bluuebunny/crossref_metadata_2025 huggingface dataset:
Using mixed treatment comparisons and meta‐regression to perform indirect comparisons to estimate the efficacy of biologic treatments in rheumatoid arthritis
Authors: Nixon R. M. , Bansback N. , Brennan A.
Published: August 2006

Mixed treatment comparison (MTC) is a generalization of meta‐analysis. Instead of the same treatment for a disease being tested in a number of studies, a number of different interventions are considered. Meta‐regression is also a generalization of meta‐analysis where an attempt is made to explain the heterogeneity between the treatment effects in the studies by regressing on study‐level covariables. Our focus is where there are several different treatments considered in a number of randomized controlled trials in a specific disease, the same treatment can be applied in several arms within a study, and where differences in efficacy can be explained by differences in the study settings. We develop methods for simultaneously comparing several treatments and adjusting for study‐level covariables by combining ideas from MTC and meta‐regression.

We use a case study from rheumatoid arthritis. We identified relevant trials of biologic verses standard therapy or placebo and extracted the doses, comparators and patient baseline characteristics. Efficacy is measured using the log odds ratio of achieving six‐month ACR50 responder status. A random‐effects meta‐regression model is fitted which adjusts the log odds ratio for study‐level prognostic factors. A different random‐effect distribution on the log odds ratios is allowed for each different treatment. The odds ratio is found as a function of the prognostic factors for each treatment. The apparent differences in the randomized trials between tumour necrosis factor alpha (TNF−∝) antagonists are explained by differences in prognostic factors and the analysis suggests that these drugs as a class are not different from each other. Copyright © 2006 John Wiley & Sons, Ltd.
Advances in statistical human genetics over the last 25 years
Authors: Elston Robert C. , Anne Spence M.
Published: August 2006

The past 25 years has seen an explosion in the number of genetic markers that can be measured on DNA samples at an ever decreasing cost. Although basic statistical methods for analysing such data gathered on samples of either independent individuals or family members, one or two markers at a time, were already well developed before this explosion occurred, there has been a corresponding burst in activity to develop multiple marker models to find disease‐causing gene variants, capitalizing on the data that have become available, to increase the power of such methods. This has required the concomitant development of faster algorithms to speed up the computation of various likelihoods. For linkage analysis, to obtain the approximate locations for genes of interest, Mendelian segregation models have been extended to be more realistic and statistical models that do not assume specific modes of inheritance have been extended to allow for the analysis of larger pedigree structures. For association analysis, to obtain more precise locations for genes of interest, the recent completion of the first stage of the HapMap project has spurred the development, still underway, of novel experimental designs and analytical methods to combat the curse of dimensionality and the resulting multiple testing problem. Perhaps the greatest current challenge concerns how best to gather and synthesize the many lines of evidence possible in order to discover the genetic determinants underlying complex diseases. Copyright © 2006 John Wiley & Sons, Ltd.
An autoregressive linear mixed effects model for the analysis of longitudinal data which show profiles approaching asymptotes
Authors: Funatogawa Ikuko , Funatogawa Takashi , Ohashi Yasuo
Published: August 2006

In longitudinal data, a continuous response sometimes shows a profile approaching an asymptote. For such data, we propose a new class of models, autoregressive linear mixed effects models in which the current response is regressed on the previous response, fixed effects, and random effects. Asymptotes can shift depending on treatment groups, individuals, and so on, and can be modelled by fixed and random effects. We also propose error structures that are useful in practice. The estimation methods of linear mixed effects models can be used as long as there is no intermittent missing. Copyright © 2006 John Wiley & Sons, Ltd.
Cobol minefield detection
Authors: Veerman Niels , Verhoeven Ernst‐Jan
Published: August 2006

In Cobol, procedures can be programmed in ways that lead to unexpected behaviour and reduced portability. This behaviour is recognized as so‐called ‘mines’: programming practices containing hidden dangers and requiring extreme caution. Cobol mines can be created intentionally or by a programming error, and can be tripped at an unforeseen moment. This leads to minefields in source code with unseen hazards, which complicate understanding and maintenance, and which can lead to costly breakdowns of business critical software systems. We discuss Cobol mines and the dangers that come with them, having implemented a mine detector for Cobol. Our detector was deployed in an industrial situation, and a number of minefields were found in production systems. By restructuring a complex legacy application, we argue that code restructuring can be used to combat minefields. Copyright © 2006 John Wiley & Sons, Ltd.
A theory of regression testing for behaviourally compatible object types
Authors: Simons Anthony J. H.
Published: August 2006

A behavioural theory of object compatibility is presented, which has implications for object‐oriented regression testing. The theory predicts that only certain models of state refinement yield compatible types, dictating the legitimate design styles to be adopted in object statecharts. The theory also predicts that conformity‐testing using regression tests is inadequate. Functionally complete test‐sets that are applied as regression tests to subtype objects are usually expected to cover the functionality of the original type, even though they are clearly not expected to cover extra functionality introduced in the subtype. However, such regression testing is proven to cover strictly less than the original state‐space in the new context and so provides much weaker confidence than expected. A different retesting model is proposed, based on full automatic test regeneration from the subtype's specification. This method can guarantee equivalent levels of confidence after retesting. The behavioural conformity desired by regression testing can then be proven by verification in the theory. Copyright © 2006 John Wiley & Sons, Ltd.
Polyyne synthesis using carbene/carbenoid rearrangements
Authors: Chalifoux Wesley A. , Tykwinski Rik R.
Published: August 2006

