bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating the roles of directed breeding and gene flow in animal domestication
Authors: Marshall Fiona B. , Dobney Keith , Denham Tim , Capriles José M.
Published: April 2014

For the last 150 y scholars have focused upon the roles of intentional breeding and genetic isolation as fundamental to understanding the process of animal domestication. This analysis of ethnoarchaeological, archaeological, and genetic data suggests that long-term gene flow between wild and domestic stocks was much more common than previously assumed, and that selective breeding of females was largely absent during the early phases of animal domestication. These findings challenge assumptions about severe genetic bottlenecks during domestication, expectations regarding monophyletic origins, and interpretations of multiple domestications. The findings also raise new questions regarding ways in which behavioral and phenotypic domestication traits were developed and maintained.
Interepithelial signaling with nephric duct is required for the formation of overlying coelomic epithelial cell sheet
Authors: Yoshino Takashi , Saito Daisuke , Atsuta Yuji , Uchiyama Chihiro , Ueda Shinya , Sekiguchi Kiyotoshi , Takahashi Yoshiko
Published: April 2014

Significance

We demonstrate that one type of epithelial tissue acts on another type and also that such interepithelial signaling is important for the coordination between different types of epithelia. When one epithelium is ablated, its adjacent epithelium becomes sensitized to external stress such as that produced by epithelial-to-mesenchymal transition (EMT) inducers. For such interactions, fibronectin serves as a prominent mediator, being translocated from one epithelium (fibronectin-producing) to the other (fibronectin-receiving). This type of interepithelial signaling and the role of fibronectin in these events are conceptually novel and thus open a new way to understand not only how epithelial tissues form in harmony but also how therapeutically to prevent EMT, a critical event in cancer initiation.
Visuospatial selective attention in chickens
Authors: Sridharan Devarajan , Ramamurthy Deepa L. , Schwarz Jason S. , Knudsen Eric I.
Published: April 2014

Significance

Top-down selective attention, which is fundamental to cognition, has been studied extensively in humans and nonhuman primates. Here we report the behavioral hallmarks of selective attention in a nonprimate species, the domestic chicken. When provided with a spatial cue, birds exhibited dramatic improvements in accuracy, faster reaction times, and higher choice certainty in a target localization task. Our results reveal that chickens shift spatial attention rapidly and dynamically following principles remarkably similar to those documented in primates. Given the evolutionary distance (>250 million years) and enormous ethological differences between chickens and primates, our findings suggest that neural mechanisms mediating selective attention appeared early in vertebrate evolution and that they are conserved across phylogeny.
Myosin-10 produces its power-stroke in two phases and moves processively along a single actin filament under low load
Authors: Takagi Yasuharu , Farrow Rachel E. , Billington Neil , Nagy Attila , Batters Christopher , Yang Yi , Sellers James R. , Molloy Justin E.
Published: April 2014

Significance

Filopodia act as organelles for sensing and exploring the environment, as well as producing traction forces during cellular locomotion. Myosin-10 is a molecular motor crucial for intrafilopodial trafficking and filopodia formation. To decipher how myosin-10 generates force and movement, we used electron microscopy and a combination of ensemble biochemical and single molecule mechanical techniques to help elucidate its structure and mechano-chemical coupling. Our results clarify current controversies about myosin-10 structure and function by revealing that it generates an unexpectedly large biphasic power stroke and moves processively along actin, but detaches rapidly at relatively low force. These adaptations may be advantageous features for a myosin motor that carries bulky cargo within the narrow confines of the filopodium.
Radiometric
81
Kr dating identifies 120,000-year-old ice at Taylor Glacier, Antarctica
Authors: Buizert Christo , Baggenstos Daniel , Jiang Wei , Purtschert Roland , Petrenko Vasilii V. , Lu Zheng-Tian , Müller Peter , Kuhl Tanner , Lee James , Severinghaus Jeffrey P. , Brook Edward J.
Published: April 2014

Significance

Past variations in Earth’s climate and atmospheric composition are recorded in accumulating polar meteoric ice and the air trapped within it. Ice outcrops provide accessible archives of old ice but are difficult to date reliably. Here we demonstrate
81
Kr radiometric dating of ice, allowing accurate dating of up to 1.5 million-year-old ice. The technique successfully identifies valuable ice from the previous interglacial period at Taylor Glacier, Antarctica. Our method will enhance the scientific value of outcropping sites as archives of old ice needed for paleoclimatic reconstructions and can aid efforts to extend the ice core record further back in time.
Heterogeneous organization of the locus coeruleus projections to prefrontal and motor cortices
Authors: Chandler Daniel J. , Gao Wen-Jun , Waterhouse Barry D.
Published: April 2014

Significance

The locus coeruleus projection system in the brain is thought to exert uniform and synchronous modulatory effects on cells and circuits throughout the CNS by widespread release of its transmitter, norepinephrine. We challenge this notion by demonstrating that neurons in the locus coeruleus maintain segregated connections to brain regions with distinctly different functions. Specifically, cells that communicate with the prefrontal cortex, a region involved in cognition and executive function, are characterized by properties that allow for independent and asynchronous modulation of operations in this area, compared with those that project to the motor cortex and regulate movement generation. These findings have important implications for understanding the role of this system in normal brain physiology and pathologic neuropsychiatric conditions.
Interferon induction of IFITM proteins promotes infection by human coronavirus OC43
Authors: Zhao Xuesen , Guo Fang , Liu Fei , Cuconati Andrea , Chang Jinhong , Block Timothy M. , Guo Ju-Tao
Published: April 2014

