bluuebunny/crossref_metadata_2025 huggingface dataset:
Short-term effect of fuel treatments on fire behaviour in a mixed heathland: a comparative assessment in an outdoor wind tunnel
Authors: Marino Eva , Hernando Carmen , Madrigal Javier , Guijarro Mercedes
Published: November 2014

Fuel management is one of the main challenges for wildfire prevention in the Mediterranean region, where wildfires have important environmental and socioeconomic effects. Different treatments are usually applied in fire-prone shrubland to try to modify its flammability. However, a knowledge gap on the effectiveness of fuel management techniques still exists. We studied the effects of two mechanical treatments (shrub crushing and shrub clearing with removal) and of prescribed burning, on fire behaviour, and compared them with untreated vegetation. Experimental burns in 0.8 × 6 m samples of regenerated shrubs 2 years after treatments were performed in an outdoor wind tunnel. All fuel treatments effectively modified fire behaviour, but no significant difference between treatment types was observed. Shrub fuel structure was the main factor affecting fire behaviour. Reduction of fuel load and height, especially necromass fraction, decreased flame height and fire intensity but did not affect fire rate of spread. Moisture contents of live and dead fuel fractions were not significant as independent parameters, but the average moisture level of the shrub fuel complex showed a relevant effect in determining fire behaviour. Temperature regime within and above the shrubs was also related to shrub fuel structure. This study contributes to understanding fuel management in shrubland by providing information about different fuel treatments effects on fire behaviour.
The Toll/NF-κB signaling pathway is required for epidermal wound repair in
Drosophila
Authors: Carvalho Lara , Jacinto António , Matova Nina
Published: November 2014

Significance

Injury and repair of broken skin are an integral part of human existence, but the ability to heal wounds extends across species. Animals ranging from insects and worms to fish, amphibians, birds, and mammals all protect and restore body integrity. Our study reveals that the evolutionary-conserved Toll/NF-κB signaling pathway, which provides the first line of defense against microbial infection, is crucial for wound repair in the embryonic epidermis (the skin) of the insect
Drosophila melanogaster
. Toll/NF-κB signaling promotes remodeling of cellular junctions and assembly of a cytoskeletal ring around the wound. Contraction of this ring much like a “purse string” fastens the epidermal gap. The findings set the stage for a similar investigation of the pathway in wound repair in vertebrates.
Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing
Authors: Chan Rebecca W. Y. , Jiang Peiyong , Peng Xianlu , Tam Lai-Shan , Liao Gary J. W. , Li Edmund K. M. , Wong Priscilla C. H. , Sun Hao , Chan K. C. Allen , Chiu Rossa W. K. , Lo Y. M. Dennis
Published: November 2014

Significance

Through the use of massively parallel sequencing, we have demonstrated a spectrum of plasma DNA abnormalities in patients with systemic lupus erythematosus. These abnormalities include aberrant measured genomic representations, hypomethylation, and DNA fragment size shortening. The binding of anti-double–stranded DNA antibody to plasma DNA appears to be an important factor associated with these abnormalities. These findings provide valuable insights into the biology of plasma DNA in an autoimmune disease and have potential implications for the development of new molecular markers for systemic lupus erythematosus.
Reliability-dependent contributions of visual orientation cues in parietal cortex
Authors: Rosenberg Ari , Angelaki Dora E.
Published: November 2014

Significance

The world is 3D, but our eyes sense 2D projections. Constructing 3D spatial representations is consequently a complex problem the brain must solve for us to interact with the environment. Robust 3D representations can theoretically be created by combining distinct visual signals according to their reliabilities, which depend on factors such as an object’s orientation and distance. Here, we show that reliability constrains the integration of texture and disparity cues for 3D orientation in macaque parietal cortex. Consistent with human perceptual studies, the contribution of texture cues is found to increase as the object’s slant (i.e., depth variation) increases. This finding suggests that the parietal cortex is capable of combining multiple visual signals to perform statistical inference about the 3D world.
Knowledge despite falsehood
Authors: Montminy Martin
Published: November 2014

I examine the claim, made by some authors, that we sometimes acquire knowledge from falsehood. I focus on two representative cases in which a subject S infers a proposition q from a false proposition p. If S knows that q, I argue, S’s false belief that p is not essential to S’s cognition. S’s knowledge is instead due to S’s belief that p′, a proposition in the neighbourhood of p that S (dispositionally) believes (and knows). S thus knows despite her false belief. The widely accepted and plausible principle that inferential knowledge requires known premises is unscathed.
The effect of perceived streakiness on the shot‐taking behaviour of basketball players
Authors: Csapo Peter , Avugos Simcha , Raab Markus , Bar‐Eli Michael
Published: November 2014

We examine behavioural changes of basketball players arising from the hot‐hand belief and use data of 1216 National Basketball Association games to measure the effect of cold and hot streaks on three proxies of shot difficulty. We find that the more consecutive shots players make (miss), the more difficult (easier) shots become along the three dimensions. Furthermore, most players' performance seems to improve during hot streaks because they attempt more difficult shots while no significant decrease in shooting accuracy takes place. This might explain why most previous studies could not find empirical evidence for the hot‐hand belief in basketball when considering in‐game field goal shooting.
The construction of spatial mental models—A new view on the continuity effect
Authors: Nejasmic Jelica , Bucher Leandra , Knauff Markus
Published: November 2014

