bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of shallow flooding on vegetation and carbon pools in boreal peatlands
Authors: Asada Taro , Warner Barry G. , Schiff Sherry L.
Published: February 2009

Question:What are the effects of shallow flooding on boreal peatlands on vegetation composition and size of carbon pools in the living and dead vegetation?

Location:Lake 979, Experimental Lakes Area, northwestern Ontario, Canada.

Methods:A boreal basin peatland complex with treed bog, open bog, and open water was experimentally flooded by raising water level ca. 1.3 m. Vegetation and above‐ground biomass were compared between pre‐flood conditions and those nine years after flooding. Peat accumulation since flooding was also quantified.

Results:Flooding caused almost all trees to die, leading to a net loss of 86% of the above‐ground living plant biomass after nine years of the flooding. Floating up of peat was rapid in the central part of the basin, and the floating peat mats were characterized by newly established open bog community. Wetland types were diversified from bog into open bog, fen, and marsh, accompanied with great species turnover. Floating open bog community accumulated the greatest amount of peat since flooding.

Conclusions:This study shows that shallow flooding of bog vegetation can lead to quick re‐establishment of open bog vegetation upon the floating up of peat mats as well as changes to more diverse vegetation over decadal time spans. We estimate that the carbon pools in 2002 in living and dead plant biomass since 1992 are comparable to what they were in the above‐ground biomass in 1992. Flooding caused an initial net decrease in carbon stores, but carbon in the pre‐flood living plant biomass was replaced by both carbon in dead biomass of the pre‐flood vegetation and newly sequestered carbon in new peat growth and post‐flood living plant biomass. Possible vegetation change toward bog‐dominated system could lead to increasing rate of new peat growth, which could affect future carbon sink/source strength of the system.
Disturbance, seeds, restoration, and the importance of experiments and long‐term observations: the Editors' Award for 2005
Authors: White Peter S. , Chiarucci Alessandro , Collins Beverly , Díaz Sandra
Published: February 2009

Editors' Award for 2005

Disturbance ecology has become an integral part of vegetation science over the past 25 years. Understanding human disturbances and human effects on natural disturbance regimes is a key to establishing restoration goals and initiating restoration projects. However, as this literature has developed, the picture has become both more interesting and more complex: Disturbances interact; each disturbance leaves behind a patch work of effects; and particular disturbances have different effects in different seasons and from one year to another. In addition, different species respond differently to the same disturbance. We are left with questions such as: Can we predict vegetation response to fire in restoration projects? Clearly, we must understand the mechanisms of species response to disturbance in order to answer these questions and achieve a predictive science.

The Editor's Award for 2005 goes to a paper that treats interactions of fire and mowing in a long‐term experiment: “Long‐term composition responses of a South African mesic grassland to burning and mowing” by Fynn, Morris & Edwards (2005). The authors report on the 50+ year Ukulinga burning and mowing experiment at the research farm of the University of KwaZulu‐Natal in South Africa. This experiment, initiated in 1950, is remarkable: three replicates in a randomized split‐plot, full‐factorial design with four whole‐plot and 11 subplot treatments. Mowing treatments included none to early season, late season, and early‐plus‐late season. Fire treatments were none, annual, biennial, and triannual in winter, spring or autumn. In sum, plot disturbance ranged from protection over 50 years to twice summer mowing plus mowing or fire in the dormant season each year. The authors found that grasses responded to type of disturbance and fire frequency, but forbs were less sensitive to disturbance type. The disturbance combinations controlled vegetation structure and composition, with some combinations producing a short‐grass community and others a tall‐grass community. Tillering strategy (below or above ground) for grasses and habit (erect or creeping) for forbs explained many responses and are a means to predict differing responses of grasses and herbs and different responses of species within each group to disturbance combinations. The conclusion of the study suggests that the highest diversity and greatest number of species (as well as benefits for wildlife species) can be achieved by applying results at the landscape scale to create patches of diverse structures from simple combinations of disturbance type and season. The authors also found transient responses and compensatory changes among species, thus demonstrating the importance of long‐term and experimental research.
Responses of root‐crown bearing shrubs to differences in fire regimes in Pinus palustris (longleaf pine) savannas: Exploring old‐growth questions in second‐growth systems
Authors: Drewa Paul B. , Thaxton Jarrod M. , Platt William J.
Published: February 2009

Question: What are the effects of fire season and intensity on resprouting of different root‐crown bearing shrub species in second‐growth Pinus palustris (longleaf pine) savannas?

Location: northern Florida and eastern Louisiana, USA.

Methods: In Florida, quadrats were burned biennially either during the dormant season or the growing season. In Louisiana, we applied intensity treatments to quadrats by manipulating ground‐cover fuels, just prior to biennial growing season fires. Maximum fire temperatures were measured, and stem densities were censused before and after fires in both regions.

Results: After dormant season fires in Florida, stem densities were seven times greater than initial levels for Hypericum spp. In contrast, growing season fires reduced densities of H. brachyphyllum by 65%, but did not change densities of H. microsepalum. Only resprouting of H. microsepalum decreased with increased fire intensity. In Louisiana, fire intensity influenced Ilex vomitoria, but not Quercus spp. Following fires, stem densities oil. vomitoria were five times greater in fuel removal than fuel addition areas.

