bluuebunny/crossref_metadata_2025 huggingface dataset:
The family 42 carbohydrate-binding module of family 54 α-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose
Authors: Miyanaga Akimasa , Koseki Takuya , Miwa Yozo , Mese Yuichiro , Nakamura Sachiko , Kuno Atsushi , Hirabayashi Jun , Matsuzawa Hiroshi , Wakagi Takayoshi , Shoun Hirofumi , Fushinobu Shinya
Published: October 2006

α-L-Arabinofuranosidase catalyses the hydrolysis of the α-1,2-, α-1,3-, and α-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan. AkAbf54 (the glycoside hydrolase family 54 α-L-arabinofuranosidase from Aspergillus kawachii) consists of two domains, a catalytic and an arabinose-binding domain. The latter has been named AkCBM42 [family 42 CBM (carbohydrate-binding module) of AkAbf54] because homologous domains are classified into CBM family 42. In the complex between AkAbf54 and arabinofuranosyl-α-1,2-xylobiose, the arabinose moiety occupies the binding pocket of AkCBM42, whereas the xylobiose moiety is exposed to the solvent. AkCBM42 was found to facilitate the hydrolysis of insoluble arabinoxylan, because mutants at the arabinose binding site exhibited markedly decreased activity. The results of binding assays and affinity gel electrophoresis showed that AkCBM42 interacts with arabinose-substituted, but not with unsubstituted, hemicelluloses. Isothermal titration calorimetry and frontal affinity chromatography analyses showed that the association constant of AkCBM42 with the arabinose moiety is approximately 103 M−1. These results indicate that AkCBM42 binds the non-reducing-end arabinofuranosidic moiety of hemicellulose. To our knowledge, this is the first example of a CBM that can specifically recognize the side-chain monosaccharides of branched hemicelluloses.
Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies
Authors: Chakraborty Kausik , Durani Venuka , Miranda Edward Roshan , Citron Michael , Liang Xiaoping , Schleif William , Joyce Joseph G. , Varadarajan Raghavan
Published: October 2006

gp120 is a subunit of the envelope glycoprotein of HIV-1. The third variable loop region of gp120 (V3 loop) contains multiple immunodominant epitopes and is also functionally important for deciding cell-tropism of the virus. 447-52D is a monoclonal antibody that recognizes the conserved tip of the V3 loop in a β-turn conformation. This antibody has previously been shown to neutralize diverse strains of the virus. In an attempt to generate an immunogen competent to generate 447-52D-like antibodies, the known epitope of 447-52D was inserted at three different surface loop locations in the small, stable protein Escherichia coli Trx (thioredoxin). At one of the three locations (between residues 74 and 75), the insertion was tolerated, the resulting protein was stable and soluble, and bound 447-52D with an affinity similar to that of intact gp120. Upon immunization, the V3 peptide-inserted Trx scaffold was able to generate anti-V3 antibodies that could compete out 447-52D binding to gp120. Epitope mapping studies demonstrated that these anti-V3 antibodies recognized the same epitope as 447-52D. Although the 447-52D-type antibodies were estimated to be present at concentrations of 50–400 μg/ml of serum, these were not able to effect neutralization of strains like JRFL and BAL but could neutralize the sensitive MN strain. The data suggest that because of the low accessibility of the V3 loop on primary isolates such as JRFL, it will be difficult to elicit a V3-specific, 447-52D-like antibody response to effectively neutralize such isolates.
Negative regulation of the Nrf1 transcription factor by its N-terminal domain is independent of Keap1: Nrf1, but not Nrf2, is targeted to the endoplasmic reticulum
Authors: Zhang Yiguo , Crouch Dorothy H. , Yamamoto Masayuki , Hayes John D.
Published: October 2006

Nrf1 (nuclear factor-erythroid 2 p45 subunit-related factor 1) and Nrf2 regulate ARE (antioxidant response element)-driven genes. At its N-terminal end, Nrf1 contains 155 additional amino acids that are absent from Nrf2. This 155-amino-acid polypeptide includes the N-terminal domain (NTD, amino acids 1–124) and a region (amino acids 125–155) that is part of acidic domain 1 (amino acids 125–295). Within acidic domain 1, residues 156–242 share 43% identity with the Neh2 (Nrf2-ECH homology 2) degron of Nrf2 that serves to destabilize this latter transcription factor through an interaction with Keap1 (Kelch-like ECH-associated protein 1). We have examined the function of the 155-amino-acid N-terminal polypeptide in Nrf1, along with its adjacent Neh2-like subdomain. Activation of ARE-driven genes by Nrf1 was negatively controlled by the NTD (N-terminal domain) through its ability to direct Nrf1 to the endoplasmic reticulum. Ectopic expression of wild-type Nrf1 and mutants lacking either the NTD or portions of its Neh2-like subdomain into wild-type and mutant mouse embryonic fibroblasts indicated that Keap1 controls neither the activity of Nrf1 nor its subcellular distribution. Immunocytochemistry showed that whereas Nrf1 gave primarily cytoplasmic staining that was co-incident with that of an endoplasmic-reticulum marker, Nrf2 gave primarily nuclear staining. Attachment of the NTD from Nrf1 to the N-terminus of Nrf2 produced a fusion protein that was redirected from the nucleus to the endoplasmic reticulum. Although this NTD–Nrf2 fusion protein exhibited less transactivation activity than wild-type Nrf2, it was nevertheless still negatively regulated by Keap1. Thus Nrf1 and Nrf2 are targeted to different subcellular compartments and are negatively regulated by distinct mechanisms.
Developmental windows and environment as important factors in the expression of genetic information: a cardiovascular physiologist's view
Authors: Kuneš Jaroslav , Zicha Josef
Published: October 2006