Rearrangement of a carbene/carbenoid intermediate to form an acetylene moiety, known as the Fritsch–Buttenberg–Wiechell (FBW) rearrangement, was developed for the formation of polyynes and polyyne frameworks within highly conjugated organic materials. Necessary precursors can be prepared through formation of an alkynyl ketone, followed by dibromoolefination under Corey–Fuchs conditions. The carbenoid rearrangement is brought about by treatment of the dibromoolefin with BuLi under mild conditions. The success of these FBW reactions is quite solvent‐dependent, and nonpolar hydrocarbon solvents (e.g., hexanes, toluene, benzene) work quite well, while use of ethereal solvents such as diethyl ether and tetrahydrofuran (THF) does not provide the desired polyyne product. This protocol was successfully applied to the formation of silyl, alkyl, alkenyl, and aryl polyynes, including di‐, tri‐, and tetrayne products, as well as the construction of two‐dimensional carbon‐rich molecules. A one‐pot variant of this procedure is being developed and is particularly applicable toward the synthesis of polyyne natural products. Formation of a series of triisopropylsilyl end‐capped polyynes, from the triyne to decayne, was achieved. Third‐order nonlinear optical properties of these polyynes were evaluated. This study shows that the molecular second hyperpolarizabilities for the polyynes as a function of length increase at a rate that is higher than all other nonaromatic organic oligomers. © 2006 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 6: 169–182; 2006: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.20081
Co‐ordinated voltage control of DFIG wind turbines in uninterrupted operation during grid faults
Authors: Hansen Anca D. , Michalke Gabriele , Sørensen Poul , Lund Torsten , Iov Florin
Published: August 2006

Emphasis in this article is on the design of a co‐ordinated voltage control strategy for doubly fed induction generator (DFIG) wind turbines that enhances their capability to provide grid support during grid faults. In contrast to its very good performance in normal operation, the DFIG wind turbine concept is quite sensitive to grid faults and requires special power converter protection. The fault ride‐through and grid support capabilities of the DFIG address therefore primarily the design of DFIG wind turbine control with special focus on power converter protection and voltage control issues. A voltage control strategy is designed and implemented in this article, based on the idea that both converters of the DFIG (i.e. rotor‐side converter and grid‐side converter) participate in the grid voltage control in a co‐ordinated manner. By default the grid voltage is controlled by the rotor‐side converter as long as it is not blocked by the protection system, otherwise the grid‐side converter takes over the voltage control. Moreover, the article presents a DFIG wind farm model equipped with a grid fault protection system and the described co‐ordinated voltage control. The whole DFIG wind farm model is implemented in the power system simulation toolbox PowerFactory DIgSILENT. The DFIG wind farm ride‐through capability and contribution to voltage control in the power system are assessed and discussed by means of simulations with the use of a transmission power system generic model developed and delivered by the Danish Transmission System Operator Energinet.dk. The simulation results show how a DFIG wind farm equipped with voltage control can help a nearby active stall wind farm to ride through a grid fault, without implementation of any additional ride‐through control strategy in the active stall wind farm. Copyright © 2006 John Wiley &Sons, Ltd.
An analysis of refinement in an abortive paradigm
Authors: Deutsch Moshe , Henson Martin C.
Published: August 2006

This paper presents a new strand of investigation which complements our previous investigation of refinement for specifications whose semantics is given by
partial
relations (using Z as a linguistic vehicle for this semantics). It revolves around extending our mathematical apparatus so as to continue our quest for examining mathematically the essence of the lifted-totalisation semantics (which underlies the de facto standard notion of refinement in Z) and the role of the semantic elements in model-theoretic refinement, but this time in the
abortive paradigm
. The analysis is given in two salient parts. In the first part, we consider the simpler framework of
operation-refinement:
we examine the (
de facto
) standard account of operation-refinement in this regime by introducing a simpler,
normative
theory which captures the notion of
firing-conditions
refinement directly in the language and in terms of the natural properties of preconditions and postconditions. In the second part, we generalise our analysis to a more intricate investigation of
simulation-based
data-refinement
. The proof-theoretic approach we undertake in the formal analysis provides us with a mathematical apparatus which enables us to examine
precisely
the relationships amongst the various theories of refinement. This enables us to examine the general mathematical role that the values play in model-theoretic refinement in the abortive paradigm, as well as the significance of the unique interaction of these values with the notions of
lifting
(of data simulations) and
lifted-totalisation
(of operations) in this regime. Furthermore, we generalise this mathematical analysis to a more
conceptual
one which also involves
extreme specifications
.
Impact of Polypropylene Amount on Functional Outcome and Quality of Life after Inguinal Hernia Repair by the TAPP Procedure Using Pure, Mixed, and Titanium‐coated Meshes
Authors: Horstmann Ruediger , Hellwig Matthias , Classen Claus , Röttgermann Susanne , Palmes Daniel
Published: August 2006

Background

Laparoscopic inguinal hernia repair requires the use of prosthetic material. This prospective, single‐center study was intended to investigate the impact of the amount of polypropylene (PP) mesh used in hernia repair on functional results and quality of life.