Many studies show that spatial reasoning with information that describe relations between two or more objects relies on the construction and inspection of mental models. This article mainly focuses on the phenomenon that humans have more difficulties in processing spatial information that is not directly related to each other—for example, presented discontinuously—what is also known as the continuity effect. The article investigates how humans integrate such information into one unified mental model. In four experiments, we investigated the question whether (a) reasoners construct more than one (preliminary) model, with the first two premises presented in a discontinuous description, and integrate the models afterwards, or alternatively (b) construct one preliminary model that is later modified in the light of the last parts of problem description. The results support the second assumption and offer a new view on the continuity effect and the fundamental principles of model construction and variation in human spatial reasoning.
Phospholipase D1 facilitates second-phase myoblast fusion and skeletal muscle regeneration
Authors: Teng Shuzhi , Stegner David , Chen Qin , Hongu Tsunaki , Hasegawa Hiroshi , Chen Li , Kanaho Yasunori , Nieswandt Bernhard , Frohman Michael A. , Huang Ping
Published: November 2014

Myoblast differentiation and fusion is a well-orchestrated multistep process that is essential for skeletal muscle development and regeneration. Phospholipase D1 (PLD1) has been implicated in the initiation of myoblast differentiation in vitro. However, whether PLD1 plays additional roles in myoblast fusion and exerts a function in myogenesis in vivo remains unknown. Here we show that PLD1 expression is up-regulated in myogenic cells during muscle regeneration after cardiotoxin injury and that genetic ablation of PLD1 results in delayed myofiber regeneration. Myoblasts derived from PLD1-null mice or treated with PLD1-specific inhibitor are unable to form mature myotubes, indicating defects in second-phase myoblast fusion. Concomitantly, the PLD1 product phosphatidic acid is transiently detected on the plasma membrane of differentiating myocytes, and its production is inhibited by PLD1 knockdown. Exogenous lysophosphatidylcholine, a key membrane lipid for fusion pore formation, partially rescues fusion defect resulting from PLD1 inhibition. Thus these studies demonstrate a role for PLD1 in myoblast fusion during myogenesis in which PLD1 facilitates the fusion of mononuclear myocytes with nascent myotubes.
PAS kinase is activated by direct SNF1-dependent phosphorylation and mediates inhibition of TORC1 through the phosphorylation and activation of Pbp1
Authors: DeMille Desiree , Badal Bryan D. , Evans J. Brady , Mathis Andrew D. , Anderson Joseph F. , Grose Julianne H.
Published: November 2014

We describe the interplay between three sensory protein kinases in yeast: AMP-regulated kinase (AMPK, or SNF1 in yeast), PAS kinase 1 (Psk1 in yeast), and the target of rapamycin complex 1 (TORC1). This signaling cascade occurs through the SNF1-dependent phosphorylation and activation of Psk1, which phosphorylates and activates poly(A)- binding protein binding protein 1 (Pbp1), which then inhibits TORC1 through sequestration at stress granules. The SNF1-dependent phosphorylation of Psk1 appears to be direct, in that Snf1 is necessary and sufficient for Psk1 activation by alternate carbon sources, is required for altered Psk1 protein mobility, is able to phosphorylate Psk1 in vitro, and binds Psk1 via its substrate-targeting subunit Gal83. Evidence for the direct phosphorylation and activation of Pbp1 by Psk1 is also provided by in vitro and in vivo kinase assays, including the reduction of Pbp1 localization at distinct cytoplasmic foci and subsequent rescue of TORC1 inhibition in PAS kinase–deficient yeast. In support of this signaling cascade, Snf1-deficient cells display increased TORC1 activity, whereas cells containing hyperactive Snf1 display a PAS kinase–dependent decrease in TORC1 activity. This interplay between yeast SNF1, Psk1, and TORC1 allows for proper glucose allocation during nutrient depletion, reducing cell growth and proliferation when energy is low.
The interplay of Hrd3 and the molecular chaperone system ensures efficient degradation of malfolded secretory proteins
Authors: Mehnert Martin , Sommermeyer Franziska , Berger Maren , Kumar Lakshmipathy Sathish , Gauss Robert , Aebi Markus , Jarosch Ernst , Sommer Thomas
Published: November 2014

