added concentrations (slope = 0.990 ± 0.01) and were linear in the tested range (0–52.7 nmol mol−1). The analyzer was sensitive to changes in H2O concentration of 1.3 nmol mol−1 based on 3σ of the calibration curve intercept for a weighted linear fit. Local PH3 absorption features that could not be distinguished from the H2O line were present in the purified PH3 spectra and resulted in an additional systematic uncertainty of 9.0 nmol mol−1. Equilibration to changing H2O levels at a flow rate of 80 std cm3 min−1 PH3 occurred in 10–30 minutes. The results indicate that cavity ring-down spectroscopy (CRDS) at 1392.53 nm may be useful for applications such as on-line monitoring (and dry-down) of phosphine gas delivery lines or the quality control of cylinder sources.
Diffusion Measurements in Binary Liquid Mixtures by Raman Spectroscopy
Authors: Berg Rolf W. , Hansen Susanne Brunsgaard , Shapiro Alexander A. , Stenby Erling H.
Published: April 2007

It is shown that Raman spectroscopy allows determination of the molar fractions in mixtures subjected to molecular diffusion. Spectra of three binary systems, benzene/n-hexane, benzene/cyclohexane, and benzene/acetone, were obtained during vertical (exchange) diffusion at several different heights ( z) as a function of time. A procedure to determine time-dependent concentration profiles and diffusion coefficients is described in detail for one system, and results are given for the two other cases. For the system benzene/cyclohexane, much lower diffusion coefficients than reported in the literature were found, even in a thermostatically controlled diffusion cell, recording spectra through circulating water. For the system benzene/acetone, the determined diffusion coefficients were in good agreement with the literature data. The limitations of the Raman method are discussed, and it is concluded that many more systems ought to be studied. It is pointed out that diffusion profiles can be obtained in ternary and higher systems, where proper measurements are almost nonexistent.
Client-driven biotechnology research for poor farmers: a case study from India
Authors: Clark Norman , Reddy Pakki , Hall Andrew
Published: April 2007

This paper explores an attempt to bring biotechnology more directly within the ambit of civil society in general and resource-poor farmers in particular. The Andhra Pradesh Netherlands Biotechnology Programme (APNLBP) was one of four country programmes initiated by Dutch aid in the
early 1990s. It is coming to an end as an aid project next year. The broad objective of the programme was to contribute to poverty alleviation through biotechnologies but to do so in a rather unique way. Instead of having R&D laboratories develop a raft of new technologies and then disseminating
these to farmers, the emphasis was put on direct interaction with farmers and related stakeholder groups such as non-governmental organizations (NGOs). The paper describes the programme's inception and evolution, outlines key governance aspects and sets the analytical discussion within the
context of modern innovation systems discourse. Two aspects in particular are emphasized. The first is the degree of connectivity among the different stakeholders that are part of the system. It is now well recognized that it is the flow of information across stakeholder groups that often
determines the degree of technological development that occurs, although clearly there are other factors also involved. The second is the importance of institutions and institutional change in enabling successful innovation to take place.
An analysis of factors influencing the development of new products in the Thai food industry
Authors: Huq M , Toyama M
Published: April 2007

The paper examines the role played by various factors in the development of new products in the Thai food industry. Data collected from a sample survey covering 62 firms in the four main subsectors of the Thai food industry are examined using both multiple regression and pair comparison
analyses. From the regression analysis based on six selected independent variables (firm-size, age, ownership, market orientation, promotional status and product type), only firm-size was found to be a statistically significant determinant of technological capability for the development of
new products. However, the pair-comparison analysis shows that various other factors can also be influential. These include senior management values, policy and strategy, management and administration, the system of rewards and promotion, information flows and links, and R&D activities.
Creating an Australian community public sphere: the role of community radio
Authors: Meadows Michael , Forde Susan , Ewart Jacqui , Foxwell Kerrie
Published: April 2007