Methods

For this series, 672 consecutive patients with primary inguinal hernia undergoing transabdominal preperitoneal hernia repair (TAPP) using a heavyweight PP mesh (Prolene 10 × 15 cm, 1.5 g, group I, n = 232), a mixed PP‐ and Polyglactin mesh (Vypro II, 10 × 15 cm, 0.53 g, group II, n = 217), or a light‐weight titanized PP mesh (Ti‐Mesh, 10 × 15 cm, 0.24 g, group III, n = 223) were compared in terms of postoperative complications (seroma, wound healing disorders), quality of life score (pain development, physical condition, urologic disorders), and hernia recurrence.

Results

During a 12‐month follow‐up there were no significant differences in the recurrence rate (1.3%‐1.7%). Patients with a pure PP mesh (group I) showed significantly more postoperative seromas (12.1% versus 4.1%/1.8%), foreign body sensations (9.1% versus 5.5%/3.5%), and sensitivity to weather changes (5.6% versus 3.2%/2.2%) compared to groups II and III. In all groups, the quality of life score was improved postoperatively. However, among those patients in our series with few preoperative complaints, the postoperative quality of life was worsened when heavy‐weight PP meshes (group I+II) were used but significantly improved when light‐weight titanized PP meshes were used.

Conclusions

Comparable functional results, fewer postoperative complications, and improved quality of life can be achieved by reducing the amount of PP in meshes used for laparoscopic hernia repair by TAPP procedure.
Comparison of Spinal Cord Protection Utilizing Left Atrial‐Femoral with Femoral‐Femoral Bypass in Patients with Traumatic Rupture of the Aortic Isthmus
Authors: Weiman Darryl S. , Gurbuz A. Tayfun , Gursky Andrei , Valaulikar Ganpat , Pate James W.
Published: August 2006

Introduction

Postoperative paraplegia remains a dreaded complication of repair of traumatic rupture of the aortic isthmus. Claims have been made that left atrial‐femoral bypass provides better spinal cord protection. To test the hypothesis that left atrial‐femoral bypass is better than femoral vein‐to‐femoral artery bypass in regard to postoperative paraplegia, we concurrently compared the two techniques.

Methods

We compared the occurrence of paraplegia in 18 patients whose ruptures were repaired utilizing left atrial‐femoral bypass with 10,000 units of systemic heparin (group A) and 72 patients with femoral‐femoral bypass with heparin 300 units/kg and an oxygenator (group B) operated on between January 1995 and July 2004.

Results

The mortality rate was 5.6% (5/90), with no statistical difference between the two groups. Postoperative paraplegia was present in three (16.7%) group A patients and five group B (6.9%) patients. However, the specific etiology of the neurologic defect was not clear, as one patient’s paraplegia was transient following a period of cardiac arrest, and four others had had neurologic injuries prior to the aortic repair. Median aortic cross‐clamp times were shorter in group A (34 minutes vs. 49 minutes). No patient required reexploration for bleeding, and no patient developed a graft infection.

Conclusions

Paraplegia rates were higher in the left atrial‐femoral group, but the difference was not statistically significant. This occurred despite the decreased cross‐clamp times in this group. In patients undergoing repair of traumatic rupture of the aortic isthmus, left atrial‐femoral bypass does not provide better spinal cord protection than femoral‐femoral bypass.
Retrosternal Goiter: The Need for Median Sternotomy
Authors: Ahmed Mohamed E. , Ahmed Elnazeer O. , Mahadi Seif I.
Published: August 2006

Introduction

The aim of this study was to analyze the features of patients with goiter who underwent thyroidectomy via a cervical incision and a median sternotomy in Khartoum.

Methods

A total of 267 thyroidectomies were performed in Khartoum Teaching Hospital during the period from January 2002 to December 2003. There were 40 patients with evidence of retrosternal goiter (15%). Of those 40 patients, 13 had clinical and radiologic evidence of deep retrosternal extension of the goiter possibly necessitating sternotomy. Only 9 of the 13 patients actually required sternotomy, which accounted for 3.4% of all thyroidectomies performed (n = 267). The clinical, radiologic, and pathologic findings of those 9 sternotomy patients were analyzed and compared to those of the 258 patients who underwent cervical thyroidecomy.

Results

Total thyroidectomy was undertaken in all nine patients. Six of them had retrosternal extension on the right side of the mediastinum, and three had bilateral extension. Seven patients had symptoms of respiratory distress, and two were asymptomatic. The duration of the goiter ranged between 7 and 30 years. The chest radiograph and computed tomography scan revealed that the retrosternal part was below the level of the aortic knuckle at the tracheal bifurcation in all cases. The histopathology revealed a simple multinodular goiter in eight of the nine patients (89%) and in one patient with papillary carcinoma. Five of the nine patients underwent intraoperative prophylactic tracheostomy due to tracheomalacia.

