bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity and expression of nitrogen fixation genes in bacterial symbionts of marine sponges
Authors: Mohamed Naglaa M. , Colman Albert S. , Tal Yossi , Hill Russell T.
Published: August 2008

Marine sponges contain complex assemblages of bacterial symbionts, the roles of which remain largely unknown. We identified diverse bacterial nifH genes within sponges and found that nifH genes are expressed in sponges. This is the first demonstration of the expression of any protein‐coding bacterial gene within a sponge. Two sponges Ircinia strobilina and Mycale laxissima were collected from Key Largo, Florida and had δ15N values of c. 0–1‰ and 3–4‰ respectively. The potential for nitrogen fixation by symbionts was assessed by amplification of nifH genes. Diverse nifH genes affiliated with Proteobacteria and Cyanobacteria were detected, and expression of nifH genes affiliated with those from cyanobacteria was detected. The nifH genes from surrounding seawater were similar to those of Trichodesmium and clearly different from the cyanobacterial nifH genes detected in the two sponges. This study advances understanding of the role of bacterial symbionts in sponges and suggests that provision of fixed nitrogen is a means whereby symbionts benefit sponges in nutrient‐limited reef environments. Nitrogen fixation by sponge symbionts is possibly an important source of new nitrogen to the reef environment that heretofore has been neglected and warrants further investigation.
Peer advisers compared with specialist health professionals in delivering a training programme on self‐management to people with diabetes: a randomized controlled trial
Authors: Baksi A. K. , Al‐Mrayat M. , Hogan D. , Whittingstall E. , Wilson P. , Wex J.
Published: August 2008

Aims  To assess the effectiveness and acceptability of peer advisers in diabetes in delivering a programme of training on self‐management for people with diabetes.

Methods  Adults with diabetes were randomly allocated to an education programme delivered either by trained peer advisers or by specialist health professionals. The primary outcome measure was change in knowledge tested before and at the conclusion of the four courses, each consisting of six sessions. Glycated haemoglobin and Diabetes Care Profile were assessed at baseline and at 6 months. Sessional and end‐of‐course evaluation responses were analysed, as was the attendance record.

Results  Eighty‐three patients were randomized. Of these, 14 failed to attend and two were excluded. Knowledge scores improved significantly in both groups, but there was no difference between the groups for any of the knowledge domains. No difference was noted in the Diabetes Care Profiles or in glycated haemoglobin. The attendance record was similar in both groups. In the post‐sessional evaluations, both groups scored highly, with the health professionals significantly more so. The post‐course questionnaire exploring patients’ understanding and confidence in self‐management of specific aspects of diabetes care revealed no difference between the groups.

Conclusions  Trained patients are as effective in imparting knowledge to their peers as specialist health professionals. Both are also acceptable to patients as trainers. However, lay tutors require to be given appropriate training, specific to the education programme they would be expected to deliver.
COMBINING REVEALED AND STATED PREFERENCE DATA TO ESTIMATE THE NONMARKET VALUE OF ECOLOGICAL SERVICES: AN ASSESSMENT OF THE STATE OF THE SCIENCE
Authors: Whitehead John C. , Pattanayak Subhrendu K. , Van Houtven George L. , Gelso Brett R.
Published: August 2008

Abstract This paper reviews the marketing, transportation and environmental economics literature on the joint estimation of revealed preference (RP) and stated preference (SP) data. The RP and SP approaches are first described with a focus on the strengths and weaknesses of each. Recognizing these strengths and weaknesses, the potential gains from combining data are described. A classification system for combined data that emphasizes the type of data combination and the econometric models used is proposed. A methodological review of the literature is pursued based on this classification system. Examples from the environmental economics literature are highlighted. A discussion of the advantages and disadvantages of each type of jointly estimated model is then presented. Suggestions for future research, in particular opportunities for application of these models to environmental quality valuation, are presented.
PROTECTION OF PROPERTY RIGHTS AND GROWTH AS POLITICAL EQUILIBRIA
Authors: Asoni Andrea
Published: August 2008

AbstractThis paper presents a survey of the literature on property rights and economic growth. Different theoretical mechanisms that relate property rights to economic development are discussed. Lack of protection of property rights can result in slow economic growth through different channels: expropriation of private wealth, corruption of civil servants, excessive taxation and barriers to adoption of new technologies. The origins of property rights are also considered. Different theories are illustrated but more attention is paid to the ‘social conflict view’ and its success and limitations. The second part of the paper illustrates relevant empirical works on property rights and growth.
THE RECEPTION OF DIONYSIUS UP TO MAXIMUS THE CONFESSOR
Authors: LOUTH ANDREW
Published: August 2008

There are various odd features about the initial reception of the Corpus Dionysiacum in the sixth century. The reception was, at first, slow and mainly concerned the few, controversial Christological assertions of the CD. The influence of the CD was mediated through a single edition, complete with introduction, variant readings, and scholia, all furnished by John of Scythopolis. The initial reception of the CD in the Syriac world seems very different: independent (at least to begin with) of Scythopolis’ edition, and deeply Origenistic. Yet, in other ways, the CD reflects the kind of historical interests we find elsewhere in the sixth century.
ALBERT, AQUINAS, AND DIONYSIUS
Authors: BURRELL DAVID , MOULIN ISABELLE
Published: August 2008