Genetic studies in humans and rodent models should help to identify altered genes important in the development of cardiovascular diseases, such as hypertension. Despite the considerable research effort, it is still difficult to identify all of the genes involved in altered blood pressure regulation thereby leading to essential hypertension. We should keep in mind that genetic hypertension and other cardiovascular diseases might develop as a consequence of early errors in well-co-ordinated systems regulating cardiovascular homoeostasis. If these early abnormalities in the ontogenetic cascade of expression of genetic information occur in critical periods of development (developmental windows), they can adversely modify subsequent development of the cardiovascular system. The consideration that hypertension and/or other cardiovascular diseases are late consequences of abnormal ontogeny of the cardiovascular system could explain why so many complex interactions among genes and environmental factors play such a significant role in the pathogenesis of these diseases. The detailed description and precise time resolution of major developmental events occurring during particular stages of ontogeny in healthy individuals (including advanced knowledge of gene expression) could facilitate the detection of abnormalities crucial for the development of cardiovascular alterations characteristic of the respective diseases. Transient gene switch-on or switch-off in specific developmental windows might be a useful approach for in vivo modelling of pathological processes. This should help to elucidate the mechanisms underlying cardiovascular diseases (including hypertension) and to develop strategies to prevent the development of such diseases.
Influence of pre-analytical and analytical factors on soluble CD40L measurements
Authors: Varo Nerea , Nuzzo Rebecca , Natal Cristina , Libby Peter , Schönbeck Uwe
Published: October 2006

The soluble form of CD40L (CD40 ligand), a pro-atherogenic mediator, has emerged as a diagnostic and prognostic marker for cardiovascular events. However, as platelets can shed CD40L upon activation, accurate measurement has proved challenging. The present study addresses the controversy regarding the appropriate specimen and preparation for laboratory evaluation of blood sCD40L (soluble CD40L). Serum and plasma (collected in EDTA, citrate or heparin) were collected from healthy volunteers (n=20), and sCD40L was analysed by ELISA immediately or after one to three freeze–thaw cycles and at different centrifugation speeds. Urine sCD40L levels were measured in subjects with low- and high-plasma sCD40L levels. Serum sCD40L levels (5.45±4.55 ng/ml; P<0.001) were higher than in citrate, EDTA or heparin plasma (1.03±1.07, 1.43±1.03 or 1.80±1.25 ng/ml respectively), with no significant differences between plasma preparations. Increasing g values (200–13000 g), which gradually deplete plasma of platelets, yielded lower sCD40L levels. Repeated freeze–thaw cycles significantly (P<0.05) increased sCD40L concentrations in platelet-rich, but not platelet-depleted, plasma (up to 2.4-fold). Bilirubin and haemoglobin interfered positively, and triacylglycerols (triglycerides) and cholesterol quenched CD40L signalling. No sCD40L was detected in urine samples. In conclusion, serum yields higher sCD40L concentrations than plasma; accurate measurements of sCD40L require exclusion of platelets and avoiding their post-hoc activation. Samples with high concentrations of bilirubin, haemoglobin and/or triacylglycerols should be excluded, as these substances interfere with the assay.
Comparative toxicity of fatty acids on a macrophage cell line (J774)
Authors: Martins de Lima Thais , Cury-Boaventura Maria Fernanda , Giannocco Gisele , Nunes Maria Tereza , Curi Rui
Published: October 2006

In the present study, the cytotoxicity of palmitic, stearic, oleic, linoleic, arachidonic, docosahexaenoic and eicosapentaenoic acids on a macrophage cell line (J774) was investigated. The induction of toxicity was investigated by changes in cell size, granularity, membrane integrity, DNA fragmentation and phosphatidylserine externalization by using flow cytometry. Fluorescence microscopy was used to determine the type of cell death (Acridine Orange/ethidium bromide assay). The possible mechanisms involved were examined by measuring mitochondrial depolarization, lipid accumulation and PPARγ (peroxisome-proliferator-activated receptor γ) activation. The results demonstrate that fatty acids induce apoptosis and necrosis of J774 cells. At high concentrations, fatty acids cause macrophage death mainly by necrosis. The cytotoxicity of the fatty acids was not strictly related to the number of double bonds in the molecules: palmitic acid>docosahexaenoic acid>stearic acid=eicosapentaenoic acid=arachidonic acid>oleic acid>linoleic acid. The induction of cell death did not involve PPARγ activation. The mechanisms of fatty acids to induce cell death involved changes in mitochondrial transmembrane potential and intracellular neutral lipid accumulation. Fatty acids poorly incorporated into triacylglycerol had the highest toxicity.
CETP (cholesteryl ester transfer protein) promoter −1337 C>T polymorphism protects against coronary atherosclerosis in Japanese patients with heterozygous familial hypercholesterolaemia
Authors: Takata Mutsuko , Inazu Akihiro , Katsuda Shoji , Miwa Kenji , Kawashiri Masa-aki , Nohara Atsushi , Higashikata Toshinori , Kobayashi Junji , Mabuchi Hiroshi , Yamagishi Masakazu
Published: October 2006

