bluuebunny/crossref_metadata_2025 huggingface dataset:
HaploPool: improving haplotype frequency estimation through DNA pools and phylogenetic modeling
Authors: Kirkpatrick Bonnie , Armendariz Carlos Santos , Karp Richard M. , Halperin Eran
Published: September 2007

Motivation: The search for genetic variants that are linked to complex diseases such as cancer, Parkinson's;, or Alzheimer's; disease, may lead to better treatments. Since haplotypes can serve as proxies for hidden variants, one method of finding the linked variants is to look for case-control associations between the haplotypes and disease. Finding these associations requires a high-quality estimation of the haplotype frequencies in the population. To this end, we present, HaploPool, a method of estimating haplotype frequencies from blocks of consecutive SNPs.

Results: HaploPool leverages the efficiency of DNA pools and estimates the population haplotype frequencies from pools of disjoint sets, each containing two or three unrelated individuals. We study the trade-off between pooling efficiency and accuracy of haplotype frequency estimates. For a fixed genotyping budget, HaploPool performs favorably on pools of two individuals as compared with a state-of-the-art non-pooled phasing method, PHASE. Of independent interest, HaploPool can be used to phase non-pooled genotype data with an accuracy approaching that of PHASE.

We compared our algorithm to three programs that estimate haplotype frequencies from pooled data. HaploPool is an order of magnitude more efficient (at least six times faster), and considerably more accurate than previous methods. In contrast to previous methods, HaploPool performs well with missing data, genotyping errors and long haplotype blocks (of between 5 and 25 SNPs).

Availability: The HaploPool software is available at: http://haplopool.icsi.berkeley.edu/haplopool/

Contact:  bbkirk@eecs.berkeley.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
CellMontage: similar expression profile search server
Authors: Fujibuchi Wataru , Kiseleva Larisa , Taniguchi Takeaki , Harada Hajime , Horton Paul
Published: September 2007

Summary: The establishment and rapid expansion of microarray databases has created a need for new search tools. Here we present CellMontage, the first server for expression profile similarity search over a large database—69 000 microarray experiments derived from NCBI's; GEO site. CellMontage provides a novel, content-based search engine for accessing gene expression data. Microarray experiments with similar overall expression to a user-provided expression profile (e.g. microarray experiment) are computed and displayed—usually within 20 s. The core search engine software is downloadable from the site.

Availability:  http://cellmontage.cbrc.jp/

Contact:  horton-p@aist.go.jp

Supplementary information:  http://cellmontage.cbrc.jp/supplementary/
TandTRAQ: an open-source tool for integrated protein identification and quantitation
Authors: Laderas Ted , Bystrom Cory , McMillen Debra , Fan Guang , McWeeney Shannon
Published: September 2007

Summary: Integrating qualitative protein identification with quantitative protein analysis is non-trivial, given incompatibility in output formats. We present TandTRAQ, a standalone utility that integrates results from i-Tracker, an open-source iTRAQ quantitation program with the search results from X?Tandem, an open-source proteome search engine. The utility runs from the command-line and can be easily integrated into a pipeline for automation.

Availability: The TandTRAQ Perl scripts are freely available for download at http://www.ohsucancer.com/isrdev/tandtraq/

Contact:  laderast@ohsu.edu
Business Groups and the Big Push: Meiji Japan's Mass Privatization and Subsequent Growth
Authors: Morck Randall , Nakamura Masao
Published: September 2007

Paul Rosenstein-Rodan argues that economic development requires coordinated investment in many interdependent industries, and prescribes a flood of state-controlled investment across all sectors—a so-called big push. Widespread government failure defeated twentieth-century ‘big push’ schemes. But spillovers across firms and industries, and from public goods, hold-up problems, and capital market limitations are real, and justify coordinated growth across sectors if it can be done without government failures. Large, extensively diversified pyramidal business groups of listed firms dominate the histories of developed economies and the economies of developing economies. Arguing that such groups provided this coordination in prewar Japan after a state-run big push failed, we propose that pyramidal business groups are private-sector mechanisms for coordinating big push growth, and that competition between rival groups induces efficiency unattainable in a state-run big push. We postulate that a successful business-group led big push requires economic openness, basic public goods, rule of law, separation of the state from business, and a timely demise of business groups when the big push phase is complete.Where these criteria are not met, growth stalls and oligarchic families become too powerful to dislodge.
Voice pitch predicts reproductive success in male hunter-gatherers
Authors: Apicella C.L , Feinberg D.R , Marlowe F.W
Published: September 2007

The validity of evolutionary explanations of vocal sexual dimorphism hinges upon whether or not individuals with more sexually dimorphic voices have higher reproductive success than individuals with less dimorphic voices. However, due to modern birth control methods, these data are rarely described, and mating success is often used as a second-rate proxy. Here, we test whether voice pitch predicts reproductive success, number of children born and child mortality in an evolutionarily relevant population of hunter-gatherers. While we find that voice pitch is not related to reproductive outcomes in women, we find that men with low voice pitch have higher reproductive success and more children born to them. However, voice pitch in men does not predict child mortality. These findings suggest that the association between voice pitch and reproductive success in men is mediated by differential access to fecund women. Furthermore, they show that there is currently selection pressure for low-pitch voices in men.
Variable fledging age according to group size: trade-offs in a cooperatively breeding bird
Authors: Raihani N.J , Ridley A.R
Published: September 2007