Beyond the usual distinction between East and West, Albert the Great and Thomas Aquinas stand not only as commentators, but also appear to be close readers, of Dionysius' works. While Albert's own metaphysics of the Good tends to underline the diffusive dimension of the Good in a creation conceived of as an emanation, Thomas uses Dionysius to elaborate his notion of God as a free creator and to define His unique relation to creatures. If Albert's own via negativa is closer to Dionysius than one might have expected, it nonetheless stands within the same scope as Thomas' conception of proximity to God, as they both borrow the Dionysian exitus/reditus pattern to offer a divinization process of salvation through peace and praise.
DIONYSIUS AND SOME LATE MEDIEVAL MYSTICAL THEOLOGIANS OF NORTHERN EUROPE
Authors: TURNER DENYS
Published: August 2008

Though the authority of Dionysius as a virtually apostolic theological source remains unchallenged in the late Middle Ages, ownership of his inheritance is much disputed, in connection with two issues of “mystical theology” principally. The first controversy (broadly between “Intellectualist” and “affectivist” readings of Dionysius' Mystical Theology) concerns whether the soul, united to God by grace, is made one with God principally by knowledge or by love. The second controversy is well exemplified by the disagreement between Jean Gerson and Denys the Carthusian as to whether Ruusbroec's account of the nature of that union of the soul with God amounts to a heretical extinction of the identity of the created soul. But both Gerson's critique of Ruusbroec and Denys the Carthusian's rebuttal of it are equally superficial, and the theologies of Eckhart and Nicholas of Cusa show why: Eckhart and Cusa retained, while Gerson and Denys had lost, their grip on the “dialectics” of “sameness” and “difference” expounded in Mystical Theology.
DIONYSIAN THOUGHT IN SIXTEENTH‐CENTURY SPANISH MYSTICAL THEOLOGY
Authors: GIRÓN‐NEGRÓN LUIS M.
Published: August 2008

This essay reviews the nature and scope of Dionysius’ influence on the Hispano‐Christian mystics, especially John of the Cross and Theresa of Ávila. As background, it first surveys the broader reception of Dionysius in sixteenth‐century Spain, especially among the ascetico‐mystical precursors and contemporaries of both Carmelite saints. This will allow us to reconnoiter with some historical precision how and to what extent Dionysian themes were interpreted and woven into signature components of their mystical theology: John's taxonomy of dark nights and Theresa's views on the suspension of the faculties as a preamble to unio mystica.
DIONYSIUS, DERRIDA, AND THE CRITIQUE OF “ONTOTHEOLOGY”
Authors: RUBENSTEIN MARY‐JANE
Published: August 2008

This essay explores Dionysius' work in light of the critique of ontotheology, focusing on Jacques Derrida's work on justice and the messianic. Ultimately, it suggests that the extent to which Dionysius troubles the ontotheological waters depends on the status of hierarchical and teleological relationships in Dionysius. Does hierarchy for Dionysius function strictly “vertically,” bringing a few chosen souls into union with God, or does it also establish ethical relations between and among creatures? And does the via negativa, as Derrida suggests, draw the soul along a pre‐determined path from hyperessence to hyperessence, or might it remain sufficiently indeterminate to welcome the unimaginable?
Periocular dermatitis: a report of 401 patients
Authors: Temesvári E , Pónyai G , Németh I , Hidvégi B , Sas A , Kárpáti S
Published: August 2008

Background  Periocular contact dermatitis may appear as contact conjunctivitis, contact allergic and/or irritative eyelid and periorbital dermatitis, or a combination of these symptoms. The clinical symptoms may be induced by several environmental and therapeutic contact allergens.

Objectives  The aim of the present study was to map the eliciting contact allergens in 401 patients with periocular dermatitis (PD) by patch testing with environmental and ophthalmic contact allergens.

Methods  Following the methodics of international requirements, 401 patients were tested with contact allergens of the standard environmental series, 133 of 401 patients with the Brial ophthalmic basic and supplementary series as well.

Results  Contact hypersensitivity was detected in 34.4% of the patients. Highest prevalence was seen in cases of PD without other symptoms (51.18%), in patients of PD associated with ophthalmic complaints (OC; 30.4%), and PD associated with atopic dermatitis (AD; 27.9%). In the subgroup of PD associated with seborrhoea (S) and rosacea (R), contact hypersensitivity was confirmed in 17.6%. Most frequent sensitisers were nickel sulphate (in 8.9% of the tested 401 patients), fragrance mix I (4.5%), balsam of Peru (4.0%), paraphenylendiamine (PPD) (3.7%), and thiomersal (3.5%). By testing ophthalmic allergens, contact hypersensitivity was observed in nine patients (6.7% of the tested 133 patients). The most common confirmed ophthalmic allergens were cocamidopropyl betaine, idoxuridine, phenylephrine hydrochloride, Na chromoglycinate, and papaine.

Limitations  Patients with symptoms of PD were tested from 1996 to 2006.

Conclusions  The occurence of contact hypersensitivity in PD patients was in present study 34.4%. A relatively high occurence was seen in cases of PD without other symptoms, in PD + OC and in PD + AD patients. The predominance of environmental contact allergens was remarkable: most frequent sensitizers were nickel sulphate, fragrance mix I, balsam of Peru, thiomersal, and PPD. The prevalence of contact hypersensitivity to ophthalmic allergens did not exceed l.5%.

