bluuebunny/crossref_metadata_2025 huggingface dataset:
Loss of Sprouty2 in human high‐grade serous ovarian carcinomas promotes EGF‐induced E‐cadherin down‐regulation and cell invasion
Authors: So Wai-Kin , Cheng Jung-Chien , Fan Qianlan , Wong Alice S.T. , Huntsman David G. , Gilks C. Blake , Leung Peter C.K.
Published: December 2014

Sprouty (SPRY) proteins are well‐characterized factors that inhibit receptor tyrosine kinase signaling. Our Human Exonic Evidence‐Based Oligonucleotide (HEEBO) microarray results showed that the mRNA levels of SPRY2, but not of SPRY1 or SPRY4, are down‐regulated in high‐grade serous ovarian carcinoma (HGSC) tissues and epithelial ovarian cancer (EOC) cell lines. Molecular inversion probe (MIP) copy number analysis showed the deletion of the SPRY2 locus in HGSC. Overexpression of SPRY2 reduced EGF‐induced cell invasion by attenuating EGF‐induced E‐cadherin down‐regulation. Moreover, a positive correlation between SPRY2 and E‐cadherin protein levels was observed in HGSC tissues. This study reveals the loss of SPRY2 in HGSC and indicates an important tumor‐suppressive role for SPRY2 in mediating the stimulatory effect of EGF on human EOC progression.
Associations between child and sibling levels of vigorous physical activity in low-income minority families
Authors: Liu Gilbert C. , Wiehe Sarah E. , Aalsma Matthew C.
Published: December 2014

Background and objectives:

A child’s level of habitual physical activity is partly determined by a familial component, but the literature is limited regarding sibling influences. Multiple studies suggest that targeting siblings is an effective strategy for improving child health behaviors.

Patients and methods:

We analyze Moving to Opportunity for Fair Housing (MTO) data to study associations between the odds of a child attaining 20 min or more of vigorous physical activity at least 3 days every week and parallel measures from an older sibling and a parent. We include covariates representing the social environment such as household income and neigh-borhood safety.

Results:

There were 1347 study units that consisted of a child (age 11.2 y ± 2.6), an older sib-ling (age 14.8 y ± 2.8), and a parent (age 38.3 y ± 7.5). A child’s odds of vigorous physical ac-tivity for 20 min or more was increased if the older sibling (OR 1.67; 95% CI 1.32-2.11) or parent (OR 1.36; 95% CI 1.08-1.72) had a comparable activity level compared to children whose older siblings or parents did not exhibit a comparable level of activity.

Conclusions:

A younger sibling’s level of physical activity is positively associated with an older sibling’s and/or parent’s level of physical activity. Family-based approaches, especially those incorporating siblings, may be effective at increasing physical activity in children.
Inadvertent puncture of the aortic noncoronary cusp during postoperative left atrial tachycardia ablation
Authors: Aras Dursun , Ozeke Ozcan , Cay Serkan , Ozcan Firat , Kara Meryem , Topaloglu Serkan
Published: December 2014

Transseptal catheterization has become part of the interventional electrophysiologist's technical armamentarium since the development of left atrial catheter ablation and percutaneous technologies for treating mitral and aortic valve disease. Although frequently performed, the procedure's most feared complication is aortic root penetration. Focal atrial tachycardia has been described as the most common late sequela of surgical valve replacements. We present a complicated case involving the inadvertent delivery of an 8 French sheath across the noncoronary cusp during radiofrequency catheter ablation for left atrial tachycardia originating from the mitral annulus in a patient with prior mitral valve replacement.
“I Did Not Think it Was An Effective Use of Questioning”: Collective Critical Observation and Reflection of Social Studies Pedagogy
Authors: Jaffee Ashley Taylor , Marri Anand R. , Shuttleworth Jay , Hatch Thomas
Published: December 2014