The first comprehensive study of the Australian community radio sector at the turn of the millennium revealed insights into the contemporary operations of the sector, particularly in terms of its connections to communities, production of local content, and creation of a citizens media.
It offered an analysis of the people working in community radio their training levels, skills, personal profile, career goals and so on. This article looks specifically at the processes of the formation of a community public sphere in Australia through the activities of around 25,000 volunteers
and 4 million listeners each week in the sector across the country. It is particularly relevant in light of the recent trials and transmission of access radio in the United Kingdom, and the growth of community radio across Europe. As Australia was one of the few countries to legislate for
community radio in the early 1970s, the experience and development of community radio here is relevant to the sector's global development. The discussion considers some early findings from the first qualitative audience study of the sector by the authors.
Evaluation of Hoop-Net Size and Bait Selection for Sampling Channel Catfish in Iowa Impoundments
Authors: Flammang Mark K. , Schultz Randall D.
Published: April 2007

We compared seasonal catches of channel catfish Ictalurus punctatus between large (76-cm-diameter frames; 25-mm bar measure mesh) and small (61-cm-diameter frames; 19-mm bar measure mesh) tandem hoop-net series and between two different bait types (soybean cake and waste cheese) during 2004. Size structure data collected by both gears provided similar estimates of proportional stock density (PSD) for the gear and bait types within impoundments. Catch across seasons was similar within impoundments; however, estimates of PSD varied by season. Large hoop nets captured substantially more fish than the small hoop nets. Bait type did not significantly affect catch per unit effort (CPUE) of hoop nets except in summer, when nets baited with soybean cake captured significantly more (>1.5 times) channel catfish than nets baited with waste cheese. The CPUE precision was greatest for large hoop nets baited with soybean cake during summer or fall. We suggest use of large hoop nets and soybean cake as a standard summer sampling regime. Large hoop nets baited with soybean cake caught more fish, provided the most precise estimates of CPUE, had low levels of fish mortality, and were convenient for use during the summer, when management biologists have time to devote to channel catfish sampling. In addition, soybean cake is preferred over waste cheese because it produces less odor, has fewer storage problems, and can be obtained easily from local suppliers.
Assessing Coastwide Effects of Power Plant Entrainment and Impingement on Fish Populations: Atlantic Menhaden Example
Authors: Heimbuch Douglas G. , Lorda Ernesto , Vaughan Douglas , Barnthouse Lawrence W. , Uphoff Jim , Van Winkle Webster , Kahnle Andy , Young Byron , Young John , Kline Lisa
Published: April 2007

A method was developed for assessing coastwide effects of power plant impingement and entrainment on managed fish stocks. The method imbeds an assessment of anthropogenic effects that occur during the first year of life of fish (the period when most entrainment and impingement occur) into a standard age-structured stock assessment that addresses age-1 and older fish. The method thereby provides a straightforward means for comparing the effects of entrainment and impingement mortality to other forms of anthropogenic mortality affecting coastwide fish stocks. The method uses standard equations from fishery science that represent the relationships among independent competing forces of mortality, stock abundance, and landings. Power plant mortality is treated like fishing mortality, and power plant losses are treated like fishery landings. The total age-0 natural mortality rate is allocated to the individual age-0 life stages based on a power function relating daily natural mortality rates to age-specific dry weights of fish. An illustrative example of the use of the method is presented for the Atlantic coast stock of Atlantic menhaden Brevoortia tyrannus, which was chosen because it is a coastwide stock, has a coastwide fishery, and is described by high-quality fisheries-dependent data. However, because available entrainment and impingement data were not adequate to support defensible coastwide estimates of the annual numbers killed by entrainment and impingement, actual estimates of the effects of entrainment and impingement on the coastwide Atlantic menhaden stock could not be computed. The method could be used to address the effects of any form of anthropogenic mortality affecting age-0 fish, including loss of habitat, effects of toxic substances, fishing mortality, and fishery bycatch, provided that valid coastwide estimates of the annual numbers of fish killed by the source of mortality are available.
Evaluation of a Management Strategy to Control the Spread of Myxobolus cerebralis in a Lower Columbia River Tributary
Authors: Bartholomew Jerri L. , Lorz Harriet V. , Atkinson Stephen D. , Hallett Sascha L. , Stevens Donald G. , Holt Richard A. , Lujan Kenneth , Amandi Antonio
Published: April 2007

