bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinesin-1 heavy chain mediates microtubule sliding to drive changes in cell shape
Authors: Jolly Amber L. , Kim Hwajin , Srinivasan Divya , Lakonishok Margot , Larson Adam G. , Gelfand Vladimir I.
Published: June 2010

Microtubules are typically observed to buckle and loop during interphase in cultured cells by an unknown mechanism. We show that lateral microtubule movement and looping is a result of microtubules sliding against one another in interphase
Drosophila
S2 cells. RNAi of the kinesin-1 heavy chain (KHC), but not dynein or the kinesin-1 light chain, eliminates these movements. KHC-dependent microtubule sliding powers the formation of cellular processes filled with parallel microtubule bundles. The growth of these cellular processes is independent of the actin cytoskeleton. We further observe cytoplasmic microtubule sliding in
Xenopus
and Ptk2 cells, and show that antibody inhibition of KHC in mammalian cells prevents sliding. We therefore propose that, in addition to its well established role in organelle transport, an important universal function of kinesin-1 is to mediate cytoplasmic microtubule–microtubule sliding. This provides the cell with a dedicated mechanism to transport long and short microtubule filaments and drive changes in cell shape.
Chronic lymphocytic leukemia modeled in mouse by targeted
miR-29
expression
Authors: Santanam Urmila , Zanesi Nicola , Efanov Alexey , Costinean Stefan , Palamarchuk Alexey , Hagan John P. , Volinia Stefano , Alder Hansjuerg , Rassenti Laura , Kipps Thomas , Croce Carlo M. , Pekarsky Yuri
Published: June 2010

B-cell chronic lymphocytic leukemia (B-CLL), the most common leukemia in the Western world, occurs in two forms, aggressive (showing for the most part high ZAP-70 expression and unmutated IgH V
H
) and indolent (showing low ZAP-70 expression and mutated IgH V
H
). We found that
miR-29a
is up-regulated in indolent human B-CLL as compared with aggressive B-CLL and normal CD19
+
B cells. To study the role of
miR-29
in B-CLL, we generated Eμ-
miR-29
transgenic mice overexpressing
miR-29
in mouse B cells. Flow cytometric analysis revealed a markedly expanded CD5
+
population in the spleen of these mice starting at 2 mo of age, with 85% (34/40) of
miR-29
transgenic mice exhibiting expanded CD5
+
B-cell populations, a characteristic of B-CLL. On average, 50% of B cells in these transgenic mice were CD5 positive. At 2 y of age the mice showed significantly enlarged spleens and an increase in the CD5
+
B-cell population to ∼100%. Of 20 Eμ-
miR-29
transgenic mice followed to 24–26 mo of age, 4 (20%) developed frank leukemia and died of the disease. These results suggest that dysregulation of
miR-29
can contribute to the pathogenesis of indolent B-CLL.
Nonconsecutive disulfide bond formation in an essential integral outer membrane protein
Authors: Ruiz Natividad , Chng Shu-Sin , Hiniker Annie , Kahne Daniel , Silhavy Thomas J.
Published: June 2010

The Gram-negative bacterial envelope is bounded by two membranes. Disulfide bond formation and isomerization in this oxidizing environment are catalyzed by DsbA and DsbC, respectively. It remains unknown when and how the Dsb proteins participate in the biogenesis of outer membrane proteins, which are transported across the cell envelope after their synthesis. The
Escherichia coli
protein LptD is an integral outer membrane protein that forms an essential complex with the lipoprotein LptE. We show that oxidation of LptD is not required for the formation of the LptD/E complex but it is essential for function. Remarkably, none of the cysteines in LptD are essential because either of two nonconsecutive disulfide bonds suffices for function. Oxidation of LptD, which is efficiently catalyzed by DsbA, does not involve the isomerase DsbC, but it requires LptE. Thus, oxidation is completed only after LptD interacts with LptE, an interaction that occurs at the outer membrane and seems necessary for LptD folding.
Smg1 is required for embryogenesis and regulates diverse genes via alternative splicing coupled to nonsense-mediated mRNA decay
Authors: McIlwain David R. , Pan Qun , Reilly Patrick T. , Elia Andrew J. , McCracken Susan , Wakeham Andrew C. , Itie-Youten Annick , Blencowe Benjamin J. , Mak Tak W.
Published: June 2010

Smg1 is a PI3K-related kinase (PIKK) associated with multiple cellular functions, including DNA damage responses, telomere maintenance, and nonsense-mediated mRNA decay (NMD). NMD degrades transcripts that harbor premature termination codons (PTCs) as a result of events such as mutation or alternative splicing (AS). Recognition of PTCs during NMD requires the action of the Upstream frameshift protein Upf1, which must first be phosphorylated by Smg1. However, the physiological function of mammalian Smg1 is not known. By using a gene-trap model of Smg1 deficiency, we show that this kinase is essential for mouse embryogenesis such that Smg1 loss is lethal at embryonic day 8.5. High-throughput RNA sequencing (RNA-Seq) of RNA from cells of Smg1-deficient embryos revealed that Smg1 depletion led to pronounced accumulation of PTC-containing splice variant transcripts from approximately 9% of genes predicted to contain AS events capable of eliciting NMD. Among these genes are those involved in splicing itself, as well as genes not previously known to be subject to AS-coupled NMD, including several involved in transcription, intracellular signaling, membrane dynamics, cell death, and metabolism. Our results demonstrate a critical role for Smg1 in early mouse development and link the loss of this NMD factor to major and widespread changes in the mammalian transcriptome.
APC: More than a beta (catenin) blocker
Authors: Leslie Mitch
Published: June 2010