Group living can provide individuals with several benefits, including cooperative vigilance and lower predation rates. Individuals in larger groups may be less vulnerable to predation due to dilution effects, efficient detection or greater ability to repel predators. Individuals in smaller groups may consequently employ alternative behavioural tactics to compensate for their greater vulnerability to predators. Here, we describe how pied babbler (
Turdoides bicolor
) fledging age varies with group size and the associated risk of nestling predation. Nestling predation is highest in smaller groups, but there is no effect of group size on fledgling predation. Consequently, small groups fledge young earlier, thereby reducing the risk of predation. However, there is a cost to this behaviour as younger fledglings are less mobile than older fledglings: they move shorter distances and are less likely to successfully reach the communal roost tree. The optimal age to fledge young appears to depend on the trade-off between reduced nestling predation and increased fledgling mobility. We suggest that such trade-offs may be common in species where group size critically affects individual survival and reproductive success.
A foetal energy balance equation based on maternal exercise and diet
Authors: Thomas Diana M , Clapp James F , Shernce Susan
Published: September 2007

Empirical data indicate that the maternal diet composition has a direct impact on foetal fat mass and resulting birth weights. Weight-bearing maternal exercise influences the placental volume, which has also been correlated to birth weight. A foetal energy balance equation, based on the first law of thermodynamics, that incorporates maternal diet and exercise is developed. Model parameters and validity are evaluated using published data.
Resummation and the semiclassical theory of spectral statistics
Authors: Keating Jonathan P , Müller Sebastian
Published: September 2007

We address the question as to why, in the semiclassical limit, classically chaotic systems generically exhibit universal quantum spectral statistics coincident with those of random-matrix theory. To do so, we use a semiclassical resummation formalism that explicitly preserves the unitarity of the quantum time evolution by incorporating duality relations between short and long classical orbits. This allows us to obtain both the non-oscillatory and the oscillatory contributions to spectral correlation functions within a unified framework, thus overcoming a significant problem in previous approaches. In addition, our results extend beyond the universal regime to describe the system-specific approach to the semiclassical limit.
Void fraction measurements in breaking waves
Authors: Blenkinsopp C.E , Chaplin J.R
Published: September 2007

This paper describes detailed measurements and analysis of the time-varying distribution of void fractions in three different breaking waves under laboratory conditions. The measurements were made with highly sensitive optical fibre phase detection probes and document the rapid spatial and temporal evolutions of both the bubble plume generated beneath the free surface and the splashes above. Integral properties of the measured void fraction fields reveal a remarkable degree of similarity between characteristics of the two-phase flow in different breaker types as they evolve with time. Depending on the breaker type, the energy expended in entraining air and generating splash accounts for a minimum of between 6.5 and 14% of the total energy dissipated during wave breaking.
Non-local elastic plate theories
Authors: Lu Pin , Zhang P.Q , Lee H.P , Wang C.M , Reddy J.N
Published: September 2007

A non-local plate model is proposed based on Eringen's theory of non-local continuum mechanics. The basic equations for the non-local Kirchhoff and the Mindlin plate theories are derived. These non-local plate theories allow for the small-scale effect which becomes significant when dealing with micro-/nanoscale plate-like structures. As illustrative examples, the bending and free vibration problems of a rectangular plate with simply supported edges are solved and the exact non-local solutions are discussed in relation to their corresponding local solutions.
Exact solutions for Sturm–Liouville problems on trees via novel substitute systems and the Wittrick–Williams algorithm
Authors: Williams Fred W , Watson Andrew , Paul Howson W , Jones Antonia J
Published: September 2007

Since 1970, the Wittrick–Williams algorithm has been applied with increasing sophistication in structural mechanics to guarantee that eigenvalues cannot be missed and are calculated accurately. The underlying theorem enables its application to any discipline requiring eigenvalues of self-adjoint systems of differential equations. Its value in mathematics was recently illustrated by studying Sturm–Liouville equations on large homogeneous trees with Dirichlet boundary conditions and
n
(≤43) levels.
Recursive subsysteming
was applied
n
−1 times to assemble the tree progressively from sub-trees. Hence, numerical results confirmed the recent theoretical bounds of Sobolev & Solomyak for
n
→∞. In addition, a structural mechanics analogy yielded a proof that many eigenvalues had high multiplicities determined by
n
and the branching number
b
.

