bluuebunny/crossref_metadata_2025 huggingface dataset:
Camouflaged or tanned: plasticity in freshwater snail pigmentation
Authors: Ahlgren Johan , Yang Xi , Hansson Lars-Anders , Brönmark Christer
Published: September 2013

By having phenotypically plastic traits, many organisms optimize their fitness in response to fluctuating threats. Freshwater snails with translucent shells, e.g. snails from the
Radix
genus, differ considerably in their mantle pigmentation patterns, with snails from the same water body ranging from being completely dark pigmented to having only a few dark patterns. These pigmentation differences have previously been suggested to be genetically fixed, but we propose that this polymorphism is owing to phenotypic plasticity in response to a fluctuating environment. Hence, we here aimed to assess whether common stressors, including ultraviolet radiation (UVR) and predation, induce a plastic response in mantle pigmentation patterns of
Radix balthica
. We show, in contrast to previous studies, that snails are plastic in their expression of mantle pigmentation in response to changes in UVR and predator threats, i.e. differences among populations are not genetically fixed. When exposed to cues from visually hunting fish,
R. balthica
increased the proportion of their dark pigmentation, suggesting a crypsis strategy. Snails increased their pigmentation even further in response to UVR, but this also led to a reduction in pattern complexity. Furthermore, when exposed to UVR and fish simultaneously, snails responded in the same way as in the UVR treatment, suggesting a trade-off between photoprotection and crypsis.
The molecular signal for the adaptation to cold temperature during early life on Earth
Authors: Groussin Mathieu , Boussau Bastien , Charles Sandrine , Blanquart Samuel , Gouy Manolo
Published: September 2013

Several lines of evidence such as the basal location of thermophilic lineages in large-scale phylogenetic trees and the ancestral sequence reconstruction of single enzymes or large protein concatenations support the conclusion that the ancestors of the bacterial and archaeal domains were thermophilic organisms which were adapted to hot environments during the early stages of the Earth. A parsimonious reasoning would therefore suggest that the last universal common ancestor (LUCA) was also thermophilic. Various authors have used branch-wise non-homogeneous evolutionary models that better capture the variation of molecular compositions among lineages to accurately reconstruct the ancestral G + C contents of ribosomal RNAs and the ancestral amino acid composition of highly conserved proteins. They confirmed the thermophilic nature of the ancestors of Bacteria and Archaea but concluded that LUCA, their last common ancestor, was a mesophilic organism having a moderate optimal growth temperature. In this letter, we investigate the unknown nature of the phylogenetic signal that informs ancestral sequence reconstruction to support this non-parsimonious scenario. We find that rate variation across sites of molecular sequences provides information at different time scales by recording the oldest adaptation to temperature in slow-evolving regions and subsequent adaptations in fast-evolving ones.
An energetic model for macromolecules unfolding in stretching experiments
Authors: De Tommasi D. , Millardi N. , Puglisi G. , Saccomandi G.
Published: September 2013

We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, to describe the unfolding of multi-domain macromolecules (proteins, silks, polysaccharides, nanopolymers). The model is fully analytical and enlightens the role of the different energetic components regulating the unfolding evolution. As an explicit example, we compare the analytical results with a titin atomic force microscopy stretch-induced unfolding experiment showing the ability of the model to quantitatively reproduce the experimental behaviour. In the thermodynamic limit, the sawtooth force–elongation unfolding curve degenerates to a constant force unfolding plateau.
Use of kernel-based Bayesian models to predict late osteolysis after hip replacement
Authors: Aram P. , Kadirkamanathan V. , Wilkinson J. M.
Published: September 2013

We studied the relationship between osteolysis and polyethylene wear, age at surgery, body mass index and height in 463 subjects (180 osteolysis and 283 controls) after cemented Charnley total hip arthroplasty (THA), in order to develop a kernel-based Bayesian model to quantitate risk of osteolysis. Such tools may be integrated into decision-making algorithms to help personalize clinical decision-making. A predictive model was constructed, and the estimated posterior probability of the implant failure calculated. Annual wear provided the greatest discriminatory information. Age at surgery provided additional predictive information and was added to the model. Body mass index and height did not contain valuable discriminatory information over the range in which observations were densely sampled. The robustness and misclassification rate of the predictive model was evaluated by a five-times cross-validation method. This yielded a 70% correct predictive classification of subjects into osteolysis versus non-osteolysis groups at a mean of 11 years after THA. Finally, the data were divided into male and female subsets to further explore the relationship between wear rate, age at surgery and incidence of osteolysis. The correct classification rate using age and wear rate in the model was approximately 66% for males and 74% for females.
The locking-decoding frontier for generic dynamics
Authors: Dupuis Frédéric , Florjanczyk Jan , Hayden Patrick , Leung Debbie
Published: September 2013