This study examines how one student teaching seminar employed collective critical observation and reflection of an experienced high school social studies teacher's pedagogy using a multimedia representation of teaching. Pre-service teachers watched this teacher implement two full class lessons and reflections on teaching about freedom of speech. This study's pre-service social studies teachers exhibited a developing ability, through collective observation, to critically reflect on their individual methodological and philosophical goals, social studies teaching and learning, and professional and curricular visions in relation to their student teaching experiences and future practice. The study's findings offer implications for how pre-service social studies teachers critically reflect on their practice, while also developing knowledge of learners, subject matter, and teaching social studies.
Prevention of Pressure Ulcers Among People With Spinal Cord Injury: A Systematic Review
Authors: Groah Suzanne L. , Schladen Manon , Pineda Cynthia G. , Hsieh Ching‐Hui J.
Published: December 2014

Objectives

To evaluate the literature on the effectiveness of bed and wheelchair positioning and repositioning in the prevention of pressure ulcers (PUs) in both the spinal cord injury (SCI) and non‐SCI populations.

Design

Systematic review.

Methods

PubMed, CINAHL, PsycINFO, and EMBASE were queried with the subject heading terms “pressure sore,” “pressure ulcer,” “position or turn in bed, wheelchair,” “pressure relief,” and “pressure release.” All study design types that assessed the effectiveness of bed and wheelchair positioning and pressure relief maneuvers in any patient group and in any setting were sought. Three independent reviewers extracted and summarized details of eligible trials using a standardized method. Two independent reviewers assessed the methodological quality of each trial using the American Academy of Neurology guidelines. When reviewers were not able to reach consensus, a third independent reviewer served as tiebreaker.

Results

We identified 2820 publications, of which 49 met inclusion criteria. Of these publications, the subject population was 2834 (923 persons with SCI, 717 persons without SCI, and 1194 healthy control subjects). Among studies examining pressure related to position or repositioning in bed or sitting, procedures for measuring skin pressure and metabolism were highly variable by anatomic location, measurement technique, outcome measure, study site, participant characteristics, and description of position/turning for bed and seated interventions. Numerous factors can influence tissue interface pressures, and no prospective studies had been performed to determine a causal relationship between interface pressure and skin breakdown. Several studies suggest that skin response to pressure differs between subjects with and without SCI. Conflicting results and insufficient evidence for optimal bed and seated positioning and turning and pressure relief maneuvers to prevent PUs in both SCI and non‐SCI populations were limiting factors.

Conclusions

Although there is no clear optimal positioning or turning frequency in bed, the evidence suggests avoiding the 90° lateral position because of high pressures and PU risk over the trochanters. During sitting, pressures are linearly redistributed from the sitting area during recline and tilt; however, reclining carries with it an increased risk of shear forces on this skin. The evidence does not support conclusive guidelines on positioning or repositioning techniques for PU prevention in bed or during sitting. We conclude that PU risk is highly individualized, with the SCI population at a higher risk, which demands flexible PU prevention strategies for bed/seated positioning and pressure relief maneuvers. Education has and will remain our most powerful ally to thwart this pervasive public health problem.
Best Practices for Surgically Implanting Acoustic Transmitters in Spotted Seatrout
Authors: Reese Robillard Megan M. , Payne Laura M. , Vega Robert R. , Stunz Gregory W.
Published: December 2014

Technological advances have made acoustic tracking of fish an effective means to collect unprecedented migration data. However, one must ensure that fish survive the surgical implantation and retain transmitters, and that their health and behavior are not adversely affected. We performed a laboratory study to examine the most effective surgery technique and suture material for implanting acoustic transmitters into Spotted Seatrout Cynoscion nebulosus. Six treatment groups were used to investigate two ventral incision locations (midline and off‐midline) and three suture materials (braid, monofilament, and staples). Overall survival was high for all fish undergoing surgery (75% for surgical controls, and 74% for surgically implanted fish), suggesting that acoustic transmitter implantation can be very successful for Spotted Seatrout. However, female fish had significantly higher survival (85.7%) than male fish (41.2%). Surgery time ranged from 73 to 270 s, and our results suggest that for every second that the surgery time was reduced the odds of increasing survival are 1.5%. Moreover, the surgery process versus tagging material or incision location is the primary cause of mortality. Overall, there was no one treatment that showed distinct differences in survival and transmitter retention; however, for future telemetry studies using Vemco V13 transmitters with Spotted Seatrout, we recommend researchers (1) target fish greater than 425 mm TL, (2) minimize surgery time (preferably 160 s or less), and (3) use an off‐midline incision placement closed with two sutures using braid suture material. These techniques will help ensure successful field acoustic tracking studies by increasing the likelihood of Spotted Seatrout survival and transmitter retention. Finally, these methods have applicability to other fishes, particularly Sciaenids, with high potential for success.