Conflicts of interest

None declared
‘Go! Sterilise the fertile with thy rage’ Envy as embittered desire
Authors: Meredith‐Owen William
Published: August 2008

Abstract:  This paper is concerned with the operation of envy: it considers its origins and their repercussions, in particular its compulsion to sterilize the evidence of fertility, exemplified by Roger Money‐Kyrle's evocation of ‘the parental intercourse as the supremely creative act’. The inevitable impact on the analytic relationship is considered in the context of two clinical examples of impasse. It is argued that such fundamentally negative transferences, one full of overt aggression and enactment, the other more covertly sabotaging, derive from envious retaliatory impulses originating in experiences—whether phantasied or factual—of exclusion from the anticipated ‘good’. Significant recent Jungian contributions to this area are considered and the absence of references to ‘envy’—so characteristic of Kleinian discourse—is noted. The ongoing value of integrating Jungian and Kleinian approaches is affirmed.
The Information Content of Private Debt Placements
Authors: Chandra Uday , Nayar Nandkumar (Nandu)
Published: August 2008

Abstract: Private placements of straight nonbank debt by publicly traded firms elicit a positive stock price reaction on average, consistent with a market perception that they confer significant certification and monitoring benefits on borrowers. However, long‐run stock returns following the debt issues are significantly lower than benchmarks. Our results are consistent with the view that firms issue private debt prior to a decline in operating performance, and they disclose overly optimistic information in the pre‐issue period which prevents information on the upcoming downturn from reaching the market in a timely manner. Lenders have private information on the post‐issue performance decline prior to their lending decision, and take steps to protect their investment which do not benefit equity investors. Our results are inconsistent with certification and monitoring benefits accruing to equity investors from private nonbank debt.
Improving Health Care Efficiency and Quality Using Tablet Personal Computers to Collect Research‐Quality, Patient‐Reported Data
Authors: Abernethy Amy P. , Herndon James E. , Wheeler Jane L. , Patwardhan Meenal , Shaw Heather , Lyerly H. Kim , Weinfurt Kevin
Published: August 2008

Objective. To determine whether e/Tablets (wireless tablet computers used in community oncology clinics to collect review of systems information at point of care) are feasible, acceptable, and valid for collecting research‐quality data in academic oncology.

Data/Setting. Primary/Duke Breast Cancer Clinic.

Design. Pilot study enrolling sample of 66 breast cancer patients.

Methods. Data were collected using paper‐ and e/Tablet‐based surveys: Functional Assessment of Cancer Therapy General, Functional Assessment of Cancer Therapy‐Breast, MD Anderson Symptom Inventory, Functional Assessment of Chronic Illness Therapy (FACIT), Self‐Efficacy; and two questionnaires: feasibility, satisfaction.

Principal Findings. Patients supported e/Tablets as: easy to read (94 percent), easy to respond to (98 percent), comfortable weight (87 percent). Generally, electronic responses validly reflected responses provided by standard paper data collection on nearly all subscales tested.

Conclusions. e/Tablets offer a valid, feasible, acceptable method for collecting research‐quality, patient‐reported outcomes data in outpatient academic oncology.
Steering Patients to Safer Hospitals? The Effect of a Tiered Hospital Network on Hospital Admissions
Authors: Scanlon Dennis P. , Lindrooth Richard C. , Christianson Jon B.
Published: August 2008

Objective. To determine if a tiered hospital benefit and safety incentive shifted the distribution of admissions toward safer hospitals.

Data Sources/Study Setting. A large manufacturing company instituted the hospital safety incentive (HSI) for union employees. The HSI gave union patients a financial incentive to choose hospitals that met the Leapfrog Group's three patient safety “leaps.” The analysis merges data from four sources: claims and enrollment data from the company, the American Hospital Association, the AHRQ HCUP‐SID, and a state Office of the Insurance Commissioner.

Study Design. Changes in hospital admissions' patterns for union and nonunion employees using a difference‐in‐difference design. We estimate the probability of choosing a specific hospital from a set of available alternatives using conditional logistic regression.

Principal Findings. Patients affiliated with the engineers' union and admitted for a medical diagnosis were 2.92 times more likely to select a hospital designated as safer in the postperiod than in the preperiod, while salaried nonunion (SNU) patients (not subject to the financial incentive) were 0.64 times as likely to choose a compliant hospital in the post‐ versus preperiod. The difference‐in‐difference estimate, which is based on the predictions of the conditional logit model, is 0.20. However, the machinists' union was also exposed to the incentive and they were no more likely to choose a safer hospital than the SNU patients. The incentive did not have an effect on patients admitted for a surgical diagnosis, regardless of union status. All patients were averse to travel time, but those union patients selecting an incentive hospital were less averse to travel time.