Tumor suppressor could stop cancer through its effect on actin cytoskeleton.
Adenomatous polyposis coli protein nucleates actin assembly and synergizes with the formin mDia1
Authors: Okada Kyoko , Bartolini Francesca , Deaconescu Alexandra M. , Moseley James B. , Dogic Zvonimir , Grigorieff Nikolaus , Gundersen Gregg G. , Goode Bruce L.
Published: June 2010

The tumor suppressor protein adenomatous polyposis coli (APC) regulates cell protrusion and cell migration, processes that require the coordinated regulation of actin and microtubule dynamics. APC localizes in vivo to microtubule plus ends and actin-rich cortical protrusions, and has well-documented direct effects on microtubule dynamics. However, its potential effects on actin dynamics have remained elusive. Here, we show that the C-terminal “basic” domain of APC (APC-B) potently nucleates the formation of actin filaments in vitro and stimulates actin assembly in cells. Nucleation is achieved by a mechanism involving APC-B dimerization and recruitment of multiple actin monomers. Further, APC-B nucleation activity is synergistic with its in vivo binding partner, the formin mDia1. Together, APC-B and mDia1 overcome a dual cellular barrier to actin assembly imposed by profilin and capping protein. These observations define a new function for APC and support an emerging view of collaboration between distinct actin assembly–promoting factors with complementary activities.
Type I IFN enhances follicular B cell contribution to the T cell–independent antibody response
Authors: Swanson Cristina L. , Wilson Timothy J. , Strauch Pamela , Colonna Marco , Pelanda Roberta , Torres Raul M.
Published: June 2010

Humoral immunity to viruses and encapsulated bacteria is comprised of T cell–independent type 2 (TI-2) antibody responses that are characterized by rapid antibody production by marginal zone and B1 B cells. We demonstrate that toll-like receptor (TLR) ligands influence the TI-2 antibody response not only by enhancing the overall magnitude but also by skewing this response to one that is dominated by IgG isotypes. Importantly, TLR ligands facilitate this response by inducing type I interferon (IFN), which in turn elicits rapid and significant amounts of antigen-specific IgG2c predominantly from FO (follicular) B cells. Furthermore, we show that although the IgG2c antibody response requires B cell–autonomous IFN-α receptor signaling, it is independent of B cell–intrinsic TLR signaling. Thus, innate signals have the capacity to enhance TI-2 antibody responses by promoting participation of FO B cells, which then elaborate effective IgG anti-pathogen antibodies.
ATM-deficient thymic lymphoma is associated with aberrant tcrd rearrangement and gene amplification
Authors: Zha Shan , Bassing Craig H. , Sanda Takaomi , Brush James W. , Patel Harin , Goff Peter H. , Murphy Michael M. , Tepsuporn Suprawee , Gatti Richard A. , Look A. Thomas , Alt Frederick W.
Published: June 2010

Ataxia telangiectasia mutated (ATM) deficiency predisposes humans and mice to T lineage lymphomas with recurrent chromosome 14 translocations involving the T cell receptor α/δ (Tcra/d) locus. Such translocations have been thought to result from aberrant repair of DNA double-strand breaks (DSBs) during Tcra locus V(D)J recombination, and to require the Tcra enhancer (Eα) for Tcra rearrangement or expression of the translocated oncogene. We now show that, in addition to the known chromosome 14 translocation, ATM-deficient mouse thymic lymphomas routinely contain a centromeric fragment of chromosome 14 that spans up to the 5′ boundary of the Tcra/d locus, at which position a 500-kb or larger region centromeric to Tcra/d is routinely amplified. In addition, they routinely contain a large deletion of the telomeric end of one copy of chromosome 12. In contrast to prior expectations, the recurrent translocations and amplifications involve V(D)J recombination–initiated breaks in the Tcrd locus, as opposed to the Tcra locus, and arise independently of the Eα. Overall, our studies reveal previously unexpected mechanisms that contribute to the oncogenic transformation of ATM-deficient T lineage cells.
Prolonged Colonization with the Methicillin-Resistant Staphylococcus aureus Strain USA300 among Residents of Extended Care Facilities
Authors: Shurland Simone M. , Stine O. Colin , Venezia Richard A. , Johnson Jennifer K. , Zhan Min , Furuno Jon P. , Miller Ram R. , Pelser Colleen , Roghmann Mary-Claire
Published: June 2010

We performed a retrospective cohort study (n = 129) to assess whether residents of extended care facilities who were initially colonized or infected with the methicillin-resistant Staphylococcus aureus (MRSA) strain USA300 were less likely to have prolonged colonization than were residents colonized or infected with other MRSA strains. We found no difference in prolonged colonization (adjusted odds ratio, 1.1 [95% confidence interval, 0.5–2.4]).
Transmission Route of Rhinovirus Type 39 in a Monodispersed Airborne Aerosol
Authors: Bischoff Werner E.
Published: June 2010