Conclusions

A long‐standing goiter with deep (below the aortic knuckle) mediastinal extension and tracheal space compromise can be postulated to increase the likelihood of sternotomy.
Bycatch: complementary information for understanding fish behaviour. Namibian Cape hake (M. capensis and M. paradoxus) as a case study
Authors: Gordoa Ana , Lesch Heinrich , Rodergas Silvia
Published: August 2006

To identify spatio-temporal distribution in Namibian Cape hake (M. paradoxus and M. capensis), incidental hake catch by the horse mackerel fleet and targeted catch by the hake fleet were analysed for the period 1999–2004. The targeted catch, 45 955 fishing days, came from hake fishery logbooks and the incidental catch, 24 689 trawls, from observers' sample data collected aboard vessels of the horse mackerel fleet. A strong negative relationship between monthly catch rates (cpue) and bycatch was observed, confirming that the seasonal change in catchability is caused by differences in hake vertical dispersion. The October trends were an exception: both cpue and bycatch were negative. A drop in catchability at different depths of the fishing grounds indicates that M. capensis migrates to shallower water (<200 m) at the peak of spawning. Although there was no significant relationship between annual catch rates and bycatch, probably because of the short length of the time-series, annual bycatch should not be discarded as an indicator of hake recruitment. The results highlight the potential informative component of bycatch in identifying population patterns that cannot be extracted from the targeted catch.
Interpreting catch per unit effort data to assess the status of individual stocks and communities
Authors: Maunder Mark N. , Sibert John R. , Fonteneau Alain , Hampton John , Kleiber Pierre , Harley Shelton J.
Published: August 2006

Despite being one of the most common pieces of information used in assessing the status of fish stocks, relative abundance indices based on catch per unit effort (cpue) data are notoriously problematic. Raw cpue is seldom proportional to abundance over a whole exploitation history and an entire geographic range, because numerous factors affect catch rates. One of the most commonly applied fisheries analyses is standardization of cpue data to remove the effect of factors that bias cpue as an index of abundance. Even if cpue is standardized appropriately, the resulting index of relative abundance, in isolation, provides limited information for management advice or about the effect of fishing. In addition, cpue data generally cannot provide information needed to assess and manage communities or ecosystems. We discuss some of the problems associated with the use of cpue data and some methods to assess and provide management advice about fish populations that can help overcome these problems, including integrated stock assessment models, management strategy evaluation, and adaptive management. We also discuss the inappropriateness of using cpue data to evaluate the status of communities. We use tuna stocks in the Pacific Ocean as examples.
On the construction of discretized configuration space of manipulators
Authors: Wu X. J. , Tang J. , Heng K. H.
Published: August 2006

In this research, we study the construction of configuration space (C-space) of manipulators. The proposed approach is based upon precomputing the global topology of a robot's free space, and consists of an offline phase and an online phase. In the offline phase, a C-space obstacle database (COD) for a given robot is developed in which the C-space obstacle (C-obstacle) maps are stored and indexed by the cells of the workspace; in the online phase when the same robot is operated in a real environment, those maps whose indices match the real obstacle cells are identified and then extracted from the COD. The superposition of these maps forms forbidden region in operation. This proposed approach is a generic one and can be applied to manipulators with arbitrary kinematic structures and geometries. The construction of the COD, which is generally the most time-consuming step, is implemented in the offline phase, and the online computing only involves the identification of the components matching the COD indices. Therefore, this proposed approach for C-space construction can be realized in a real-time online fashion and is especially suitable for robot manipulation under dynamic operations. We carry out analyses on several types of manipulators to verify and demonstrate the feasibility and efficiency of the proposed approach.
Introduction
Authors: FISHER KATHLEEN
Published: August 2006

The Ninth ACM SIGPLAN International Conference on Functional Programming (ICFP) took place on September 19–21 2004 in Snowbird, Utah. The scope of ICFP includes all languages that encourage programming with functions, with topics ranging from principles to practice, foundations to features, and abstractions to applications. The program committee, which I chaired, selected 21 papers from 80 submissions for presentation at the conference. Afterwards, the program committee invited the authors of nine papers to submit extended versions for this special issue of JFP. The seven papers that appear in this volume were reviewed, revised, and accepted following standard Journal of Functional Programming procedures. Reflecting the scope of the conference, the papers cover the theoretical foundations, implementation, design, programming techniques, and applications of functional languages.
Monadic regions
Authors: FLUET MATTHEW , MORRISETT GREG
Published: August 2006

Region-based type systems provide programmer control over memory management without sacrificing type-safety. However, the type systems for region-based languages, such as the ML-Kit or Cyclone, are relatively complicated, and proving their soundness is non-trivial. This paper shows that the complication is in principle unnecessary. In particular, we show that plain old parametric polymorphism, as found in Haskell, is all that is needed. We substantiate this claim by giving a type- and meaning-preserving translation from a variation of the region calculus of Tofte and Talpin to a monadic variant of System F with region primitives whose types and operations are inspired by (and generalize) the ST monad of Launchbury and Peyton Jones.
Generics for the masses
Authors: HINZE RALF
Published: August 2006