Conclusions. Patient price incentives and quality/safety information may influence hospital selection decisions, particularly for medical admissions, though the optimal incentive level for financial return to the plan sponsor is not clear.
Advancing Forest Cover Development on a High‐Elevation Sierra Nevada Mine Site with Nutritional Amendments
Authors: Walker Roger F.
Published: August 2008

Selected nutrient amendments were evaluated for their capacity to enhance growth and nutrition of established but stunted Jeffrey pine (Pinus jeffreyiGrev. & Balf.) saplings on an acidic Sierra Nevada surface mine. The amendments were applied by topdressing at three rates each and consisted of Forestcote 22‐4‐6 + Minors, a controlled‐release formulation; Free Flow 29‐3‐4 and Hydro Agri 21‐7‐14, two conventional fertilizers, with the former featuring urea as the predominant N source, whereas that for the latter was exclusively ammoniacal and nitrate forms; and Milorganite 6‐2‐0 + Iron, an organic amendment based on municipal biosolids. All formulations reinvigorated sapling growth, generally more so as the amounts supplied increased, with the Free Flow and Hydro Agri amendments marginally more stimulative than Forestcote and Milorganite. Foliar analysis revealed that fertilized saplings had more N, with concentrations that generally rose with amounts supplied, and P but less Mn and Al than the control. Enhanced N nutrition in particular but also that of P probably accounted for most of the growth stimulation by the amendments, as availability of both in the soil was limiting. Of the two metallic elements, reduced Mn was likely most critical because concentrations encountered here were exceedingly elevated overall, including that in the soil, although soil Al was also high. These results suggest that a variety of nutritional amendments can be employed in forest restoration on surface mine sites and those similarly degraded, including sites for which dry climates greatly influence the selection of remedial practices.
Changes in Soil Properties Following 55 Years of Secondary Forest Succession at Fort Benning, Georgia, U.S.A.
Authors: Maloney Kelly O. , Garten Charles T. , Ashwood Tom L.
Published: August 2008

We present results on changes in soil properties following land use change over an approximately 55‐year period at Fort Benning, Georgia, U.S.A. Soil cores were taken at 129 locations that were categorized as reforested (field/bare ground in 1944 and forest in 1999), disturbed (field/bare ground in 1944 and 1999), or reference forests (forest in 1944 and 1999). Soil disturbance included historic agriculture (pre‐1944) and military training (post‐1944). Density in mineral soils exhibited a historic land use legacy effect (reference < reforested < disturbed). Rates of change in bulk density decreased with depth and estimated total times to reach reference forest levels ranged from 83 (0–10 cm) to 165 (30–40 cm) years. A land use legacy effect on C stock was apparent in the O‐horizon and in 30‐ to 40‐cm soil increment (reference > reforested > disturbed). Soil C stock in all other increments and in particulate organic matter was affected by disturbance; however, no legacy was apparent (reference = reforested > disturbed). For the entire soil profile (O‐horizon to 40 cm), rate of C accrual was 28 g m−2 yr−1 (1.5%/yr). Nitrogen stocks were affected by disturbance in the O‐horizon and 0‐ to 10‐cm increment; however, no legacy effect was detected (reference = reforested > disturbed). Nitrogen accumulated at 0.56 g m−2 yr−1 (0.6%/yr) for the entire soil profile. At Fort Benning, soil C and N stocks of reforested stands were similar to those of reference forested stands after approximately 55 years. However, soil bulk density was greater on reforested stands than reference forest stands at 55 years and may require an additional century to reach reference levels.
Wetland Restoration in the New Millennium: Do Research Efforts Match Opportunities?
Authors: Wagner Kelly I. , Gallagher Sally K. , Hayes Matthew , Lawrence Beth A. , Zedler Joy B.
Published: August 2008

Of 311 papers on wetland restoration, only 15 concerned large‐scale experimentation in restoration sites. Most papers described what happened, reported on small field experiments, or discussed restoration targets. While these are important topics, our opinion is that we lose significant opportunities to learn how to recover populations, community structure, and ecosystem processes, and we limit our ability to document variability and whole‐system responses, when we do not experiment at large scales. We suggest that, wherever possible, large projects facilitate field tests of alternative restoration approaches. Furthermore, we encourage researchers to take advantage of major restoration efforts by conducting large field experiments, assessing multiple responses, and offering restoration guidance in an adaptive framework.
Washing of drained blood does not alter immediate immune effects of retransfusion
Authors: Volk Thomas , Doering Kristin , Granitza Lucille , Perka Carsten , Spies Claudia D. , Heymann Christian von
Published: August 2008

BACKGROUND: Retransfusion of postoperatively drained wound blood may be associated with adverse immune effects induced by many mediators present in unwashed filtered blood.

STUDY DESIGN AND METHODS: In this randomized trial, the hypothesis that a washing procedure alters the course of markers of immune and inflammatory responses after retransfusion of blood collected from patients after endoprosthetic surgery is tested. Mean volume of blood reinfused was 363 ± 173 mL in Group A and 352 ± 180 mL in Group B. Five hours postoperatively patients either received washed (Group A) or unwashed (Group B) blood collected during the postoperative period. Circulating cytokines (tumor necrosis factor [TNF]‐α, interleukin [IL]‐6, IL‐8, IL‐10, monocyte chemoattractant protein [MCP]‐1) and lipopolysaccharide (LPS)‐stimulated TNF‐α secretion were measured at several time points pre‐ and postoperatively.