Conclusions: Past use of dormant season fires likely contributed to increased abundances of some species of root‐crown bearing shrubs observed today in old‐growth savannas. Reintroduction of growing season fires will be effective in maintaining or decreasing stem densities, depending on species and fuel type. Genet mortality and stem density reductions appear most likely in areas at localized scales where tree falls and needle coverage create hotspots in Pinus palustris savannas.
Hydrological landscape settings of base‐rich fen mires and fen meadows: an overview
Authors: Grootjans A.P. , Adema E.B. , Bleuten W. , Joosten H. , Madaras M. , Janáková M.
Published: February 2009

Question: Why do similar fen meadow communities occur in different landscapes? How does the hydrological system sustain base‐rich fen mires and fen meadows?

Location: Interdunal wetlands and heathland pools in The Netherlands, percolation mires in Germany, Poland, and Siberia, and calcareous spring fens in the High Tatra, Slovakia.

Methods: This review presents an overview of the hydrological conditions of fen mires and fen meadows that are highly valued in nature conservation due to their high biodiversity and the occurrence of many Red List species. Fen types covered in this review include: (1) small hydrological systems in young calcareous dune areas, and (2) small hydrological systems in decalcified old cover sand areas in The Netherlands; (3) large hydrological systems in river valleys in Central‐Europe and western‐Siberia, and (4) large hydrological systems of small calcareous spring fens with active precipitation of travertine in mountain areas of Slovakia.

Results: Different landscape types can sustain similar nutrient poor and base‐rich habitats required by endangered fen meadow species. The hydrological systems of these landscapes are very different in size, but their ground water flow pattern is remarkably similar. Paleoecological research showed that travertine forming fen vegetation types persisted in German lowland percolation mires from 6000 to 3000 BP. Similar vegetation types can still be found in small mountain mires in the Slovak Republic. Small pools in such mires form a cascade of surface water bodies that stimulate travertine formation in various ways. Travertine deposition prevents acidification of the mire and sustains populations of basiphilous species that elsewhere in Europe are highly endangered.

Conclusion: Very different hydrological landscape settings can maintain a regular flow of groundwater through the top soil generating similar base‐rich site conditions. This is why some fen species occur in very different landscape types, ranging from mineral interdunal wetlands to mountain mires.
Late‐Holocene fire history in a forest‐grassland mosaic in southern Brasil: Implications for conservation
Authors: Behling Hermann , Pillar Valério D. , Müller Sandra C. , Overbeck Gerhard E.
Published: February 2009

Question: Is the diverse mosaic of forest/grassland (Campos) vegetation on the hills in the Porto Alegre region natural or of anthropogenic origin? What are the best approaches to management and conservation of forest/grassland mosaics in southern Brazil?

Location: 280 m a.s.l., Rio Grande do Sul State (30°04′32″S; 51°06′05″W, southern Brazil.

Methods: A 50‐cm long radiocarbon dated sediment core from a swamp on Morro Santana was analysed for pollen and charcoal, and multivariate data analysis was used to reconstruct past vegetation and fire dynamics.

Results: The formation of swamp deposits is related to a change to wetter climatic conditions since 1230 cal yr BP. The diverse forest/grassland mosaic existed already at that time and can be seen as natural in origin as it has been also shown from other studies in southern Brazil. Since 580 cal yr BP, forests expanded continuously. The marked higher occurrence of the pioneer Myrsine during the last 70 years, indicates a change in the disturbance regime. In the past, vegetation has been influenced by mostly anthropogenic fire, set first by Amerindians and later by European settlers.

Conclusions: Management for conservation of forest/grassland mosaics should take into account, first, that grasslands are remnants of earlier drier Holocene periods and not a result of deforestation and, second, the history of disturbance by grazing and fire. Suppression of grazing and burning has likely resulted in a trend towards more woody vegetation under modern wet climatic conditions. If management for conservation excludes fire, the present grassland patches will tend to disappear due to forest expansion under the modern humid climate. Maintaining or reintroducing cattle grazing in conservation areas could be an alternative to fire.
Type 1 and Type 2 Diabetic-Erectile Dysfunction: Same Diagnosis (ICD-9), Different Disease?
Authors: Chitaley Kanchan
Published: February 2009

Introduction

Although hyperglycemia is a common defining feature of both type 1 and type 2 diabetes, many unique characteristics distinguish these diseases, including insulin and lipid levels, obesity status, and inflammatory agent profiles. In the laboratory, the presence of erectile dysfunction (ED) has been established in animal models of both type 1 and type 2 diabetes.

Aim

The purpose of this study was to determine whether unique mechanisms underlie ED in type 1 vs. type 2 diabetic animal models.

Main Outcome Measures

Many mechanisms can underlie ED, including impaired dilatory signaling, heightened contractile sensitivity, and veno-occlusive disorder.

Methods

Using PubMed, the literature was mined to evaluate what is known about which mechanism underlie ED in type 1 vs. type 2 diabetic animal models.