Received January 29, 2014; accepted September 9, 2014
Definitions of Kant’s categories
Authors: Nunez Tyke
Published: December 2014

The consensus view in the literature is that, according to Kant, definitions in philosophy are impossible. While this is true prior to the advent of transcendental philosophy, I argue that with Kant’s Copernican Turn definitions of some philosophical concepts, the categories become possible. Along the way I discuss issues like why Kant introduces the ‘Analytic of Concepts’ as an analysis of the understanding, how this faculty, as the faculty for judging, provides the principle for the complete exhibition of the categories, how the pure categories relate to the schematized categories, and how the latter can be used on empirical objects.
Characterization of three putative xylulose 5-phosphate/fructose 6-phosphate phosphoketolases in the cyanobacterium Anabaena sp. PCC 7120
Authors: Moriyama Takashi , Tajima Naoyuki , Sekine Kohsuke , Sato Naoki
Published: December 2014

Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp) is a key enzyme in the central carbohydrate metabolism in heterofermentative bacteria, in which enzymatic property of Xfps is well characterized. This is not the case in other microbes. The cyanobacterium Anabaena sp. PCC 7120 possesses three putative genes encoding Xfp, all1483, all2567, and alr1850. We purified three putative Xfps as recombinant proteins. The results of gel filtration indicated that these proteins form homomultimer complex. All1483 and All2567 showed phosphoketolase activity, whereas Alr1850 did not show the activity. Kinetic analyses demonstrated that substrates, fructose 6-phosphate and inorganic phosphate, are cooperatively bound to enzymes positively and negatively, respectively.
The thematic hierarchy in sentence comprehension: A study on the interaction between verb class and word order in Spanish
Authors: Gattei Carolina A. , Dickey Michael W. , Wainselboim Alejandro J. , París Luis
Published: December 2014

Linking is the theory that captures the mapping of the semantic roles of lexical arguments to the syntactic functions of the phrases that realize them. At the sentence level, linking allows us to understand “who did what to whom” in an event. In Spanish, linking has been shown to interact with word order, verb class, and case marking. The current study aims to provide the first piece of experimental evidence about the interplay between word order and verb type in Spanish. We achieve this by adopting role and reference grammar and the extended argument dependency model. Two different types of clauses were examined in a self-paced reading task: clauses with object–experiencer psychological verbs and activity verbs. These types of verbs differ in the way that their syntactic and semantic structures are linked, and thus they provide interesting evidence on how information that belongs to the syntax–semantics interface might influence the predictive and integrative processes of sentence comprehension with alternative word orders. Results indicate that in Spanish, comprehension and processing speed is enhanced when the order of the constituents in the sentence mirrors their ranking on a semantic hierarchy that encodes a verb's lexical semantics. Moreover, results show that during online comprehension, predictive mechanisms based on argument hierarchization are used rapidly to inform the processing system. Our findings corroborate already existing cross-linguistic evidence on the issue and are briefly discussed in the light of other sentence-processing models.
The Economics of Collective Reputation: Evidence from the Wine Industry
Authors: Castriota Stefano , Delmastro Marco
Published: December 2014