The common cold affects millions of people. Unfortunately, it remains unknown whether cold viruses enter the respiratory tract only through the nose and mouth or whether they can also enter through the tear ducts. Transocular exposure to an airborne infectious dose of human rhinovirus did not lead to infection.
ℬ(ℓ^{𝓅}) is never amenable
Authors: Runde Volker
Published: June 2010

We show that if

E
E

is a Banach space with a basis satisfying a certain condition, then the Banach algebra

ℓ
∞

(

K

(

ℓ
2

⊕
E
)
)

\ell ^\infty ({\mathcal K}(\ell ^2 \oplus E))

is not amenable; in particular, this is true for

E
=

ℓ
p

E = \ell ^p

with

p
∈
(
1
,
∞
)

p \in (1,\infty )

. As a consequence,

ℓ
∞

(

K

(
E
)
)

\ell ^\infty ({\mathcal K}(E))

is not amenable for any infinite-dimensional

L

p

{\mathcal L}^p

-space. This, in turn, entails the non-amenability of

B

(

ℓ
p

(
E
)
)

{\mathcal B}(\ell ^p(E))

for any

L

p

{\mathcal L}^p

-space

E
E

, so that, in particular,

B

(

ℓ
p

)

{\mathcal B}(\ell ^p)

and

B

(

L
p

[
0
,
1
]
)

{\mathcal B}(L^p[0,1])

are not amenable.
Noether-Lefschetz theory and the Yau-Zaslow conjecture
Authors: Klemm A. , Maulik D. , Pandharipande R. , Scheidegger E.
Published: June 2010

The Yau-Zaslow conjecture predicts the genus 0 curve counts of

K
3

K3

surfaces in terms of the Dedekind

η
\eta

function. The classical intersection theory of curves in the moduli of

K
3

K3

surfaces with Noether-Lefschetz divisors is related to 3-fold Gromov-Witten invariants via the

K
3

K3

curve counts. Results by Borcherds and Kudla-Millson determine these classical intersections in terms of vector-valued modular forms. Proven mirror transformations can often be used to calculate the 3-fold invariants which arise.

Via a detailed study of the STU model (determining special curves in the moduli of

K
3

K3

surfaces), we prove the Yau-Zaslow conjecture for all curve classes on

K
3

K3

surfaces. Two modular form identities are required. The first, the Klemm-Lerche-Mayr identity relating hypergeometric series to modular forms after mirror transformation, is proven here. The second, the Harvey-Moore identity, is proven by D. Zagier and presented in the paper.
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
Authors: Otto Thomas D. , Sanders Mandy , Berriman Matthew , Newbold Chris
Published: June 2010

Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy.

Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications.

Availability: The software is available at http://icorn.sourceforge.net

Contact:  tdo@sanger.ac.uk; cnewbold@hammer.imm.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis
Authors: Brunel Helena , Gallardo-Chacón Joan-Josep , Buil Alfonso , Vallverdú Montserrat , Soria José Manuel , Caminal Pere , Perera Alexandre
Published: June 2010

Motivation: Finding association between genetic variants and phenotypes related to disease has become an important vehicle for the study of complex disorders. In this context, multi-loci genetic association might unravel additional information when compared with single loci search. The main goal of this work is to propose a non-linear methodology based on information theory for finding combinatorial association between multi-SNPs and a given phenotype.

Results: The proposed methodology, called MISS (mutual information statistical significance), has been integrated jointly with a feature selection algorithm and has been tested on a synthetic dataset with a controlled phenotype and in the particular case of the F7 gene. The MISS methodology has been contrasted with a multiple linear regression (MLR) method used for genetic association in both, a population-based study and a sib-pairs analysis and with the maximum entropy conditional probability modelling (MECPM) method, which searches for predictive multi-locus interactions. Several sets of SNPs within the F7 gene region have been found to show a significant correlation with the FVII levels in blood. The proposed multi-site approach unveils combinations of SNPs that explain more significant information of the phenotype than their individual polymorphisms. MISS is able to find more correlations between SNPs and the phenotype than MLR and MECPM. Most of the marked SNPs appear in the literature as functional variants with real effect on the protein FVII levels in blood.

Availability: The code is available at http://sisbio.recerca.upc.edu/R/MISS_0.2.tar.gz

Contact:  helena.brunel@upc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Manipulation of FASTQ data with Galaxy
Authors: Blankenberg Daniel , Gordon Assaf , Von Kuster Gregory , Coraor Nathan , Taylor James , Nekrutenko Anton ,   the Galaxy Team
Published: June 2010

Summary: Here, we describe a tool suite that functions on all of the commonly known FASTQ format variants and provides a pipeline for manipulating next generation sequencing data taken from a sequencing machine all the way through the quality filtering steps.