Inspired by the structural mechanics analogy, we now prove that all eigenvalues of the tree are obtainable from
n
substitute chains
r
(=1, 2, …, 
n
) which involve only
r
consecutively linked differential equations and which have only singlefold eigenvalues. Equations are also derived for the multiplicities these eigenvalues have for the tree. Hence, double precision calculations on a PC readily gave eigenvalues for
n
=10
6
and
b
=10, i.e. ≃10
999 999
linked Sturm–Liouville equations. Moreover, a simple equation is derived which gives all the eigenvalues of uniform trees with Dirichlet conditions at both ends, and band-gap spectra are numerically demonstrated and theoretically justified for trees with the Dirichlet conditions at either end replaced by Neumann ones. Additionally, even if each multiple eigenvalue would be counted as if it were singlefold, the proportion of eigenvalues that are multiple is proved to approach unity as
n
→∞.
Human cooperation in social dilemmas: comparing the Snowdrift game with the Prisoner's Dilemma
Authors: Kümmerli Rolf , Colliard Caroline , Fiechter Nicolas , Petitpierre Blaise , Russier Flavien , Keller Laurent
Published: September 2007

Explaining the evolution of cooperation among non-relatives is one of the major challenges for evolutionary biology. In this study, we experimentally examined human cooperation in the iterated Snowdrift game (ISD), which has received little attention so far, and compared it with human cooperation in the iterated Prisoner's Dilemma (IPD), which has become the paradigm for the evolution of cooperation. We show that iteration in the ISD leads to consistently higher levels of cooperation than in the IPD. We further demonstrate that the most successful strategies known for the IPD (generous Tit-for-Tat and Pavlov) were also successfully used in the ISD. Interestingly, we found that female players cooperated significantly more often than male players in the IPD but not in the ISD. Moreover, female players in the IPD applied Tit-for-Tat-like or Pavlovian strategies significantly more often than male players, thereby achieving significantly higher pay-offs than male players did. These data demonstrate that the willingness to cooperate does not only depend on the type of the social dilemma, but also on the class of individuals involved. Altogether, our study shows that the ISD can potentially explain high levels of cooperation among non-relatives in humans. In addition, the ISD seems to reflect the social dilemma more realistically than the IPD because individuals obtain immediate direct benefits from the cooperative acts they perform and costs of cooperation are shared between cooperators.
Duetting in space: a radio-telemetry study of the black-bellied wren
Authors: Logue David M
Published: September 2007

In many birds, individuals ‘answer’ the songs of their pair-mates to produce vocal ‘duets’. One hypothesized function of song answering is that it prevents extra-pair birds from intruding into the duetting pair's territory to obtain copulations or usurp one of the pair-mates. In this capacity, answering may signal that the pair-mates are close together, and so are prepared to defend against such an intrusion. Another functional hypothesis states that answering helps pair-mates maintain contact, and so predicts that a bird is more likely to approach its mate after a duet than after a solo song. I used radio-telemetry to monitor the distance between mated black-bellied wrens (
Pheugopedius fasciatoventris
). I found that birds of both sexes were more likely to answer their mate's song when the mate was close, and that maximum duet length was negatively related to the distance between pair-mates. Furthermore, song answering positively affected the likelihood of one pair-mate approaching the other after a song. In a significant majority of the approaches after duet songs, the answering bird approached the initiator. I conclude that in the black-bellied wren, (i) the occurrence and duration of vocal duets covary with physical closeness and (ii) contact maintenance is a secondary function of duet participation.
Producing sons reduces lifetime reproductive success of subsequent offspring in pre-industrial Finns
Authors: Rickard Ian J , Russell Andrew F , Lummaa Virpi
Published: September 2007

Life-history theory states that reproductive events confer costs upon mothers. Many studies have shown that reproduction causes a decline in maternal condition, survival or success in subsequent reproductive events. However, little attention has been given to the prospect of reproductive costs being passed onto subsequent offspring, despite the fact that parental fitness is a function of the reproductive success of progeny. Here we use pedigree data from a pre-industrial human population to compare offspring life-history traits and lifetime reproductive success (LRS) according to the cost incurred by each individual's mother in the previous reproductive event. Because producing a son versus a daughter has been associated with greater maternal reproductive cost, we hypothesize that individuals born to mothers who previously produced sons will display compromised survival and/or LRS, when compared with those produced following daughters. Controlling for confounding factors such as socio-economic status and ecological conditions, we show that those offspring born after elder brothers have similar survival but lower LRS compared with those born after elder sisters. Our results demonstrate a maternal cost of reproduction manifested in reduced LRS of subsequent offspring. To our knowledge, this is the first time such a long-term intergenerational cost has been shown in a mammal species.
Shrinking to fit: fluid jettison from a haemocoelic hydrostatic skeleton during defensive withdrawals of a gastropod larva
Authors: Page Louise R
Published: September 2007

Although most of the basic animal body plans are supported by hydrostatic skeletons consisting of fluid maintained at constant volume, studies on how animals have solved biomechanical scaling dilemmas during evolution of large body size have emphasized cases where skeletons are formed by rigid solids. Larvae of gastropod molluscs swim using ciliated velar lobes supported by a constant volume hydrostatic skeleton. Defensive behaviour involves rapid withdrawal of the velar lobes and foot into a protective biomineralized shell. Some gastropod larvae grow to giant size and the velar lobes enlarge allometrically, but the lobes and foot of many can still withdraw completely into the mineral-stiffened shell. I dyed internal fluid of a large gastropod larva with fluorescein to show that fluid supporting the extended velar lobes is expelled from discrete release sites during defensive withdrawals. Scanning electron microscopy suggested that release sites are distinctive papillae on the upper velar epidermis. Ultrathin sections revealed that branched tracks of microvilli-free membrane on the surface of these papillae were formed by very thin epithelial cells, which may rupture and re-anneal during and after defensive withdrawals. Behaviours facilitated by fluid discharge from a haemocoelic (non-coelomic) body compartment have been rarely reported among aquatic invertebrates, but may be more widespread than currently recognized.
Climatic zonation drives latitudinal variation in speciation mechanisms
Authors: Kozak Kenneth H , Wiens John J
Published: September 2007