Significance

Here we report that all three types of IFNs, the primary mediators of host innate and adaptive antiviral responses, promote infection by human coronavirus HCoV-OC43. They do so through the IFN-induced transmembrane proteins that normally restrict a broad spectrum of viruses but serve as entry factors for HCoV-OC43 to infect its host cells. Our finding reveals a unique mechanism by which HCoV-OC43 evades host antiviral immune responses and suggests that the cytokine response to infection or noninfectious stimuli can be co-opted to promote the infection and spreading of opportunistic pathogens that have evolved adaptations similar to that of HCoV-OC43.
Control of dopaminergic neuron survival by the unfolded protein response transcription factor XBP1
Authors: Valdés Pamela , Mercado Gabriela , Vidal Rene L. , Molina Claudia , Parsons Geoffrey , Court Felipe A. , Martinez Alexis , Galleguillos Danny , Armentano Donna , Schneider Bernard L. , Hetz Claudio
Published: April 2014

Significance

The selective loss of dopaminergic neurons is characteristic of Parkinson disease (PD). Protein folding stress is a salient feature of PD. This study uncovers a previously undefined function of a major unfolded protein response (UPR) transcription factor (XBP1) in supporting the survival of nigral dopaminergic neurons at basal levels and under pathological conditions. Our results reveal an important role for a canonical UPR pathway in the maintenance of dopaminergic neuron proteostasis, which also could be relevant to understand the selective neuronal vulnerability observed in Parkinson disease.
Crystal structure ofStreptococcus pyogenesEndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies
Authors: Trastoy Beatriz , Lomino Joseph V. , Pierce Brian G. , Carter Lester G. , Günther Sebastian , Giddens John P. , Snyder Greg A. , Weiss Thomas M. , Weng Zhiping , Wang Lai-Xi , Sundberg Eric J.
Published: April 2014

Significance

Because bacteria colonize hostile environments they have evolved immune evasion mechanisms, including the expression of enzymes that specifically modify host immune system proteins.Streptococcus pyogenessecretes an enzyme called EndoS that removes carbohydrates specifically from human antibodies, impairing their ability to activate immune defenses. Because of its high substrate specificity, EndoS is also being developed as a treatment for autoimmune diseases and is a key enzyme used in the production of antibodies bearing customized carbohydrates. We have determined the three-dimensional structure of EndoS and present a molecular model depicting how EndoS engages antibodies with high specificity. Our data provide a roadmap for engineering EndoS variants with unique activities for clinical and biotechnological applications.
Automatic ultrarapid activation and inhibition of cortical motor systems in spoken word comprehension
Authors: Shtyrov Yury , Butorina Anna , Nikolaeva Anastasia , Stroganova Tatiana
Published: April 2014

Significance

The mechanisms through which our brain generates complex cognitive percepts from simple sensory and motor events remain unknown. An important question is whether the basic brain structures controlling movements and perceptions directly participate in higher-order cognitive processes such as language comprehension. Using neurophysiology, we found ultrarapid (starting at ∼80 ms) activations in the human motor cortex in response to unattended action-related verbs and nouns, with words related to different body parts activating corresponding body representations. Accompanying this category-specific activity was activation suppression by words with area-incompatible meaning, demonstrating operation of the neurophysiological principles of lateral/surround inhibition in language processing. These instant activations and deactivations emerging for words of different types in the absence of attention advocate automatic involvement of neural sensorimotor circuits in language comprehension.
Solid MRI contrast agents for long-term, quantitative in vivo oxygen sensing
Authors: Liu Vincent H. , Vassiliou Christophoros C. , Imaad Syed M. , Cima Michael J.
Published: April 2014

Significance

Information on tissue oxygen tension is critical to the successful treatment of many human diseases. Clinical decisions for diseases such as cancer benefit from knowing how oxygen tension changes in response to treatment. Acquiring this knowledge obviously requires a series of measurements and is limited currently by the use of invasive oxygen electrodes. We have developed an oxygen-sensitive MRI contrast agent for chronic oxygen tension measurements. This contrast agent can be delivered with a small-gauge needle that is minimally invasive, and subsequent measurements are entirely noninvasive. The material is stable in the body for at least 1 mo, and we envision that other types of responsive contrast agents can be used with this technology to detect different metabolites.
Crystal structure of
Arabidopsis
glutamyl-tRNA reductase in complex with its stimulator protein
Authors: Zhao Aiguo , Fang Ying , Chen Xuemin , Zhao Shun , Dong Wei , Lin Yajing , Gong Weimin , Liu Lin
Published: April 2014