CETP (cholesteryl ester transfer protein) and HL (hepatic lipase) play a role in the metabolism of plasma lipoproteins, but the effects of CETP and LIPC (gene encoding HL) genotypes on coronary atherosclerosis may be dependent on LDL (low-density lipoprotein)-receptor activity. Recently, the −1337 C>T polymorphism in the CETP gene has been reported in REGRESS (Regression Growth Evaluation Statin Study) to be a major determinant of promoter activity and plasma CETP concentration. In the present study, we have investigated the effects of the CETP promoter −1337 C>T and LIPC promoter −514 C>T polymorphisms on serum lipid profiles and risk of coronary atherosclerosis in 206 patients (154 males) with heterozygous FH (familial hypercholesterolaemia). To evaluate coronary atherosclerosis, we used CSI (coronary stenosis index) calculated from coronary angiograms. The CETP −1337 T allele was less frequent in subjects with a CSI ≥14 (mean value) in the group with coronary artery disease (P=0.04, as determined by χ2 test). ANOVA revealed that HDL-C (high-density lipoprotein-cholesterol) and triacylglycerol (triglyceride) levels were not significantly higher in the presence of the CETP promoter −1337 T allele. Combined with LIPC promoter polymorphisms, HDL-C levels were highest and CSI were lowest with CETP −1337 CT+TT and LIPC −514 CC genotypes, but a significant interaction was not shown. A multiple logistic regression analysis revealed that, in patients with coronary atherosclerosis, the CETP− 1337 CC genotype was a significant genetic risk factor in FH (odds ratio=2.022; P=0.0256). These results indicate that the CETP promoter −1337C>T polymorphism is associated with the progression of coronary atherosclerosis in Japanese patients with FH, independent of HDL-C and triacylglycerol levels.
Gender and the Colonial Encounter in the Arab World: Examining Women's Experiences and Narratives
Authors: Garcia-Ramon Maria-Dolors
Published: October 2006

It has been asserted that women's travel narratives are fundamentally different from those of men. The differential access of women to the dominant imperial position produced a gaze on the Orient that registered differences in less pejorative ways. However, the analysis of the intersection of gender, class, nation, and race discourses problematizes this view, and gives evidence that in women's narratives and life experiences one can find sites of resistance to colonialism as well as sites of complicity, depending on the individual women's positioning in this intersection. But even if women's narratives and life experiences do not necessarily deviate from the predominant Orientalist discourse, their texts are nevertheless specifically gendered. In this paper I study two women travelers, Isabelle Eberhardt (1877 – 1904) and Gertrude Bell (1868 – 1926). Eberhardt, born in Geneva (although with a Russian background), traveled to Tunisia and Algeria, wrote in French, and became a legendary figure in France. Gertrude Bell, born in County Durham (United Kingdom), spent most of her adult life in the Middle East and, at the service of the British Government, played a major role in the creation of its modern political map (in particular in Iraq). The study and comparison of these two women shed light on the complexity of attitudes towards colonialism that can result from a combined analysis of gender, class, nation, and race. Eberhardt was frequently torn between identifying with her race and class or with her gender, and among French colonial officers held a reputation of being an enemy of France as well as profoundly Algerianized; but, in the end, she gradually reached a compromised position in relation to France's colonial policies in the Sahara. In contrast, Bell was a traveler and a scholar who used her knowledge and her travels to promote the cause of the British Empire. But although she was unambiguously imperial in her outlook, she also managed to achieve a personal closeness with many Arabs and was a champion of their history and culture.
Art of the Demolition Derby: Gender, Space, and Antiproduction
Authors: Haller Aurian
Published: October 2006

Geographers have productively employed recent theories of performativity to investigate the ways in which space and identity (that is, gender, sexuality, and race) are interdependent, in that they produce and reinforce each other. Expanding on such work, in this paper I explore the spatial and performative aspects of artist Bill Featherston's representation of the sports and pastimes of his working-class hometown, specifically that of demolition derbies. Such theatrical spaces, both actual and represented, present a somewhat unusual challenge to geographers interested in how meaning and identity are negotiated within and through the production of specific sites. I examine how gender and the performance of capitalist production are at once reinforced and subverted through the creation and consumption of the spaces of realist art.
Beyond Belief? Consumer Culture, Complementary Medicine, and the Dis-Ease of Everyday Life
Authors: Doel Marcus A , Segrott Jeremy
Published: October 2006

The increasing popularity of complementary and alternative medicine (CAM) in the West raises profound questions for social scientists, not least because it is as much about consumerism as it is about health care. Although the sociology of CAM is well developed, its geography remains almost wholly unexplored. In this paper we argue that one of the main reasons for this neglect is the fact that (post)medical geography has found it extremely difficult to come to terms with the disconcerting fusion of health care and consumer culture, and its dispersion across a vast array of materials and practices that are often far removed from the established concerns of the subdiscipline. Accordingly, in this paper we approach the dispersed geography of CAM through two key sources of consumer information: a range of ‘popular’ health-related magazines produced for the UK market, contextualized in relation to a sample of twenty-four British-based patient support groups. Specifically, we consider three critical issues that are shaping the mass mediation of CAM: the displacement of efficacy; the abrogation of authority; and the cultivation of anxiety. The paper concludes with a brief consideration of a profoundly geographical problem: the difficulty of constructing effective pathways through a profusion of disparate materials and practices in a context that is literally beyond belief.
Hawala Discourses and the War on Terrorist Finance
Authors: de Goede Marieke
Published: October 2006