It is known that the maximum classical mutual information, which can be achieved between measurements on pairs of quantum systems, can drastically underestimate the quantum mutual information between them. In this article, we quantify this distinction between classical and quantum information by demonstrating that after removing a logarithmic-sized quantum system from one half of a pair of perfectly correlated bitstrings, even the most sensitive pair of measurements might yield only outcomes essentially independent of each other. This effect is a form of information locking but the definition we use is strictly stronger than those used previously. Moreover, we find that this property is generic, in the sense that it occurs when removing a random subsystem. As such, the effect might be relevant to statistical mechanics or black hole physics. While previous works had always assumed a uniform message, we assume only a min-entropy bound and also explore the effect of entanglement. We find that classical information is strongly locked almost until it can be completely decoded. Finally, we exhibit a quantum key distribution protocol that is ‘secure’ in the sense of accessible information but in which leakage of even a logarithmic number of bits compromises the secrecy of all others.
Forced cubic Schrödinger equation with Robin boundary data: large-time asymptotics
Authors: Kaikina Elena I.
Published: September 2013

We consider the initial-boundary-value problem for the cubic nonlinear Schrödinger equation, formulated on a half-line with inhomogeneous Robin boundary data. We study traditionally important problems of the theory of nonlinear partial differential equations, such as the global-in-time existence of solutions to the initial-boundary-value problem and the asymptotic behaviour of solutions for large time.
Determining the effects of surface elasticity and surface stress by measuring the shifts of resonant frequencies
Authors: Zhang Y. , Zhuo L. J. , Zhao H. S.
Published: September 2013

Both surface elasticity and surface stress can result in changes of resonant frequencies of a micro/nanostructure. There are infinite combinations of surface elasticity and surface stress that can cause the same variation for one resonant frequency. However, as shown in this study, there is only one combination resulting in the same variations for two resonant frequencies, which thus provides an efficient and practical method of determining the effects of both surface elasticity and surface stress other than an atomistic simulation. The errors caused by the different models of surface stress and mode shape change due to axial loading are also discussed.
Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting
Authors: Friedman Matt , Keck Benjamin P. , Dornburg Alex , Eytan Ron I. , Martin Christopher H. , Hulsey C. Darrin , Wainwright Peter C. , Near Thomas J.
Published: September 2013

Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (
ca
135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene (
ca
65–57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography.
Classification of grass pollen through the quantitative analysis of surface ornamentation and texture
Authors: Mander Luke , Li Mao , Mio Washington , Fowlkes Charless C. , Punyasena Surangi W.
Published: September 2013

Taxonomic identification of pollen and spores uses inherently qualitative descriptions of morphology. Consequently, identifications are restricted to categories that can be reliably classified by multiple analysts, resulting in the coarse taxonomic resolution of the pollen and spore record. Grass pollen represents an archetypal example; it is not routinely identified below family level. To address this issue, we developed quantitative morphometric methods to characterize surface ornamentation and classify grass pollen grains. This produces a means of quantifying morphological features that are traditionally described qualitatively. We used scanning electron microscopy to image 240 specimens of pollen from 12 species within the grass family (Poaceae). We classified these species by developing algorithmic features that quantify the size and density of sculptural elements on the pollen surface, and measure the complexity of the ornamentation they form. These features yielded a classification accuracy of 77.5%. In comparison, a texture descriptor based on modelling the statistical distribution of brightness values in image patches yielded a classification accuracy of 85.8%, and seven human subjects achieved accuracies between 68.33 and 81.67%. The algorithmic features we developed directly relate to biologically meaningful features of grass pollen morphology, and could facilitate direct interpretation of unsupervised classification results from fossil material.
Presence of subclinical infection in gene-targeted human prion protein transgenic mice exposed to atypical bovine spongiform encephalopathy
Authors: Wilson Rona , Dobie Karen , Hunter Nora , Casalone Cristina , Baron Thierry , Barron Rona M.
Published: September 2013

The transmission of bovine spongiform encephalopathy (BSE) to humans, leading to variant Creutzfeldt–Jakob disease has demonstrated that cattle transmissible spongiform encephalopathies (TSEs) can pose a risk to human health. Until recently, TSE disease in cattle was thought to be caused by a single agent strain, BSE, also known as classical BSE, or BSE-C. However, due to the initiation of a large-scale surveillance programme throughout Europe, two atypical BSE strains, bovine amyloidotic spongiform encephalopathy (BASE, also named BSE-L) and BSE-H have since been discovered. To model the risk to human health, we previously inoculated these two forms of atypical BSE (BASE and BSE-H) into gene-targeted transgenic (Tg) mice expressing the human prion protein (PrP) (HuTg) but were unable to detect any signs of TSE pathology in these mice. However, despite the absence of TSE pathology, upon subpassage of some BASE-challenged HuTg mice, a TSE was observed in recipient gene-targeted bovine PrP Tg (Bov6) mice but not in HuTg mice. Disease transmission from apparently healthy individuals indicates the presence of subclinical BASE infection in mice expressing human PrP that cannot be identified by current diagnostic methods. However, due to the lack of transmission to HuTg mice on subpassage, the efficiency of mouse-to-mouse transmission of BASE appears to be low when mice express human rather than bovine PrP.
The human immunodeficiency virus type 1 Vpr protein upregulates PVR via activation of the ATR-mediated DNA damage response pathway
Authors: Vassena Lia , Giuliani Erica , Matusali Giulia , Cohen Éric A. , Doria Margherita
Published: September 2013