Many groups of organisms show greater species richness in the tropics than in the temperate zone, particularly in tropical montane regions. Forty years ago, Janzen suggested that more limited temperature seasonality in the tropics leads to greater climatic zonation and more climatic barriers to organismal dispersal along elevational gradients in the tropics relative to temperate regions. These factors could lead to differences in how species arise in tropical versus temperate regions and possibly contribute to greater tropical diversity. However, no studies have compared the relationships among climate, elevational distribution and speciation in a group inhabiting both tropical and temperate regions. Here, we compare elevational and climatic divergence among 30 sister-species pairs (14 tropical, 16 temperate) within a single family of salamanders (Plethodontidae) that reaches its greatest species richness in montane Mesoamerica. In support of Janzen's hypothesis, we find that sister species are more elevationally and climatically divergent in the tropics than in the temperate zone. This pattern seemingly reflects regional variation in the role of climate in speciation, with niche conservatism predominating in the temperate zone and niche divergence in the tropics. Our study demonstrates how latitudinal differences in elevational climatic zonation may increase opportunities for geographical isolation, speciation and the associated build-up of species diversity in the tropics relative to the temperate zone.
Language processing in the natural world
Authors: Tanenhaus Michael K , Brown-Schmidt Sarah
Published: September 2007

The authors argue that a more complete understanding of how people produce and comprehend language will require investigating real-time spoken-language processing in natural tasks, including those that require goal-oriented unscripted conversation. One promising methodology for such studies is monitoring eye movements as speakers and listeners perform natural tasks. Three lines of research that adopt this approach are reviewed: (i) spoken word recognition in continuous speech, (ii) reference resolution in real-world contexts, and (iii) real-time language processing in interactive conversation. In each domain, results emerge that provide insights which would otherwise be difficult to obtain. These results extend and, in some cases, challenge standard assumptions about language processing.
The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis
Authors: Wirth Thierry , Morelli Giovanna , Kusecek Barica , van Belkum Alex , van der Schee Cindy , Meyer Axel , Achtman Mark
Published: September 2007

The nosocomial human pathogen Moraxella catarrhalis is one the most important agents of human respiratory tract infections. This species is composed of two distinct lineages, one of only moderate virulence, the so-called serosensitive subpopulation, and a second, the seroresistant one, which is enriched among strains that harbor two major virulence traits: complement resistance and adherence to epithelial cells. Using a suite of population genetics tools, we show that the seroresistant lineage is also characterized by higher homologous recombination and mutation rates at housekeeping genes relative to its less pathogenic counterpart. Thus, sex and virulence have evolved in tandem in M. catarrhalis. Moreover, phylogenetic and Bayesian analyses that take into account recombination between the two clades show that the ancestral group was avirulent, is possibly 70 million years old, and must have infected mammals prior to the evolution of humans, which occurred later. The younger seroresistant isolates went through an important population expansion some 5 million years ago, coincident with the hominid expansion. This rise and spread was possibly coupled with a host shift and the acquisition of virulence genes.
Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21
Authors: Lyle Robert , Prandini Paola , Osoegawa Kazutoyo , ten Hallers Boudewijn , Humphray Sean , Zhu Baoli , Eyras Eduardo , Castelo Robert , Bird Christine P. , Gagos Sarantos , Scott Carol , Cox Antony , Deutsch Samuel , Ucla Catherine , Cruts Marc , Dahoun Sophie , She Xinwei , Bena Frederique , Wang Sheng-Yue , Van Broeckhoven Christine , Eichler Evan E. , Guigo Roderic , Rogers Jane , de Jong Pieter J. , Reymond Alexandre , Antonarakis Stylianos E.
Published: September 2007

The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. This region contains extensive euchromatic-like sequence and includes on average one transcript every 100 kb. These transcripts show multiple inter- and intrachromosomal copies, and extensive copy number and sequence variability. The sequencing of the “heterochromatic” regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information.
Increased susceptibility of Sf1+/– mice to azoxymethane‐induced colon tumorigenesis
Authors: Shitashige Miki , Satow Reiko , Honda Kazufumi , Ono Masaya , Hirohashi Setsuo , Yamada Tesshi
Published: September 2007