Availability and Implementation: This open-source toolset was implemented in Python and has been integrated into the online data analysis platform Galaxy (public web access: http://usegalaxy.org; download: http://getgalaxy.org). Two short movies that highlight the functionality of tools described in this manuscript as well as results from testing components of this tool suite against a set of previously published files are available at http://usegalaxy.org/u/dan/p/fastq

Contact:  james.taylor@emory.edu; anton@bx.psu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System
Authors: Ondov Brian D. , Cochran Charles , Landers Mark , Meredith Gavin D. , Dudas Miroslav , Bergman Nicholas H.
Published: June 2010

Summary: Bisulfite sequencing allows cytosine methylation, an important epigenetic marker, to be detected via nucleotide substitutions. Since the Applied Biosystems SOLiD System uses a unique di-base encoding that increases confidence in the detection of nucleotide substitutions, it is a potentially advantageous platform for this application. However, the di-base encoding also makes reads with many nucleotide substitutions difficult to align to a reference sequence with existing tools, preventing the platform's potential utility for bisulfite sequencing from being realized. Here, we present SOCS-B, a reference-based, un-gapped alignment algorithm for the SOLiD System that is tolerant of both bisulfite-induced nucleotide substitutions and a parametric number of sequencing errors, facilitating bisulfite sequencing on this platform. An implementation of the algorithm has been integrated with the previously reported SOCS alignment tool, and was used to align CpG methylation-enriched Arabidopsis thaliana bisulfite sequence data, exhibiting a 2-fold increase in sensitivity compared to existing methods for aligning SOLiD bisulfite data.

Availability: Executables, source code, and sample data are available at http://solidsoftwaretools.com/gf/project/socs/

Contact:  bergmann@nbacc.net

Supplementary information:  Supplementary data are available at Bioinformatics online.
Hatha Yoga Practices: Energy Expenditure, Respiratory Changes and Intensity of Exercise
Authors: Ray Uday Sankar , Pathak Anjana , Tomer Omveer Singh
Published: June 2010

The aim of this study was to critically observe the energy expenditure, exercise intensity and respiratory changes during a full yoga practice session. Oxygen consumption (), carbon dioxide output (), pulmonary ventilation (E), respiratory rate (Fr) and tidal volume (VT), were measured in 16 physical posture (asanas), five yoga breathing maneuvers (BM) and two types of meditation. Twenty male (age 27.3 ± 3.5 years, height 166.6 ± 5.4 cm and body weight 58.8 ± 9.6 kg) yoga instructors were studied. Their maximal oxygen consumption () was recorded. The exercise intensity in asanas was expressed in percentage
. In asanas, exercise intensity varied from 9.9 to 26.5% of

. Highest energy cost was 3.02 kcal min-1. In BM highest E was 53.7 ± 15.5 l min-1. VT was 0.97 ± 0.59, 1.41 ± 1.27 and 1.28 ± l/breath with corresponding Fr of 14.0 ± 5.3, 10.0 ± 6.35, 10.0 ± 5.8 breaths/min. Average energy expenditure in asanas, BM and meditation were 2.29, 1.91 and 1.37 kcal min-1, respectively. Metabolic rate was generally in the range of 1‐2 metabolic equivalents (MET) except in three asanas where it was >2 MET.
was 0.27 ± 0.05 and 0.24 ± 0.04 l min-1 in meditation and Shavasana, respectively. Although yogic practices are low intensity exercises within lactate threshold, physical performance improvement is possible owing to both better economy of breathing by BM and also by improvement in cardiovascular reserve. Other factors such as psycho‐physiological and better relaxation may contribute to it.
Morphometric ratios of six commercially landed species of skate from the Portuguese continental shelf, and their utility for identification
Authors: Serra-Pereira Bárbara , Farias Inês , Moura Teresa , Gordo Leonel Serrano , Santos Miguel , Figueiredo Ivone
Published: June 2010

Serra-Pereira, B., Farias, I., Moura, T., Gordo, L. S., Santos, M., and Figueiredo, I. 2010. Morphometric ratios of six commercially landed species of skate from the Portuguese continental shelf, and their utility for identification. – ICES Journal of Marine Science, 67: 1596–1603. European skate landings have traditionally been reported under a generic landing category, because of problems with species identification. To address this data deficiency, the ICES Working Group on Elasmobranch Fishes compiled conversion factors, including the relationships between different body measurements, for the main elasmobranch species. Size conversion factors for six common NE Atlantic skate species, Leucoraja naevus, Raja brachyura, R. clavata, R. miraletus, R. montagui, and R. undulata are compiled, and the capability of morphometric data to assist species discrimination is evaluated, highlighting the case of similar species such as R. brachyura and R. montagui. The estimated size conversion factors displayed some variability between areas and sexes for most species, the allometric relationship between weight and total length did not differ significantly between sexes, and some morphometric ratios proved adequate in discriminating between rajid species (misclassification error 0.12). Leucoraja naevus was fully discriminated from the remaining species. Species with a similar dorsal colour, e.g. R. brachyura and R. montagui, showed good discrimination based on their morphometry, with just 6–11% misclassification between the two.
Biological parameters of immature, ripening, and non-reproductive, mature northeast Arctic cod in 1984–2006
Authors: Yaragina Natalia A.
Published: June 2010