Significance

The glutamyl-tRNA reductase (GluTR)-catalyzed reduction of glutamyl-tRNA is the rate-limiting and a pivotal regulation step in the tetrapyrrole biosynthetic pathway. In chloroplast-containing photosynthetic organisms, GluTR binding protein (GluBP) is a newly identified spatial regulator that allocates GluTR for synthesis of different tetrapyrrole products. We find that GluBP stimulates GluTR catalytic efficiency. The structure of the GluTR–GluBP complex shows that GluBP binding promotes GluTR to a hydride-transferring state, the second step of the glutamyl-tRNA reduction, revealing structural details for the catalytic process. These findings clarify a series of arguments regarding the activation and regulation of GluTR. The GluBP structure also suggests that GluBP may have a novel role in heme metabolism.
Theory for plasticity of face-centered cubic metals
Authors: Jo Minho , Koo Yang Mo , Lee Byeong-Joo , Johansson Börje , Vitos Levente , Kwon Se Kyun
Published: April 2014

Significance

The ultimate goal of materials science can be reached only from a thorough understanding of the underlying physics of the materials properties. Accordingly, the present global need for high-technology metallic materials strongly depends on the development of robust theoretical understandings that can help to elucidate and optimize their performance. Although plastic deformation is a common denominator in many of these problems, no reliable microscopic theory of plasticity has been presented to date. We demonstrate that fundamental concepts in atomic theory provide a unified solution to plasticity and invite multidisciplinary contributions to deepen and extend the scope to a number of engineering applications. The present work will form a solid basis for many scientific and engineering disciplines.
GTP activator and dNTP substrates of HIV-1 restriction factor SAMHD1 generate a long-lived activated state
Authors: Hansen Erik C. , Seamon Kyle J. , Cravens Shannen L. , Stivers James T.
Published: April 2014

Significance

The degradative dNTP triphosphohydrolase activity of the sterile α-motif/histidine-aspartate domain-containing protein 1 (SAMHD1) enzyme helps maintain optimal dNTP balances for DNA replication and also serves as an HIV-1 restriction factor in resting CD4
+
target cells of HIV by depleting dNTP substrates of reverse transcriptase. This study shows that full activation of SAMHD1 involves ordered binding of GTP and substrate dNTPs to activator and substrate sites on the enzyme, leading to ordered assembly of the tetramer active form. After the enzyme is activated, it no longer communicates with free activator nucleotides, which contributes to efficient depletion of dNTP pools in resting T cells.
Decreased abundance of type III secretion system-inducing signals in
Arabidopsis mkp1
enhances resistance against
Pseudomonas syringae
Authors: Anderson Jeffrey C. , Wan Ying , Kim Young-Mo , Pasa-Tolic Ljiljana , Metz Thomas O. , Peck Scott C.
Published: April 2014

Significance

Pathogenic bacteria inject effector proteins into the host to suppress its defenses. However, bacteria produce the effector proteins and injection machinery only upon recognition of a potential host. Here we identified an
Arabidopsis
mutant,
mapk phosphatase 1
(
mkp1
), with decreased levels of chemical signals recognized by the bacterium, thus making the plant more resistant by suppressing the ability of the pathogen,
Pseudomonas syringae
, to express and inject effector proteins. Reapplying these chemical signals not only eliminated resistance in the
mkp1
mutant but also suppressed resistance in wild-type plants with a preinduced immune response. These results demonstrate an important layer in determining the biological outcome during host–pathogen interactions and may provide new targets for enhancing resistance against bacterial pathogens.
Endoscopic photoconversion reveals unexpectedly broad leukocyte trafficking to and from the gut
Authors: Morton Angela M. , Sefik Esen , Upadhyay Rabi , Weissleder Ralph , Benoist Christophe , Mathis Diane
Published: April 2014

Significance

Gut-microbiota/immune-cell interactions play important roles in immune system homeostasis and responsiveness, but surprisingly little is known about the movement of immune cells into and, particularly, out of the gut. We used a minimally invasive system to monitor immigration of diverse innate and adaptive immune-cell types to the intestine from a distant lymph node, and a novel endoscopic adaptation of the system to follow their emigration from the distal colon to nearby and distal lymphoid organs. We uncovered an unexpectedly broad movement of leukocytes to and from the gut at steady state, as well as subset-specific migration proclivities. Moreover, we evidenced a critical cellular link between an intestinal microbe, segmented filamentous bacteria, and an extraintestinal autoinflammatory disease, the K/BxN model of arthritis.
Music and Contemplation in the Twelfth-Century Dulcis Jesu memoria
Authors: Deeming Helen
Published: April 2014

The music of the twelfth-century song Dulcis Jesu memoria has been almost entirely neglected in modern scholarship, though its text (or rather a version of it) is well known in settings by fifteenth- and sixteenth-century composers. This article presents a new edition and translation of the song, and seeks to interpret its music and text as partners in an exegetical whole. The song's complicated relationship with the sequence genre proves a fruitful backdrop against which to interpret both text and melody, and analysis of the song's only notated manuscript source leads to new conclusions about the purpose to which the song may have been put by the manuscript's first readers.
Pilot randomised controlled trial of school‐based humanistic counselling for psychological distress in young people: Outcomes and methodological reflections
Authors: Pybis Joanne , Cooper Mick , Hill Andy , Cromarty Karen , Levesley Ruth , Murdoch Jamie , Turner Nick
Published: April 2014

Aim

The purpose of this study was to replicate and extend a pilot evaluation of the effectiveness of school‐based humanistic counselling for psychological distress in young people.