A generic function is a function that can be instantiated on many data types to obtain data type specific functionality. Examples of generic functions are the functions that can be derived in Haskell, such as show, read, and ‘==’. The recent years have seen a number of proposals that support the definition of generic functions. Some of the proposals define new languages, some define extensions to existing languages. As a common characteristic none of the proposals can be made to work within Haskell 98: they all require something extra, either a more sophisticated type system or an additional language construct. The purpose of this paper is to show that one can, in fact, program generically within Haskell 98 obviating to some extent the need for fancy type systems or separate tools. Haskell's type classes are at the heart of this approach: they ensure that generic functions can be defined succinctly and, in particular, that they can be used painlessly. We detail three different implementations of generics both from a practical and from a theoretical perspective.
PHYSICS AND ASTRONOMY: ARISTOTLE'S PHYSICS II.2.193b22–194a12
Authors: MUELLER IAN
Published: August 2006

In the first part of chapter 2 of book II of the Physics Aristotle addresses the issue of the difference between mathematics and physics. In the course of his discussion he says some things about astronomy and the ‘ ‘ more physical branches of mathematics”. In this paper I discuss historical issues concerning the text, translation, and interpretation of the passage, focusing on two cruxes, ( I ) the first reference to astronomy at 193b25–26 and ( II ) the reference to the more physical branches at 194a7–8. In section I, I criticize Ross’s interpretation of the passage and point out that his alteration of ( I ) has no warrant in the Greek manuscripts. In the next three sections I treat three other interpretations, all of which depart from Ross's: in section II that of Simplicius, which I commend; in section III that of Thomas Aquinas, which is importantly influenced by a mistranslation of ( II ), and in section IV that of Ibn Rushd, which is based on an Arabic text corresponding to that printed by Ross. In the concluding section of the paper I describe the modern history of the Greek text of our passage and translations of it from the early twelfth century until the appearance of Ross's text in 1936.
IBN BĀJJA AND THE CLASSIFICATION OF THE SCIENCES IN AL-ANDALUS
Authors: FORCADA MIQUEL
Published: August 2006

Coinciding with the scientific flourishing of the 5th / 11th century, which was favoured by the cultural policy of the Andalusī kingdoms ( mulūk al-tawā'if ), Abū ‘ Umar ibn ‘ Abd al-Barr, Ibn Hazm and Sā‘ id al-Andalusī all dealt with the classification of the sciences in many works that are already known. Ibn Bājja began his career at the end of this period. In his glosses to al-Fārābī’s commentary to the Isagoge he wrote a text on this subject that has not yet been analysed. The present paper studies Ibn Bājja's classification in connection with his predecessors and with the scientific and philosophical background of Andalusī culture. In their classifications of the sciences, all these authors express and stress important factors of the evolution of Andalusī science and thought, such as the dialectic between religious and rational sciences and the importance of the scientific method derived from Aristotle's logic. Sā‘ id al-Andalusī and Ibn Bājja ( and, to a lesser extent, Ibn Hazm ) show the profound influence exerted by al-Fārābī’s works, particularly the Ihsā' al-‘ ulūm. Thus, Ibn Bājja foreshadows the evolution of sciences in the next century and the movement headed by Ibn Rushd, Ibn Tufayl and others, characterized by the search for concordance with the postulates set forth by philosophical disciplines.
Introduction: an atlas of the urban icons project
Authors: ETHINGTON PHILIP J. , SCHWARTZ VANESSA R.
Published: August 2006

When the World Trade Center towers collapsed on 11 September 2001, many commentators noted that in their short lives, the towers had come to represent many things: American-led global capitalism, the United States and, most of all, New York City. Their brief role as a shorthand way of saying ‘New York City’ provoked us to ask about ‘urban icons’ more generally. But we did not need such cataclysm to provoke us to consider the topic of icons and their functioning in contemporary global culture. To help illuminate the usefulness of the concept of ‘urban icons’ we held an international conference in order to determine whether the category can be used as a conceptual grid for studying the intersection of visual culture and urban history.
The iconiCITY of ancient Rome
Authors: FAVRO DIANE
Published: August 2006

Urban icons were common in the Roman world, with monuments, cityscapes and personifications all used as metonyms. Yet an icon for the most important city of all is not easily identified. Rome was always sui generis, too large to be easily captured visually. Filled with innumerable wonders, no single structure or artwork stood for the whole. Representing the collective, as well as the great extent of the empire, the city could not be encapsulated in a single image.
‘It has to go away, but at the same time it has to be kept’: the Berlin Wall and the making of an urban icon
Authors: SCHLÖR JOACHIM
Published: August 2006

For 28 years, from 13 August 1961 through 9 November 1989, the city of Berlin was divided by a wall. The borderline was the symbol for the Cold War and the political partition between East and West – but it was also an element of the urban structure: Berliners in the two parts of the city had to live with it and to define themselves in relation to it. After the fall of the wall and its destruction in the euphoric mood of re-unification, a huge inner-urban wasteland became the symbol for the need of a new politics of memory: the missing Berlin Wall became an urban icon.