Misfolded proteins of the secretory pathway are extracted from the endoplasmic reticulum (ER), polyubiquitylated by a protein complex termed the Hmg-CoA reductase degradation ligase (HRD-ligase), and degraded by cytosolic 26S proteasomes. This process is termed ER-associated protein degradation (ERAD). We previously showed that the membrane protein Der1, which is a subunit of the HRD-ligase, is involved in the export of aberrant polypeptides from the ER. Unexpectedly, we also uncovered a close spatial proximity of Der1 and the substrate receptor Hrd3 in the ER lumen. We report here on a mutant Hrd3KR that is selectively defective for ERAD of soluble proteins. Hrd3KR displays subtle structural changes that affect its positioning toward Der1. Furthermore, increased quantities of the ER-resident Hsp70-type chaperone Kar2 and the Hsp40-type cochaperone Scj1 bind to Hrd3KR. Of note, deletion of SCJ1 impairs ERAD of model substrates and causes the accumulation of client proteins at Hrd3. Our data imply a function of Scj1 in the removal of malfolded proteins from the receptor Hrd3, which facilitates their delivery to downstream-acting components like Der1.
The formin FMNL3 assembles plasma membrane protrusions that participate in cell–cell adhesion
Authors: Gauvin Timothy J. , Young Lorna E. , Higgs Henry N.
Published: November 2014

FMNL3 is a vertebrate-specific formin protein previously shown to play a role in angiogenesis and cell migration. Here we define the cellular localization of endogenous FMNL3, the dynamics of GFP-tagged FMNL3 during cell migration, and the effects of FMNL3 suppression in mammalian culture cells. The majority of FMNL3 localizes in a punctate pattern, with >95% of these puncta being indistinguishable from the plasma membrane by fluorescence microscopy. A small number of dynamic cytoplasmic FMNL3 patches also exist, which enrich near cell–cell contact sites and fuse with the plasma membrane at these sites. These cytoplasmic puncta appear to be part of larger membranes of endocytic origin. On the plasma membrane, FMNL3 enriches particularly in filopodia and membrane ruffles and at nascent cell–cell adhesions. FMNL3-containing filopodia occur both at the cell–substratum interface and at cell–cell contacts, with the latter being 10-fold more stable. FMNL3 suppression by siRNA has two major effects: decrease in filopodia and compromised cell–cell adhesion in cells migrating as a sheet. Overall our results suggest that FMNL3 functions in assembly of actin-based protrusions that are specialized for cell–cell adhesion.
Reglucosylation by UDP-glucose:glycoprotein glucosyltransferase 1 delays glycoprotein secretion but not degradation
Authors: Tannous Abla , Patel Nishant , Tamura Taku , Hebert Daniel N.
Published: November 2014

UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1) is a central quality control gatekeeper in the mammalian endoplasmic reticulum (ER). The reglucosylation of glycoproteins supports their rebinding to the carbohydrate-binding ER molecular chaperones calnexin and calreticulin. A cell-based reglucosylation assay was used to investigate the role of UGT1 in ER protein surveillance or the quality control process. UGT1 was found to modify wild-type proteins or proteins that are expected to eventually traffic out of the ER through the secretory pathway. Trapping of reglucosylated wild-type substrates in their monoglucosylated state delayed their secretion. Whereas terminally misfolded substrates or off-pathway proteins were most efficiently reglucosylated by UGT1, the trapping of these mutant substrates in their reglucosylated or monoglucosylated state did not delay their degradation by the ER-associated degradation pathway. This indicated that monoglucosylated mutant proteins were actively extracted from the calnexin/calreticulin binding-reglucosylation cycle for degradation. Therefore trapping proteins in their monoglucosylated state was sufficient to delay their exit to the Golgi but had no effect on their rate of degradation, suggesting that the degradation selection process progressed in a dominant manner that was independent of reglucosylation and the glucose-containing A-branch on the substrate glycans.
Methionine sulfoxide reductase 2 reversibly regulates Mge1, a cochaperone of mitochondrial Hsp70, during oxidative stress
Authors: Allu Praveen Kumar , Marada Adinarayana , Boggula Yerranna , Karri Srinivasu , Krishnamoorthy Thanuja , Sepuri Naresh Babu V.
Published: November 2014

Peptide methionine sulfoxide reductases are conserved enzymes that reduce oxidized methionines in protein(s). Although these reductases have been implicated in several human diseases, there is a dearth of information on the identity of their physiological substrates. By using Saccharomyces cerevisiae as a model, we show that of the two methionine sulfoxide reductases (MXR1, MXR2), deletion of mitochondrial MXR2 renders yeast cells more sensitive to oxidative stress than the cytosolic MXR1. Our earlier studies showed that Mge1, an evolutionarily conserved nucleotide exchange factor of Hsp70, acts as an oxidative sensor to regulate mitochondrial Hsp70. In the present study, we show that Mxr2 regulates Mge1 by selectively reducing MetO at position 155 and restores the activity of Mge1 both in vitro and in vivo. Mge1 M155L mutant rescues the slow-growth phenotype and aggregation of proteins of mxr2Δ strain during oxidative stress. By identifying the first mitochondrial substrate for Mxrs, we add a new paradigm to the regulation of the oxidative stress response pathway.
The Cdc15 and Imp2 SH3 domains cooperatively scaffold a network of proteins that redundantly ensure efficient cell division in fission yeast
Authors: Ren Liping , Willet Alaina H. , Roberts-Galbraith Rachel H. , McDonald Nathan A. , Feoktistova Anna , Chen Jun-Song , Huang Haiming , Guillen Rodrigo , Boone Charles , Sidhu Sachdev S. , Beckley Janel R. , Gould Kathleen L.
Published: November 2014