RESULTS: IL‐6 and IL‐8 slightly increased immediately after retransfusion in both groups (by 48 ± 37 and 5 ± 2 pg/mL, respectively, in Group A; by 74 ± 60 and 17 ± 13 pg/mL in Group B). IL‐10 and MCP‐1 were unaltered and both circulating TNF‐α and LPS stimulated capacity in TNF‐α secretion decreased (by 5 ± 13 and 1 ± 31 pg/mL, respectively, in Group A; by 3 ± 14 and 29 ± 39 pg/mL in Group B), independent from a washing procedure.

CONCLUSION: For small reinfusion volumes a washing procedure does not alter the ex vivo capacity of LPS induced TNF‐α secretion and the selected cytokine profile after retransfusion of postoperatively drained and filtered blood.
Adaptive Management: A Paradigm for Remediation of Public Facilities Following a Terrorist Attack
Authors: Whicker Jeffrey J. , Janecky David R. , Doerr Ted B.
Published: August 2008

Terrorist actions are aimed at maximizing harm (health, psychological, economical, and political) through the combined physical impacts of the act and fear. Immediate and effective response to a terrorist act is critical to limit human and environmental harm, effectively restore facility function, and maintain public confidence. Though there have been terrorist attacks in public facilities that we have learned from, overall our experiences in restoration of public facilities following a terrorist attack are limited. Restoration of public facilities following a release of a hazardous material is inherently far more complex than in industrial settings and has many unique technical, economic, social, and political challenges. For example, there may be a great need to quickly restore the facility to full operation and allow public access even though it was not designed for easy or rapid restoration, and critical information is needed for quantitative risk assessment and effective restoration must be anticipated to be incomplete and uncertain. Whereas present planning documents have substantial linearity in their organization, the “adaptive management” paradigm provides a constructive parallel paradigm for restoration of public facilities that anticipates and plans for uncertainty, inefficiencies, and stakeholder participation. Adaptive management grew out of the need to manage and restore natural resources in highly complex and changing environments with limited knowledge about causal relationships and responses to restoration actions. Similarities between natural resource management and restoration of a public facility after a terrorist attack suggest that integration of adaptive management principles explicitly into restoration processes will result in substantially enhanced and flexible responses necessary to meet the uncertainties of potential terrorist attacks.
Quantitative ultrasound (QUS): a useful tool for monitoring bone health in preterm infants?
Authors: Fewtrell MS , Loh KL , Chomtho S , Kennedy K , Hawdon J , Khakoo A
Published: August 2008

Preterm infants are at risk of osteopenia and metabolic bone disease (MBD) of prematurity. There is a need for simple, reliable methods to detect and monitor this condition.

Aims: The aims were first to describe longitudinal changes in speed of sound (SOS) measured using quantitative ultrasound (QUS; Sunlight Omnisense, Israel) in preterm neonates: and second to determine whether SOS predicts the development of MBD.

Methods: SOS was measured in the tibia in 99 preterm infants (mean (SD)) gestation 29.7 (3.6) weeks; birthweight 1340 (550) g, with longitudinal measurements in 75. SOS z‐scores were generated for gestation and sex. Clinical data were recorded.

Results: Baseline SOS (but not SOS z‐score) was positively associated with gestational age. SOS and SOS z‐score fell with age. In multivariate models, peak ALP, minimum phosphate concentrations and markers of illness severity were not predictors of the fall in SOS z‐score, and baseline SOS measurements did not predict the development of high peak ALP or low phosphate.

Interpretation: Speed of sound measurements fell with age in all infants, but we found no evidence that this measurement could predict biochemical indicators of MBD. We cannot exclude the possibility that this technique could be useful in monitoring the response to interventions designed to improve bone health in this population.
ΔG‐based prediction and experimental confirmation of SYCRP1‐binding sites on the Synechocystis genome
Authors: Omagari Katsumi , Yoshimura Hidehisa , Suzuki Takayuki , Takano Mitunori , Ohmori Masayuki , Sarai Akinori
Published: August 2008

DNA‐binding sites for SYCRP1, which is a regulatory protein of the cyanobacterium Synechocystis sp. PCC6803, were predicted for the whole genome sequence by estimating changes in the binding free energy () for SYCRP1 for those sites. The values were calculated by summing ΔΔG values derived from systematic single base‐pair substitution experiments (symmetrical and cooperative binding model). Of the calculated binding sites, 23 sites with a value < 3.9 kcal·mol−1 located upstream or between the ORFs were selected as putative binding sites for SYCRP1. In order to confirm whether SYCRP1 actually binds to these binding sites or not, 11 sites with the lowest values were tested experimentally, and we confirmed that SYCRP1 binds to ten of the 11 sites with a ΔΔGtotal value < 3.9 kcal·mol−1. The best correlation coefficient between and the observed ΔΔGtotal for binding of SYCRP1 to those sites was 0.78. These results suggest that the ΔΔG values derived from systematic single base‐pair experiments may be used to screen for potential binding sites of a regulatory protein in the genome sequence.
Estimation of Item Response Theory Parameters in the Presence of Missing Data
Authors: Finch Holmes
Published: August 2008