What business do we have in Berlin? Memories.

Uwe Johnson
Lawn cemeteries: the emergence of a new landscape of death
Authors: RUGG JULIE
Published: August 2006

The provision of space for burial is a common but rarely discussed feature of urban existence. Shifts in cemetery aesthetics reflect changing views on what might be thought appropriate landscapes in which to bury the dead. This article, for the first time in a UK context, describes and analyses the introduction of the lawn cemetery in the twentieth century, and gives the rise of cremation a central place in explaining the need to ‘reinvent’ the cemetery aesthetic.
Do nitrogen inputs stimulate dissolved organic carbon production in upland peat bogs?
Authors: Worrall F. , Burt T. P. , Adamson J.
Published: August 2006

This study uses a 10‐year record of precipitation, soil, and stream concentration of nutrient and carbon species from an upland peat catchment to examine whether or not changes in nutrient inputs can explain long‐term increases in DOC flux from peat. The study uses time series analysis and particularly the derivation of impulse response functions to provide an alternative approach to environmental manipulations and experimental additions of nitrogen. The study shows that (1) the catchment has a fixed capacity for nitrogen uptake and as such nitrogen flux from the catchment is controlled by precipitation inputs; (2) the DOC flux from the catchment shows no relationship with precipitation inputs and flux from the peat itself continues to increase over the period; (3) impulse response functions suggest that high DOC concentrations suppress nutrient flux from the catchment and not the other way around; and (4) no significant correlation could be found between nutrient time series and the residual of the DOC concentrations after removing the effects of both temperature and changes in water table. The study can find no evidence of a link between nutrient inputs and the release of DOC from the peat profile. The DOC flux corrected for rainfall inputs and the residual time series of regression all show sharp step changes in the DOC release after severe drought.
Contribution of agricultural liming to riverine bicarbonate export and CO2 sequestration in the Ohio River basin
Authors: Oh Neung‐Hwan , Raymond Peter A.
Published: August 2006

Chemical weathering of silicates and carbonates is essential in the global cycles of many elements, including carbon. Chemical weathering affects regional and global carbon budgets through the export of bicarbonate, much of which can originate from the atmosphere. Agricultural practices may accelerate chemical weathering from the Mississippi River basin directly or indirectly. Here we investigated one of the direct effects of agricultural practices, liming, on stream bicarbonate export and the carbon budget of agricultural systems. Using geographic information systems (GIS) layers extracted from various sources such as USGS National Land Cover Data set, U.S. Census of Agriculture data, USGS water data, NADP atmospheric acid deposition data, and NASS‐USDA crop production data, we estimated the contributions of liming inputs on both the riverine bicarbonate export and atmospheric CO2 sequestration for a subset of agricultural and forested watersheds within the Ohio River basin. Liming rates have slightly decreased from 23.6 to 19.4 g CaCO3 m−2 cropland yr−1 from 1954–1970 to 1971–1987 in six highly agricultural watersheds. The largest decrease was observed in watersheds located in the state of Ohio while a slight increase was observed in watersheds located in the state of Illinois where agricultural practices are the most intense. An average of 21.1 and 22.4 g CaCO3 m−2 yr−1 were applied to the two most highly agricultural watersheds (91% agricultural in 1992) located in the state of Illinois during 1954–1970 and 1971–1987, respectively. Using a calcium mass balance, we estimated that 29% of the total riverine bicarbonate export from the two most agricultural watersheds was by liming and thus liming is important to the cation/anion balance and buffering capacity of streams. The on‐site net atmospheric C sequestration by liming from the two most agricultural watersheds was estimated to be 0.95 g C m−2 yr−1. However, considering 0.85 g C m−2 yr−1 is estimated to be released as CO2 during the production, transport, and spreading of lime, liming as a C sequestration strategy is not attractive.
Integral pumping test analyses of linearly sorbed groundwater contaminants using multiple wells: Inferring mass flows and natural attenuation rates
Authors: Bayer‐Raich Martí , Jarsjö Jerker , Liedl Rudolf , Ptak Thomas , Teutsch Georg
Published: August 2006

This paper addresses a field‐scale application of the integral pumping test (IPT) method, which is a method for quantitative characterization of contaminant plumes (e.g., benzene, toluene, ethylbenzene, and xylenes (BTEX), chlorinated hydrocarbons, and polyaromatic hydrocarbons) in groundwater. We extend the associated analytical framework by formal consideration of linear, instantaneous sorption/retardation and provide novel nonrecursive analytical solutions for estimation of field‐scale contaminant mass flows. We find that estimates of the average concentration obtained through IPTs are independent of the retardation factor under equilibrium conditions, although linear retardation due to sorption decreases the investigation volume in comparison with the nonretarded case. Furthermore, whereas previous studies were based on single‐well analyses, we present in this paper developments relevant for multiple‐well analyses by introducing a simple, analytical multiple‐well framework for evaluation of IPTs considering overall water budgets. Although single‐well analyses provide consistent results in isolation, their applicability on multiwell systems suffer from the fact that the theory does not include mass balance considerations for the gallery of wells that constitutes a control plane. Through application of the developed multiple‐well methods to measurement data from the field we show that the estimated total mass flows across well galleries can differ considerably from corresponding estimates using single‐well methods, which to some extent, also influences natural attenuation (NA) rate estimates. We believe that the developments presented here can provide a useful basis for biogeochemical studies of field‐scale NA processes, including assessments of changes in isotope ratios.
Evaluating uncertainty in predicting spatially variable representative elementary scales in fractured aquifers, with application to Turkey Creek Basin, Colorado
Authors: Wellman Tristan P. , Poeter Eileen P.
Published: August 2006