Viral infection may induce the cell-surface expression of PVR (CD155) that, upon recognition by its cognate activating DNAM-1 receptor present on cytotoxic lymphocytes, may promote antiviral immune responses. Here we show that expression of the human immunodeficiency virus type 1 (HIV-1) Vpr protein in Jurkat T cells increases cell-surface and total PVR levels. Analysis of mutated Vpr variants indicated that Vpr uses the same protein surfaces, and hence probably the same mechanisms, to upregulate PVR and arrest the cell cycle in the G2 phase. Moreover, we found that PVR upregulation by Vpr relied on the ability of the protein to activate the ATR kinase that triggers the DNA damage response pathway and G2 arrest. Finally, we showed that Vpr contributes to PVR up-modulation in HIV-infected CD4+ T lymphocytes and inhibits the PVR downregulating activity of the viral Nef protein.
Nucleo-cytoplasmic shuttling of VPg encoded by Wheat yellow mosaic virus requires association with the coat protein
Authors: Sun Liying , Jing Bian , Andika Ida Bagus , Hu Yingchun , Sun Bingjian , Xiang Rong , Kondo Hideki , Chen Jianping
Published: September 2013

VPg (virus protein, genome-linked) is a multifunctional protein that plays important roles in viral multiplication in the cytoplasm. However, a number of VPgs encoded by plant viruses target the nucleus and this appears to be biologically significant. These VPgs may therefore be translocated between nuclear and cytoplasmic compartments during virus infection, but such nucleo-cytoplasmic transport has not been demonstrated. We report that VPg encoded by Wheat yellow mosaic virus (WYMV, genus Bymovirus, family Potyviridae) accumulated in both the nucleus and cytoplasm of infected cells, but localized exclusively in the nucleus when expressed alone in plants. Computational analyses predicted the presence of a nuclear localization signal (NLS) and a nuclear export signal (NES) in WYMV VPg. Mutational analyses showed that both the N-terminal and the NLS domains of VPg contribute to the efficiency of nuclear targeting. In vitro and in planta assays indicated that VPg interacts with WYMV coat protein (CP) and proteinase 1 (P1) proteins. Observation of VPg fused to a fluorescent protein and subcellular fractionation experiments showed that VPg was translocated to the cytoplasm when co-expressed with CP, but not with P1. Mutations in the NES domain or treatment with leptomycin B prevented VPg translocation to the cytoplasm when co-expressed with CP. Our results suggest that association with CP facilitates the nuclear export of VPg during WYMV infection.
Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies
Authors: Martin Simon H. , Dasmahapatra Kanchon K. , Nadeau Nicola J. , Salazar Camilo , Walters James R. , Simpson Fraser , Blaxter Mark , Manica Andrea , Mallet James , Jiggins Chris D.
Published: September 2013

Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting the extent and timing of admixture between diverging species can clarify the role of geographic isolation in speciation. Here we use new methodology to quantify admixture at different stages of divergence inHeliconiusbutterflies, based on whole-genome sequences of 31 individuals. Comparisons between sympatric and allopatric populations ofH. melpomene,H. cydno, andH. timaretarevealed a genome-wide trend of increased shared variation in sympatry, indicative of pervasive interspecific gene flow. Up to 40% of 100-kb genomic windows clustered by geography rather than by species, demonstrating that a very substantial fraction of the genome has been shared between sympatric species. Analyses of genetic variation shared over different time intervals suggested that admixture between these species has continued since early in speciation. Alleles shared between species during recent time intervals displayed higher levels of linkage disequilibrium than those shared over longer time intervals, suggesting that this admixture took place at multiple points during divergence and is probably ongoing. The signal of admixture was significantly reduced around loci controlling divergent wing patterns, as well as throughout the Z chromosome, consistent with strong selection for Müllerian mimicry and with known Z-linked hybrid incompatibility. Overall these results show that species divergence can occur in the face of persistent and genome-wide admixture over long periods of time.
A Kinetic Analysis of the Auxin Transcriptome Reveals Cell Wall Remodeling Proteins That Modulate Lateral Root Development inArabidopsis
Authors: Lewis Daniel R. , Olex Amy L. , Lundy Stacey R. , Turkett William H. , Fetrow Jacquelyn S. , Muday Gloria K.
Published: September 2013