Results

Impaired cavernosal vasodilation has been established in type 1 diabetic rodents. This dysfunction appears to be mediated by a severe defect in non-adrenergic–non-cholinergic nerve signaling, as well as impairment in penile endothelial function. In contrast, type 2 diabetic animals appear to have minimal impairment in parasympathetic-mediated dilatory function, but do have evidence of endothelial dysfunction. Type 2 diabetic models also exhibit a significant and striking increase in cavernosal contractile sensitivity, and a significant veno-occlusive disorder, neither of which is consistently reported in type 1 diabetic animals.

Conclusions

With the distinct mechanisms underlying the ED phenotype in animal models of type 1 and type 2 diabetes, tailoring therapeutic treatments for diabetic-ED to the specific mechanisms underlying this disease complication may be warranted. Further examination of mechanisms underlying ED in diabetic human patients may thus lead to significant changes in the way urologists diagnose, code, and treat diabetic-ED.
Adenosine Signaling, Priapism and Novel Therapies
Authors: Dai Yingbo , Zhang Yujin , Phatarpekar Prasad , Mi Tiejuan , Zhang Hong , Blackburn Michael R. , Xia Yang
Published: February 2009

Introduction

Priapism is defined as abnormal prolonged penile erection lasting at least for 4 hours occurring without sexual interest. Forty percent of sickle cell disease (SCD) patients display priapism. The disorder is dangerous and urgent given its association with ischemia-mediated erectile tissue damage and subsequent erectile dysfunction. Current strategies to manage the disorder are poor due to lack of fundamental understanding of the molecular mechanisms of priapism. Adenosine is a signaling nucleoside that elicits many pathophysiological effects by engaging membrane receptors. Recent evidence shows that adenosine may play an important role in priapism via adenosine receptor.

Aim

To summarize the recent findings on the importance of adenosine signaling in the pathogenesis of priapism.

Main Outcome Measures

Evidence in the literature on the association between adenosine signaling and the development of priapism.

Methods

This article reviews the literature that relates to the contributory role of adenosine signaling in priapism in multiple animal models and humans.

Results

Excessive adenosine accumulation in the penis, coupled with increased A2BR signaling, contributes to priapism in two independent lines of mutant mice. One is adenosine deaminase (ADA)-deficient mice, the only animal displaying spontaneously prolonged penile erection, and the other is SCD transgenic mice, a well-accepted priapic animal model. Both polyethylene glycol-modified ADA (PEG-ADA) enzyme therapy and A2BR antagonists are capable of inhibiting potent corpus cavernosal vascular relaxation associated with priapic-like activity seen in both ADA-deficient mice and SCD transgenic mice, indicating that PEG-ADA enzyme therapy is likely to be a novel therapy for such a dangerous urological disorder.

Conclusions

Overall, the research reviewed here raises the intriguing possibility that elevated adenosine signaling contributes to priapism in general and that this signaling pathway represents a potentially important therapeutic target for the treatment of priapism.
Role of Immunophilins in Recovery of Erectile Function After Cavernous Nerve Injury
Authors: Sezen Sena F. , Lagoda Gwen , Burnett Arthur L.
Published: February 2009

Introduction

Immunophilin ligands provide potentially new alternatives for the treatment of erectile dysfunction (ED), which occurs after injury of the cavernous nerves (CNs).

Aim

To review and update current knowledge of the neurotrophic effects and likely mechanism of action of immunophilin proteins with emphasis on the FK506-binding protein (FKBP) subfamily and the role of immunophilin ligands for the treatment of CN injury-induced ED.

Methods

Review of available reports of studies investigating the effects and neurotrophic mechanisms of immunophilin ligands involved in erectile function recovery in rodent models of CN injury.

Main Outcome Measures

Erection parameters and molecular correlations associated with CN injury and functional recovery.

Results

Treatment with prototype immunosuppressive immunophilin ligands FK506 (FK) and rapamycin (Rapa) improve erectile function in animal models of CN injury. Similarly, non-immunosuppressive analogs such as GPI-1046 and FK1706 are effective in recovery of erections after CN injury. Neuronal nitric oxide may influence the erection recovery effects of immunophilin ligands after CN injury. FKBPs 38 and 65 expression changes in the penis and its innervation coincide with the neurotrophic effects of immunophilin ligands. Antioxidative actions of immunophilin ligands contribute to their neurotrophic effects. Immunophilins are localized to nerves coursing in human prostate and penile tissue.

Conclusions

The findings support the hypothesis that immunophilin ligands, working through specific receptor mechanisms that are specific to injured CN, are potentially useful to sustain erectile function in men following radical prostatectomy.
Nerve Growth Factor Modulation of the Cavernous Nerve Response to Injury
Authors: Bella Anthony J. , Lin Guiting , Lin Ching-Shwun , Hickling Duane R. , Morash Christopher , Lue Tom F.
Published: February 2009

Introduction

Surgical therapies for prostate cancer and other pelvic malignancies often result in neuronal damage and debilitating loss of sexual function due to cavernous nerve (CN) trauma. Advances in the neurobiology of growth factors have heightened clinical interest in the development of protective and regenerative neuromodulatory strategies targeting CN recovery following injury.