Computational limitations and sparse field data often mandate use of continuum representation for modeling hydrologic processes in large‐scale fractured aquifers. Selecting appropriate element size is of primary importance because continuum approximation is not valid for all scales. The traditional approach is to select elements by identifying a single representative elementary scale (RES) for the region of interest. Recent advances indicate RES may be spatially variable, prompting unanswered questions regarding the ability of sparse data to spatially resolve continuum equivalents in fractured aquifers. We address this uncertainty of estimating RES using two techniques. In one technique we employ data‐conditioned realizations generated by sequential Gaussian simulation. For the other we develop a new approach using conditioned random walks and nonparametric bootstrapping (CRWN). We evaluate the effectiveness of each method under three fracture densities, three data sets, and two groups of RES analysis parameters. In sum, 18 separate RES analyses are evaluated, which indicate RES magnitudes may be reasonably bounded using uncertainty analysis, even for limited data sets and complex fracture structure. In addition, we conduct a field study to estimate RES magnitudes and resulting uncertainty for Turkey Creek Basin, a crystalline fractured rock aquifer located 30 km southwest of Denver, Colorado. Analyses indicate RES does not correlate to rock type or local relief in several instances but is generally lower within incised creek valleys and higher along mountain fronts. Results of this study suggest that (1) CRWN is an effective and computationally efficient method to estimate uncertainty, (2) RES predictions are well constrained using uncertainty analysis, and (3) for aquifers such as Turkey Creek Basin, spatial variability of RES is significant and complex.
Smallpox transmission and control: Spatial dynamics in Great Britain
Authors: Riley Steven , Ferguson Neil M.
Published: August 2006

Contingency planning for the possible deliberate reintroduction of smallpox has become a priority for many national public health organizations in recent years. We used an individual-based spatial model of smallpox transmission in Great Britain and census-derived journey-to-work data to accurately describe the spatiotemporal dynamics of an outbreak of smallpox in the community. A Markov chain Monte-Carlo algorithm was developed to generate sociospatial contact networks that were consistent with demographic and commuting data. We tested the sensitivity of model predictions to key epidemiological parameters before choosing three representative scenarios from within the range explored. We examined the spatiotemporal dynamics for these illustrative scenarios and assessed the efficacy of symptomatic case isolation, contact tracing with vaccination, and reactive regional mass vaccination as policy options for control. We conclude that case isolation and contact tracing with vaccination would be sufficient to halt ongoing transmission rapidly, unless policy effectiveness was compromised by resource or other constraints. A slight reduction in the expected size and duration of an outbreak could be achieved with regional mass vaccination, but these benefits are small and do not justify the high numbers of vaccine doses required and their associated negative side effects.
Myosin-X is a molecular motor that functions in filopodia formation
Authors: Bohil Aparna B. , Robertson Brian W. , Cheney Richard E.
Published: August 2006

Despite recent progress in understanding lamellipodia extension, the molecular mechanisms regulating filopodia formation remain largely unknown. Myo10 is a MyTH4-FERM myosin that localizes to the tips of filopodia and is hypothesized to function in filopodia formation. To determine whether endogenous Myo10 is required for filopodia formation, we have used scanning EM to assay the numerous filopodia normally present on the dorsal surfaces of HeLa cells. We show here that siRNA-mediated knockdown of Myo10 in HeLa cells leads to a dramatic loss of dorsal filopodia. Overexpressing the coiled coil region from Myo10 as a dominant- negative also leads to a loss of dorsal filopodia, thus providing independent evidence that Myo10 functions in filopodia formation. We also show that expressing Myo10 in COS-7 cells, a cell line that normally lacks dorsal filopodia, leads to a massive induction of dorsal filopodia. Because the dorsal filopodia induced by Myo10 are not attached to the substrate, Myo10 can promote filopodia by a mechanism that is independent of substrate attachment. Consistent with this observation, a Myo10 construct that lacks the FERM domain, the region that binds to integrin, retains the ability to induce dorsal filopodia. Deletion of the MyTH4-FERM region, however, completely abolishes Myo10's filopodia-promoting activity, as does deletion of the motor domain. Additional experiments on the mechanism of Myo10 action indicate that it acts downstream of Cdc42 and can promote filopodia in the absence of VASP proteins. Together, these data demonstrate that Myo10 is a molecular motor that functions in filopodia formation.
Inhibition of protein aggregation
in vitro
and
in vivo
by a natural osmoprotectant
Authors: Ignatova Zoya , Gierasch Lila M.
Published: August 2006