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction. Several clusters were enriched with genes encoding proteins involved in cell wall modification, opening the possibility for understanding mechanistic details of cell structural changes that result in root formation following auxin treatment. Mutants with insertions in 72 genes annotated with a cell wall remodeling function were examined for alterations in IAA-regulated root growth and development. This reverse-genetic screen yielded eight mutants with root phenotypes. Detailed characterization of seedlings with mutations in CELLULASE3/GLYCOSYLHYDROLASE9B3 and LEUCINE RICH EXTENSIN2, genes not normally linked to auxin response, revealed defects in the early and late stages of lateral root development, respectively. The genes identified here using kinetic insight into expression changes lay the foundation for mechanistic understanding of auxin-mediated cell wall remodeling as an essential feature of lateral root development.
Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis
Authors: Lowry David B. , Logan Tierney L. , Santuari Luca , Hardtke Christian S. , Richards James H. , DeRose-Wilson Leah J. , McKay John K. , Sen Saunak , Juenger Thomas E.
Published: September 2013

The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression.
The Membrane-Bound NAC Transcription Factor ANAC013 Functions in Mitochondrial Retrograde Regulation of the Oxidative Stress Response in Arabidopsis
Authors: De Clercq Inge , Vermeirssen Vanessa , Van Aken Olivier , Vandepoele Klaas , Murcha Monika W. , Law Simon R. , Inzé Annelies , Ng Sophia , Ivanova Aneta , Rombaut Debbie , van de Cotte Brigitte , Jaspers Pinja , Van de Peer Yves , Kangasjärvi Jaakko , Whelan James , Van Breusegem Frank
Published: September 2013

Upon disturbance of their function by stress, mitochondria can signal to the nucleus to steer the expression of responsive genes. This mitochondria-to-nucleus communication is often referred to as mitochondrial retrograde regulation (MRR). Although reactive oxygen species and calcium are likely candidate signaling molecules for MRR, the protein signaling components in plants remain largely unknown. Through meta-analysis of transcriptome data, we detected a set of genes that are common and robust targets of MRR and used them as a bait to identify its transcriptional regulators. In the upstream regions of these mitochondrial dysfunction stimulon (MDS) genes, we found a cis-regulatory element, the mitochondrial dysfunction motif (MDM), which is necessary and sufficient for gene expression under various mitochondrial perturbation conditions. Yeast one-hybrid analysis and electrophoretic mobility shift assays revealed that the transmembrane domain–containing NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON transcription factors (ANAC013, ANAC016, ANAC017, ANAC053, and ANAC078) bound to the MDM  cis-regulatory element. We demonstrate that ANAC013 mediates MRR-induced expression of the MDS genes by direct interaction with the MDM  cis-regulatory element and triggers increased oxidative stress tolerance. In conclusion, we characterized ANAC013 as a regulator of MRR upon stress in Arabidopsis thaliana.
Risk of retained placenta in women previously delivered by caesarean section: a population‐based cohort study
Authors: Belachew J , Cnattingius S , Mulic‐Lutvica A , Eurenius K , Axelsson O , Wikström AK
Published: September 2013

Objective

To evaluate whether women with a caesarean section at their first delivery have an increased risk of retained placenta at their second delivery.

Design

Population‐based cohort study.

Setting

Sweden.

Population

All women with their first and second singleton deliveries in Sweden during the years 1994–2006 (n = 258 608). Women with caesarean section or placental abruption in their second pregnancy were not included in the study population.

Methods

The risk of retained placenta at second delivery was estimated for women with a first delivery by caesarean section (n = 19 458), using women with a first vaginal delivery as reference (n = 239 150). Risks were calculated as odds ratios by unconditional logistic regression analysis with 95% confidence intervals (95%) after adjustments for maternal, delivery, and infant characteristics.

Main outcome measures

Retained placenta with normal (≤1000 ml) and heavy (>1000 ml) bleeding.

Results

The overall rate of retained placenta was 2.07%. In women with a previous caesarean section and in women with previous vaginal delivery, the corresponding rates were 3.44% and 1.96%, respectively. Compared with women with a previous vaginal delivery, women with a previous caesarean section had an increased risk of retained placenta (adjusted OR 1.45; 95% CI 1.32–1.59), and the association was more pronounced for retained placenta with heavy bleeding (adjusted OR 1.61; 95% CI 1.44–1.79).