Aim

The aim of this review was to offer an examination of current and future nerve growth factor (NGF) modulation of the CN response to injury with a focus on brain-derived nerve growth factor (BDNF), growth differentiation factor-5 (GDF-5), and neurturin (NTN).

Methods

Information for this presentation was derived from a current literature search using the National Library of Medicine PubMed Services producing publications relevant to this topic. Search terms included neuroprotection, nerve regeneration, NGFs, neurotrophic factors, BDNF, GDF-5, NTN, and CNs.

Main Outcome Measures

Basic science studies satisfying the search inclusion criteria were reviewed.

Results

In this session, BDNF, atypical growth factors GDF-5 and NTN, and their potential influence upon CN recovery after injury are reviewed, as are the molecular pathways by which their influence is exerted.

Conclusions

Compromised CN function is a significant cause of erectile dysfunction development following prostatectomy and serves as the primary target for potential neuroprotective or regenerative strategies utilizing NGFs such as BDNF, GDF-5, and NTN, and/or targeted novel therapeutics modulating signaling pathways.
Phase II study of S‐1 and irinotecan combination chemotherapy as a first‐line therapy for patients with advanced gastric cancer. Korean Cancer Study Group Protocol ST05‐02
Authors: KANG Hye J , CHO Sang H , OH Suk J , YANG Sung H , LEE Moon H , SONG Eun‐Kee , CHUNG Hyun C , NA Im I , RYOO Baek‐Yeol
Published: February 2009

Background:  Irinotecan plus intravenous 5‐fluorouracil (5‐FU) with leucovorin is effective against gastrointestinal cancer. S‐1 is an oral fluoropyrimidine derivative and has a high response rate of about 40% for patients with advanced gastric cancer (AGC). We evaluated the antitumor activity and toxicities of an S‐1 and irinotecan combination as a first‐line therapy for patients with AGC.

Methods:  Patients with histologically confirmed unresectable or metastatic AGC were treated with S‐1 40 mg/m2 PO twice daily on days 1–14 and irinotecan 150 mg/m2 i.v. on day 1 every 3 weeks until disease progression or unacceptable toxicities resulted.

Results:  A total of 45 patients were enrolled between September 2005 and March 2007. After a median of seven cycles of chemotherapy (range: 1–20, total: 350), 42 and 44 patients were evaluable for response and toxicity, respectively. On the intention‐to‐treat analysis, the overall response rate was 48.9% (95% C.I. 34.3–63.5%). The median time to progression was 5.7 months (95% C.I. 4.3–7.1) and the median overall survival was 10.4 months (95% C.I. 6.1–14.7). The commonly observed grade 3/4 adverse events were neutropenia (29.5% of patients) and vomiting (13.6%).

Conclusion:  An S‐1 and irinotecan combination chemotherapy is active and tolerable as a first‐line therapy for AGC.
EGFR mutation testing in NSCLC: Patterns of care and outcomes in Western Australia
Authors: WEBB Suzanne , THOMAS Marc , METCALF Cecily , SEGAL Amanda , NOWAK Anna K , BENTEL Jacqueline , MILLWARD Michael
Published: February 2009

Aims:  This study evaluated the EGFR mutation status, administration of gefitinib or erlotinib and outcomes of patients assessed for EGFR mutations since the commencement of testing in Western Australia.

Methods:  A retrospective study identified patients with NSCLC who undergone EGFR mutation testing in the Department of Anatomical Pathology, Royal Perth Hospital, Western Australia from March 2005 until May 2007. Patient characteristics, cancer history, treatment, outcomes and survival were collected from the medical records and pathology reports.

Results:  Tumor samples from 64 patients were sequenced for mutations in exons 18–21 EGFR and, of these, 53 patients with NSCLC were included in the analysis. The mean age at diagnosis was 61 years (range 19–80) and most of the tumor samples tested were from female patients (76%). Overall 36% of patients tested were mutation‐positive with 95% of mutations occurring in exons 19 or 21. A total of 63% of mutation‐positive and 18% of mutation‐negative patients were treated with gefitinib or erlotinib. Of these, 83% of patients whose tumors had an EGFR mutation had a favorable response following treatment, compared to 17% of mutation‐negative patients. The duration of treatment was longer in mutation‐positive patients (mean 30 weeks vs 9 weeks).

Conclusion:  EGFR mutation testing is not routinely performed in NSCLC in Western Australia. Referral for testing is at the discretion of the treating physician, accounting for the high proportion of women and adenocarcinoma histology. Selection of mutation‐positive tumors for treatment with gefitinib or erlotinib is associated with good responses to treatment. This study supports the use of gefitinib or erlotinib in routine clinical practice in patients with NSCLC carrying an EGFR mutation.
An ArcGIS®Approach to Include Tectonic Structures in Point Data Regionalization
Authors: Darsow Andreas , Schafmeister Maria‐Theresia , Hofmann Thilo
Published: February 2009