Schizosaccharomyces pombe cdc15 homology (PCH) family members participate in numerous biological processes, including cytokinesis, typically by bridging the plasma membrane via their F-BAR domains to the actin cytoskeleton. Two SH3 domain–containing PCH family members, Cdc15 and Imp2, play critical roles in S. pombe cytokinesis. Although both proteins localize to the contractile ring, with Cdc15 preceding Imp2, only cdc15 is an essential gene. Despite these distinct roles, the SH3 domains of Cdc15 and Imp2 cooperate in the essential process of recruiting other proteins to stabilize the contractile ring. To better understand the connectivity of this SH3 domain–based protein network at the CR and its function, we used a biochemical approach coupled to proteomics to identify additional proteins (Rgf3, Art1, Spa2, and Pos1) that are integrated into this network. Cell biological and genetic analyses of these SH3 partners implicate them in a range of activities that ensure the fidelity of cell division, including promoting cell wall metabolism and influencing cell morphogenesis.
Sport: A Very Short Introduction
Authors: Cronin Mike
Published: November 2014

Sport is big business, international in nature, and the focus of much media and cultural attention. Sport: A Very Short Introduction charts the history of sport, from its traditional origins in folk football and cock fighting to its position as a global phenomenon today. Looking at a variety of sports from team games such as rugby, cricket, and football to games for individuals such as golf, tennis, and skiing, it considers how these first emerged and captivated the interest of ordinary people, and how sport has been transformed within our daily lives. This VSI also explores the relationship between sport and class, gender, commerce, identity, and ethics.
Revisiting the Supplemental Nutrition Assistance Program cycle of food intake: Investigating heterogeneity, diet quality, and a large boost in benefit amounts
Authors: Todd Jessica E.
Published: November 2014

The monthly cycle of daily food intake among adult participants in the Supplemental Nutrition Assistance Program is examined using data from the 2007–10 National Health and Nutrition Examination Survey. Exogenous variation in interview and benefit receipt dates provides means for identification, and a difference‐in‐differences specification is used to account for the large boost in benefits that began in April 2009 via the American Recovery and Reinvestment Act (ARRA). Caloric intake declined as much as 25% at the end of the month prior to ARRA, but not after implementation. Few differences were observed for diet quality measures or among subgroups. Increases in SNAP benefit amounts may help smooth food intake over the benefit month.
Mechanotransduction map: simulation model, molecular pathway, gene set
Authors: Dent Jennifer E. , Devescovi Valentina , Li Han , Di Lena Pietro , Lu Youtao , Liu Yuanhua , Nardini Christine
Published: November 2014

Motivation: Mechanotransduction—the ability to output a biochemical signal from a mechanical input—is related to the initiation and progression of a broad spectrum of molecular events. Yet, the characterization of mechanotransduction lacks some of the most basic tools as, for instance, it can hardly be recognized by enrichment analysis tools, nor could we find any pathway representation. This greatly limits computational testing and hypothesis generation on mechanotransduction biological relevance and involvement in disease or physiological mechanisms.

Results: We here present a molecular map of mechanotransduction, built in CellDesigner to warrant that maximum information is embedded in a compact network format. To validate the map’s necessity we tested its redundancy in comparison with existing pathways, and to estimate its sufficiency, we quantified its ability to reproduce biological events with dynamic simulations, using Signaling Petri Networks.

Availability and implementation: SMBL language map is available in the Supplementary Data: core_map.xml, basic_map.xml.

Contact: christine.nardini.rsrc@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells
Authors: Keane Peter , Ceredig Rhodri , Seoighe Cathal
Published: November 2014

Motivation: The expression of tissue-restricted antigens (TRAs) in the thymus is required to ensure efficient negative selection of potentially auto-reactive T lymphocytes and avoid autoimmune disease. This promiscuous expression is under the control of the autoimmune regulator (AIRE), a transcription factor expressed in medullary thymic epithelial cells (mTECs). Tissue-specific alternative splicing may also produce TRAs but the extent to which splice isoforms that are restricted to specific tissues are expressed in mTECs is yet to be investigated.

Results: We reanalyzed microarray and RNA-Seq datasets from mouse mTECs and other epithelial and non-epithelial cell types and found that the diversity of splice isoforms in mTECs was greater than in any of the other cell types or tissues studied. We identified tissue-specific isoforms from a panel of mouse tissues and found several examples of such isoforms that are expressed in mTECs. The number of isoforms with restricted expression found in mTECs was significantly higher than for comparable cell types. Furthermore, we found evidence that AIRE influences the increased splicing diversity observed in mTECs as the genes for which tissue restricted isoforms are produced in mTECs were significantly more likely than other genes to be differentially spliced between AIRE knock-out and wild-type samples. Our results suggest that developing T lymphocytes are exposed to diverse tissue-restricted splice isoforms in the thymus and that AIRE has a direct or indirect role in this process, representing a novel aspect of its role in the maintenance of immune self-tolerance.