Method

Data were available on 32 young people who were randomised to either school‐based humanistic counselling or waiting list conditions for one school term. The primary outcome measure was of psychological distress using the Young Person's CORE (YP‐CORE), at six and 12 weeks post‐assessment. Secondary measures at these time‐points were of psychological difficulties, self‐esteem, levels of depression, and attainment of personal goals; with longitudinal evaluation of outcomes at six months post‐assessment.

Results

On the primary outcome measure, participants who received counselling were significantly less distressed at six weeks than those in the waiting list group but not at 12 weeks, with effect sizes (Cohen's d) of 0.59 and 0.39 respectively. Reductions in psychological distress were maintained at follow‐up.

Discussion

Although the present findings, in isolation, are equivocal, they contribute to a body of evidence that supports the effectiveness of school‐based humanistic counselling. However, the principal lesson learnt from this study was the need for rigorous training of researchers, counsellors and pastoral care teachers to ensure adherence to protocols.
A Working Memory Account of the Interaction between Numbers and Spatial Attention
Authors: van Dijck Jean-Philippe , Abrahamse Elger L. , Acar Freya , Ketels Boris , Fias Wim
Published: April 2014

Rather than reflecting the long-term memory construct of a mental number line, it has been proposed that the relation between numbers and space is of a more temporary nature and constructed in working memory during task execution. In three experiments we further explored the viability of this working memory account. Participants performed a speeded dot detection task with dots appearing left or right, while maintaining digits or letters in working memory. Just before presentation of the dot, these digits or letters were used as central cues. These experiments show that the “attentional SNARC-effect” (where SNARC is the spatial–numerical association of response codes) is not observed when only the lastly perceived number cue—and no serially ordered sequence of cues—is maintained in working memory (Experiment 1). It is only when multiple items (numbers in Experiment 2; letters in Experiment 3) are stored in working memory in a serially organized way that the attentional cueing effect is observed as a function of serial working memory position. These observations suggest that the “attentional SNARC-effect” is strongly working memory based. Implications for theories on the mental representation of numbers are discussed.
Examining the lag effect under incidental encoding: Contributions of semantic priming and reminding
Authors: Bui Dung C. , Maddox Geoffrey B. , Zou Fan , Hale Sandra S.
Published: April 2014

Memory is better when repeated learning events are spaced than when they are massed (spacing effect), as well as when material is processed semantically than when it is processed graphemically (levels-of-processing effect). Examination of the relationship between levels of processing and spacing for both deeply and shallowly encoded items has shown a spacing effect for items processed deeply, but not shallowly. A semantic priming account of spacing was proposed to explain the interaction between levels of processing and spacing on memory. The current study manipulated levels of processing and the amount of spacing (lag) that occurred between repetitions of items that were incidentally encoded. Results from Experiments 1A and 1B revealed lag effects in test performance when items were deeply and shallowly encoded. Although these findings are inconsistent with a semantic priming account, they can be interpreted within a reminding account, which is explored in Experiment 2. Results from the second experiment indicate that bringing reminding under conscious control benefited items that were presented at a long lag but not at a shorter lag. Together, this study provides evidence that is difficult to accommodate with a semantic priming account of spacing and instead provides additional support for a reminding account suggesting that automatic and controlled processes may both underlie the reminding process.
BARP suppresses voltage-gated calcium channel activity and Ca2+-evoked exocytosis
Authors: Béguin Pascal , Nagashima Kazuaki , Mahalakshmi Ramasubbu N. , Vigot Réjan , Matsunaga Atsuko , Miki Takafumi , Ng Mei Yong , Ng Yu Jin Alvin , Lim Chiaw Hwee , Tay Hock Soon , Hwang Le-Ann , Firsov Dmitri , Tang Bor Luen , Inagaki Nobuya , Mori Yasuo , Seino Susumu , Launey Thomas , Hunziker Walter
Published: April 2014

Voltage-gated calcium channels (VGCCs) are key regulators of cell signaling and Ca2+-dependent release of neurotransmitters and hormones. Understanding the mechanisms that inactivate VGCCs to prevent intracellular Ca2+ overload and govern their specific subcellular localization is of critical importance. We report the identification and functional characterization of VGCC β-anchoring and -regulatory protein (BARP), a previously uncharacterized integral membrane glycoprotein expressed in neuroendocrine cells and neurons. BARP interacts via two cytosolic domains (I and II) with all Cavβ subunit isoforms, affecting their subcellular localization and suppressing VGCC activity. Domain I interacts at the α1 interaction domain–binding pocket in Cavβ and interferes with the association between Cavβ and Cavα1. In the absence of domain I binding, BARP can form a ternary complex with Cavα1 and Cavβ via domain II. BARP does not affect cell surface expression of Cavα1 but inhibits Ca2+ channel activity at the plasma membrane, resulting in the inhibition of Ca2+-evoked exocytosis. Thus, BARP can modulate the localization of Cavβ and its association with the Cavα1 subunit to negatively regulate VGCC activity.
PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity
Authors: Kane Lesley A. , Lazarou Michael , Fogel Adam I. , Li Yan , Yamano Koji , Sarraf Shireen A. , Banerjee Soojay , Youle Richard J.
Published: April 2014