We use original data regarding the array of Italian winery coalitions (wine denominations) to analyze the economics and determinants of collective reputation. We first run a cross‐sectional analysis with 2008 data and the full set of control variables, then move to the dynamics of collective reputation with panel data analysis on a 30‐year time span (1978–2008). Group reputation is history‐dependent. In particular, past bad collective behavior increases the probability of being stuck in a “bad reputation trap.” Minimum quality standards and effective enforcement are fundamental drivers of group reputation. The relationship between group size and collective reputation is non‐linear: free entry may not be optimal due to free‐riding problems. Finally, institutional signals such as the wine classification system are useful because they can be used by consumers as easily available proxies for information that is much more difficult to acquire.
The Cyni framework for network inference in Cytoscape
Authors: Guitart-Pla Oriol , Kustagi Manjunath , Rügheimer Frank , Califano Andrea , Schwikowski Benno
Published: December 2014

Motivation: Research on methods for the inference of networks from biological data is making significant advances, but the adoption of network inference in biomedical research practice is lagging behind. Here, we present Cyni, an open-source ‘fill-in-the-algorithm’ framework that provides common network inference functionality and user interface elements. Cyni allows the rapid transformation of Java-based network inference prototypes into apps of the popular open-source Cytoscape network analysis and visualization ecosystem. Merely placing the resulting app in the Cytoscape App Store makes the method accessible to a worldwide community of biomedical researchers by mouse click. In a case study, we illustrate the transformation of an ARACNE implementation into a Cytoscape app.

Availability and implementation: Cyni, its apps, user guides, documentation and sample code are available from the Cytoscape App Store http://apps.cytoscape.org/apps/cynitoolbox

Contact:  benno.schwikowski@pasteur.fr
CDvist: a webserver for identification and visualization of conserved domains in protein sequences
Authors: Adebali Ogun , Ortega Davi R. , Zhulin Igor B.
Published: December 2014

Summary: Identification of domains in protein sequences allows their assigning to biological functions. Several webservers exist for identification of protein domains using similarity searches against various databases of protein domain models. However, none of them provides comprehensive domain coverage while allowing bulk querying and their visualization schemes can be improved. To address these issues, we developed CDvist (a comprehensive domain visualization tool), which combines the best available search algorithms and databases into a user-friendly framework. First, a given protein sequence is matched to domain models using high-specificity tools and only then unmatched segments are subjected to more sensitive algorithms resulting in a best possible comprehensive coverage. Bulk querying and rich visualization and download options provide improved functionality to domain architecture analysis.

Availability and implementation: Freely available on the web at http://cdvist.utk.edu

Contact:  oadebali@vols.utk.edu or ijouline@utk.edu
Cardiorespiratory Fitness Is Associated With Cognitive Performance in Older But Not Younger Adults
Authors: Hayes Scott M. , Forman Daniel E. , Verfaellie Mieke
Published: December 2014

Objectives:

Aging is associated with declines in executive function and episodic memory. Cardiorespiratory fitness (CRF) has been associated with enhanced executive function in older adults (OA), but the relationship with episodic memory remains unclear. The purpose of the study was to examine the relationship between CRF and cognition in young and OA and whether CRF mitigates age-related cognitive decline.

Methods:

Participants completed exercise testing to evaluate CRF (peak VO 2 ) and neuropsychological testing to assess cognition.

Results:

In OA, peak VO 2 was positively related to executive function, as well as to accuracy on an experimental face–name memory task and visual episodic memory. In young adults (YA), a relationship between peak VO 2 and cognition was not evident. High-fit OA performed as well as YA on executive function measures. On episodic memory measures, YA performed better than high-fit OA, who in turn performed better than low-fit OA.

Conclusions:

CRF is positively associated with executive function and episodic memory in OA and attenuates age-related cognitive decline. We provide preliminary support for the age-dependence hypothesis, which posits that cognition and CRF relationships may be most readily observed during lifetime periods of significant neurocognitive development.
Binary black hole accretion during inspiral and merger
Authors: Farris Brian D. , Duffell Paul , MacFadyen Andrew I. , Haiman Zoltán
Published: December 2014