Contact: cathal.seoighe@nuigalway.ie

Supplementary information:  Supplementary data are available at Bioinformatics online.
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data
Authors: Fermin Damian , Avtonomov Dmitry , Choi Hyungwon , Nesvizhskii Alexey I.
Published: November 2014

We present LuciPHOr2, a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data. As an extension of the original LuciPHOr (version 1) for phosphorylation site localization, the new software provides a site-level localization score for generic PTMs and associated false discovery rate called the false localization rate. We describe several novel features such as operating system independence and reduced computation time through multiple threading. We also discuss optimal parameters for different types of data and illustrate the new tool on a human skeletal muscle dataset for lysine-acetylation.

Availability and implementation: The software is freely available on the SourceForge website http://luciphor2.sourceforge.net.

Contact:  hyung_won_choi@nuhs.edu.sg, nesvi@med.umich.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Decreasing predation levels and increasing landings challenge the paradigm of non-management of North Sea brown shrimp (Crangon crangon)
Authors: Temming Axel , Hufnagl Marc
Published: November 2014

The North Sea brown shrimp fishery is currently regulated neither with quotas nor with effort management. The current paradigm of non-management was based on an analysis of the total predation by cod and whiting in relation to commercial catches for the period 1970–1995 and the estimated total dominance of natural mortality. However, since this period, the North Sea ecosystem has undergone pronounced changes with overfishing and climate change causing a substantial decline in predator stocks, namely cod and whiting. In addition, both predators have shifted their range of distribution causing a reduced overlap with brown shrimp. Here, we extend the previous assessment of brown shrimp predation for the years 1996–2011 using updated stock assessment and predator distribution data. For the first time, predation estimates are used together with commercial landings to partition independent estimates of total mortality into fishing and predation mortality. We demonstrate that the decline of key predators of brown shrimp in combination with a shift in the distributional range of the predators has caused a new situation, in which the fishery has become the main mortality source of adult brown shrimp (>50 mm). Average landings since 2000 have been ∼40% higher than in the 1980s and 1990s, indicating that humans have at least partly taken over the share previously taken by juvenile whiting and cod. We discuss that this situation is likely to continue, because three marine mammal species have built up a combined population of over 80 000 individuals, which hunt for potential brown shrimp predators mainly in the distribution area of brown shrimp. The application of two yield-per-recruit models of different complexity indicates potential growth overfishing of brown shrimp and reopens the discussion of management.
Interactive effects of temperature and light during deep convection: a case study on growth and condition of the diatom Thalassiosira weissflogii
Authors: Walter B. , Peters J. , van Beusekom J. E. E. , St. John M. A.
Published: November 2014

Aim of this study was to expose phytoplankton to growth conditions simulating deep winter convection in the North Atlantic and thereby to assess changes in physiology enabling their survival. Growth rate, biochemical composition, and photosynthetic activity of the diatom Thalassiosira weissflogii were determined under two different light scenarios over a temperature range of 5–15°C to simulate conditions experienced by cells during winter deep convection. These metrics were examined under a low light scenario (20 µmol m−2 s−1, 12/12 h light/dark), and compared with a scenario of short light pulses of a higher light intensity (120 µmol m−2 s−1, 2/22 h light/dark). Both experimental light conditions offered the same daily light dose. No growth was observed at temperatures below 8°C. Above 8°C, growth rates were significantly higher under low light conditions compared with those of short pulsed light exposures, indicating a higher efficiency of light utilization. This could be related to (i) a higher content of Chl a per cell in the low light trial and/or (ii) a more efficient transfer of light energy into growth as indicated by constantly low carbohydrate levels. In contrast, pulsed intense light led to an accumulation of carbohydrates, which were catabolized during the longer dark period for maintaining metabolism. Light curves measured via Chl a fluorescence indicated low light assimilation for the algae exposed to short pulsed light. We postulate that our trial with short light pluses did not provide sufficient light to reach full light saturation. In general, photosynthesis was more strongly affected by temperature under pulsed light than under low light conditions. Our results indicate that model estimates of primary production in relation to deep convection, which are based on average low light conditions, not considering vertical transportation of algae will lead to an overestimation of in situ primary production.
Aggressive behaviour of spotted spiny lobsters (Panulirus guttatus) in different social contexts: the influence of sex, size, and missing limbs
Authors: Briones-Fourzán Patricia , Domínguez-Gallegos Roberto , Lozano-Álvarez Enrique
Published: November 2014