Conclusions

Our report shows an increased risk for retained placenta in women previously delivered by caesarean section, a finding that should be considered in discussions of mode of delivery.
Intrapartum management of trial of labour after caesarean delivery: evidence and experience
Authors: Scott JR
Published: September 2013

Few studies have focused specifically on the intrapartum management of patients following a prior caesarean delivery. Contemporary assessments and recommendations on attempting vaginal birth after caesarean delivery (VBAC) vary. The actual conduct of labour and delivery of the infant in an uncomplicated trial of labour after caesarean (TOLAC) is similar to the management of a patient without a previous caesarean. Intrapartum management of TOLAC differs primarily in the need for caution with induction of labour in women with an unfavourable cervix, the avoidance of overstimulation with oxytocin augmentation, and surveillance for prompt recognition of the rare case of uterine rupture.
The Threat of Disease Increases as Species Move Toward Extinction
Authors: HEARD MATTHEW J. , SMITH KATHERINE F. , RIPP KELSEY J. , BERGER MELANIE , CHEN JANE , DITTMEIER JUSTIN , GOTER MAGGIE , MCGARVEY STEPHEN T. , RYAN ELIZABETH
Published: September 2013

At local scales, infectious disease is a common driver of population declines, but globally it is an infrequent contributor to species extinction and endangerment. For species at risk of extinction from disease important questions remain unanswered, including when does disease become a threat to species and does it co‐occur, predictably, with other threats? Using newly compiled data from the International Union for Conservation of Nature (IUCN) Red List, we examined the relative role and co‐occurrence of threats associated with amphibians, birds, and mammals at 6 levels of extinction risk (i.e., Red List status categories: least concern, near threatened, vulnerable, endangered, critically endangered, and extinct in the wild/extinct). We tested the null hypothesis that the proportion of species threatened by disease is the same in all 6 Red List status categories. Our approach revealed a new method for determining when disease most frequently threatens species at risk of extinction. The proportion of species threatened by disease varied significantly between IUCN status categories and linearly increased for amphibians, birds, and all species combined as these taxa move from move from least concern to critically endangered. Disease was infrequently the single contributing threat. However, when a species was negatively affected by a major threat other than disease (e.g., invasive species, land‐use change) that species was more likely to be simultaneously threatened by disease than species that had no other threats. Potential drivers of these trends include ecological factors, clustering of phylogenetically related species in Red List status categories, discovery bias among species at greater risk of extinction, and availability of data. We echo earlier calls for baseline data on the presence of parasites and pathogens in species when they show the first signs of extinction risk and arguably before.

La Amenaza de Enfermedades Incrementa a Medida que las Especies se Aproximan a la Extinción
Use of Inverse Spatial Conservation Prioritization to Avoid Biological Diversity Loss Outside Protected Areas
Authors: KAREKSELA SANTTU , MOILANEN ATTE , TUOMINEN SEPPO , KOTIAHO JANNE S.
Published: September 2013

Globally expanding human land use sets constantly increasing pressure for maintenance of biological diversity and functioning ecosystems. To fight the decline of biological diversity, conservation science has broken ground with methods such as the operational model of systematic conservation planning (SCP), which focuses on design and on‐the‐ground implementation of conservation areas. The most commonly used method in SCP is reserve selection that focuses on the spatial design of reserve networks and their expansion. We expanded these methods by introducing another form of spatial allocation of conservation effort relevant for land‐use zoning at the landscape scale that avoids negative ecological effects of human land use outside protected areas. We call our method inverse spatial conservation prioritization. It can be used to identify areas suitable for economic development while simultaneously limiting total ecological and environmental effects of that development at the landscape level by identifying areas with highest economic but lowest ecological value. Our method is not based on a priori targets, and as such it is applicable to cases where the effects of land use on, for example, individual species or ecosystem types are relatively small and would not lead to violation of regional or national conservation targets. We applied our method to land‐use allocation to peat mining. Our method identified a combination of profitable production areas that provides the needed area for peat production while retaining most of the landscape‐level ecological value of the ecosystem. The results of this inverse spatial conservation prioritization are being used in land‐use zoning in the province of Central Finland.
Plastic Collapse Moment for Weld Overlay Pipe With Multiple Circumferential Flaws
Authors: Hasegawa Kunio , Li Yinsheng , Shimomoto Masayoshi
Published: September 2013

Weld overlay is one of the useful repair methods for cracked piping that has been successfully applied for piping in many nuclear power plants. This paper proposes an approach for predicting plastic collapse moment for weld overlaid piping with single and multiple circumferential part-through flaws, using a new flaw depth parameter for weld overlay. The formulas for plastic collapse moments for weld overlaid pipes can be simply expressed by similar equations for a single flaw and multiple flaws using the parameter.
Correction to Design Equation for Spring Diametral Growth Upon Compression
Authors: Bockwoldt T. S. , Munsick G. A.
Published: September 2013

In the textbook by Wahl (1963, Mechanical Springs, 2nd ed., McGraw-Hill, New York, Chap. 20), he derived an equation predicting the diametral growth of a helical spring as the spring is compressed from free to solid height, and the spring's ends are free to rotate. A recent comparison with test data for growth of compression springs revealed that the calculated growth predicted by the Wahl formula did not agree well with measured values. Review of the Wahl derivation uncovered an arithmetic error that, when corrected, brought the calculated and measured diameters into closer agreement. The corrected diametral growth equation presented herein bounds the original data provided by Wahl, better matches an alternate growth equation derived by Ancker and Goodier for most springs evaluated, predicts larger growth than the original Wahl equation, and is a better fit to recent measured data.
Postnatal Soluble FGFR3 Therapy Rescues Achondroplasia Symptoms and Restores Bone Growth in Mice
Authors: Garcia Stéphanie , Dirat Béatrice , Tognacci Thomas , Rochet Nathalie , Mouska Xavier , Bonnafous Stéphanie , Patouraux Stéphanie , Tran Albert , Gual Philippe , Le Marchand-Brustel Yannick , Gennero Isabelle , Gouze Elvire
Published: September 2013