Yaragina, N. A. 2010. Biological parameters of immature, ripening, and non-reproductive, mature northeast Arctic cod in 1984–2006. – ICES Journal of Marine Science, 67: 2033–2041. Russian samples of cod caught in the Barents Sea during November–February, the period of migration to the overwintering and spawning grounds, were re-analysed by grouping the maturity stages recorded in three classes: immature, ripening, and apparently mature fish, with gonads of uncertain status. When treated by age class and gender, these three classes were characterized by significant differences in size (length and weight) and condition (somatic and a liver index). Within an age group, the group with uncertain status was on average consistently larger than the ripening fish and the latter group was on average larger than the immature component. However, in terms of condition, fish of uncertain status resembled the immature fish. Males and females displayed very similar patterns, although the levels were consistently lower for the former. The patterns are consistent with the interpretation that the gonads of uncertain status represent non-reproductive, mature fish. At the population level, the percentage of mature fish that presumably skip spawning varied annually between 4 and 21%, but this has little effect on the perception of the overall development in spawning-stock biomass. No correlation was found between the non-reproductive fraction and environmental factors examined.
Isozoanthus primnoidus, a new species of zoanthid (Cnidaria: Zoantharia) associated with the gorgonian Callogorgia verticillata (Cnidaria: Alcyonacea)
Authors: Carreiro-Silva M. , Braga-Henriques A. , Sampaio I. , de Matos V. , Porteiro F. M. , Ocaña O.
Published: June 2010

Carreiro-Silva, M., Braga-Henriques, A., Sampaio, I., de Matos, V., Porteiro, F. M., and Ocaña, O. 2011. Isozoanthus primnoidus, a new species of zoanthid (Cnidaria: Zoantharia) associated with the gorgonian Callogorgia verticillata (Cnidaria: Alcyonacea). – ICES Journal of Marine Science, 68: 408–415. In the Azores, Northeast Atlantic, an undescribed epizoan zoanthid is often found in association with the cold-water gorgonian Callogorgia verticillata at 110–800 m depth. This zoanthid was identified as a new species, Isozoanthus primnoidus sp. nov., based on morphological and anatomical characters of the polyps and type of cnidae. The distinguishing features of I. primnoidus are coenenchyme, column, and oral disc light brown, with short, translucent tentacles. Contracted polyps have column diameter up to 3 mm and height up to 2 mm. Ectoderm and outer mesogloea are densely encrusted with mineral particles and gorgonian sclerites. Capitulum bears a maximum of 14 distinctive ridges. Isozoanthus primnoidus was associated with 17% of C. verticillata colonies studied, and covered 14 ± 5% of the gorgonian colony. There was strong evidence of a parasitic relationship whereby I. primoidus progressively eliminates gorgonian tissue and uses the gorgonian axis for structure and support, and sclerites for protection.
The effect of temporal changes in life-history traits on reproductive potential in an exploited population of Pacific cod, Gadus macrocephalus
Authors: Narimatsu Yoji , Ueda Yuji , Okuda Takehiro , Hattori Tsutomu , Fujiwara Kunihiro , Ito Masaki
Published: June 2010

Narimatsu, Y., Ueda, Y., Okuda, T., Hattori, T., Fujiwara, K., and Ito, M. 2010. The effect of temporal changes in life-history traits on reproductive potential in an exploited population of Pacific cod, Gadus macrocephalus. – ICES Journal of Marine Science, 67: 1659–1666. The population size of Pacific cod (Gadus macrocephalus) in the northeastern Pacific has fluctuated at high levels during the past 10 years, despite heavy exploitation from the juvenile stage. Annual changes in growth, age, and standard length (SL) at maturity, potential fecundity (PF), and total egg production are evaluated in relation to the population fluctuations. Most 4-year-old females were mature, and the SL at which 50% of 3-year-old females matured fluctuated very little over the years. However, the proportion of mature 3-year-old females varied significantly among years. The values of PF-at-age also varied among years and were explained by a model containing SL, condition factor, and oocyte diameter. The population size was negatively correlated with the proportion of mature females and the PF of females 3 years old, so the range of total egg production was smaller than that of spawning-stock biomasses. Eggs were produced mainly by young adults (3 and 4 years of age). The age of adult females did not affect recruitment success. It is suggested that plasticity of life-history traits allowed for compensation of total egg production and that the compensation contributed to maintaining the abundance of a population consisting mainly of young fish.
Circular Data in Political Science and How to Handle It
Authors: Gill Jeff , Hangartner Dominik
Published: June 2010

There has been no attention to circular (purely cyclical) data in political science research. We show that such data exist and are mishandled by models that do not take into account the inherently recycling nature of some phenomenon. Clock and calendar effects are the obvious cases, but directional data are observed as well. We describe a standard maximum likelihood regression modeling framework based on the von Mises distribution, then develop a general Bayesian regression procedure for the first time, providing an easy-to-use Metropolis-Hastings sampler for this approach. Applications include a chronographic analysis of U.S. domestic terrorism and directional party preferences in a two-dimensional ideological space for German Bundestag elections. The results demonstrate the importance of circular models to handle periodic and directional data in political science.
Reply to “Time is Not A Theoretical Variable”
Authors: Carter David B. , Signorino Curtis S.
Published: June 2010