PINK1 kinase activates the E3 ubiquitin ligase Parkin to induce selective autophagy of damaged mitochondria. However, it has been unclear how PINK1 activates and recruits Parkin to mitochondria. Although PINK1 phosphorylates Parkin, other PINK1 substrates appear to activate Parkin, as the mutation of all serine and threonine residues conserved between Drosophila and human, including Parkin S65, did not wholly impair Parkin translocation to mitochondria. Using mass spectrometry, we discovered that endogenous PINK1 phosphorylated ubiquitin at serine 65, homologous to the site phosphorylated by PINK1 in Parkin’s ubiquitin-like domain. Recombinant TcPINK1 directly phosphorylated ubiquitin and phospho-ubiquitin activated Parkin E3 ubiquitin ligase activity in cell-free assays. In cells, the phosphomimetic ubiquitin mutant S65D bound and activated Parkin. Furthermore, expression of ubiquitin S65A, a mutant that cannot be phosphorylated by PINK1, inhibited Parkin translocation to damaged mitochondria. These results explain a feed-forward mechanism of PINK1-mediated initiation of Parkin E3 ligase activity.
Improved HSC reconstitution and protection from inflammatory stress and chemotherapy in mice lacking granzyme B
Authors: Carnevalli Larissa S. , Scognamiglio Roberta , Cabezas-Wallscheid Nina , Rahmig Susann , Laurenti Elisa , Masuda Kohei , Jöckel Lars , Kuck Andrea , Sujer Stefanie , Polykratis Apostolos , Erlacher Miriam , Pasparakis Manolis , Essers Marieke A.G. , Trumpp Andreas
Published: April 2014

The serine protease granzyme B (GzmB) is stored in the granules of cytotoxic T and NK cells and facilitates immune-mediated destruction of virus-infected cells. In this study, we use genetic tools to report novel roles for GzmB as an important regulator of hematopoietic stem cell (HSC) function in response to stress. HSCs lacking the GzmB gene show improved bone marrow (BM) reconstitution associated with increased HSC proliferation and mitochondrial activity. In addition, recipients deficient in GzmB support superior engraftment of wild-type HSCs compared with hosts with normal BM niches. Stimulation of mice with lipopolysaccharide strongly induced GzmB protein expression in HSCs, which was mediated by the TLR4–TRIF–p65 NF-κB pathway. This is associated with increased cell death and GzmB secretion into the BM environment, suggesting an extracellular role of GzmB in modulating HSC niches. Moreover, treatment with the chemotherapeutic agent 5-fluorouracil (5-FU) also induces GzmB production in HSCs. In this situation GzmB is not secreted, but instead causes cell-autonomous apoptosis. Accordingly, GzmB-deficient mice are more resistant to serial 5-FU treatments. Collectively, these results identify GzmB as a negative regulator of HSC function that is induced by stress and chemotherapy in both HSCs and their niches. Blockade of GzmB production may help to improve hematopoiesis in various situations of BM stress.
Elucidation of the enigmatic IgD class-switch recombination via germline deletion of the IgH 3′ regulatory region
Authors: Rouaud Pauline , Saintamand Alexis , Saad Faten , Carrion Claire , Lecardeur Sandrine , Cogné Michel , Denizot Yves
Published: April 2014

Classical class-switch recombination (cCSR) substitutes the Cμ gene with Cγ, Cε, or Cα, thereby generating IgG, IgE, or IgA classes, respectively. This activation-induced deaminase (AID)–driven process is controlled by the IgH 3′ regulatory region (3′RR). Regulation of rare IgD CSR events has been enigmatic. We show that μδCSR occurs in mouse mesenteric lymph node (MLN) B cells and is AID-dependent. AID attacks differ from those in cCSR because they are not accompanied by extensive somatic hypermutation (SHM) of targeted regions and because repaired junctions exhibit features of the alternative end-joining (A-EJ) pathway. In contrast to cCSR and SHM, μδCSR is 3′RR-independent, as its absence affects neither breakpoint locations in Sμ- and Sδ-like (σδ) nor mutation patterns at Sμ-σδ junctions. Although mutations occur in the immediate proximity of the μδ junctions, SHM is absent distal to the junctions within both Sμ and rearranged VDJ regions. In conclusion, μδCSR is active in MLNs, occurs independently of 3′RR-driven assembly, and is even dramatically increased in 3′RR-deficient mice, further showing that its regulation differs from cCSR.
Type I IFN suppresses Cxcr2 driven neutrophil recruitment into the sensory ganglia during viral infection
Authors: Stock Angus T. , Smith Jeffrey M. , Carbone Francis R.
Published: April 2014