Point data derived from drilling logs must often be regionalized. However, aquifers may show discontinuous surface structures, such as the offset of an aquitard caused by tectonic faults. One main challenge has been to incorporate these structures into the regionalization process of point data. We combined ordinary kriging and inverse distance weighted (IDW) interpolation to account for neotectonic structures in the regionalization process. The study area chosen to test this approach is the largest porous aquifer in Austria. It consists of three basins formed by neotectonic events and delimited by steep faults with a vertical offset of the aquitard up to 70 m within very short distances. First, ordinary kriging was used to incorporate the characteristic spatial variability of the aquitard location by means of a variogram. The tectonic faults could be included into the regionalization process by using breaklines with buffer zones. All data points inside the buffer were deleted. Last, IDW was performed, resulting in an aquitard map representing the discontinuous surface structures. This approach enables one to account for such surfaces using the standard software package ArcGIS®; therefore, it could be adopted in many practical applications.
Vulnerability in Research: Individuals with Limited Financial and/or Social Resources
Authors: Grady Christine
Published: February 2009

Vulnerability in research is often understood as a diminished ability to protect one's own interests, manifested by a compromised capacity to give informed or voluntary consent. Certain groups of people are thought to be more vulnerable than others and therefore are at risk of being exploited or mistreated in research. Accordingly, the federal regulations call for additional safeguards to protect vulnerable groups.

There remains some ambiguity and contradiction, however, regarding what groups are vulnerable in research and why,3 since the available codes of research ethics and regulations describe many groups as vulnerable. When so many groups are considered vulnerable, but no specification is offered as to how they are vulnerable or what particular protections are appropriate, the possibility of meaningful safeguards is diminished. In addition, current concepts of vulnerability are usually applied to whole groups of people, without distinguishing between individuals in a group who might truly have a compromised capacity to protect their own interests from those who do not.
The Vulnerability of the Very Sick
Authors: Menikoff Jerry
Published: February 2009

Suppose that someone has a serious illness. The illness will likely lead to significant disabilities, and may even cause death. Existing treatments are unsatisfactory. The patient learns about a clinical trial, in which some allegedly promising new treatment for that illness is being tested.

Such seriously ill patients for whom existing treatments are unsatisfactory have sometimes been categorized as medically vulnerable in the literature. Should these patients indeed be considered vulnerable subjects and be provided with special protections? And if the answer is yes, then what are those special protections? This article explores the possible answers to these questions.

The federal regulations for the protection of research subjects have several provisions addressing the concept of vulnerability. The three subparts Subparts B (pregnant women, fetuses, and neonates), C (prisoners), and D (children) deal with specific categories of vulnerable subjects, but do relatively little to address broader issues relating to vulnerability that might apply to a category such as the medically vulnerable. The Common Rule (Subpart A) is the only section containing general discussions of vulnerability.
A Walk in the Park: A Case Study in Research Ethics
Authors: Lazzarini Zita , Case Patricia , Thomas Cecil J.
Published: February 2009

Can researchers, interested in novel ways to assess HIV seroprevalence among populations which are otherwise hidden, collect condoms that have been discarded on the ground in a public sex environment (PSE) and test them for HIV? Does the Code of Federal Regulations address this question, and if not, what areas of research ethics might provide guidance to an IRB considering such a study? These questions arose as part of a preliminary study to test the feasibility of collecting discarded condoms from a public sex environment in Massachusetts, and testing contained semen for HIV. Although the methodology of this study is somewhat unusual, the questions raised are not. Researchers, who wish to use other types of abandoned samples such as discarded syringes, hair or saliva samples, or even excess biological samples, commonly confront similar issues, and the analysis utilized here could guide design and review of other studies.
Prejudice and the Medical Profession: A Five-Year Update
Authors: Clark Peter A.
Published: February 2009

Over the past decades the mortality rate in the United States has decreased and life expectancy has increased. Yet a number of recent studies have drawn Americans attention to the fact that racial and ethnic disparities persist in health care. It is clear that the U.S. health care system is not only flawed for many reasons including basic injustices, but may be the cause of both injury and death for members of racial and ethnic minorities.

In 2002, an Institute of Medicine (IOM) report requested by Congress listed more than 100 studies documenting a wide range of disparities in the United States health care system. This report found that people belonging to racial and ethnic minorities often receive lower quality of health care than do people of European descent, even when their medical insurance coverage and income levels are the same as that of the latter.
Africa's Linguistic Diversity
Authors: Sands Bonny
Published: February 2009

African language classification in the latter half of the 20th century has been dominated by Joseph Greenberg's work classifying African languages into four linguistic genetic groupings: Afroasiatic, Niger‐Kordofanian, Nilo‐Saharan, and Khoisan. Current research indicates that there are a minimum of 20 unrelated African language families or isolates. Africa's linguistic diversity will remain poorly documented unless significant efforts are made to document some of the continent's most endangered, underdescribed languages and language families.
Characterizing the Structure and Photocycle of PR 2D Crystals with CD and FTIR Spectroscopy†
Authors: Schäfer Gabriela , Shastri Sarika , Verhoefen Mirka‐Kristin , Vogel Vitali , Glaubitz Clemens , Wachtveitl Josef , Mäntele Werner
Published: February 2009