Aberrant transactivation of a certain set of target genes by the β‐catenin and T‐cell factor‐4 nuclear complex has been considered crucial for the initiation of colorectal carcinogenesis. We previously identified splicing factor‐1 (SF1) as a novel component of the β‐catenin and T‐cell factor‐4 complex, and showed that the overexpression of SF1 inhibited the gene transactivational activity of the complex and markedly suppressed β‐catenin‐evoked colony formation by human embryonic kidney 293 cells. However, the involvement of SF1 in the process of carcinogenesis in vivo remains unclear. In the present study, we established SF1‐knockout mice using the gene trapping method. Homozygous mice (Sf1−/–) died during embryonic development before embryonic day (E)8.5, whereas heterozygous (Sf1+/–) mice were born alive and developed normally. Azoxymethane (AOM) was given at a dose of 10 mg/kg body weight once a week for 6 weeks to 7‐week‐old Sf1+/– and Sf1+/+ mice. At 23 weeks after the start of AOM the average number (5.5 ± 0.6 versus 2.2 ± 0.2 in females [P = 0.003, Mann–Whitney U‐test], 3.7 ± 0.2 versus 1.7 ± 0.7 in males [P = 0.014]) and volume of colon tumors per mouse (8.7 ± 1.6 versus 2.2 ± 0.5 mm3 per female [P = 0.0008], 11.3 ± 3.4 versus 0.6 ± 0.2 mm3 per male [P = 0.001]) were significantly higher in Sf1+/– than in Sf1+/+ mice. The increased susceptibility of Sf1+/– mice to AOM‐induced colon tumorigenesis indicates the crucial involvement of SF1 in the β‐catenin‐mediated regulation of proliferation and differentiation of intestinal epithelial cells. (Cancer Sci 2007; 98: 1862–1867)
Thyrotoxic hypokalaemic periodic paralysis in a Turkish population: three new case reports and analysis of the case series
Authors: Cesur Mustafa , Bayram Fahri , Temel Mehtap Akcil , Ozkaya Mesut , Kocer Abdulkadir , Ertorer Melek Eda , Koc Filiz , Kaya Ahmet , Gullu Sevim
Published: September 2007

Objective  Thyrotoxic hypokalaemic periodic paralysis (THPP) is an uncommon condition with intermittent episodes of muscle weakness and occasionally severe paralysis. THPP is a common complication of hyperthyroidism in Asian populations, and has also been reported in other ethnic groups including Caucasians. This study aimed to conduct an analysis of THPP in a Turkish population, and is to our knowledge the first analysis of a homogeneous Caucasian group.

Subjects  Forty cases with THPP were identified in the Turkish population. Three out of the 40 were new cases and were assigned as index cases. Two cases were not included in the analysis because of lack of data.

Results  THPP was diagnosed in 10 cases during the first attack and was observed to have a significant shorter complete recovery time statistically in this group (P < 0·01). The majority of cases were hypokalaemic, while there were two normokalaemic cases. Classification of the cases according to their potassium (K) levels revealed that the group with K levels < 2·5 mEq/l had a statistically longer amelioration time than the group with K levels ≥ 2·5 mEq/l. When the cases were classified according to intravenous or oral application of K, the mean amelioration time was 6·8 ± 3·6 h for the intravenous group and 13·1 ± 7·6 for the oral group. Mean complete recovery times of the groups were 29·4 ± 16·2 h and 52·8 ± 18·0 h, respectively. The intravenous group had a shorter amelioration time and complete recovery time, and both were statistically significant (P < 0·05 for each).

Conclusions  THPP may be seen among Caucasians. Diagnosing THPP during the first attack might decrease the recovery time. The level of hypokalaemia seems to affect the recovery time and initial low K levels may lead to more deterioration in a patient's health compared with mild or near‐normal levels. Intravenous, rather than oral, application of K may be advantageous for shortening both the amelioration and complete recovery times.
Detection and significance of koi herpesvirus (KHV) in freshwater environments
Authors: MATSUI KAZUAKI , HONJO MIE , KOHMATSU YUKIHIRO , UCHII KIMIKO , YONEKURA RYUJI , KAWABATA ZEN'ICHIRO
Published: September 2007

1. Koi herpesvirus (KHV) disease, a lethal disease in carp and koi, has spread rapidly since the late 1990s. Only a few studies have focused on the ecology of KHV in natural freshwater environments, although characterization and the diagnosis of KHV disease have been intensively studied. This is mainly due to the lack of reliable detection methods for KHV in natural environments.

2. Three different approaches have been used to detect KHV in fish samples: (i) isolation and identification of the virus using cultured cell lines; (ii) detection of viral DNA with target DNA amplification techniques; and (iii) detection of anti‐KHV antibodies using an enzyme‐linked immunosorbent assay (ELISA). Among these methods, DNA amplification techniques have become most popular because of their sensitivity and simplicity.

3. In contrast to KHV detection in fish samples, detection of KHV from water and sediment samples has not been reported. This is the result of a lack of reliable KHV concentration methods for water and sediment samples, although methodology from public health and marine microbiology may be applicable to determine KHV concentration in such samples.

4. Few reports have evaluated the environmental factors (e.g. temperature, UV irradiation) that affect the fate of KHV in water bodies. Mass mortality of wild carp caused by KHV infection would result in the removal of a large omnivorous fish from freshwater ecosystems and may thus alter community structure and ecosystem functioning.
Emergent body size of mayfly survivors
Authors: ALEXANDER ALEXA C. , HEARD KRISTIE S. , CULP JOSEPH M.
Published: September 2007

1. Employing field‐deployed mesocosms, we examined the effects of 12‐h pulse and 20‐day press (continuous) exposures of the common agricultural insecticide, imidacloprid, on nymph abundance, emergence patterns and adult body size of Epeorus spp. (Heptageniidae) and Baetis spp. (Baetidae).

2. In press exposures, reduced nymph density was driven by reduced survivorship; in pulse exposures, reduced nymph density may reflect increased emergence because of stress.

3. Once exposed to imidacloprid, Epeorus and Baetis mayflies developed less and emerged smaller than their control counterparts. Concentrations as low as 0.1 μg L−1 (12‐h pulse) reduced head length in Baetis and thorax length in Epeorus.