In this paper I argue that the informal hawala money-transfer networks, which were made to take much of the blame for terrorist financing in the wake of the September 11 attacks, are not ‘underground’ banking systems but are connected to Western banking in a myriad of ways. I argue that negative stereotyping of hawala in press and policy discourses has implicitly constructed Western banking as the normal and legitimate space of international finance and has deflected calls for regulation of Western investment banking. I discuss how hawala is connected to the financial exclusion of migrant workers in the West. In the war on terrorist finance, discourses of hawala have led to the underestimation of the complexity of cutting off terrorist funding, while criminalising remittance networks.
Collective Memory and Productive Nostalgia: Anglo-Indian Homemaking at McCluskieganj
Authors: Blunt Alison
Published: October 2006

Memory and nostalgia have attracted an increasing amount of critical interest in recent years. Whereas sites of memory often invoke, but also extend far beyond, spaces of home, nostalgia invokes home in its very meaning. And yet, whereas spatial narratives explore the sites and landscapes of memory, nostalgia is usually described in temporal terms rather than in spatial terms and is understood as a wider “desire for desire” [Stewart S, 1993 On Longing: Narratives of the Miniature, the Gigantic, the Souvenir, the Collection (Duke University Press, Durham, NC), page 23] rather than as a desire for home. In this paper I show how memory and nostalgia informed the establishment and promotion of an Anglo-Indian homeland called McCluskieganj in Bihar in the 1930s. Homemaking at McCluskieganj was enacted in gendered and racialized ways that inscribed and yet erased the collective memory of mixed descent shared by its Anglo-Indian residents. Whereas an imperial lineage was imagined through the figure of a British forefather, an Indian maternal ancestor was more usually refigured as Mother India. In this paper I examine Anglo-Indian homemaking at McCluskieganj in terms of productive nostalgia. First, rather than a nostalgic desire for home being apolitical or confining, settlement at McCluskieganj showed its liberatory potential for Anglo-Indians. Second, rather than focus on nostalgia solely in narrative or the imagination, I show that productive nostalgia implies its embodiment and enactment in practice. Third, rather than nostalgia being seen in terms of loss, mourning, and the impossibility of return, productive nostalgia is oriented towards the present and the future as well as towards the past. Fourth, rather than focus on the temporality of home as a site of origin and an unattainable past, I show how productive nostalgia refocuses on the desire for both proximate homes and more distant homes. Anglo-Indian homemaking at McCluskieganj enacted a productive nostalgia that was oriented towards the present and future as well as towards the past, and revealed an attachment to both India and Britain as home.
The ‘Place’ of Street Children in Kampala, Uganda: Marginalisation, Resistance, and Acceptance in the Urban Environment
Authors: Young Lorraine
Published: October 2006

In this paper I examine the ‘place’ of street children in Kampala, Uganda, highlighting their ingenious and resourceful use of the urban environment. Considered ‘out of place’ in urban public space, street children create their own niches in the marginal spaces of the city. By looking at untouchable spaces, underground spaces, and rooftop spaces I show how they develop their own place identities. For survival, street children react to their exclusion by resisting this out-of-place image and encroaching into crowded spaces or by dominating the street under the cover of darkness. However, in certain city spaces, street children are also legitimised and accepted by other street users if they conform to the desired behaviours of that space. The place of street children in Kampala is one which is contested, resulting in a multiplicity of street children's niches being created which vary both spatially and temporally.
Urban Ethnocracy: Ethnicization and the Production of Space in an Israeli ‘Mixed City’
Authors: Yiftachel Oren , Yacobi Haim
Published: October 2006

In this paper we offer a critical analysis of ethnic relations in an Israeli ‘mixed city’. Similar to other sites shaped by the logics of settling ethnonationalism and capitalism, the ‘mixed city’ is characterized by stark patterns of segregation between a dominant majority and a subordinate minority, as well as by ethnoclass fragmentation within each group. ‘Mixed’ spaces are both exceptional and involuntary, often resulting from the process of ethnicization prevalent in contested urban spaces. We theorize this setting as an ‘ urban ethnocracy’, where a dominant group appropriates the city apparatus to buttress its domination and expansion. In such settings, conspicuous tensions accompany the interaction between the city's economic and ethnoterritorial logics, producing sites of conflict and instability, and essentializing group identities and ethnic geographies. Empirically, the paper focuses on the city of Lod or Lydda, Israel, where the production of contested urban space has been linked to the construction of an exclusionary Israeli-Jewish national identity and to the establishment of hierarchical ethnic citizenship. Like other previously Arab cities, Lod has been the target of a concerted strategy of Judaization, which has formed the city's central planning goal since the late 1940s. We analyze in detail various aspects and sites of the Judaization process, and of the ensuing urban conflicts. We point to the chronic instability of urban ethnocracies, and to the need of planning to rise above narrow ethnocentric considerations in order for the ‘mixed city’ to prosper as the home for all communities.
Scary Monsters? Software Formats, Peer-to-Peer Networks, and the Spectre of the Gift
Authors: Leyshon Andrew
Published: October 2006