We present here a study on proteorhodopsin (PR) 2D crystals with analytical ultracentrifugation, circular dichroism and Fourier transform infrared (FTIR) spectroscopy. The aim of our experiments was to test the activity of 2D crystal sample preparations and to gain further insight in PR structure, stability and function with these techniques. Our results demonstrate higher stability compared to detergent‐solubilized or reconstituted samples. For different pH values, low pH 2D crystals tend to form bigger aggregates and are less stable than at basic pH. The pH 9 sample shows a sharp phase transition during heat denaturation and there is also evidence for protein–protein interaction due to the close proximity of the proteins in the 2D crystals. In the FTIR measurements at cryogenic temperatures (77 K), we characterized the first step in the PR photocycle. At pH 9, the K intermediate could be observed and the samples showed no orientation effects. At pH 5, we could trap the K/L intermediate, characterized by its negative IR signal at 1741 cm−1. In rapid‐scan FTIR experiments, we could also identify the M intermediate of the photocycle at basic pH. We conclude that the PR 2D crystals exhibit a fully functional photocycle and are therefore well suited for further studies on the proton transport mechanism of PR.
Genesis and Mixing/Mingling of Mafic and Felsic Magmas of Back‐Arc Granite: Miocene Tsushima Pluton, Southwest Japan
Authors: Shin Ki‐Cheol , Kurosawa Masanori , Anma Ryo , Nakano Takanori
Published: February 2009

The Middle Miocene Tsushima granite pluton is composed of leucocratic granites, gray granites and numerous mafic microgranular enclaves (MME). The granites have a metaluminous to slightly peraluminous composition and belong to the calc‐alkaline series, as do many other coeval granites of southwestern Japan, all of which formed in relation to the opening of the Sea of Japan. The Tsushima granites are unique in that they occur in the back‐arc area of the innermost Inner Zone of Southwest Japan, contain numerous miarolitic cavities, and show shallow crystallization (2–6 km deep), based on hornblende geobarometry. The leucocratic granite has higher initial 87Sr/86Sr ratios (0.7065–0.7085) and lower εNd(t) (−7.70 to −4.35) than the MME of basaltic–dacitic composition (0.7044–0.7061 and −0.53 to −5.24), whereas most gray granites have intermediate chemical and Sr–Nd isotopic compositions (0.7061–0.7072 and −3.75 to −6.17). Field, petrological, and geochemical data demonstrate that the Tsushima granites formed by the mingling and mixing of mafic and felsic magmas. The Sr–Nd–Pb isotope data strongly suggest that the mafic magma was derived from two mantle components with depleted mantle material and enriched mantle I (EMI) compositions, whereas the felsic magma formed by mixing of upper mantle magma of EMI composition with metabasic rocks in the overlying lower crust. Element data points deviating from the simple mixing line of the two magmas may indicate fractional crystallization of the felsic magma or chemical modification by hydrothermal fluid. The miarolitic cavities and enrichment of alkali elements in the MME suggest rapid cooling of the mingled magma accompanied by elemental transport by hydrothermal fluid. The inferred genesis of this magma–fluid system is as follows: (i) the mafic and felsic magmas were generated in the mantle and lower crust, respectively, by a large heat supply and pressure decrease under back‐arc conditions induced by mantle upwelling and crustal thinning; (ii) they mingled and crystallized rapidly at shallow depths in the upper crust without interaction during the ascent of the magmas from the middle to the upper crust, which (iii) led to fluid generation in the shallow crust. The upper mantle in southwest Japan thus has an EMI‐like composition, which plays an important role in the genesis of igneous rocks there.
DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix
Authors: LANGHOFF PIA , AUTHIER ASTRID , BUCKLEY THOMAS R. , DUGDALE JOHN S. , RODRIGO ALLEN , NEWCOMB RICHARD D.
Published: February 2009

Molecular techniques such as DNA barcoding have become popular in assisting species identification especially for cryptic species complexes. We have analysed data from a 468‐bp region of the mitochondrial cytochrome oxidase subunit I (COI) gene from 200 specimens of 12 species of endemic New Zealand leafroller moths (Tortricidae) from the genera Planotortrix and Ctenopseustis to assess whether the DNA barcoding region can distinguish these species. Among the 200 sequences analysed, 72 haplotypes were recovered, with each genus forming a separate major clade. Maximum likelihood phylogenetic methods were used to test whether species fell into reciprocally monophyletic clades. The optimal phylogeny showed that four species within the genus Ctenopseustis (C. obliquana, C. herana, C. filicis and C. fraterna) and three within Planotortrix (P. octo, P. excessana and P. avicenniae) are polyphyletic. Shimodaira–Hasegawa tests rejected a null hypothesis of monophyly for the species C. obliquana, C. herana, P. octo and P. excessana. Comparisons of within and between species levels of sequence divergence for the same set of seven species showed cases where maximum levels of within‐species divergence were greater than some levels of between‐species divergence. DNA barcoding using this region of the COI gene is able to distinguish the two genera and some species within each genus; however, many species cannot be identified using this method. Finally, we discuss the possible reasons for this polyphyly, including incomplete lineage sorting, introgression, horizontal gene transfer and incorrect taxonomy.
New polymorphic microsatellite loci in the house sparrow, Passer domesticus
Authors: GARNIER S. , DURAND P. , ARNATHAU C. , RISTERUCCI A. M. , ESPARZA‐SALAS R. , CELLIER‐HOLZEM E. , SORCI G.
Published: February 2009