4. In all of the Baetis and Epeorus examined, effects were only found in males. Male survivorship and body size can affect population dynamics. Sublethal doses of this widely applied agricultural insecticide have the potential to reduce reproductive success of mayfly populations.
A real spectral analysis of the deformation of a homogenous electric field over a thin bed – A Hartley transform approach
Authors: Sundararajan N. , Al‐Garni Mansour A. , Ramabrahmam G. , Srinivas Y.
Published: September 2007

Spectral analysis of the deformation of a homogenous electric field caused by a long, thin inclined bed, which is of considerable importance in the exploration of ground water and minerals, is presented using the Hartley transform. The Hartley transform is an alternative and real replacement for the well‐known complex Fourier transform in the field of spectral analysis. The thickness of the bed and the inclination are given as functions of frequency by simple expressions. A theoretical example illustrates the method while the applicability is demonstrated by the field examples from the fractured crystalline basement complex in Burkina Faso, Africa and the Precambrian limestones of the Cuddapah basin, Andhra Pradesh, India. The results obtained by this method agree well with those of the drilling.
Importance of borehole deviation surveys for monitoring of hydraulic fracturing treatments
Authors: Bulant Petr , Eisner Leo , Pšenčík Ivan , Calvez Joël Le
Published: September 2007

During seismic monitoring of hydraulic fracturing treatment, it is very common to ignore the deviations of the monitoring or treatment wells from their assumed positions. For example, a well is assumed to be perfectly vertical, but in fact, it deviates from verticality. This can lead to significant errors in the observed azimuth and other parameters of the monitored fracture‐system geometry derived from microseismic event locations. For common hydraulic fracturing geometries, a 2° deviation uncertainty on the positions of the monitoring or treatment well survey can cause a more than 20° uncertainty of the inverted fracture azimuths. Furthermore, if the positions of both the injection point and the receiver array are not known accurately and the velocity model is adjusted to locate perforations on the assumed positions, several‐millisecond discrepancies between measured and modeled SH‐P traveltime differences may appear along the receiver array. These traveltime discrepancies may then be misinterpreted as an effect of anisotropy, and the use of such anisotropic model may lead to the mislocation of the detected fracture system. The uncertainty of the relative positions between the monitoring and treatment wells can have a cumulative, nonlinear effect on inverted fracture parameters. We show that incorporation of borehole deviation surveys allows reasonably accurate positioning of the microseismic events. In this study, we concentrate on the effects of horizontal uncertainties of receiver and perforation positions. Understanding them is sufficient for treatment of vertical wells, and also necessary for horizontal wells.
Changes in spring arrival of Nearctic‐Neotropical migrants attributed to multiscalar climate
Authors: MACMYNOWSKI DENA P. , ROOT TERRY L. , BALLARD GRANT , GEUPEL GEOFFREY R.
Published: September 2007

Climate‐related changes associated with the California marine ecosystem have been documented; however, there are no studies assessing changes in terrestrial vertebrate phenology on the Pacific coast of western North America. We analyze the spring phenology of 21 Nearctic‐Neotropical migratory songbird species in central and northern CA. Using observational and banding data at multiple sites, we evaluate evidence for a change in arrival timing being linked to either nonclimatic or multiscalar climatic explanations. Using correlation analysis, of the 13 species with a significant (P<0.10) change in arrival, the arrival timing of 10 species (77%) is associated with both temperature and a large‐scale climate oscillation index (El Niño Southern Oscillation, ENSO; North Atlantic Oscillation, NAO; and/or Pacific Decadal Oscillation, PDO) at least at one location. Eight of the 13 species (62%) are advancing their migratory timing. All species for which spring arrival is associated with climate at multiple locations are exhibiting changes (n=5) and all species lacking evidence for association between migration phenology and climate (n=3) exhibit no change. Migrants tend to arrive earlier in association with warmer temperatures, positive NAO indices, and stronger ENSO indices. Twelve species negatively correlate (P≤0.05) with local or regional temperature at least at one location; five species negatively correlate with ENSO. Eleven species' arrival is correlated (P≤0.05) with NAO; 10 are negatively associated. After an exhaustive literature search, this is apparently the first documentation of an association between NAO and migratory phenology in western North America.
Compromised CD4+ CD25high regulatory T‐cell function in patients with relapsing‐remitting multiple sclerosis is correlated with a reduced frequency of FOXP3‐positive cells and reduced FOXP3 expression at the single‐cell level
Authors: Venken Koen , Hellings Niels , Thewissen Marielle , Somers Veerle , Hensen Karen , Rummens Jean‐Luc , Medaer Robert , Hupperts Raymond , Stinissen Piet
Published: September 2007