We thank Neal Beck for his comments. In general, there is little difference in our theoretical and practical positions. We all agree that in some applications, time dummies can be problematic; controlling for temporal dependence is important for less-biased estimation of the coefficients on our substantive regressors; a smoothed function of time (whether via a cubic polynomial or spline) is a useful way to model temporal dependence in grouped binary data; and viewing the graph of the hazard can be informative.
Enhancement of Plant Metabolite Fingerprinting by Machine Learning
Authors: Scott Ian M. , Vermeer Cornelia P. , Liakata Maria , Corol Delia I. , Ward Jane L. , Lin Wanchang , Johnson Helen E. , Whitehead Lynne , Kular Baldeep , Baker John M. , Walsh Sean , Dave Anuja , Larson Tony R. , Graham Ian A. , Wang Trevor L. , King Ross D. , Draper John , Beale Michael H.
Published: June 2010

Metabolite fingerprinting of Arabidopsis (Arabidopsis thaliana) mutants with known or predicted metabolic lesions was performed by 1H-nuclear magnetic resonance, Fourier transform infrared, and flow injection electrospray-mass spectrometry. Fingerprinting enabled processing of five times more plants than conventional chromatographic profiling and was competitive for discriminating mutants, other than those affected in only low-abundance metabolites. Despite their rapidity and complexity, fingerprints yielded metabolomic insights (e.g. that effects of single lesions were usually not confined to individual pathways). Among fingerprint techniques, 1H-nuclear magnetic resonance discriminated the most mutant phenotypes from the wild type and Fourier transform infrared discriminated the fewest. To maximize information from fingerprints, data analysis was crucial. One-third of distinctive phenotypes might have been overlooked had data models been confined to principal component analysis score plots. Among several methods tested, machine learning (ML) algorithms, namely support vector machine or random forest (RF) classifiers, were unsurpassed for phenotype discrimination. Support vector machines were often the best performing classifiers, but RFs yielded some particularly informative measures. First, RFs estimated margins between mutant phenotypes, whose relations could then be visualized by Sammon mapping or hierarchical clustering. Second, RFs provided importance scores for the features within fingerprints that discriminated mutants. These scores correlated with analysis of variance F values (as did Kruskal-Wallis tests, true- and false-positive measures, mutual information, and the Relief feature selection algorithm). ML classifiers, as models trained on one data set to predict another, were ideal for focused metabolomic queries, such as the distinctiveness and consistency of mutant phenotypes. Accessible software for use of ML in plant physiology is highlighted.
DTH8 Suppresses Flowering in Rice, Influencing Plant Height and Yield Potential Simultaneously
Authors: Wei Xiangjin , Xu Junfeng , Guo Hongnian , Jiang Ling , Chen Saihua , Yu Chuanyuan , Zhou Zhenling , Hu Peisong , Zhai Huqu , Wan Jianmin
Published: June 2010

The three most important agronomic traits of rice (Oryza sativa), yield, plant height, and flowering time, are controlled by many quantitative trait loci (QTLs). In this study, a newly identified QTL, DTH8 (QTL for days to heading on chromosome 8), was found to regulate these three traits in rice. Map-based cloning reveals that DTH8 encodes a putative HAP3 subunit of the CCAAT-box-binding transcription factor and the complementary experiment increased significantly days to heading, plant height, and number of grains per panicle in CSSL61 (a chromosome segment substitution line that carries the nonfunctional DTH8 allele) with the Asominori functional DTH8 allele under long-day conditions. DTH8 is expressed in most tissues and its protein is localized to the nucleus exclusively. The quantitative real-time PCR assay revealed that DTH8 could down-regulate the transcriptions of Ehd1 (for Early heading date1) and Hd3a (for Heading date3a; a rice ortholog of FLOWERING LOCUS T) under long-day conditions. Ehd1 and Hd3a can also be down-regulated by the photoperiodic flowering genes Ghd7 and Hd1 (a rice ortholog of CONSTANS). Meanwhile, the transcription of DTH8 has been proved to be independent of Ghd7 and Hd1, and the natural mutation of this gene caused weak photoperiod sensitivity and shorter plant height. Taken together, these data indicate that DTH8 probably plays an important role in the signal network of photoperiodic flowering as a novel suppressor as well as in the regulation of plant height and yield potential.
Political Variables in Cross‐country Growth Analysis
Authors: Brunetti Aymo
Published: June 2010

The recent boom in cross‐country growth analysis has renewed the empirical interest in political sources of economic growth. A large number of studies have tested political variables in growth regressions and a very heterogenous set of variables has been proposed to measure economically relevant differences in the political systems of countries. This paper distinguishes five categories of relevant political variables: democracy, government stability, political violence, policy volatility, and subjective perception of politics. For each of these categories, the specification, testing method, and results of the most relevant studies are presented and are critically discussed. The paper concludes that measures of democracy are least successful and measures of policy volatility and subjective perception of politics most successful as explanatory variables in cross‐country growth regressions.
Learning and Bounded Rationality
Authors: Williamson Paul
Published: June 2010

Sargent, Thomas J., Bounded Rationality in Economics

Kirkman, Alan and Salmon, Mark, Learning and Rationality in Economics
Technological Diffusion: Alternative Theories and Historical Evidence
Authors: Sarkar Jayati
Published: June 2010