We developed 13 new polymorphic microsatellite loci in the house sparrow (Passer domesticus), which exhibited from 2 to 15 alleles. Observed and expected heterozygosities ranged from 0.17 to 0.77 and from 0.35 to 0.85, respectively. We detected no linkage disequilibrium between loci. Allele frequencies supported Hardy–Weinberg equilibrium for 8 loci out of 13 after Bonferroni correction. Combined with loci previously isolated in the house sparrow, these new microsatellite markers provide valuable tools to study population genetics of this species.
KINALYZER, a computer program for reconstructing sibling groups
Authors: ASHLEY M. V. , CABALLERO I. C. , CHAOVALITWONGSE W. , DASGUPTA B. , GOVINDAN P. , SHEIKH S. I. , BERGER‐WOLF T. Y.
Published: February 2009

A software suite KINALYZER reconstructs full‐sibling groups without parental information using data from codominant marker loci such as microsatellites. KINALYZER utilizes a new algorithm for sibling reconstruction in diploid organisms based on combinatorial optimization. KINALYZER makes use of a Minimum 2‐Allele Set Cover approach based on Mendelian inheritance rules and finds the smallest number of sibling groups that contain all the individuals in the sample. Also available is a ‘Greedy Consensus’ approach that reconstructs sibgroups using subsets of loci and finds the consensus of the partial solutions. Unlike likelihood methods for sibling reconstruction, KINALYZER does not require information about population allele frequencies and it makes no assumptions regarding the mating system of the species. KINALYZER is freely available as a web‐based service.
Isolation and characterization of microsatellite loci in the plant‐ant Pseudomyrmex ferrugineus (Formicidae: Pseudomyrmecinae) and cross‐testing for two congeneric species
Authors: KAUTZ STEFANIE , SCHMID VOLKER S. , TRINDL ANDREAS , HEINZE JÜRGEN , BALLHORN DANIEL J. , HEIL MARTIN
Published: February 2009

To investigate the population structure of the obligate plant‐ant Pseudomyrmex ferrugineus, we developed primers for 12 microsatellite loci. We tested the variability of the markers on 11 individuals from each of two populations (totalling 22 individuals) and found two to 12 alleles per locus and population. No deviations from Hardy–Weinberg equilibrium were detected. Observed and expected heterozygosities at each locus ranged from 0.00 to 0.50 and from 0.08 to 0.46, respectively. We also investigated suitability of these primers in two congeneric species.
Isolation of nine nuclear microsatellites in the common Mediterranean sea urchin, Paracentrotus lividus (Lamarck)
Authors: CALDERÓN I. , TURON X. , PASCUAL M.
Published: February 2009

Nine polymorphic microsatellite loci were isolated and characterized for the edible common sea urchin Paracentrotus lividus. Loci were obtained from two genomic libraries enriched with different di‐, tri‐ and tetranucleotides. Most microsatellites obtained were imperfect dinucleotides. Allelic variation was screened for a total of 56 individuals from two populations from North‐Western Mediterranean. Microsatellites showed a number of alleles ranging from 13 to 35. Linkage disequilibrium was not detected between any pair of loci, and all loci showed a significant departure from Hardy–Weinberg equilibrium which is not likely to be the result of null alleles, suggesting that demographic features may be acting upon this commercially interesting species.
Reddish Green: A Challenge for Modal Claims About Phenomenal Structure1
Authors: NIDA‐RÜMELIN MARTINE , SUAREZ JUAN
Published: February 2009

We discuss two modal claims about the phenomenal structure of color experiences: (i) violet experiences are necessarily experiences of a color that is for the subject on that occasion phenomenally composed of red and blue (the modal claim about violet) and (ii) no subject can possibly have an experience of a color that is for it then phenomenally composed of red and green (the modal claim about reddish green). The modal claim about reddish green is undermined by empirical results. We discuss whether these empirical results cast doubt on the other modal claims as well. We argue that this not the case. Our argument is based on the thesis that the best argument for the modal claim about violet is quite different from the best argument for the modal claim about reddish green. To argue for this disanalogy we propose a reconstruction of the best available justification for both claims.
Conditional Monte Carlo Gradient Estimation in Economic Design of Control Limits
Authors: Fu Michael C. , Lele Shreevardhan , Vossen Thomas W. M.
Published: February 2009

The economic approach to determining the optimal control limits of control charts requires estimating the gradient of the expected cost function. Simulation is a very general methodology for estimating the expected costs, but for estimating the gradient, straightforward finite difference estimators can be inefficient. We demonstrate an alternative approach based on smoothed perturbation analysis (SPA), also known as conditional Monte Carlo. Numerical results and consequent design insights are obtained in determining the optimal control limits for exponentially weighted moving average and Bayes charts. The results indicate that the SPA gradient estimators can be significantly more efficient than finite difference estimators, and that a simulation approach using these estimators provides a viable alternative to other numerical solution techniques for the economic design problem.
Product Design and Supply Chain Coordination Under Extended Producer Responsibility
Authors: Subramanian Ravi , Gupta Sudheer , Talbot Brian
Published: February 2009