In this paper I focus upon a sociotechnical network made possible through the combination of software, the Internet, and peer-to-peer computer networks. These sociotechnical networks have destabilised the regime of governance that supports what I describe in the paper as copyright capitalism by creating a series of gift economies where the products of those industries are given away. This development has significance for a wide range of creative industries that are dependent upon copyright protection for their reproduction, including motion pictures, publishing, and software engineering. The main empirical focus of this paper is the music industry because it is there that the challenge to the mode of reproduction of copyright capitalism has been most acute. I look at the origins of these gift economies, which can be traced back to the academic roots of the Internet. A musical gift economy centred upon MP3 (a software format) emerged during the early 1990s, but was only constituted as a problem for the music industry after the commercial invasion of the Internet during the late 1990s. Dot.com start-ups transformed the specialised knowledge that was once the preserve of hackers and hobbyists into generic knowledge through the development of ‘user-friendly’ file-exchange systems, thereby providing mass access to a once underground musical gift economy. Copyright capitalists mobilised the powers of law enforcement to reassert their control over the circulation of recorded music, and have successfully tamed many of the firms that sought to extend this gift economy for commercial gain. However, there has emerged a set of networks that are both ideologically and substantively opposed to the interests of copyright capitalism, and that are more resistant to attempts to reassert the control of the large corporations. In this paper I argue that the continued existence of these networks will undermine the ability of large media companies to control copyright in the way they have in the past. Although the communities that facilitate such economies are themselves unstable and rely, like other ‘alternative’ economic systems, upon a narrow band of active participants, such gift economies may emerge as the most significant and problematic legacy of the ‘new economy’.
Reflection positivity, rank connectivity, and homomorphism of graphs
Authors: Freedman Michael , Lovász László , Schrijver Alexander
Published: October 2006

It is shown that a graph parameter can be realized as the number of homomorphisms into a fixed (weighted) graph if and only if it satisfies two linear algebraic conditions: reflection positivity and exponential rank connectivity. In terms of statistical physics, this can be viewed as a characterization of partition functions of vertex coloring models.
Intermediate subfactors with no extra structure
Authors: Grossman Pinhas , Jones Vaughan
Published: October 2006

IfN⊆P,Q⊆MN\subseteq P,Q\subseteq Mare type II1_1factors withN′∩M=CidN’\cap M =\mathbb C idand[M:N]>∞[M:N]>\inftywe show that restrictions on the standard invariants of the elementary inclusionsN⊆PN\subseteq P,N⊆QN\subseteq Q,P⊆MP\subseteq MandQ⊆MQ\subseteq Mimply drastic restrictions on the indices and angles between the subfactors. In particular we show that if these standard invariants are trivial and the conditional expectations ontoPPandQQdo not commute, then[M:N][M:N]is66or6+426+4\sqrt 2. In the former caseNNis the fixed point algebra for an outer action ofS3S_3onMMand the angle isπ/3\pi /3, and in the latter case the angle iscos−1⁡(2−1)\cos ^{-1}(\sqrt 2-1)and an example may be found in the GHJ subfactor family. The techniques of proof rely heavily on planar algebras.
Universal characteristic factors and Furstenberg averages
Authors: Ziegler Tamar
Published: October 2006

Let

X
=
(

X
0

,

B

,
μ
,
T
)

X=(X^0,\mathcal {B},\mu ,T)

be an ergodic probability measure-preserving system. For a natural number

k
k

we consider the averages
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartLayout 1st Row with Label left-parenthesis asterisk right-parenthesis EndLabel StartFraction 1 Over upper N EndFraction sigma-summation Underscript n equals 1 Overscript upper N Endscripts product Underscript j equals 1 Overscript k Endscripts f Subscript j Baseline left-parenthesis upper T Superscript a Super Subscript j Superscript n Baseline x right-parenthesis EndLayout">

(*)

1
N

∑

n
=
1

N

∏

j
=
1

k

f
j

(

T

a
j

n

x
)

\begin{equation*} \tag {*} \frac {1}{N}\sum _{n=1}^N \prod _{j=1}^k f_j(T^{a_jn}x) \end{equation*}

where

f
j

∈

L

∞

(
μ
)

f_j \in L^{\infty }(\mu )

, and

a
j

a_j

are integers. A factor of

X
X

is characteristic for averaging schemes of length

k
k

(or

k
k

-characteristic) if for any nonzero distinct integers

a
1

,
…
,

a
k

a_1,\ldots ,a_k

, the limiting

L
2

(
μ
)

L^2(\mu )

behavior of the averages in (*) is unaltered if we first project the functions

f
j

f_j

onto the factor. A factor of

X
X

is a

k
k

-universal characteristic factor (

k
k

-u.c.f.) if it is a

k
k

-characteristic factor, and a factor of any

k
k

-characteristic factor. We show that there exists a unique

k
k

-u.c.f., and it has the structure of a

(
k
−
1
)

(k-1)

-step nilsystem, more specifically an inverse limit of

(
k
−
1
)

(k-1)

-step nilflows. Using this we show that the averages in (*) converge in

L
2

(
μ
)

L^2(\mu )

. This provides an alternative proof to the one given by Host and Kra.
Representations of affine Hecke algebras and based rings of affine Weyl groups
Authors: Xi Nanhua
Published: October 2006

In this paper we show that the Deligne-Langlands-Lusztig classification of simple representations of an affine Hecke algebra remains valid if the parameter is not a root of the corresponding Poincaré polynomial. This verifies a conjecture of Lusztig proposed in 1989.
A ‘large infrequent disturbance’ in an East African savanna
Authors: Gillson Lindsey
Published: October 2006