We present the results of 2D, moving mesh, viscous hydrodynamical simulations of accretion on to merging supermassive black hole (SMBH) binaries. We include viscous heating, shock heating, and radiative cooling, and simulate the transition from the ‘pre-decoupling’ epoch, where the inspiral time-scale is longer than the viscous time-scale, to the ‘post-decoupling’ epoch, where the inspiral time-scale is shorter than the viscous time-scale. We find that there is no abrupt halt to the accretion at decoupling, but rather the accretion shows a slow decay, with significant accretion well after the expected decoupling. Moreover, we find that the luminosity in X-rays is significantly higher prior to the merger, as orbital energy from the SMBH binary is converted to heat via strong shocks inside the cavity, and radiated away. Following the merger, the cavity refills viscously and the accretion rate relaxes to the Shakura–Sunyaev value, while the X-ray luminosity drops as the shocks quickly dissipate.
CC Sculptoris: Eclipsing SU UMa-type intermediate polar
Authors: Kato Taichi , Hambsch Franz-Josef , Oksanen Arto , Starr Peter , Henden Arne
Published: December 2014

We observed the 2014 superoutburst of the SU UMa-type intermediate polar CC Scl. We detected superhumps with a mean period of 0.05998(2) d during the superoutburst plateau and during three nights after the fading. During the post-superoutburst stage after three nights, a stable superhump period of 0.059523(6) d was detected. We found that this object is an eclipsing system with an orbital period of 0.058567233(8) d. By assuming that the disk radius in the post-superoutburst phase is similar to those in other SU UMa-type dwarf novae, we obtained a mass ratio of q = 0.072(3) from the dynamical precession rate of the accretion disk. The eclipse profile during outbursts can be modeled by an inclination of 80 $_{.}^{\circ}$6 ± 0 $_{.}^{\circ}$5. The 2014 superoutburst was preceded by a precursor outburst and the overall appearance of the outburst was similar to superoutbursts in ordinary SU UMa-type dwarf novae. We showed that the standard thermal-tidal instability model can explain the outburst behavior in this system and suggest that inner truncation of the disk by magnetism of the white dwarf does not strongly affect the behavior in the outer part of the disk.
Expansion of theHSFYgene family in pig lineages
Authors: Skinner Benjamin M , Lachani Kim , Sargent Carole A , Yang Fengtang , Ellis Peter , Hunt Toby , Fu Beiyuan , Louzada Sandra , Churcher Carol , Tyler-Smith Chris , Affara Nabeel A
Published: December 2014

Amplified gene families on sex chromosomes can harbour genes with important biological functions, especially relating to fertility. TheHSFYfamily has amplified on the Y chromosome of the domestic pig (Sus scrofa), in an apparently independent event to anHSFYexpansion on the Y chromosome of cattle (Bos taurus). Although the biological functions ofHSFYgenes are poorly understood, they appear to be involved in gametogenesis in a number of mammalian species, and, in cattle,HSFYgene copy number correlates with levels of fertility.

We have investigated theHSFYfamily in domestic pigs, and other suid species including warthogs, bushpigs, babirusas and peccaries. The domestic pig contains at least two amplified variants ofHSFY, distinguished predominantly by presence or absence of a SINE within the intron. Both these variants are expressed in testis, and both are present in approximately 50 copies each in a single cluster on the short arm of the Y. The longer form has multiple nonsense mutations rendering it likely non-functional, but many of the shorter forms still have coding potential. Other suid species also have these two variants ofHSFY, and estimates of copy number suggest theHSFYfamily may have amplified independently twice during suid evolution. Given the association ofHSFYgene copy number with fertility in cattle,HSFYis likely to play an important role in spermatogenesis in pigs also.
Using Bayesian multilevel whole-genome regression models for partial pooling of estimation sets in genomic prediction
Authors: Technow Frank , Totir L. Radu
Published: December 2014