Infection induces the expression of inflammatory chemokines that recruit immune cells to the site of inflammation. Whereas tissues such as the intestine and skin express unique chemokines during homeostasis, whether different tissues express distinct chemokine profiles during inflammation remains unclear. With this in mind, we performed a comprehensive screen of the chemokines expressed by two tissues (skin and sensory ganglia) infected with a common viral pathogen (herpes simplex virus type 1). After infection, the skin and ganglia showed marked differences in their expression of the family of Cxcr2 chemokine ligands. Specifically, Cxcl1/2/3, which in turn controlled neutrophil recruitment, was up-regulated in the skin but absent from the ganglia. Within the ganglia, Cxcl2 expression and subsequent neutrophil recruitment was inhibited by type I interferon (IFN). Using a combination of bone marrow chimeras and intracellular chemokine staining, we show that type I IFN acted by directly suppressing Cxcl2 expression by monocytes, abrogating their ability to recruit neutrophils to the ganglia. Overall, our findings describe a novel role for IFN in the direct, and selective, inhibition of Cxcr2 chemokine ligands, which results in the inhibition of neutrophil recruitment to neuronal tissue.
Well-posedness of the linearized plasma-vacuum interface problem in ideal incompressible MHD
Authors: Morando Alessandro , Trakhinin Yuri , Trebeschi Paola
Published: April 2014

We study the free boundary problem for the plasma-vacuum interface in ideal incompressible magnetohydrodynamics (MHD). In the vacuum region the magnetic field is described by the div-curl system of pre-Maxwell dynamics, while at the interface the total pressure is continuous and the magnetic field is tangent to the boundary. Under a suitable stability condition satisfied at each point of the plasma-vacuum interface, we prove the well-posedness of the linearized problem in Sobolev spaces.
Efficient Bayesian inference under the structured coalescent
Authors: Vaughan Timothy G. , Kühnert Denise , Popinga Alex , Welch David , Drummond Alexei J.
Published: April 2014

Motivation: Population structure significantly affects evolutionary dynamics. Such structure may be due to spatial segregation, but may also reflect any other gene-flow-limiting aspect of a model. In combination with the structured coalescent, this fact can be used to inform phylogenetic tree reconstruction, as well as to infer parameters such as migration rates and subpopulation sizes from annotated sequence data. However, conducting Bayesian inference under the structured coalescent is impeded by the difficulty of constructing Markov Chain Monte Carlo (MCMC) sampling algorithms (samplers) capable of efficiently exploring the state space.

Results: In this article, we present a new MCMC sampler capable of sampling from posterior distributions over structured trees: timed phylogenetic trees in which lineages are associated with the distinct subpopulation in which they lie. The sampler includes a set of MCMC proposal functions that offer significant mixing improvements over a previously published method. Furthermore, its implementation as a BEAST 2 package ensures maximum flexibility with respect to model and prior specification. We demonstrate the usefulness of this new sampler by using it to infer migration rates and effective population sizes of H3N2 influenza between New Zealand, New York and Hong Kong from publicly available hemagglutinin (HA) gene sequences under the structured coalescent.

Availability and implementation: The sampler has been implemented as a publicly available BEAST 2 package that is distributed under version 3 of the GNU General Public License at http://compevol.github.io/MultiTypeTree.

Contact:  tgvaughan@gmail.com

Supplementary information:  Supplementary Data are available at Bioinformatics online.
A model for fast extragalactic radio bursts
Authors: Lyubarsky Yuri
Published: April 2014

Bursts of millisecond duration were recently discovered in the 1 GHz band. There is a strong evidence that they come from ∼1 Gpc distances, which implies extraordinary high-brightness temperature. I propose that these bursts could be attributed to synchrotron maser emission from relativistic, magnetized shocks. At the onset of the magnetar flare, a strongly magnetized pulse is formed, which propagates away through the relativistic magnetar wind and eventually reaches the nebula inflated by the wind within the surrounding medium. I show that the observed radio bursts could be generated at shocks formed via the interaction of the magnetic pulse with the plasma within the nebula. The model predicts strong millisecond bursts in the TeV band, which could be observed even from distant galaxies.
Video-Assisted Thoracoscopic Resection of Recurrent Intrapulmonary Bronchogenic Cyst after Thoracotomy
Authors: Hynes Conor F. , Marshall M. Blair
Published: April 2014

Intrapulmonary bronchogenic cysts are typically treated surgically by lobectomy to completely excise the cyst to minimize risk for recurrence. Video-assisted thoracoscopic surgery is being used with increasing frequency to manage intrathoracic pathology. We present a patient who underwent resection of a bronchogenic cyst 20 years before. She developed a symptomatic recurrence, and video-assisted thoracoscopic surgery was used to lyse adhesions from her previous posterolateral thoracotomy and perform an intraparenchymal dissection to resect the pathologic lesion while sparing the remaining parenchyma of her right upper lobe. At 2 years of follow-up, the patient is without evidence of recurrence.
Experience with Thoracoscopic Pneumonectomies at a Single Institution
Authors: Kim Anthony W. , Fonseca Annabelle L. , Boffa Daniel J. , Detterbeck Frank C.
Published: April 2014

Objective

The aim of this study was to review a single-institution experience with video-assisted thoracoscopic pneumonectomy (VATP).

Methods

From July 2008 through December 2012, the medical records of all patients undergoing pneumonectomy (total and completion) for lung cancer were reviewed. Clinical parameters were recorded and analyzed.