There is growing interest in large infrequent disturbances (LIDs), but by definition they occur rarely and long‐term data are needed in order to study their effects and frequency. Palaeoecological records have the potential to provide information on the effects and frequency of LIDs. By comparing recent sedimentary records with known historical data, the effects of LIDs on pollen, charcoal and sedimentary sequences can be assessed. In this study, a LID in East Africa is described, and its representation in the palaeoecological record is explored. Historical records show that there was severe drought and famine in East Africa at the end of the 19th century. Fossil pollen and charcoal records from this period show evidence of a disturbance event that occurred at approximately this time. Statistical comparison of pollen and charcoal data from before, during and after the disturbance event identified it as a LID. The data also suggest that an erosion event occurred part way through the drought, indicating that an environmental threshold was exceeded.
CD80/CD28 co-stimulation in human brucellosis
Authors: Skendros P , Boura P , Kamaria F , Raptopoulou-Gigi M
Published: October 2006

Despite treatment, 10–30% of brucellosis patients develop chronic disease, characterized by atypical clinical picture and/or relapses. A defective T helper 1 (Th1) response and a long percentage of CD4+/CD25+ cells have been described in chronic brucellosis patients. CD80/CD28 co-stimulation is critical for an efficient Th1 response and has not been studied previously in human brucellosis. In order to investigate the role of CD80/CD28 co-stimulation, 13 acute brucellosis patients (AB), 22 chronic brucellosis patients (CB, 12/22 relapsing type-CB1 and 10/22 atypical type-CB2), 11 ‘cured’ subjects and 15 healthy volunteers (controls) were studied. The percentage of CD4+/CD28+ T lymphocytes and CD14+/CD80+ monocytes were analysed by flow cytometry both ex vivo and after phytohaemagglutinin (PHA)-stimulation with or without heat-killed Brucella abortus (HkBA). Ex vivo analysis showed no differences between all groups studied. PHA stimulation up-regulated the percentage of CD80+ monocytes in AB compared to ‘cured’ subjects and controls (P < 0·001), although the proportion of CD4+/CD28+ cells did not alter. A higher percentage of CD80+ monocytes was observed in the CB1 subgroup, compared to AB, ‘cured’ subjects and controls (P = 0·042, < 0·001 and < 0·001, respectively). CB2 was characterized by a lower percentage of CD80+ monocytes in comparison to CB1 (P = 0·020). HkBA in PHA cultures down-regulated the percentage of CD80+ monocytes compared to PHA alone in all groups, especially in AB and CB patients (P < 0·001 and P = 0·007, respectively). In conclusion, the diminished percentage of CD4+/CD25+ T cells in CB is not associated with inadequate CD80/CD28 co-stimulation. We speculate that differential frequency of CD80+ monocytes after PHA stimulation could serve as a qualitative parameter of disease status, related to the different clinical forms of chronic brucellosis.
Cokriging particle size fractions of the soil
Authors: Lark R. M. , Bishop T. F. A.
Published: October 2006

It is often necessary to predict the distribution of mineral particles in soil between size fractions, given observations at sample sites. Because the contents in each fraction necessarily sum to 100%, these values constitute a composition, which we may assume is drawn from a random compositional variate. Elements of a D‐component composition are subject to non‐stochastic constraints; they are constrained to lie on a D– 1 dimensional simplex. This means we cannot treat them as realizations of unbounded random variables such as the multivariate Gaussian. For this reason, there are theoretical reasons not to use ordinary cokriging (or ordinary kriging) to map particle size distributions. Despite this, the compositional constraints on data on particle size fractions are not always accounted for by soil scientists.

The additive log‐ratio (alr) transform can be used to transform data from a compositional variate into a form that can be treated as a realization of an unbounded random variable. Until now, while soil scientists have made use of the alr transform for the spatial prediction of particle size, there has been concern that the simple back‐transform of the optimal estimate of the alr‐transformed variables does not yield the optimal estimate of the composition. A numerical approximation to the conditional expectation of the composition has been proposed, but we are not aware of examples of its application and it has not been used in soil science.

In this paper, we report two case studies in which we predicted clay, silt and sand contents of the soil at test sites by ordinary cokriging of the alr‐transformed data followed by both the direct (biased) back‐transform of the estimates and the unbiased back‐transform. We also computed estimates by ordinary cokriging of the untransformed data (which ignores the compositional constraints on the variables) for comparison.

In one of our case studies, the benefit of using the alr transform was apparent, although there was no consistent advantage in using the unbiased back‐transform. In the other case study, there was no consistent advantage in using the alr transform, although the bias of the simple back‐transform was apparent. The differences between these case studies could be explained with respect to the distribution on the simplex of the particle size fractions at the two sites.
Modelling the transformations and sequestration of soil organic matter in two contrasting ecosystems of the Andes
Authors: Pansu M. , Sarmiento L. , Metselaar K. , Hervé D. , Bottner P.
Published: October 2006