A recombinant soluble fibroblast growth factor receptor 3 (FGFR3) restored normal skeletal growth and prevented disease-related complications in a mouse model of achondroplasia.
A Step Closer to Therapy for Leaky Vessels.
Authors: Balcells Mercedes
Published: September 2013

Vascular permeability can be regulated by specifically blocking a microRNA that targets VE-cadherin.
Zoning In on Obesity
Authors: Mahfuz Mustafa
Published: September 2013

Zonulin may be a useful marker of gut microbiota-associated systemic micro-inflammation in obese patients.
Perturbation of Cytochrome
c
Maturation Reveals Adaptability of the Respiratory Chain in Mycobacterium tuberculosis
Authors: Small Jennifer L. , Park Sae Woong , Kana Bavesh D. , Ioerger Thomas R. , Sacchettini James C. , Ehrt Sabine
Published: September 2013

Mycobacterium tuberculosis
depends on aerobic respiration for growth and utilizes an
aa
3
-type cytochrome
c
oxidase for terminal electron transfer. Cytochrome
c
maturation in bacteria requires covalent attachment of heme to apocytochrome
c
, which occurs outside the cytoplasmic membrane. We demonstrate that in
M. tuberculosis
the thioredoxin-like protein Rv3673c, which we named CcsX, is required for heme insertion in cytochrome
c
. Inactivation of CcsX resulted in loss of
c
-type heme absorbance, impaired growth and virulence of
M. tuberculosis
, and induced cytochrome
bd
oxidase. This suggests that the bioenergetically less efficient
bd
oxidase can compensate for deficient cytochrome
c
oxidase activity, highlighting the flexibility of the
M. tuberculosis
respiratory chain. A spontaneous mutation in the active site of vitamin K epoxide reductase (VKOR) suppressed phenotypes of the CcsX mutant and abrogated the activity of the disulfide bond-dependent alkaline phosphatase, which shows that VKOR is the major disulfide bond catalyzing protein in the periplasm of
M. tuberculosis.

IMPORTANCE
Mycobacterium tuberculosis
requires oxygen for growth; however, the biogenesis of respiratory chain components in mycobacteria has not been explored. Here, we identified a periplasmic thioredoxin, CcsX, necessary for heme insertion into cytochrome
c
. We investigated the consequences of disrupting cytochrome
c
maturation (CCM) for growth and survival of
M. tuberculosis in vitro
and for its pathogenesis. Appearance of a second-site suppressor mutation in the periplasmic disulfide bond catalyzing protein VKOR indicates the strong selective pressure for a functional cytochrome
c
oxidase. The observation that
M. tuberculosis
is able to partially compensate for defective CCM by upregulation of the cytochrome
bd
oxidase exposes a functional role of this alternative terminal oxidase under normal aerobic conditions and during pathogenesis. This suggests that targeting both oxidases simultaneously might be required to effectively disrupt respiration in
M. tuberculosis
.
Canine Distemper Virus (CDV) in Another Big Cat: Should CDV Be Renamed Carnivore Distemper Virus?
Authors: Terio Karen A. , Craft Meggan E.
Published: September 2013

One of the greatest threats to the conservation of wild cat populations may be dogs or, at least, one of their viruses. Canine distemper virus (CDV), a single-stranded RNA virus in the
Paramyxoviridae
family and genus
Morbillivirus
, infects and causes disease in a variety of species, not just canids. An outbreak of CDV in wild lions in the Serengeti, Tanzania, in 1994 was a wake-up call for conservationists, as it demonstrated that an infectious disease could swiftly impact a previously healthy felid population. To understand how this virus causes disease in noncanid hosts, researchers have focused on specific mutations in the binding site of the CDV hemagglutinin gene. Now, Seimon et al. provide information on CDV in its latest feline victim, the endangered wild Amur tiger (
Panthera tigris altaica
) [T. A. Seimon et al., mBio 4(4):e00410-13, 2013, doi:10.1128/mBio.00410-13]. Their findings of CDV strains infecting tigers, in combination with recent information from other felids, paints a different picture, one in which CDV strains from a variety of geographic lineages and with a variety of amino acid residues in the hemagglutinin gene binding site can infect cats and cause disease. Although CDV has been known as a multihost disease since its discovery in domestic dogs in 1905, perhaps it is time to reconsider whether these noncanid species are not just incidental or “spillover” hosts but, rather, a normal part of the complex ecology of this infectious disease.
Renal infarction due to spontaneous dissection of the renal artery: an unusual cause of non-visceral type abdominal pain
Authors: Kang James H-E , Kang Jin-Yong , Morgan Robert
Published: September 2013