Extended Producer Responsibility (EPR) legislation focuses on the life‐cycle environmental performance of products and has significant implications for management theory and practice. In this paper, we examine the influence of EPR policy parameters on product design and coordination incentives in a durable product supply chain. We model a manufacturer supplying a remanufacturable product to a customer over multiple periods. The manufacturer invests in two design attributes of the product that impact costs incurred by the supply chain— performance, which affects the environmental impact of the product during use, and remanufacturability, which affects the environmental impact post‐use. Consistent with the goals of EPR policies, the manufacturer and the customer are required to share the environmental costs incurred over the product's life cycle. The customer has a continuing need for the services of the product and optimizes between the costs of product replacement and the costs incurred during use. We demonstrate how charges during use and post‐use can be used as levers to encourage environmentally favorable product design. We analyze the impact of supply chain coordination on design choices and profit and discuss contracts that can be used to achieve coordination, both under symmetric and asymmetric information about customer attributes.
Nonlinear Viscoelastic Finite Element Analysis of Physical Aging in an Encapsulated Transformer
Authors: Neidigk M. A. , Shen Y.-L.
Published: February 2009

The generation of thermal stresses is a major cause for mechanical failure in encapsulated electronic components. In this study numerical modeling is employed to analyze thermal stresses in a high-voltage transformer encapsulated with filled epoxy. The transformer assembly consists of materials with an extremely disparate range of thermomechanical properties. The thermal histories considered mimic those in the operational condition. It is found that, upon thermal cooling from elevated temperature, the ceramic core can be under local tensile stress although it is entirely surrounded by materials with much greater coefficients of thermal expansion. The unique aspect of this paper originates from the fact that the volume shrinkage of the viscoelastic encapsulant during physical aging contributes to an increase in stress over time, thus increasing the tendency of fracture. This counter intuitive result (stress increase due to nonlinear viscoelastic physical aging) can now be predicted using constitutive models recently developed at Sandia National Laboratories. When a silicone coating between the core and the encapsulation is included, the stress is significantly reduced. The modeling result is shown to corroborate with the actual performance of the transformer.
A General Methodology to Predict Fatigue Life in Lead-Free Solder Alloy Interconnects
Authors: Pierce David M. , Sheppard Sheri D. , Vianco Paul T.
Published: February 2009

The ubiquitous eutectic tin-lead (Sn–Pb) solder alloys are soon to be replaced with lead-free alternatives. In light of this transition, new computational tools for predicting the fatigue life of lead-free solders are required. A fatigue life prediction methodology was developed, based on stress-strain, creep, and isothermal fatigue data; the latter generated using a double lap-shear (DLS) test assembly. The proposed fatigue life prediction methodology builds on current practices in fatigue prediction for solder alloys, particularly the concepts of unpartitioned energy methods in finite element analysis (FEA) and continuum damage mechanics. As such, the current state of these fields is briefly discussed. Next, the global and local FEA simulations of the DLS test assembly are detailed. A correlation is then made between the empirical data and the FEA simulations. A general fatigue life prediction methodology is next described in detail. Finally, this methodology is tested and verified against the empirical data.
Thermal Management of Electronic Chips in a Channel Using Input Power to Control Flow Velocity
Authors: Alawadhi Esam M.
Published: February 2009

In this research, thermal management of an electronic device using the input power is investigated numerically using the finite element method. The considered geometry consists of a horizontal channel with three volumetrically heated chips mounted on the bottom wall of the channel. The magnitude of the channel’s inlet velocity is varied with the variation of heat generation in the chips. The thermal characteristics of the system are presented, and compared with thermal characteristics of a system at a steady state condition. The effect of the Reynolds number and the oscillating period of the heat generation on the chips’ average temperature and Nusselt number is presented. The pressure drop in the channel is also calculated. The results indicated that the transient operating condition causes temperature to be higher than steady state by more than 45%, and difference between the transient and steady operations is reduced if the frequency is high. However, flow frequency has nearly no effect on the pressure drop in the channel.
Input-Output Analysis and Control Design Applied to a Linear Model of Spatially Developing Flows
Authors: Bagheri S. , Henningson D. S. , Hœpffner J. , Schmid P. J.
Published: February 2009

This review presents a framework for the input-output analysis, model reduction, and control design for fluid dynamical systems using examples applied to the linear complex Ginzburg–Landau equation. Major advances in hydrodynamics stability, such as global modes in spatially inhomogeneous systems and transient growth of non-normal systems, are reviewed. Input-output analysis generalizes hydrodynamic stability analysis by considering a finite-time horizon over which energy amplification, driven by a specific input (disturbances/actuator) and measured at a specific output (sensor), is observed. In the control design the loop is closed between the output and the input through a feedback gain. Model reduction approximates the system with a low-order model, making modern control design computationally tractable for systems of large dimensions. Methods from control theory are reviewed and applied to the Ginzburg–Landau equation in a manner that is readily generalized to fluid mechanics problems, thus giving a fluid mechanics audience an accessible introduction to the subject.