This paper presents an interpretive survey of the neoclassical and evolutionary approaches to modeling the process of technological diffusion, with an orientation that is distinct in two important respects from existing surveys. First, the present survey is designed to provide a comparative overview of the alternative approaches within a unified framework of analysis. The objective is to bring out the areas of convergence as well as divergence between the approaches, and address the issue of whether the approaches could be considered as complementary rather than as alternatives. Second, the survey attempts to link the theoretical methodologies to the variety of empirical and historical evidence, and evaluate how the theories best fit the evidence on the dynamics of the technological diffusion process.
The Distributional Effects of Public Expenditure
Authors: Schwartz Gerd , Ter‐Minassian Teresa
Published: June 2010

It is commonly agreed that economic policies, including budgetary policies, can have potentially strong distributional effects. Traditional economic analysis held that economic policies affected the income distribution primarily through their impact on the rate of growth. More recently, it has come to be recognised that qualitative aspects of economic growth are probably more important than the rate of growth itself. While recent research has confirmed the potential role of expenditure policies as a redistributive tool, it has also shown that redistribution does not necessarily have to come at the expense of economic growth and efficiency. Although there are substantial analytical and technical problems to be faced in the design of equitable and cost‐effective public expenditure programmes, unfavourable distributional outcomes of these programmes can usually be traced more to political and institutional pressures than to purely technical factors. JEL Classification number: H5
Unique strategies for therapeutic gene transfer in haemophilia A and haemophilia B. WFH State‐of‐the‐Art Session on Therapeutic Gene Transfer Buenos Aires, Argentina
Authors: MONTGOMERY R. R. , MONAHAN P. E. , OZELO M. C.
Published: June 2010

Summary.  Gene therapy of haemophilia has been initiated through a number of approaches including expression in muscle, liver and omental implanted fibroblasts, or i.v. injection of an expression construct under the control of a ubiquitous promoter. In all these approaches, the goal was to have factor VIII (FVIII) or factor IX (FIX) synthesized so that it restored the levels of the missing protein in blood. The three talks in this session are totally, or at least in part, directed at strategies that may be clinically effective even in the absence of correction of the missing plasma clotting factor, although the haematopoietic stem cell or blood outgrowth endothelial cell therapy could achieve plasma correction as well. Two of the approaches achieve localized coagulation factor expression without necessarily correcting the systemic defect – one is with synthesis of FVIII or FIX within the joint space and the other is with the local release of FVIII (or FIX) by platelets at the site of vascular injury. All of the three approaches have demonstrated efficacy in small animal models and are now the subject of larger animal studies. None has yet to progress to human trials.
The application of genetics to inherited bleeding disorders
Authors: JAMES P. , DI PAOLA J.
Published: June 2010

Summary.  Most bleeding disorders encountered in clinical practice will be diagnosed, at least initially, by phenotypic assays. However, since the characterization of the genes that encode coagulation factors in the 1980s, significant progress has been made in translating this knowledge for diagnostic and therapeutic purposes. For the haemophilias, in particular, molecular genetic testing to determine carrier status, prenatal diagnosis and prediction of the likelihood of inhibitor development has now become an established component of comprehensive clinical management. For von Willebrand’s disease (VWD), significant recent advances have allowed for the establishment of genotype–phenotype correlations that have improved our understanding of the disease. The availability of high density single nucleotide polymorphism (SNP) maps will allow investigators to probe the genetic basis of the general symptoms of bleeding and bruising using a comprehensive genome‐wide approach. This article will review the state‐of‐the‐art for molecular diagnostics for both haemophilia and VWD and will end with a discussion of plans for an international genome‐wide association study (GWAS) designed to improve our understanding of blood coagulation.
Considerations in the laboratory assessment of haemostasis
Authors: McCRAW A. , HILLARP A. , ECHENAGUCIA M.
Published: June 2010

Summary.  This review outlines a number of key issues when performing laboratory testing of homeostasis. The effect pre‐analytical variables have on the reliability and consistency of screening tests is often forgotten due to a lack of understanding and awareness. This can be improved through educating healthcare professionals who are involved in taking blood for assessment. Recent advances in coagulation testing have not enabled laboratories to replace the Prothrombin Time (PT) and Activated Partial Thromboplastin Time (APTT) screening tests with more advanced assays and they continue to play an important role with the advantage of being easily automated. However, there are many analysers on the market, each with varying sensitivity to coagulation defects and it is important to keep this in mind when interpreting results.
Tests of global haemostasis and their applications in bleeding disorders
Authors: NAIR S. C. , DARGAUD Y. , CHITLUR M. , SRIVASTAVA A.
Published: June 2010

Summary.  There is a potential for significant paradigm shift in the assessment of haemostasis from the conventional plasma recalcification times, such as prothrombin time (PT) and activated partial thromboplastin time (APTT), which correspond to artificially created compartments of haemostasis to tests that assess the entire process in a more physiological and holistic manner. These include the thrombin generation test, thromboelastogram and the clot wave form analysis. While these tests have been described many years ago, there is renewed interest in their use with modified technology for assessing normal haemostasis and its disorders. Although early data suggest that they can provide much greater information regarding the overall haemostasis process and its disorders, many challenges remain. Some of them are possible only on instruments that are proprietary technology, expensive and are not widely available. Furthermore, these tests need to be standardized with regard to their reagents, methodology and interpretation, and finally, much more data need to be collected regarding clinical correlations with the parameters measured.
State‐of‐the‐art imaging techniques for the evaluation of haemophilic arthropathy: present and future
Authors: DORIA A. S.
Published: June 2010