In October 2001, Myxobolus cerebralis, the myxozoan parasite that causes salmonid whirling disease, was detected in juvenile rainbow trout Oncorhynchus mykiss from a private hatchery that received water from Clear Creek, a tributary of the Clackamas River, Oregon. The Oregon Department of Fish and Wildlife closed the surface water portion of the hatchery in March 2003 and initiated a monitoring program to evaluate the success of the closure in containing further parasite spread. From 2002 to 2005, rainbow trout sentinels were held in live cages for 2 weeks at locations upstream, downstream, and within the area of the facility and then were tested for M. cerebralis infection. Infection prevalence in groups held in the hatchery pond, the outflow, and downstream of the facility was initially high; however, by May 2004 infection was no longer detected in Clear Creek, although the parasite continued to be detected in the hatchery pond. A single rainbow trout collected approximately 18 river kilometers upstream of the facility in 2002 was infected with M. cerebralis. The parasite was not detected in fish collected from other portions of the Clackamas River drainage, indicating that the introduction was limited. Tubifex tubifex, the invertebrate host for the parasite, were abundant in the hatchery ponds, but only a single specimen was identified in the main stem of Clear Creek. Actinospores of M. cerebralis were only detected in the hatchery waters. The monitoring indicated that the parasite had not become widely established in Clear Creek and that partial closure of the hatchery removed the primary source of infection for fish.
Comparison between Model‐Predicted and Field‐Measured Stream Habitat Features for Evaluating Fish Assemblage‐Habitat Relationships
Authors: Brenden Travis O. , Wang Lizhu , Clark Richard D. , Seelbach Paul W. , Lyons John
Published: April 2007

The use of model‐predicted, local‐scale habitat data as inputs in analyses intended to evaluate multiscale fish assemblage‐habitat relationships in streams has become increasingly common as the scale at which such studies are conducted has increased. We used fish assemblage and habitat data from 208 wadeable streams in Wisconsin and Michigan to determine whether model‐predicted habitat data would yield results similar to those of field‐measured data in multiscale analyses of fish assemblage‐habitat relationships. Predictions of local habitat features from landscape variables were generated by means of generalized additive modeling with likelihood‐based boosting. Relationships between fish assemblage measures and landscape and local habitat features were studied via partial constrained multivariate ordination analyses. The total variation explained in the fish assemblage data sets was similar for model‐predicted local habitat features and field‐measured data, as was the proportion of variation explained that was due independently to local and regional (i.e., landscape) habitat features. We observed dissimilar results in the magnitude of ordination scores for local habitat features and the directional relationships between local habitat ordination scores and individual species and assemblage metric scores. Our findings indicate that model‐predicted, local‐scale habitat data can be useful for evaluating the relative strengths of local and regional habitat features in structuring fish assemblages, but caution may be necessary when evaluating species‐habitat or assemblage metric‐habitat relationships.
Cold Summer Temperature Regimes Cause a Recruitment Bottleneck in Age‐0 Colorado River Cutthroat Trout Reared in Laboratory Streams
Authors: Coleman Mark A. , Fausch Kurt D.
Published: April 2007

Native salmonids are increasingly restricted to upstream habitats that may be too cold to sustain recruitment, and recruitment limitation owing to cold temperatures is a main hypothesis to explain translocation failures of native cutthroat trout Oncorhynchus clarkii in high‐elevation streams in the southern Rocky Mountains. We subjected Colorado River cutthroat trout O. c. pleuriticus fry to one of three temperature regimes (cold, intermediate, or warm), which averaged 7.0, 8.5, and 10.0°C during the warmest summer month, in each of 2 years. The regimes mimicked those of natural streams where translocated fish had died out or produced populations of cutthroat trout of low or high abundance. The mean fry survival rate from hatching through swim‐up was high during both experiments, ranging from 97% in the warm regime to 85% in the cold. After swim‐up, fry in the warm regime grew more than 60% more on average than those in the cold regime by the onset of winter in 2003 during a 22‐week period. Survival rates through midwinter were also higher in the warm regime (76%) than in the intermediate (62%) and cold (29%) regimes. A similar pattern of temperature‐related growth and mortality was apparent in the 2004 experiment (12 weeks), in which survival rates to early winter ranged from 44% in the warm regime to 10% in the cold. Most mortality in all three treatments occurred during a recruitment bottleneck encompassing a 4‐6‐week period following swim‐up. Analyses of size and percent dry weight indicated that the energy content of fry after swim‐up was lower in colder regimes and declined during the recruitment bottleneck in all three regimes. Our findings indicate a strong recruitment bottleneck after swim‐up when temperature‐related energy deficits apparently cause significant mortality. Managers may increase the viability of these translocated populations by selecting sites that accumulate more than 900 degree‐days during summer.