The mechanisms linking soil respiration to climate and soil physical properties are important for modelling transformation and sequestration of C and N in the soil. We investigated them by incubating 14C and 15N labelled straw in soils of the dry puna (Bolivian altiplano, semi‐arid shrubland at 3789 m above sea level) and the humid paramo (Venezuelan tropical alpine vegetation at 3400 m). These two ecosystems of the high Andes are comparable in terms of altitude, mean temperature and land use, but are very different regarding organic matter content, rainfall patterns and soil physical properties. Total 14C and 15N, microbial‐biomass 14C and 15N, soil moisture and meteorological data were recorded over 2 years. Daily soil moisture was predicted from a water balance model. The data from the paramo site were used to calibrate MOMOS‐6, a model of organic matter decomposition based on microbial activity and requiring only kinetic constant parameters to describe: (i) inputs to microbial biomass from plant debris and microbial metabolites, and (ii) losses from the biomass by mortality and respiration (respiration coefficient and microbial metabolic quotient qCO2). The simulated qCO2–14C agrees well with qCO2–14C and qCO2 measured at the calibration site and with published data. To apply MOMOS‐6 to the puna site, only the respiration coefficient of the biomass was re‐estimated. The dynamics of 14C and 15N were very different in the two systems. In the puna, the transformation processes stop during the long dry periods, though total annual mineralization is greater than in the paramo. The change in the value of the respiration coefficient enables us to predict that the amount of C and N sequestered in the stable humus is greater in the paramo than in the puna. The data in this paper can be used to estimate values of the respiration coefficient so that MOMOS‐6 can be applied to other systems.
Visualization of root growth in heterogeneously contaminated soil using neutron radiography
Authors: Menon M. , Robinson B. , Oswald S. E. , Kaestner A. , Abbaspour K. C. , Lehmann E. , Schulin R.
Published: October 2006

We used neutron radiography (NR), a non‐invasive and in situ technique, to study living plant roots in soil. Plant roots have a larger water content than their unsaturated surrounding media. As water strongly attenuates a neutron‐beam, NR can identify root structures in detail. We investigated the use of NR to visualize the root growth of lupin in quartz sand and in a loamy sand field soil. Further experiments elucidated the root growth of lupin in the loamy sand heterogeneously contaminated with 10 and 20 mg kg−1 boron (B) and 100 mg kg−1 zinc (Zn). We obtained high‐quality images of root growth dynamics in both media with a resolution range of 110–270 μm. The images with quartz sand revealed fine structures such as proteoid roots that are difficult to locate in situ by other methods without destruction of the soil. Though quartz sand provided excellent visibility of roots, it proved to be a poor medium for growing plants, probably because of its bulk density (1.8 Mg m−3). The images with field soil showed normal root growth with slightly less contrast than the quartz sand. The poorer contrast was due to the greater neutron interaction with soil water and soil organic matter. In the heterogeneously contaminated soil, root growth was significantly reduced in the contaminated part of the soil in all B and Zn treatments. This study shows that NR has potential as a non‐invasive method to investigate root growth over time as well as the response of roots to various abiotic stress factors.
Transit towards floristic homogenization on oceanic islands in the south‐eastern Pacific: comparing pre‐European and current floras
Authors: Castro Sergio A. , Muñoz Mélica , Jaksic Fabian M.
Published: October 2006

Aim  To quantify the occurrence of processes of homogenization or differentiation in the vascular flora of six oceanic islands.

Location  Six islands in the south‐eastern Pacific drawn from the Desventuradas Archipelago, Easter Island and the Juan Fernández Archipelago.

Methods  Using published floristic studies, we determined the floristic composition of each island at two different stages: (1) pre‐European colonization and (2) current flora. We compared changes in the number of shared plants and the floristic similarity among islands for each stage.

Results  The number of plant species doubled from 263 in pre‐European flora to 531 species currently. Only three native species became extinct, four natives were translocated among the islands and 271 plant species were introduced from outside. The frequency of plant species shared by two or more islands is higher in the post‐European floras than prior to European contact, and the level of floristic similarity between islands increased slightly.

Main conclusions  Considering the low naturalization rate of alien plants, the small number of extinctions and the meagre increase in floristic similarity, these islands are undergoing a slow process of floristic homogenization.
A mid‐Holocene environmental change in Amazonian savannas
Authors: De Toledo Mauro B. , Bush Mark B.
Published: October 2006

Aim  The main goal of this study was to investigate how climate and human activities may have influenced ecotonal areas of disjoint savannas within Brazilian Amazonia.

Location  Eastern Brazilian Amazonia, Amapá State.

Methods  The fossil pollen and charcoal records of two lakes in Amapá (Marcio and Tapera) were used to provide a Holocene palaeoecological history of eastern Amazonian savannas. Detrended correspondence analysis was used to enhance the patterns of sample distribution along the sediment core.

Results  Even though sedimentary hiatuses were recognized in the sediment cores from both lakes, a marked change in vegetation from closed forests with swamp elements to open flooded savanna at c. 5000 yr bp was evident from the pollen record. Charcoal analysis revealed a pattern of increased accumulation of charred particles coincident with the establishment of savanna vegetation, suggesting higher fire frequency near the lakes. Because the timing of the sedimentary hiatus overlapped with the highest Holocene sea level, which would have increased the local water table preventing the lakes from drying out, we infer that both lakes used to depend heavily on flood waters, and the sedimentary gap was caused by reduced discharge from the Amazon River, due to a dry period in the Andes, when precipitation levels markedly decreased between 8000 and 5000 yr bp. The lack of Andean pollen (probably river transported) in the sediment record after this event and the existence of similar records near the study site make this interpretation more appealing. The resumption of sedimentation in Lake Marcio, contemporaneous with falling sea level and increasingly wet conditions in the Andes after 5000 yr bp, indicates that Holocene sea‐level variation did not play an important role in maintaining lake levels.