Panulirus guttatus is a sedentary spiny lobster that exhibits cryptic behaviour and a low degree of gregariousness. Because these lobsters are obligate coral reef-dwellers and avoid sandy expanses, they are potentially distributed in relatively small, discrete populations with variable social contexts, which can strongly influence the expression of aggression. The present study examined the relative importance of sex, size, and the number of missing limbs in the shelter-related aggressive behaviour of replicated groups of four lobsters that differed in social context (i.e. same-sex and mixed-sex groups). Each group was held in a seawater tank with a single artificial cave-like shelter. The interior of the cave was video-recorded for 72 h and the number of aggressions performed by each individual was quantified in a 10-min segment of video per hour. Most aggressions were related to occupancy of the shelter inner space and tended to end when individuals were sufficiently spaced out. In general, per-capita rates of aggression were higher at night and size was an important predictor of aggressiveness among individuals of the same sex. Males were substantially more aggressive than females, but the number of missing limbs significantly impacted the degree of aggressiveness in males. In mixed-sex groups, fewer aggressions occurred when the largest individual was a male than when it was a female, suggesting that it may take longer for smaller males to assert themselves. Our results provide insights into some potential consequences of increase in fishing pressure and loss of habitat complexity in Caribbean reefs for the social behaviour and population dynamics of these lobsters.
Evaluation of the eazyplex® SuperBug CRE system for rapid detection of carbapenemases and ESBLs in clinical Enterobacteriaceae isolates recovered at two Spanish hospitals
Authors: García-Fernández Sergio , Morosini María-Isabel , Marco Francesc , Gijón Desirèe , Vergara Andrea , Vila Jordi , Ruiz-Garbajosa Patricia , Cantón Rafael
Published: November 2014

Objectives

To evaluate the performance of the eazyplex® SuperBug CRE system, a loop-mediated isothermal amplification (LAMP)-based system, for confirming the presence of carbapenemases in addition to CTX-M-type ESBLs in previously genotypically and/or phenotypically characterized clinical Enterobacteriaceae isolates recovered in two centres in Spain.

Methods

A collection of 94 carbapenemase-producing strains previously characterized by conventional PCR and sequencing and a total of 45 prospectively collected isolates with phenotypes compatible with the presence of a carbapenemase were tested with the eazyplex® SuperBug CRE system. In both cases, the presence of an ESBL was also assessed. Results were evaluated to establish the accuracy of this rapid LAMP-based system as well as to determine the concordance between all approaches.

Results

The eazyplex® SuperBug CRE system correctly detected bla carbapenemase genes with or without blaCTX-M genes in 100% of the molecularly characterized strains. Absolute concordance (100%) was also observed in the case of isolates with phenotypes compatible with the presence of a carbapenemase with or without an ESBL inferred by susceptibility patterns and phenotypic inhibitory profiles. Determinations performed with the eazyplex® SuperBug CRE system took 15 min.

Conclusions

The eazyplex® SuperBug CRE system proved to be a powerful tool for the detection of different carbapenemases as well as CTX-M-type ESBLs in Enterobacteriaceae with a rapid resolution time. The test has the high-performance parameters attributable to the sensitivity and specificity already demonstrated by LAMP-based assays. These results assure the usefulness of this test for routine rapid confirmation of carbapenemase-producing Enterobacteriaceae.
BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers
Authors: Abo Ryan P. , Ducar Matthew , Garcia Elizabeth P. , Thorner Aaron R. , Rojas-Rudilla Vanesa , Lin Ling , Sholl Lynette M. , Hahn William C. , Meyerson Matthew , Lindeman Neal I. , Van Hummelen Paul , MacConaill Laura E.
Published: November 2014

Genomic structural variation (SV), a common hallmark of cancer, has important predictive and therapeutic implications. However, accurately detecting SV using high-throughput sequencing data remains challenging, especially for ‘targeted’ resequencing efforts. This is critically important in the clinical setting where targeted resequencing is frequently being applied to rapidly assess clinically actionable mutations in tumor biopsies in a cost-effective manner. We present BreaKmer, a novel approach that uses a ‘kmer’ strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are predicted by realigning an assembled consensus sequence created from sequence reads that were abnormally aligned to the reference genome. Using targeted resequencing data from tumor specimens with orthogonally validated SV, non-tumor samples and whole-genome sequencing data, BreaKmer had a 97.4% overall sensitivity for known events and predicted 17 positively validated, novel variants. Relative to four publically available algorithms, BreaKmer detected SV with increased sensitivity and limited calls in non-tumor samples, key features for variant analysis of tumor specimens in both the clinical and research settings.
Do Markets Erode Social Responsibility? *
Authors: Bartling Björn , Weber Roberto A. , Yao Lan
Published: November 2014

This article studies socially responsible behavior in markets. We develop a laboratory product market in which low-cost production creates a negative externality for third parties, but where alternative production with higher costs mitigates the externality. Our first study, conducted in Switzerland, reveals a persistent preference among many consumers and firms for avoiding negative social impact in the market, reflected both in the composition of product types and in a price premium for socially responsible products. Socially responsible behavior is generally robust to varying market characteristics, such as increased seller competition and limited consumer information, and it responds to prices in a manner consistent with a model in which positive social impact is a utility-enhancing feature of a consumer product. In a second study, we investigate whether market social responsibility varies across societies by comparing market behavior in Switzerland and China. While subjects in Switzerland and China do not differ in their degree of social concern in nonmarket contexts, we find that low-cost production that creates negative externalities is significantly more prevalent in markets in China. Across both studies, consumers in markets exhibit less social concern than subjects in a comparable individual choice context.
Very Long-Run Discount Rates *
Authors: Giglio Stefano , Maggiori Matteo , Stroebel Johannes
Published: November 2014