Missing data are a common problem in a variety of measurement settings, including responses to items on both cognitive and affective assessments. Researchers have shown that such missing data may create problems in the estimation of item difficulty parameters in the Item Response Theory (IRT) context, particularly if they are ignored. At the same time, a number of data imputation methods have been developed outside of the IRT framework and been shown to be effective tools for dealing with missing data. The current study takes several of these methods that have been found to be useful in other contexts and investigates their performance with IRT data that contain missing values. Through a simulation study, it is shown that these methods exhibit varying degrees of effectiveness in terms of imputing data that in turn produce accurate sample estimates of item difficulty and discrimination parameters.
An Odds Ratio Approach for Assessing Differential Distractor Functioning Effects under the Nominal Response Model
Authors: Penfield Randall D.
Published: August 2008

Investigations of differential distractor functioning (DDF) can provide valuable information concerning the location and possible causes of measurement invariance within a multiple‐choice item. In this article, I propose an odds ratio estimator of the DDF effect as modeled under the nominal response model. In addition, I propose a simultaneous distractor‐level (SDL) test of invariance based on the results of the distractor‐level tests of DDF. The results of a simulation study indicated that the DDF effect estimator maintained good statistical properties under a variety of conditions, and the SDL test displayed substantially higher power than the traditional Mantel‐Haenszel test of no DIF when the DDF effect varied in magnitude and/or size across the distractors.
Classification System for English Language Learners: Issues and Recommendations
Authors: Abedi Jamal
Published: August 2008

High‐stakes decisions for the instruction and assessment of English language learner (ELL) students are made based on the premise that ELL classification is a valid dichotomy that distinguishes between those who are proficient in the use of the English language and those who are not. However, recent research findings draw a vague picture of the term “ELL” and call for a more valid classification system for ELL students. Thus, the purpose of this paper is twofold: (1) to reveal issues concerning the validity of the current ELL classification system based on the results of several empirical studies, and (2) to initiate a discussion on ways to improve the validity of the ELL classification system by proposing a system that uses existing multiple criteria in a stepwise manner. While the suggested system has its own limitations and controversies, we hope this discussion stimulates thoughts and brings much needed attention to this very important national issue.
Effect of the TRIPS‐Mandated Intellectual Property Rights on Foreign Direct Investment in Developing Countries: A Case Study of the Indian Pharmaceutical Industry
Authors: Rai Rajnish Kumar
Published: August 2008

The Agreement on Trade‐Related Aspects of Intellectual Property Rights is the most important as well as the most controversial instrument to date concerning intellectual property protection. What is not clear is the impact it will have on developing countries and whether it will actually meet its objective in the “… promotion of technological innovation and to the transfer and dissemination of technology …”. The proponents of a strong patent regime vehemently argue that strengthening patent protection will lead to greater technology transfer in developing countries, and consequently inflow of foreign direct investment (FDI) as it is the most important channel for technology transfer. This article takes the Indian pharmaceutical industry as an example to examine the above assertion, and argues that simply enhancing patent protection may not necessarily result in a corresponding increase in FDI in the Indian pharmaceutical sector. It shows that in addition to strong patent protection, there are equally or even more important factors that have a bearing on the inflow of FDI.
From Plant Variety Definition to Geographical Indication Protection: A Search for the Link Between Basmati Rice and India/Pakistan
Authors: Marie‐Vivien Delphine
Published: August 2008

Geographical indications (GIs) deal with local issues. Their protection generates an original scheme of governance. GIs were first protected in France and they were later harmonised in the European Union (EU) and then included in the TRIPS Agreement, which was the basis for the enactment of the GI Act in India and GI protection in Pakistan. The Basmati rice example will illustrate the different objectives of GI protection in these two countries and in Europe. Europe is an emerging market for Basmati, and therefore the EU is setting rules of importation based on its tradition of food quality. Such an increase in exports of Basmati raises the issue of a protection that is efficient in the international market, but still is adapted to Indian and Pakistani needs. On the one hand, Basmati has been defined for a long time as the name of plant varieties which now includes evolved varieties. On the other hand, Basmati is still not yet registered as a GI, because the concept of GI is a very recent development in India and Pakistan. The Basmati case raises general issues for GIs protection worldwide: tradition versus modernity, product definition versus method of production and geographical environment.
Hippocampal Sclerosis: Progress Since Sommer
Authors: Thom Maria
Published: August 2008

Hippocampal sclerosis (HS) continues to be the most common pathology identified in patients with refractory temporal lobe epilepsy undergoing surgery. Wilhelm Sommer described this characteristic pattern of neuronal loss over 120 years ago through his post‐mortem studies on patients with epilepsy. Neuropathological post‐mortem studies in the 20th century proceeded to contribute significantly to the understanding of this disease process, with regard to the varying patterns of HS and involvement of adjacent limbic structures. From studies of surgical temporal lobe specimens from the 1950s onwards it was recognized that an early cerebral injury could act as the precipitant for the sclerosis and epilepsy. Modern neuropathological studies have focused on aspects of neuronal injury, loss of specific neuronal groups and cellular reorganization to address mechanisms of epileptogenesis and the enigma of how specific hippocampal neuronal vulnerabilities and glial proliferation are both the effect and the cause of seizures.
In Vivo Absorption Spectra of the Two Stable States of the Euglena Photoreceptor Photocycle
Authors: Barsanti Laura , Coltelli Primo , Evangelista Valtere , Passarelli Vincenzo , Frassanito Anna Maria , Vesentini Nicoletta , Santoro Fabrizio , Gualtieri Paolo
Published: August 2008