Summary.  In spite of the fact that the diagnosis of haemophilia is essentially clinical and laboratory‐based, imaging has become an important tool for the evaluation of complications, diagnostic confirmation and/or complementation and therapeutic follow‐up in haemophilic arthropathy. Radiography remains the workforce horse in the diagnosis and follow‐up of haemophilic arthropathy. The radiographical findings in arthropathy follow an expected sequence of events and are overall similar in different joints. Magnetic resonance imaging (MRI) has advantages over radiography based on its capability of visualizing soft tissue and cartilage changes in haemophilic joints. The recent development and standardization of MRI scoring systems for measuring soft tissue and cartilage abnormalities may enable the comparison of pathological joint findings in clinical trials conducted at different institutions across the world. The implementation of high‐frequency transducers and colour/power Doppler capabilities has provided new insights for clinical applications of ultrasonography (US) in haemophilic arthropathy. In spite of the imaging modality's technical challenges such as operator‐dependency, US has advantages over MRI. One of these advantages is its ability of differentiating synovium hypertrophy and hemosiderin deposition, which is not possible with MRI given the presence of susceptibility artefacts from extracellular hemosiderin on gradient‐echo MR images. In addition to the aforementioned conventional imaging modalities, novel imaging techniques (blood oxygen level dependent, ultrasmall superparamagnetic iron‐oxide contrast‐enhanced, and T1 and T2 mapping MRI, ultrasound biomicroscopy, microbubble contrast‐enhanced US and positron emission tomography, among others) hold promise for early assessment of haemophilic arthropathy in the future upon completion of their clinical validation.
Electrotherapy: yesterday, today and tomorrow
Authors: TIKTINSKY R. , CHEN L. , NARAYAN P.
Published: June 2010

Summary.  The use of electrotherapy has been part of physical therapy treatment for the past few decades. There have been numerous modalities used such as TENS, interferential, diathermy, magnetic therapy, ultrasound, laser and surface electromyography to name a few. There has been an upsurge in the past decade of new and innovative modalities. There needs to be extensive research on each of these electrotherapy devices to determine the proper use of each device.
Vascular haemostasis
Authors: KEY N. S. , DE PAEPE A. , MALFAIT F. , SHOVLIN C. L.
Published: June 2010

Summary.  While the majority of this session will deal with selected inherited vascular abnormalities that may manifest as a haemorrhagic disorder, the initial discussion by Dr Key will focus on the interplay between the vessel wall and components of the coagulation system, with a focus on haemophilia A and B. Although it is generally accepted that physiological haemostasis is triggered by contact of blood with tissue factor (TF), there remains some controversy regarding the cellular origin of TF in vivo. In addition, the initiation and propagation of thrombin generation are highly dependent on the balance of pro‐ and anticoagulant functions of endothelium, a profile that varies significantly throughout the vasculature. Drs De Paepe and Malfait address heritable collagen disorders such as the Ehlers–Danlos syndromes (EDS), a heterogeneous group of diseases involving the skin, ligaments and joints, blood vessels and internal organs. Most EDS subtypes are caused by mutations in genes encoding fibrillar collagens, or in genes coding for enzymes involved in posttranslational modifications of collagens. Accurate biochemical and molecular testing is now available for most EDS subtypes and can direct genetic counselling and medical management for these disorders. Dr Shovlin reviews recent developments in hereditary haemorrhagic telengiectasia (HHT), a frequently undiagnosed disorder characterized by arteriovenous malformations in multiple organs. These abnormal blood vessels are the result of mutations in one of a number of genes whose protein products influence TGF‐beta signalling in vascular endothelial cells. Several HHT management guidelines have been published and are discussed.
Inherited disorders of platelet function and challenges to diagnosis of mucocutaneous bleeding
Authors: ISRAELS S. J. , EL‐EKIABY M. , QUIROGA T. , MEZZANO D.
Published: June 2010

Summary.  Platelets play a pivotal role in the arrest of bleeding at sites of vascular injury. Following endothelial damage, they respond rapidly by adhesion to subendothelial matrix proteins resulting in platelet activation, spreading, aggregation, secretion and recruitment of additional platelets to form the primary haemostatic plug. This mass provides a surface for thrombin generation and fibrin mesh formation that stabilizes the clot. Careful study of patients with inherited platelet disorders and, subsequently, of informative animal models, has identified structural platelet abnormalities that have enhanced our understanding of platelet function. The investigations of rare, but severe, inherited platelet disorders have led us to the discovery of causative molecular defects. One of the most informative is the rare autosomal recessive disorder Glanzmann thrombasthenia, caused by defect or deficiency in the platelet integrin αIIbβ3, resulting in absent platelet aggregation and a significant clinical bleeding diathesis. Our new challenge is to understand the mechanisms underlying more common, but less well‐defined, mucocutaneous bleeding (MCB) disorders. Present diagnostic testing for platelet function disorders and von Willebrand’s Disease often fails to identify the cause of bleeding in individuals with inherited MCB.