We estimate how households trade off immediate costs and uncertain future benefits that occur in the very long run, 100 or more years away. We exploit a unique feature of housing markets in the United Kingdom and Singapore, where residential property ownership takes the form of either leaseholds or freeholds. Leaseholds are temporary, prepaid, and tradable ownership contracts with maturities between 99 and 999 years, while freeholds are perpetual ownership contracts. The price difference between leaseholds and freeholds reflects the present value of perpetual rental income starting at leasehold expiration, and is thus informative about very long-run discount rates. We estimate the price discounts for varying leasehold maturities compared to freeholds and extremely long-run leaseholds via hedonic regressions using proprietary data sets of the universe of transactions in each country. Households discount very long-run cash flows at low rates, assigning high present value to cash flows hundreds of years in the future. For example, 100-year leaseholds are valued at more than 10% less than otherwise identical freeholds, implying discount rates below 2.6% for 100-year claims.
Regulating Consumer Financial Products: Evidence from Credit Cards
*
Authors: Agarwal Sumit , Chomsisengphet Souphala , Mahoney Neale , Stroebel Johannes
Published: November 2014

We analyze the effectiveness of consumer financial regulation by considering the 2009 Credit Card Accountability Responsibility and Disclosure (CARD) Act. We use a panel data set covering 160 million credit card accounts and a difference-in-differences research design that compares changes in outcomes over time for consumer credit cards, which were subject to the regulations, to changes for small business credit cards, which the law did not cover. We estimate that regulatory limits on credit card fees reduced overall borrowing costs by an annualized 1.6% of average daily balances, with a decline of more than 5.3% for consumers with FICO scores below 660. We find no evidence of an offsetting increase in interest charges or a reduction in the volume of credit. Taken together, we estimate that the CARD Act saved consumers $11.9 billion a year. We also analyze a nudge that disclosed the interest savings from paying off balances in 36 months rather than making minimum payments. We detect a small increase in the share of accounts making the 36-month payment value but no evidence of a change in overall payments.
Incidence of Intraoperative Hypersensitivity Reactions: A Registry Analysis
Authors: Saager Leif , Turan Alparslan , Egan Cameron , Mascha Edward J. , Kurz Andrea , Bauer Maria , Besson Hervé , Sessler Daniel I. , Hesler Brian D.
Published: November 2014

AbstractAbstract

A novel methodology combining electronic search strategies and clinical adjudication was used to identify occurrences of hypersensitivity reactions. The overall incidence of hypersensitivity reactions identified from the electronic records of 178,746 procedures performed on 120,242 patients was 1 in 677 and that of anaphylaxis was 1 in 4,583. The incidence of anaphylaxis was similar to that reported in previous studies but that of hypersensitivity reactions was nearly seven times higher.

Background:

Previously reported incidences for intraoperative hypersensitivity reactions vary more than 15-fold. The goal was to determine the incidence of intraoperative hypersensitivity events at a U.S. surgical center.

Methods:

With institutional review board (Cleveland, Ohio) approval and waiver of written/informed consent, the anesthesia records of adult patients undergoing noncardiac surgery from 2005 to 2011 at the Cleveland Clinic were queried using a novel electronic search protocol developed to identify potential hypersensitivity reactions: cardiovascular collapse defined as systolic arterial blood pressure less than 50 mmHg; administration of epinephrine; administration of diphenhydramine; physician comments in the anesthesia record suggestive of hypersensitivity reactions; laboratory tests for histamine, tryptase, or immunoglobulin-E within 24 h of surgery; and International Classification of Diseases, Ninth Revision, codes suggestive of hypersensitivity reactions. Each electronically identified candidate chart was evaluated by an adjudication committee. Hypersensitivity reactions were graded on a 5-point severity scale. From these data, the authors determined the proportion of operations having adjudicated hypersensitivity reactions, and calculated the 95% exact binomial CI.

Results:

Among 178,746 records, 4,008 charts were identified by the search strategies. After adjudication, 264 hypersensitivity cases were identified. The overall incidence of hypersensitivity reactions was 1:677 surgeries, corresponding to 15 (95% CI, 13 to 17) cases per 10,000 operations. The incidence of severe hypersensitivity reactions (grades 3 to 5) was 1:4,583, corresponding to 2 (95% CI, 2 to 3) cases per 10,000 operations.

Conclusions:

The incidence of severe hypersensitivity reactions was similar to previous reports. However, the overall incidence of hypersensitivity reactions was much greater than reported elsewhere, possibly because of a comprehensive search strategy.
Review of the Performance of Quantitative Sensory Testing Methods to Detect Hyperalgesia in Chronic Pain Patients on Long-term Opioids
Authors: Katz Nathaniel P. , Paillard Florence C. , Edwards Robert R.
Published: November 2014

AbstractAbstract

In a systematic review of 14 studies of opioid-induced hyperalgesia, most sensory modalities tested failed to demonstrate hypersensitivity to test stimuli, and additional work with stronger study designs is needed.