Small organic molecules termed osmolytes are harnessed by a variety of cell types in a wide range of organisms to counter unfavorable physiological conditions that challenge protein stability and function. Using a well characterized reporter system that we developed to allow
in vivo
observations, we have explored how the osmolyte proline influences the stability and aggregation of a model aggregation-prone protein, P39A cellular retinoic acid-binding protein. Strikingly, we find that the natural osmolyte proline abrogates aggregation both
in vitro
and
in vivo
(in an
Escherichia coli
expression system). Importantly, proline also prevented aggregation of constructs containing exon 1 of huntingtin with extended polyglutamine tracts. Although compatible osmolytes are known to stabilize the native state, our results point to a destabilizing effect of proline on partially folded states and early aggregates and a solubilizing effect on the native state. Because proline is believed to act through a combination of solvophobic backbone interactions and favorable side-chain interactions that are not specific to a particular sequence or structure, the observed effect is likely to be general. Thus, the osmolyte proline may be protective against biomedically important protein aggregates that are hallmarks of several late-onset neurodegenerative diseases including Huntington’s, Alzheimer’s, and Parkinson’s. In addition, these results should be of practical importance because they may enable protein expression at higher efficiency under conditions where aggregation competes with proper folding.
The Temporary Staffing Industry and Workforce Development: Assessing a System of Local Experiments
Authors: Doussard Marc , Theodore Nik
Published: August 2006

Local workforce authorities in liberal market states are increasingly charged with mitigating long-term unemployment rooted in macroeconomic forces beyond their immediate control. In the US, and now elsewhere, these authorities have begun to establish partnerships with the temporary staffing industry as a means of extending their limited resources and improving job placement outcomes. Such partnerships are especially prominent in the US, where the Department of Labor has sanctioned policy experiments between local workforce authorities and the temporary staffing industry. In order to appraise these experiments, we present case-study evaluations of three diverse and highly touted employment schemes undertaken by American workforce authorities in conjunction with temporary staffing agencies. We find that under even the most favourable circumstances, the modest mechanisms of these programmes are unable to produce appreciable impacts within local labour markets.
The novel gene asb11: a regulator of the size of the neural progenitor compartment
Authors: Diks Sander H. , Bink Robert J. , van de Water Sandra , Joore Jos , van Rooijen Carina , Verbeek Fons J. , den Hertog Jeroen , Peppelenbosch Maikel P. , Zivkovic Danica
Published: August 2006

From a differential display designed to isolate genes that are down-regulated upon differentiation of the central nervous system in Danio rerio embryos, we isolated d-asb11 (ankyrin repeat and suppressor of cytokine signaling box–containing protein 11). Knockdown of the d-Asb11 protein altered the expression of neural precursor genes sox2 and sox3 and resulted in an initial relative increase in proneural cell numbers. This was reflected by neurogenin1 expansion followed by premature neuronal differentiation, as demonstrated by HuC labeling and resulting in reduced size of the definitive neuronal compartment. Forced misexpression of d-asb11 was capable of ectopically inducing sox2 while it diminished or entirely abolished neurogenesis. Overexpression of d-Asb11 in both a pluripotent and a neural-committed progenitor cell line resulted in the stimulus-induced inhibition of terminal neuronal differentiation and enhanced proliferation. We conclude that d-Asb11 is a novel regulator of the neuronal progenitor compartment size by maintaining the neural precursors in the proliferating undifferentiated state possibly through the control of SoxB1 transcription factors.
γ-Tubulin Is Required for Proper Recruitment and Assembly of Kar9–Bim1 Complexes in Budding Yeast
Authors: Cuschieri Lara , Miller Rita , Vogel Jackie
Published: August 2006

Microtubule plus-end–interacting proteins (+TIPs) promote the dynamic interactions between the plus ends (+ends) of astral microtubules and cortical actin that are required for preanaphase spindle positioning. Paradoxically, +TIPs such as the EB1 orthologue Bim1 and Kar9 also associate with spindle pole bodies (SPBs), the centrosome equivalent in budding yeast. Here, we show that deletion of four C-terminal residues of the budding yeast γ-tubulin Tub4 (tub4-Δdsyl) perturbs Bim1 and Kar9 localization to SPBs and Kar9-dependant spindle positioning. Surprisingly, we find Kar9 localizes to microtubule +ends in tub4-Δdsyl cells, but these microtubules fail to position the spindle when targeted to the bud. Using cofluorescence and coaffinity purification, we show Kar9 complexes in tub4-Δdsyl cells contain reduced levels of Bim1. Astral microtubule dynamics is suppressed in tub4-Δdsyl cells, but it are restored by deletion of Kar9. Moreover, Myo2- and F-actin–dependent dwelling of Kar9 in the bud is observed in tub4-Δdsyl cells, suggesting defective Kar9 complexes tether microtubule +ends to the cortex. Overproduction of Bim1, but not Kar9, restores Kar9-dependent spindle positioning in the tub4-Δdsyl mutant, reduces cortical dwelling, and promotes Bim1–Kar9 interactions. We propose that SPBs, via the tail of Tub4, promote the assembly of functional +TIP complexes before their deployment to microtubule +ends.