CD4+ CD25high regulatory T cells (Tregs) of patients with relapsing‐remitting (RR) multiple sclerosis (MS), in contrast to those of patients with secondary progressive (SP) MS, show a reduced suppressive function. In this study, we analysed forkhead box P3 (FOXP3) at the single‐cell level in MS patients and controls (healthy individuals and patients with other neurological diseases) by means of intracellular flow cytometry. Our data revealed a reduced number of peripheral blood CD4+ CD25high FOXP3+ T cells and lower FOXP3 protein expression per cell in RR‐MS patients than in SP‐MS patients and control individuals, which was correlated with the suppressive capacity of Tregs in these patients. Interestingly, interferon (IFN)‐β‐treated RR‐MS patients showed restored numbers of FOXP3+ Tregs. Furthermore, a higher percentage of CD4+ CD25high FOXP3+ Tregs in RR‐MS patients, as compared with controls and SP‐MS patients, expressed CD103 and CD49d, adhesion molecules involved in T‐cell recruitment towards inflamed tissues. This was consistent with a significantly increased number of CD27+ CD25high CD4+ T cells in the cerebrospinal fluid (CSF), as compared with peripheral blood, in RR‐MS patients. Taken together, these data show aberrant FOXP3 expression at the single‐cell level correlated with Treg dysfunction in RR‐MS patients. Our results also suggest that Tregs accumulate in the CSF of RR‐MS patients, in an attempt to down‐regulate local inflammation in the central nervous system.
Induction of 150‐kDa adenosine deaminase that acts on RNA (ADAR)‐1 gene expression in normal T lymphocytes by anti‐CD3‐ε and anti‐CD28
Authors: Laxminarayana Dama , Khan Islam U. , O'Rourke Kenneth S. , Giri Banabihari
Published: September 2007

We and other investigators have demonstrated up‐regulation of the expression of the RNA‐editing gene 150‐kDa adenosine deaminase that acts on RNA (ADAR1) in systemic lupus erythematosus (SLE) T cells and B cells, peripheral blood mononuclear cells (PBMC), natural killer (NK) cells. The presence of a small proportion of activated T cells is the hallmark of SLE. Therefore, it was hypothesized that 150‐kDa ADAR1 gene expression is induced by the physiological activation of T cells. To examine this hypothesis, normal T cells were activated by anti‐CD3‐ε plus anti‐CD28 for various time periods from 0 to 48 hr. The expression of 110‐kDa and 150‐kDa ADAR1, and interleukin (IL)‐2 and β‐actin gene transcripts was analysed. An approximately fourfold increase in 150‐kDa ADAR1 gene expression was observed in activated T cells. ADAR2 gene transcripts are substrates for ADAR1 and ADAR2 enzymes. Therefore, we assessed the role of the 150‐kDa ADAR enzyme in editing of ADAR2 gene transcripts. In activated T cells, site‐selective editing of the −2 site was observed. Previous studies indicate that this site is predominantly edited by ADAR1. In addition to this, novel editing sites at base positions −56, −48, −45, −28, −19, −15, +46 and +69 were identified in activated T cells. On the basis of these results, it is proposed that 150‐kDa ADAR1 gene expression is selectively induced in T cells by anti‐CD3‐ε and anti‐CD28 stimulation and that it may play a role in site‐selective editing of gene transcripts and in altering the functions of several gene products of T cells during activation and proliferation.
The zinc cluster transcription factor Tac1p regulates PDR16 expression in Candida albicans
Authors: Znaidi Sadri , De Deken Xavier , Weber Sandra , Rigby Tracey , Nantel André , Raymond Martine
Published: September 2007

The Candida albicans PDR16 gene, encoding a putative phosphatidylinositol transfer protein, is co‐induced with the multidrug transporter genes CDR1 and CDR2 in azole‐resistant (AR) clinical isolates and upon fluphenazine exposure of azole‐susceptible (AS) cells, suggesting that it is regulated by Tac1p, the transcriptional activator of CDR genes. Deleting TAC1 in an AR isolate (5674) overexpressing PDR16, CDR1 and CDR2 decreased the expression of the three genes and fluconazole resistance to levels similar to those detected in the matched AS isolate (5457), demonstrating that Tac1p is responsible for PDR16 upregulation in that strain. Deleting TAC1 in the AS strain SC5314 abolished CDR2 induction by fluphenazine and decreased that of PDR16 and CDR1, uncovering the participation of an additional factor in the regulation of PDR16 and CDR1 expression. Sequencing of the TAC1 alleles identified one homozygous mutation in strain 5674, an Asn to Asp substitution at position 972 in the C‐terminus of Tac1p. Introduction of the Asp972 allele in a tac1Δ/Δ mutant caused high levels of fluconazole resistance and TAC1, PDR16, CDR1 and CDR2 constitutive induction. These results demonstrate that: (i) Tac1p controls PDR16 expression; (ii) Asn972 to Asp972 is a gain‐of‐function mutation; and (iii) Tac1p is positively autoregulated, directly or indirectly.
Elaborate spatial patterning of cell‐wall PME and PMEI at the pollen tube tip involves PMEI endocytosis, and reflects the distribution of esterified and de‐esterified pectins
Authors: Röckel Nina , Wolf Sebastian , Kost Benedikt , Rausch Thomas , Greiner Steffen
Published: September 2007