Background:

Opioid-induced hyperalgesia is a clinical syndrome whereby patients on long-term opioids become more sensitive to pain while taking opioids. Opioid-induced hyperalgesia is characterized by increased pain intensity over time, spreading of pain to other locations, and increased pain sensation to external stimuli. To characterize opioid-induced hyperalgesia, laboratory methods to measure hyperalgesia have been developed. To determine the performance of these methods, the authors conducted a systematic review of clinical studies that incorporate measures of hyperalgesia in chronic pain patients on long-term opioids.

Methods:

PubMed and Cochrane databases were searched (terms: opioid induced hyperalgesia, study or trial, and long-term or chronic). Studies published in English were selected if they were conducted in chronic pain patients on long-term opioids and incorporated measures of hyperalgesia; acute/single-dose studies and/or conducted in healthy volunteers were excluded.

Results:

Fourteen articles made the final selection (11 were selected from the search and 3 others were found from additional sources); there was one randomized controlled trial, one prospective controlled study, three prospective uncontrolled studies, and nine cross-sectional observation studies. Hyperalgesia measurement paradigms used included cold pain, heat pain, pressure pain, electrical pain, ischemic pain, and injection pain. Although none of the stimuli were capable of detecting patients’ hyperalgesia, heat pain sensitivity showed some promising results.

Conclusions:

None of the measures reviewed herein met the criteria of a definitive standard for the measurement of hyperalgesia. Additional studies that use improved study design should be conducted.
Fiber-needle Swept-source Optical Coherence Tomography System for the Identification of the Epidural Space in Piglets
Authors: Kuo Wen-Chuan , Kao Meng-Chun , Chang Kuang-Yi , Teng Wei-Nung , Tsou Mei-Yung , Chang Yin , Ting Chien-Kun
Published: November 2014

AbstractAbstract

An optical probe placed in the epidural needle coupled with swept-source optical coherence tomography can provide two-dimensional images of tissue surrounding the needle tip. Using a porcine model, high sensitivity and specificity for the identification of the epidural space were achieved.

Background:

Epidural needle insertion is traditionally a blind technique whose success depends on the experience of the operator. The authors describe a novel method using a fiber-needle–based swept-source optical coherence tomography (SSOCT) to identify epidural space.

Methods:

An optical fiber probe was placed into a hollow 18-gauge Tuohy needle. It was then inserted by an experienced anesthesiologist to continuously construct a series of two-dimensional SSOCT images by mechanically rotating the optical probe. To quantify this observation, both the average SSOCT signal intensities and their diagnostic potentials were assessed. The insertions were performed three times into both the lumbar and thoracic regions of five pigs using a paramedian approach.

Results:

A side-looking SSOCT is constructed to create a visual image of the underlying structures. The image criteria for the identification of the epidural space from the outside region were generated by the analysis of a training set (n = 100) of ex vivo data. The SSOCT image criteria for in vivo epidural space identification are high sensitivity (0.867 to 0.965) and high specificity (0.838 to 0.935). The mean value of the average signal intensities exhibits statistically significant differences (P < 0.01) and a high discriminatory capacity (area under curve = 0.88) between the epidural space and the outside tissues.

Conclusions:

This is the first study to introduce a SSOCT fiber probe embedded in a standard epidural needle. The authors anticipate that this technique will reduce the occurrence of failed epidural blocks and other complications such as dural punctures.
Rewriting the history of an extinction—was a population of Steller's sea cows (
Hydrodamalis gigas
) at St Lawrence Island also driven to extinction?
Authors: Crerar Lorelei D. , Crerar Andrew P. , Domning Daryl P. , Parsons E. C. M.
Published: November 2014

The Kommandorskiye Islands population of Steller's sea cow (
Hydrodamalis gigas
) was extirpated
ca
1768 CE. Until now, Steller's sea cow was thought to be restricted in historic times to Bering and Copper Islands, Russia, with other records in the last millennium from the western Aleutian Islands. However, Steller's sea cow bone has been obtained by the authors from St Lawrence Island, Alaska, which is significantly further north. Bone identity was verified using analysis of mitochondrial DNA. The nitrogen-15 (δ
15
N)/carbon-13 (δ
13
C) values for bone samples from St Lawrence Island were significantly (
p
≤ 0.05) different from Bering Island samples, indicating a second population. Bone samples were dated to between 1030 and 1150 BP (approx. 800–920 CE). The samples date from close to the beginning of the mediaeval warm period, which could indicate that the population at St Lawrence Island was driven to extinction by climate change. A warming of the climate in the area may have changed the availability of kelp; alternatively or in addition, the animals may have been driven to extinction by the expansion of the Inuit from the Bering Strait region, possibly due to opening waterways, maybe following bowhead whales (
Balaena mysticetus
), or searching for iron and copper. This study provides evidence for a previously unknown population of sea cows in the North Pacific within the past 1000 years and a second Steller's sea cow extirpation event in recent history.