Results

During this period, 16% (7/45) of pneumonectomies for malignancy were performed thoracoscopically. Patient selection was performed in the context of a multidisciplinary tumor board. Of the seven VATPs, five were standard (Video 1, available at http://links.lww.com/INNOV/A40 ) and two were completion pneumonectomies (Video 2, available at http://links.lww.com/INNOV/A41 ). Indications were primary lung cancer in six (three adenocarcinoma, one squamous carcinoma, one large cell neuroendocrine carcinoma, and one mixed adenocarcinoma cell and small cell lung carcinoma) and metastatic esophageal cancer in one patient. Preoperative selection was based on unfavorable location of the primary tumor, which excluded the possibility of a lesser resection such as sleeve resection while permitting an R0 resection by pneumonectomy. Pathologic staging was consistent with clinical staging except for one patient who was upstaged. There were four complications: atrial fibrillation, pneumonia, and two bronchopleural fistulas. The median length of stay was 4 days (excluding one outlier). Distant disease recurrence occurred in one patient. Kaplan-Meier survival at 24 months was 75%.

Conclusions

Introduction of VATP into the armamentarium of the experienced thoracoscopic surgeon is feasible with acceptable outcomes and a complication profile that is not dissimilar to the open pneumonectomy experience. Greater experience with this approach should provide additional data to more objectively evaluate the merits of this approach.
Use of Pledgeted Sutures in Mitral Annuloplasty
Authors: Hassan Mohammed , Windsor Jimmy , Salerno Tomas , Ricci Marco
Published: April 2014

Annuloplasty ring or band dehiscence is a possible complication of mitral valve repair surgery. It may be due to increased tension on the annuloplasty sutures, especially in ischemic mitral pathology in which a circumferential ring is used. Herein, we describe a technique for alternative suture placement in mitral annuloplasty using pledgeted sutures that may reduce the risk for ring or band dehiscence.
On integrating multi-experiment microarray data
Authors: Tsiliki Georgia , Vlachakis Dimitrios , Kossida Sophia
Published: April 2014

With the extensive use of microarray technology as a potential prognostic and diagnostic tool, the comparison and reproducibility of results obtained from the use of different platforms is of interest. The integration of those datasets can yield more informative results corresponding to numerous datasets and microarray platforms. We developed a novel integration technique for microarray gene-expression data derived by different studies for the purpose of a two-way Bayesian partition modelling which estimates co-expression profiles under subsets of genes and between biological samples or experimental conditions. The suggested methodology transforms disparate gene-expression data on a common probability scale to obtain inter-study-validated gene signatures. We evaluated the performance of our model using artificial data. Finally, we applied our model to six publicly available cancer gene-expression datasets and compared our results with well-known integrative microarray data methods. Our study shows that the suggested framework can relieve the limited sample size problem while reporting high accuracies by integrating multi-experiment data.
Hybrid indexes for repetitive datasets
Authors: Ferrada H. , Gagie T. , Hirvola T. , Puglisi S. J.
Published: April 2014

Advances in DNA sequencing mean that databases of thousands of human genomes will soon be commonplace. In this paper, we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper bounds on pattern lengths and edit distances, we pre-process the text with the lossless data compression algorithm LZ77 to obtain a filtered text, for which we store a conventional index. Later, given a query, we find all matches in the filtered text, then use their positions and the structure of the LZ77 parse to find all matches in the original text. Our experiments show that this also significantly reduces query times.
An optimal algorithm for computing all subtree repeats in trees
Authors: Flouri T. , Kobert K. , Pissis S. P. , Stamatakis A.
Published: April 2014

Given a labelled tree
T
, our goal is to group repeating subtrees of
T
into equivalence classes with respect to their topologies and the node labels. We present an explicit, simple and time-optimal algorithm for solving this problem for unrooted unordered labelled trees and show that the running time of our method is linear with respect to the size of
T
. By unordered, we mean that the order of the adjacent nodes (children/neighbours) of any node of
T
is irrelevant. An unrooted tree
T
does not have a node that is designated as root and can also be referred to as an undirected tree. We show how the presented algorithm can easily be modified to operate on trees that do not satisfy some or any of the aforementioned assumptions on the tree structure; for instance, how it can be applied to rooted, ordered or unlabelled trees.
Behavioral variation in Drosophila melanogaster: no evidence for common alleles of large- effect at the foraging gene in a population from North Carolina, USA
Authors: Turner Thomas , Giauque Christopher C , Schrider Daniel R , Kern Andrew D
Published: April 2014

It has been postulated that natural populations of Drosophila melanogaster are comprised of two behavioral morphs termed "rover" and "sitter", and that this variation is caused mainly by large-effect alleles at a single locus. Contrary to common assertions, however, published support for the existence of common large effect alleles in nature is quite limited. To further investigate, we quantified the foraging behavior of 36 sequenced strains from a natural population, performed an association study, and described patterns of molecular evolution at the foraging locus. Though there was significant variation in foraging behavior among genotypes, this variation was continuously distributed and not significantly associated with genetic variation at the foraging gene. Patterns of molecular population genetic variation at this gene also provide no support for the hypothesis that for is a target of recent balancing selection. Though our data only apply to this specific population, we propose that additional data is required to support a hypothesis of common alleles of large effect on foraging behavior in nature.
Quantitative comparison of single-cell sequencing methods using hippocampal neurons
Authors: Ning Luwen , Wang Guan , Li Zhoufang , Hu Wen , Hou Qingming , Tong Yin , Zhang Meng , Qin Li , Chen Xiaoping , Man Heng-Ye , Liu Pinghua , He Jiankui
Published: April 2014