A 44-year-old man presented with very severe right upper quadrant pain of sudden onset. This was exacerbated by movement but unaffected by food or defaecation. It was continuous—day and night —but resolved over a 1-week period. The physical examination was normal at presentation, by which time the pain had resolved. His white cell count, alanine transaminase and C reactive protein were elevated but normalised after 10 days. An abdominal CT showed low density lesions in the right kidney consistent with segmental infarcts. CT angiogram showed a dissection of the right renal artery. The patient remained asymptomatic and normotensive when reviewed 1 month later.
Giant thoracic mass: an unusual presentation of primary pulmonary Hodgkin's lymphoma
Authors: McElnay Philip James , Pawade Joya , Chandratreya Ladli , West Douglas
Published: September 2013

Primary pulmonary Hodgkin's lymphoma (PPHL) is rare. PPHL without peripheral lymphadenopathy or hepatosplenomegaly is exceptionally uncommon. We present a 61-year-old woman believed to have a solitary intrapulmonary fibrous tumour on a CT and a CT-guided biopsy, until surgical excision. Histopathology and immunohistochemistry of the excised mass confirmed PPHL. PPHL is a very rare differential diagnosis of large solitary intrapulmonary masses. A CT-guided biopsy is recommended, as it can be diagnostic, reserving excision for cases where the diagnosis remains in doubt.
Capillary refill time is a predictor of short-term mortality for adult patients admitted to a medical department: an observational cohort study
Authors: Mrgan Monija , Rytter Dorte , Brabrand Mikkel
Published: September 2013

Background

Capillary refill time (CRT) has been advocated as a tool for rapid assessment of circulatory status. The correlation between neither CRT and mortality nor CRT and markers of circulatory status has been assessed. We performed a prospective observational cohort study to assess the relationship between CRT (using two existing definitions and as a continuous variable) and short-term mortality.

Methods

We included all acutely admitted adult patients to a medical admission unit. We measured CRT, blood pressure, pulse, temperature and peripheral oxygen saturation. We presented the data descriptively. Difference between continuous data was analysed using Wilcoxon Rank Sum Test and categorical data using χ2test. The primary endpoint was 1-day all-cause mortality.

Results

3046 patients were enrolled and CRT was measured on 1935. In univariate analyses, we found increasing all-cause 1-day mortality with all definitions of CRT. Performing multivariable analysis, controlling for age, sex, mean blood pressure, pulse, temperature and peripheral oxygen saturation, we found increasing CRT as a continuous variable and according to the Schriger and Baraff definition to be associated with increased mortality. Both the Trauma score and Schriger and Baraff definitions had high negative predictive values. The calculations on the Schriger and Baraff defition were based on limited power.

Conclusions

We found a significant association between CRT measured as a continuous variable and short-term mortality. Using the definition of Schriger and Baraff also seems appropriate, but this is based on calculations of limited power.
THE MODULAR CLASS OF A LIE ALGEBROID COMORPHISM
Authors: CASEIRO RAQUEL
Published: September 2013

We introduce the definition of modular class of a Lie algebroid comorphism and exploit some of its properties.
MULTISYMPLECTIC AND POLYSYMPLECTIC STRUCTURES ON FIBER BUNDLES
Authors: FORGER MICHAEL , GOMES LEANDRO G.
Published: September 2013

We propose new definitions of the concepts of a multisymplectic structure and of a polysymplectic structure which extend previous ones so as to cover the cases that are of interest in mathematical physics: they are tailored to apply to fiber bundles, rather than just manifolds, and at the same time they are sufficiently specific to allow us to prove Darboux theorems for the existence of canonical local coordinates. A key role is played by the notion of "symbol" of a multisymplectic form, which is a polysymplectic form representing its leading order contribution, thus clarifying the relation between these two closely related but not identical concepts.
AUTOMORPHIC BLACK HOLE ENTROPY
Authors: SCHIMMRIGK ROLF
Published: September 2013

Over the past few years the understanding of the microscopic theory of black hole entropy has made important conceptual progress by recognizing that the degeneracies are encoded in partition functions which are determined by higher rank automorphic representations, in particular in the context of Siegel modular forms of genus two. In this review, some of the elements of this framework are highlighted. One of the surprising aspects is that the Siegel forms that have appeared in the entropic context are geometric in origin, arising from weight two cusp forms, hence from elliptic curves.
INITIAL CONDITIONS FOR NUMERICAL RELATIVITY: INTRODUCTION TO NUMERICAL METHODS FOR SOLVING ELLIPTIC PDEs
Authors: OKAWA HIROTADA
Published: September 2013