Main conclusions  The study site recorded long‐term occupation by pre‐Columbian peoples. However, it is still unclear whether these disjoint savannas have an anthropogenic origin. Even though locally dry environmental conditions were inferred from both records, there is no evidence of a mid‐Holocene dry climate in eastern Amazonia. Instead, the Amapá record indicates a connection between Andean climate and eastern Amazonia, demonstrating the need for a better understanding of the impacts and magnitude of climate changes.
Pathogenesis and treatment of diabetic vascular disease – illustrated by two cases
Authors: SMITH U. , LAAKSO M. , ELIASSON B. , WESSLAU C. , BORÉN J. , WIKLUND O. , ATTVALL S.
Published: October 2006

This publication is a summary of the presentations given at the First JIM Grand Round held at the Sahlgrenska University Hospital on 15 March 2006. The Grand Round was based on two case reports; a patient with type 2 diabetes and pronounced macrovascular disease and another patient with early microvascular disease combined with the macrovascular complications. The pathogenesis of the vascular complications and the current treatment regimens were discussed in relation to the history and examinations performed in these patients.
A novel ligand bound ABC transporter, LolCDE, provides insights into the molecular mechanisms underlying membrane detachment of bacterial lipoproteins
Authors: Ito Yasuko , Kanamaru Kyoko , Taniguchi Naohiro , Miyamoto Shigehiko , Tokuda Hajime
Published: October 2006

The LolCDE complex of Escherichia coli belongs to the ABC transporter superfamily and initiates the lipoprotein sorting to the outer membrane by catalysing their release from the inner membrane. LolC and/or LolE, membrane subunits, recognize lipoproteins anchored to the outer surface of the inner membrane, while LolD hydrolyses ATP on its inner surface. We report here that ligand‐bound LolCDE can be purified from the inner membrane in the absence of ATP. Liganded LolCDE represents an intermediate of the release reaction and exhibits higher affinity for ATP than the unliganded form. ATP binding to LolD weakens the interaction between LolCDE and lipoproteins and causes their dissociation in a detergent solution, while lipoprotein release from membranes requires ATP hydrolysis. Liganded LolCDE thus reveals molecular events brought about through ATP binding and hydrolysis. LolCDE is the first example of an ABC transporter purified with tightly bound native substrates. A single molecule of lipoprotein is found to bind per molecule of the LolCDE complex.
An α‐(1,4)‐amylase is essential for α‐(1,3)‐glucan production and virulence in Histoplasma capsulatum
Authors: Marion Christopher L. , Rappleye Chad A. , Engle Jacquelyn T. , Goldman William E.
Published: October 2006

Histoplasma capsulatum is a dimorphic fungus that causes respiratory and systemic disease and is capable of surviving and replicating within macrophages. The virulence of Histoplasma has been linked to cell wall α‐(1,3)‐glucan; however, the role of this polysaccharide during infection, its organization within the cell wall, and its synthesis and regulation remain poorly understood. To identify genes involved in the biosynthesis of α‐(1,3)‐glucan, we employed a forward genetics strategy to isolate physically marked mutants with reduced α‐(1,3)‐glucan. Insertional mutants were generated in a virulent strain of H. capsulatum by optimization of Agrobacterium tumefaciens‐mediated transformation. Approximately 90% of these mutants possessed single insertions with no chromosomal rearrangements or deletions in the host genome. To confirm the role and specificity of identified candidate genes, we phenocopied the disrupted locus by either RNA interference or targeted gene deletion. Our findings indicate α‐(1,3)‐glucan production requires the function of the AMY1 gene product, a novel protein with homology to the α‐amylase family of glycosyl hydrolases, and UGP1, a UTP‐glucose‐1‐phosphate uridylyltransferase which synthesizes UDP‐glucose monomers. Loss of AMY1 function attenuated the ability of Histoplasma to kill macrophages and to colonize murine lungs.
RyhB small RNA modulates the free intracellular iron pool and is essential for normal growth during iron limitation in Escherichia coli
Authors: Jacques Jean‐François , Jang Soojin , Prévost Karine , Desnoyers Guillaume , Desmarais Maxime , Imlay James , Massé Eric
Published: October 2006

The small RNA RyhB has recently been shown to negatively regulate a number of mRNAs encoding dispensable iron‐using proteins in Escherichia coli. The resulting decrease in the synthesis of iron‐using proteins is thought to spare iron in order to ensure its availability for iron‐requiring proteins that are indispensable. Indeed, the expression of RyhB from a heterologous promoter activates the iron‐sensing repressor Fur, which suggests an increase in the pool of free intracellular iron (iron‐sparing). In accordance with these observations, we report here that RyhB expression increases the concentration of free intracellular iron, as shown by direct measurements of the metal in whole cells by electron paramagnetic resonance spectroscopy. Our data also suggest that iron‐sparing originates from rapid uptake of extracellular iron and not from already internalized metal. Furthermore, RyhB is shown to be essential for normal bacterial growth and survival during iron starvation, which is consistent with previous data describing the function of the small RNA. Overall, our data demonstrate that, by regulating synthesis of nonessential iron‐using proteins, the small RNA RyhB ensures that the iron is directed towards the iron‐requiring enzymes that are indispensable.