Single-cell genomic analysis has grown rapidly in recent years and will find widespread applications in various fields of biology, including cancer biology, development, immunology, pre-implantation genetic diagnosis, and neurobiology. In this study, we amplified genomic DNA from individual hippocampal neurons using one of three single-cell DNA amplification methods (multiple annealing and looping-based amplification cycles (MALBAC), multiple displacement amplification (MDA), and GenomePlex whole genome amplification (WGA4)). We then systematically evaluated the genome coverage, GC-bias, reproducibility, and copy number variations among individual neurons. Our results showed that single-cell genome sequencing results obtained from the MALBAC and WGA4 methods are highly reproducible and have a high success rate. Chromosome-level and subchromosomal-level copy number variations among individual neurons can be detected.
Phylogenetic ANOVA: The Expression Variance and Evolution (EVE) model for quantitative trait evolution
Authors: Rohlfs Rori , Nielsen Rasmus
Published: April 2014

A number of methods have been developed for modeling the evolution of a quantitative trait on a phylogeny. These methods have received renewed interest in the context of genome-wide studies of gene expression, in which the expression levels of many genes can be modeled as quantitative traits. We here develop a new method for joint analyses of quantitative traits within and between-species, the Expression Variance and Evolution (EVE) model. The model parameterizes the ratio of population to evolutionary expression variance, facilitating a wide variety of analyses, including a test for lineage-specific shifts in expression level, and a phylogenetic ANOVA that can detect genes with increased or decreased ratios of expression divergence to diversity, analogous to the famous HKA test used to detect selection at the DNA level. We use simulations to explore the properties of these tests under a variety of circumstances and show that the phylogenetic ANOVA is more accurate than the standard ANOVA (no accounting for phylogeny) sometimes used in transcriptomics. We then apply the EVE model to a mammalian phylogeny of 15 species typed for expression levels in liver tissue. We identify genes with high expression divergence between-species as candidates for expression level adaptation, and genes with high expression diversity within-species as candidates for expression level conservation and/or plasticity. Using the test for lineage-specific expression shifts, we identify several candidate genes for expression level adaptation on the catarrhine and human lineages, including genes putatively related to dietary changes in humans. We compare these results to those reported previously using a model which ignores expression variance within-species, uncovering important differences in performance. We demonstrate the necessity for a phylogenetic model in comparative expression studies and show the utility of the EVE model to detect expression divergence, diversity, and branch-specific shifts.
Highway maintenance: impact of framework agreements on contractor performance
Authors: Lam Terence , Gale Keith
Published: April 2014

Purpose

– The construction industry in the UK has a history of client dissatisfaction. A potential solution for improvement is through use of a framework agreement, where long-term relationships between parties may focus upon performance. The purpose of this paper is to assess whether use of framework agreements for highway maintenance projects can result in significant improvement for performance when compared with engagement of contractors through traditional discrete methods.

Design/methodology/approach

– A single-case study approach is used to investigate outcomes set within the context of a major county council in the UK. Quantitative data compiled from 164 civil engineering highway maintenance projects are separated into two groups – one represents those procured using traditional discrete methods and the other within a framework agreement.

Findings

– Results from independent-samples t-tests identified significant improvements in overall performance and in time (finish on time), cost (payment accuracy) and quality (defects and health and safety) resulted from the framework agreements.

Research limitations/implications

– The results of this study are derived from one unique and typical case, but they form a baseline upon which further research can build to test their significance in many other settings for construction and maintenance programme, especially in housing, education and highways. This research does not cover the impact of framework agreements on production and transaction costs which should be treated as a separate area for further research.

Practical implications

– Councils have a statutory duty to provide and maintain a wide range of local services and facilities, including transportation and road network. Conclusions from this study support use of framework agreements within a public sector environment, leading to improvement for contractor performance due to longer term relationship with clients. This in turn enhances quality of works and hence value for money from the councils’ highway budgets.

Originality/value

– Construction frameworks are a relatively new idea. Although a number of frameworks have been concluded, there is very little analysis regarding performance outcomes. This research tested and confirmed the validity of impact of this new approach on contractor performance.
Extending theEU RenewableEnergyDirective sustainability criteria to solid bioenergy from forests
Authors: Fritsche Uwe R. , Iriarte Leire , de Jong Johnny , Agostini Alessandro , Scarlat Nicolae
Published: April 2014

Solid bioenergy from forests plays — and is expected to continue to play — a key role to fulfil the renewable energy targets at theEuropeanUnion level. When theRenewableEnergyDirective was enacted, sustainability criteria were incorporated solely for biofuels and bioliquids. Sustainability criteria for solid bioenergy are also needed in order to prevent wood and primary forest residues from posing additional environmental risks to ecosystems. Acknowledging this, theEuropeanCommission has been working on extending the biofuels and bioliquids provisions to solid biomass. An internal draft was circulated inAugust 2013 which addressed the ways to both balance and mitigate the risks in three main topics: biodiversity; sustainable forest management; and greenhouse gases. This paper presents a set of criteria and indicators, developed during workshops with experts fromGovernments, scientific institutions, businesses andNGOs, that may be considered by theEUto assure that solid biomass from forests is obtained in an environmentally sustainable way.