Euglena gracilis possesses a simple but sophisticated light detecting system, consisting of an eyespot formed by carotenoids globules and a photoreceptor. The photoreceptor of Euglena is characterized by optical bistability, with two stable states. In order to provide important and discriminating information on the series of structural changes that Euglena photoreceptive protein(s) undergoes inside the photoreceptor in response to light, we measured the in vivo absorption spectra of the two stable states A and B of photoreceptor photocycle. Data were collected using two different devices, i.e. a microspectrophotometer and a digital microscope. Our results show that the photocycle and the absorption spectra of the photoreceptor possess strong spectroscopic similarities with a rhodopsin‐like protein. Moreover, the analysis of the absorption spectra of the two stable states of the photoreceptor and the absorption spectrum of the eyespot suggests an intriguing hypothesis for the orientation of microalgae toward light.
Ten polymorphic microsatellite DNA markers for the platypus, Ornithorhynchus anatinus
Authors: KOLOMYJEC STEPHEN H. , GRANT TOM R. , BLAIR DAVID
Published: August 2008

We identified and optimized 10 microsatellite loci for the platypus, Ornithorhynchus anatinus (Monotremata: Ornithorhynchidae), and screened 21 individuals from the southern tablelands area of New South Wales, Australia. Each polymorphic locus possessed between two and 12 alleles with observed heterozygosities between 0.118 and 0.950. The intent of this effort was to provide informative loci for studies on the population genetics of this species.
Isolation and characterization of microsatellite loci in Palinurus elephas
Authors: PALERO F. , PASCUAL M.
Published: August 2008

The European spiny lobster (Palinurus elephas) mean annual catches have decreased alarmingly during recent decades along its entire distribution area due to stock over‐exploitation, which makes it a primary target for conservation plans. A total of 164 microsatellite loci were isolated from a genomic library of P. elephas enriched for CA, GA, CAA and GATA repeats. A total of 15 polymorphic loci have been screened in 48 individuals. High numbers of alleles per locus (averaging 20 ± 10.5) and observed heterozygosity (averaging 0.789 ± 0.197) have been detected. None of the pairs of loci showed significant linkage disequilibrium. Two of the loci (Pael1 and Pael2) showed significant departure from Hardy–Weinberg equilibrium in Sagres, while Pael38 showed significant departure in Tunis. These highly polymorphic markers will be useful in determining the spatial patterns of genetic diversity between and within populations of Palinurus elephas.
Double‐dose double‐phase use of second generation hepatitis B virus vaccine in patients after living donor liver transplantation: Not an effective measure in transplant recipients
Authors: Yamashiki Noriyo , Sugawara Yasuhiko , Tamura Sumihito , Kaneko Junichi , Matsui Yuichi , Togashi Junichi , Kokudo Norihiro , Omata Masao , Makuuchi Masatoshi
Published: August 2008

Aims: Post‐transplant active immunization for chronic hepatitis B patients has been attempted in several studies with controversial results. We assessed the effect of a double‐dose double‐phase vaccination regimen among partial living donor liver recipients.

Methods: Eighteen patients who underwent liver transplantation (LT) for chronic hepatitis B and two non‐hepatitis B virus (HBV)‐infected patients who received hepatitis B core antibody (HBcAb)‐positive donor organs were recruited 18–78 months after LT. All were on hepatitis B immunoglobulin (HBIG) mono‐prophylaxis before and throughout vaccination, to maintain hepatitis B surface antibody (HBsAb) titers of more than 100 IU/mL. Recombinant hepatitis B surface antigen vaccine (40 µg) was administered intramuscularly during weeks 0, 4, 8, 24, 28 and 32.

Results: The patients consisted of 15 males and five females with a median age of 52 (39–59) years. None developed a sufficient HBsAb titer above 500 IU/mL by week 48. In two patients whose maximum HBsAb titer increased to above 300 IU/mL, we attempted to skip HBIG, but shortly thereafter the titer dropped below 100 IU/mL and HBIG administration was resumed. Although the HBIG dose was reduced during and after vaccination, cessation of administration was not achieved.

Conclusion: Double‐dose double‐phase use of second generation recombinant vaccine was not effective in this study population. The selected population should be targeted for a conventional vaccine regimen, and different approaches, such as strong adjuvant or pre‐S containing protein, should be further tested in a larger number of patients after LT for chronic hepatitis B.
Nonlinear Versus Linear Stress-Strain Relations in Engine Turbulence Modeling Under Swirl and Squish Flow Conditions
Authors: Baratta Mirko , Catania Andrea E. , d’Ambrosio Stefano
Published: August 2008