Numerical relativity became a powerful tool to investigate the dynamics of binary problems with black holes or neutron stars as well as the very structure of General Relativity. Although public numerical relativity codes are available to evolve such systems, a proper understanding of the methods involved is quite important. Here, we focus on the numerical solution of elliptic partial differential equations. Such equations arise when preparing initial data for numerical relativity, but also for monitoring the evolution of black holes. Because such elliptic equations play an important role in many branches of physics, we give an overview of the topic, and show how to numerically solve them with simple examples and sample codes written in C ++ and Fortran90 for beginners in numerical relativity or other fields requiring numerical expertise.
A GA-BASED APPROACH FOR EPIPOLAR GEOMETRY ESTIMATION
Authors: KHALED NEHAL , HEMAYED ELSAYED E. , FAYEK MAGDA B.
Published: September 2013

In this paper, a genetic algorithm (GA)-based approach to estimate the fundamental matrix is presented. The aim of the proposed GA-based algorithm is to reduce the effect of noise and outliers in the corresponding points which affect the accuracy of the estimated fundamental matrix. Although in the proposed approach the GA is allowed to select the significant among all detected points, on the average half of the matched points have been determined to give optimum estimation of the fundamental matrix. Experiments with synthetic and real data show that the proposed approach is accurate especially in the presence of a high percentage of outliers. The proposed GA can always obtain good results in both high and low detailed images. Even for low detailed images which have a small number of matched points available to estimate the fundamental matrix, the proposed GA outperformed other methods.
QUANTIZATION EFFECT ON A SECOND-ORDER DYNAMICAL SYSTEM UNDER SLIDING-MODE CONTROL
Authors: YAN YAN , YU XINGHUO , YU SHUANGHE
Published: September 2013

The quantization behaviors of a sliding-mode control system with state feedback when the measurement of the state is quantized are studied. Some inherent dynamical properties for the quantized SMC systems are analyzed. The definition and the occurrence condition of "quantized sliding mode" are proposed. Theoretical results are illustrated with simulation examples.
SLIDING BIFURCATION AND GLOBAL DYNAMICS OF A FILIPPOV EPIDEMIC MODEL WITH VACCINATION
Authors: WANG AILI , XIAO YANNI
Published: September 2013

This paper proposes a Filippov epidemic model with piecewise continuous function to represent the enhanced vaccination strategy being triggered once the proportion of the susceptible individuals exceeds a threshold level. The sliding bifurcation and global dynamics for the proposed system are investigated. It is shown that as the threshold value varies, the proposed system can exhibit variable sliding mode domains and local sliding bifurcations including boundary node (focus) bifurcation, double tangency bifurcation and other sliding mode bifurcations. Model solutions ultimately approach either one of two endemic states for two structures or the pseudo-equilibrium on the switching surface, depending on the threshold level. The findings indicate that proper combinations of threshold level and enhanced vaccination rate based on threshold policy can lead disease prevalence to a previously chosen level if eradication of disease is impossible.
SYNCHRONIZATION AND STABILIZATION OF MULTI-SCROLL INTEGER AND FRACTIONAL ORDER CHAOTIC ATTRACTORS GENERATED USING TRIGONOMETRIC FUNCTIONS
Authors: XU FEI , YU PEI , LIAO XIAOXIN
Published: September 2013

Sigmoidal functions are usually used to characterize the behavior of dynamical systems, in particular, for neural networks. Recently, multilevel piecewise linear functions have been employed in cellular neural networks (CNN). In this paper, we first use the inverse trigonometric function, tan -1(x), to generate a series of trigonometric functions to obtain one-, two- and three-directional multi-scroll integer and fractional order chaotic attractors. Then, based upon the properties of the chaotic systems, simple feedback control laws are designed to stabilize or synchronize the integer and fractional order chaotic systems. Numerical simulations are presented to demonstrate the applicability of theoretical predictions.
STRONG LAWS FOR RECURRENCE QUANTIFICATION ANALYSIS
Authors: GRENDÁR M. , MAJEROVÁ J. , ŠPITALSKÝ V.
Published: September 2013

The recurrence rate and determinism are two of the basic complexity measures studied in the recurrence quantification analysis. In this paper, the recurrence rate and determinism are expressed in terms of the correlation sum, and strong laws of large numbers are given for them.
META-MONOIDS, META-BICROSSED PRODUCTS, AND THE ALEXANDER POLYNOMIAL
Authors: BAR-NATAN DROR , SELMANI SAM
Published: September 2013

We introduce a new invariant of tangles along with an algebraic framework in which it is to be interpreted. We claim that the invariant contains the classical Alexander polynomial of knots and its multivariable extension to links. We argue that of the computationally efficient members of the family of Alexander invariants, it is the most meaningful.

These are lecture notes for talks given by the first author, written and completed by the second. The talks, with handouts and videos, are available at http://www.math.toronto.edu/drorbn/Talks/Regina-1206/ . See also further comments at http://www.math.toronto.edu/drorbn/Talks/Caen-1206/#June8 .