In dicots, pectins are the major structural determinant of the cell wall at the pollen tube tip. Recently, immunological studies revealed that esterified pectins are prevalent at the apex of growing pollen tubes, where the cell wall needs to be expandable. In contrast, lateral regions of the cell wall contain mostly de‐esterified pectins, which can be cross‐linked to rigid gels by Ca2+ ions. In pollen tubes, several pectin methylesterases (PMEs), enzymes that de‐esterify pectins, are co‐expressed with different PME inhibitors (PMEIs). This raises the possibility that interactions between PMEs and PMEIs play a key role in the regulation of cell‐wall stability at the pollen tube tip. Our data establish that the PME isoform AtPPME1 (At1g69940) and the PMEI isoform AtPMEI2 (At3g17220), which are both specifically expressed in Arabidopsis pollen, physically interact, and that AtPMEI2 inactivates AtPPME1 in vitro. Furthermore, transient expression in tobacco pollen tubes revealed a growth‐promoting activity of AtPMEI2, and a growth‐inhibiting effect of AtPPME1. Interestingly, AtPPME1:YFP accumulated to similar levels throughout the cell wall of tobacco pollen tubes, including the tip region, whereas AtPMEI2:YFP was exclusively detected at the apex. In contrast to AtPPME1, AtPMEI2 localized to Brefeldin A‐induced compartments, and was found in FYVE‐induced endosomal aggregates. Our data strongly suggest that the polarized accumulation of PMEI isoforms at the pollen tube apex, which depends at least in part on local PMEI endocytosis at the flanks of the tip, regulates cell‐wall stability by locally inhibiting PME activity.
Glycated albumin levels predict long‐term survival in diabetic patients undergoing haemodialysis
Authors: FUKUOKA KOUSUKE , NAKAO KAZUSHI , MORIMOTO HISANORI , NAKAO AI , TAKATORI YUJI , ARIMOTO KATSUHIKO , TAKI MASAFUMI , WADA JUN , MAKINO HIROFUMI
Published: September 2007

Aim:  Glycated albumin (GA) is recognized as a reliable marker for monitoring glycemic control particularly in patients with end‐stage renal disease (ESRD). Here, we investigated the impact of GA levels on long‐term survival in diabetic patients with ESRD.

Methods:  We enrolled ESRD patients with diabetic nephropathy into our single‐centre prospective follow‐up study (n = 98, 66 men and 32 women; age 68.2  12.3 years) with a mean follow‐up period of 47.7 months. All patients had started haemodialysis between December 1992 and November 2003. They were categorized into two groups according to their GA levels at the initiation of haemodialysis; GA < 29% (low‐GA group; n = 54) and GA  29% (high‐GA group; n = 44).

Results:  Between low‐GA and high‐GA groups, there were no significant differences in various clinical parameters except GA and HbA1c levels. The cumulative survival rate of low‐GA group was significantly higher than that of high‐GA group (P = 0.034, log–rank test). After adjustment for age, sex, total cholesterol, C‐reactive protein and albumin, high‐GA was a significant predictor of survival (hazard ratio 1.042 per 1.0% increment of GA, 95% CI 1.014–1.070, P < 0.05), but not in the case with HbA1c. Cox proportional hazard model demonstrated that high‐GA group was a significant predictor for cardiovascular death (hazard ratio 2.971 (1.064–8.298), P = 0.038).

Conclusion:  We conclude that poor glycemic control (GA  29%) before starting haemodialysis is associated with increased cardiovascular morbidity and shortened survival in diabetic patients with ESRD.
The need for integrative approaches to understand and conserve migratory ungulates
Authors: Bolger Douglas T. , Newmark William D. , Morrison Thomas A. , Doak Daniel F.
Published: September 2007

Over the last two centuries overhunting, anthropogenic barriers and habitat loss have disrupted many ungulate migrations. We review the literature on ungulate migration disruptions and find that for many species the disruption of migratory routes causes a rapid population collapse. Previous research has focused on the proximal ecological factors that might favour migration, particularly spatiotemporal variation in resources and predation. However, this does not provide an adequate basis for understanding and mitigating anthropogenic effects on migratory populations. Migration is a complex behaviour and we advocate an integrative approach that incorporates population dynamics, evolution, genetics, behaviour and physiology, and that borrows insights and approaches from research on other taxa. We draw upon research on avian migration to illustrate research approaches that might also be fruitful in ungulates. In particular, we suggest that the migratory cycle should be evaluated in the context of seasonal population limitation, an approach we highlight with a preliminary demographic perturbation analysis of the Serengeti wildebeest (Connochaetes taurinus) population. We provide suggestions for avenues of future research and highlight areas where we believe rapid progress can be made by applying recent advances in theory, technology and analytical approaches.
Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
Authors: Tyson Gene W. , Banfield Jillian F.
Published: September 2007

Recent experimental evidence has demonstrated that bacteria acquire resistance to viruses by incorporation of short transcribed nucleotide sequences into regions of clustered regularly interspaced short palindromic repeats (CRISPR). We have analysed community genomic data from acidophilic microbial biofilms and discovered that evolution of the CRISPR regions in two distinct Leptospirillum group II bacteria occurs fast enough to promote individuality in otherwise nearly clonal populations. Comparative genomics strongly indicates very recent lateral transfer of the CRISPR locus between these populations, followed by significant loss of spacer sequences and locus expansion by unidirectional heterogeneous addition of new spacer sequences. Diversification of the CRISPR region is inferred to be a population‐level response to the rapidly changing selective pressure of phage predation. Results reinforce the importance of phage–host interactions in shaping microbial ecology and evolution over very short time scales.