A general form of the stress-strain constitutive relation was introduced for the application of two nonlinear k-ε turbulence models, namely, the algebraic Reynolds stress model of Gatski and Speziale (1993, “On Explicit Algebraic Stress Models for Complex Turbulent Flows,” J. Fluid Mech., 254, pp. 59–78) and the cubic model of Lien et al. (1996, “Low Reynolds Number Eddy-Viscosity Modeling Based on Non-Linear Stress-Strain/Vorticity Relations,” Proceedings of Third Symposium on Engineering Turbulence Modeling and Measurements, Crete, Greece), to the numerical analysis of flow fields in a test engine with flat-piston and bowl-in-piston arrangements, under swirling and no-swirling flow motored conditions. The model capabilities in capturing turbulent flow features were compared to those of the upgraded linear RNG k-ε model, which was previously indicated as a good compromise between accuracy and computational cost. Evaluations were made on the basis of the predicted flow evolution throughout the whole engine cycle, as well as of the comparison between the numerical and experimental results. Furthermore, the effect of the stress-strain relationship on the predicted averaged turbulence quantities and anisotropy-invariant values were examined, in addition to the sensitivity of the nonlinear models to the mesh quality. Finally, prospects concerning possible improvements of turbulence eddy-viscosity models were presented. The predictions were made by a newly developed CFD code embedding various accuracy-order finite-volume discretization schemes. Modified wall boundary conditions with respect to the conventional logarithmic-function approach were used, so as to make the local equilibrium hypothesis virtually ineffective.
Optical Nondestructive Condition Monitoring of Thermal Barrier Coatings
Authors: Heyes A. L. , Feist J. P. , Chen X. , Mutasim Z. , Nicholls J. R.
Published: August 2008

This paper describes recent developments of the thermal barrier sensor concept for nondestructive evaluation (NDE) of thermal barrier coatings (TBCs) and online condition monitoring in gas turbines. Increases in turbine inlet temperature in the pursuit of higher efficiency will make it necessary to improve or upgrade current thermal protection systems in gas turbines. As these become critical to safe operation, it will also be necessary to devise techniques for online condition monitoring and NDE. The authors have proposed thermal barrier sensor coatings (TBSCs) as a possible means of achieving NDE for TBCs. TBSCs are made by doping the ceramic material (currently yttria-stabilized zirconia (YSZ)) with a rare-earth activator to provide the coating with luminescence when excited with UV light. This paper describes the physics of the thermoluminescent response of such coatings and shows how this can be used to measure temperature. Calibration data are presented along with the results of comparative thermal cycle testing of TBSCs, produced using a production standard air plasma spray system. The latter show the durability of TBSCs to be similar to that of standard YSZ TBCs and indicate that the addition of the rare-earth dopant is not detrimental to the coating. Also discussed is the manufacture of functionally structured coatings with discreet doped layers. The temperature at the bond coat interface is important with respect to the life of the coating since it influences the growth rate of the thermally grown oxide layer, which in turn destabilizes the coating system as it becomes thicker. Experimental data are presented, indicating that dual-layered TBSCs can be used to detect luminescence from, and thereby the temperature within, subsurface layers covered by as much as 500 μm of standard TBC material. A theoretical analysis of the data has allowed some preliminary calculations of the transmission properties of the overcoat to be made, and these suggest that it might be possible to observe phosphorescence and measure temperature through an overcoat layer of up to approximately 1.56 mm thickness.
Natural Selection on a Major Armor Gene in Threespine Stickleback
Authors: Barrett Rowan D. H. , Rogers Sean M. , Schluter Dolph
Published: August 2008

Experimental estimates of the effects of selection on genes determining adaptive traits add to our understanding of the mechanisms of evolution. We measured selection on genotypes of the
Ectodysplasin
locus, which underlie differences in lateral plates in threespine stickleback fish. A derived allele (low) causing reduced plate number has been fixed repeatedly after marine stickleback colonized freshwater from the sea, where the ancestral allele (complete) predominates. We transplanted marine sticklebacks carrying both alleles to freshwater ponds and tracked genotype frequencies over a generation. The low allele increased in frequency once lateral plates developed, most likely via a growth advantage. Opposing selection at the larval stage and changing dominance for fitness throughout life suggest either that the gene affects additional traits undergoing selection or that linked loci also are affecting fitness.
Seeding and Propagation of Untransformed Mouse Mammary Cells in the Lung
Authors: Podsypanina Katrina , Du Yi-Chieh Nancy , Jechlinger Martin , Beverly Levi J. , Hambardzumyan Dolores , Varmus Harold
Published: August 2008

The acquisition of metastatic ability by tumor cells is considered a late event in the evolution of malignant tumors. We report that untransformed mouse mammary cells that have been engineered to express the inducible oncogenic transgenes MYC and Kras
D12
, or polyoma middle T, and introduced into the systemic circulation of a mouse can bypass transformation at the primary site and develop into metastatic pulmonary lesions upon immediate or delayed oncogene induction. Therefore, previously untransformed mammary cells may establish residence in the lung once they have entered the bloodstream and may assume malignant growth upon oncogene activation. Mammary cells lacking oncogenic transgenes displayed a similar capacity for long-term residence in the lungs but did not form ectopic tumors.
The anatomy of the normal placenta
Authors: Huppertz B
Published: August 2008

The placenta is the fetal organ providing the interchange between mother and fetus. This organ needs to provide its function such as transport and secretion even during its development and thus all developmental changes need to be in accordance with its function. This review describes development of the placenta during the first few weeks of pregnancy until the villous trees with their vasculature are established. The macroscopic anatomy of the delivered placenta as well as the microscopic anatomy and histology of this organ are also described. This includes the different types of villi and the most important cellular components of the villi such as villous trophoblast, Hofbauer cells, mesenchymal cells and endothelium. Fibrinoid and its localisation is also described.