Estimation set size is an important determinant of genomic prediction accuracy. Plant breeding programs are characterized by a high degree of structuring, particularly into populations. This hampers establishment of large estimation sets for each population. Pooling populations increases estimation set size but ignores unique genetic characteristics of each. A possible solution is partial pooling with multilevel models, which allows estimating population specific marker effects while still leveraging information across populations. We developed a Bayesian multilevel whole-genome regression model and compared its performance to that of the popular BayesA model applied to each population separately (no pooling) and to the joined data set (complete pooling). As example we analyzed a wide array of traits from the nested association mapping maize population. There we show that for small population sizes (e.g., < 50), partial pooling increased prediction accuracy over no or complete pooling for populations represented in the estimation set. No pooling was superior however when populations were large. In another example data set of interconnected biparental maize populations either partial or complete pooling were superior, depending on the trait. A simulation showed that no pooling is superior when differences in genetic effects among populations are large and partial pooling when they are intermediate. With small differences, partial and complete pooling achieved equally high accuracy. For prediction of new populations, partial and complete pooling had very similar accuracy in all cases. We conclude that partial pooling with multilevel models can maximize the potential of pooling by making optimal use of information in pooled estimation sets.
Gibberellins Interfere with Symbiosis Signaling and Gene Expression and Alter Colonization by Arbuscular Mycorrhizal Fungi in Lotus japonicus
Authors: Takeda Naoya , Handa Yoshihiro , Tsuzuki Syusaku , Kojima Mikiko , Sakakibara Hitoshi , Kawaguchi Masayoshi
Published: December 2014

Arbuscular mycorrhiza is a mutualistic plant-fungus interaction that confers great advantages for plant growth. Arbuscular mycorrhizal (AM) fungi enter the host root and form symbiotic structures that facilitate nutrient supplies between the symbionts. The gibberellins (GAs) are phytohormones known to inhibit AM fungal infection. However, our transcriptome analysis and phytohormone quantification revealed GA accumulation in the roots of Lotus japonicus infected with AM fungi, suggesting that de novo GA synthesis plays a role in arbuscular mycorrhiza development. We found pleiotropic effects of GAs on the AM fungal infection. In particular, the morphology of AM fungal colonization was drastically altered by the status of GA signaling in the host root. Exogenous GA treatment inhibited AM hyphal entry into the host root and suppressed the expression of Reduced Arbuscular Mycorrhization1 (RAM1) and RAM2 homologs that function in hyphal entry and arbuscule formation. On the other hand, inhibition of GA biosynthesis or suppression of GA signaling also affected arbuscular mycorrhiza development in the host root. Low-GA conditions suppressed arbuscular mycorrhiza-induced subtilisin-like serine protease1 (SbtM1) expression that is required for AM fungal colonization and reduced hyphal branching in the host root. The reduced hyphal branching and SbtM1 expression caused by the inhibition of GA biosynthesis were recovered by GA treatment, supporting the theory that insufficient GA signaling causes the inhibitory effects on arbuscular mycorrhiza development. Most studies have focused on the negative role of GA signaling, whereas our study demonstrates that GA signaling also positively interacts with symbiotic responses and promotes AM colonization of the host root.
Challenging the maximum rooting depth paradigm in grasslands and savannas
Authors: Nippert Jesse B. , Holdo Ricardo M.
Published: December 2014

For many grassland and savanna ecosystems, water limitation is a key regulator of individual plant, community and ecosystem processes. Maximum rooting depth is commonly used to characterize the susceptibility of plant species to drought. This rests on the assumption that deep‐rooted plant species would have a greater total volume of soil water to exploit and should be less susceptible to episodic changes in water availability.

Independent of maximum rooting depth, rooting strategies based on differences in biomass allocation with depth, uptake plasticity in relation to water availability and variation in water transport capability may all influence growth responses and susceptibility to drought. Many examples from grasslands and savannas reflect these rooting strategies among coexisting grass, forb and woody species.

Here, we use a dynamic model of plant water uptake and growth to show how changes in root distribution, functional plasticity and root hydraulic conductivity have the potential to influence aboveground biomass and competitive outcomes, even when maximum rooting depth remains constant. We also show theoretically that shifts in root distribution to surface soils without changes in maximum depth can potentially outweigh the benefits of increased maximum rooting depth.

Combining our current reliance on biogeographic descriptions of maximum rooting depth with insights about other, more subtle aspects of root structure and function are likely to improve our understanding of ecosystem responses to dynamic water limitation.
Is successional research nearing its climax? New approaches for understanding dynamic communities
Authors: Meiners Scott J. , Cadotte Marc W. , Fridley Jason D. , Pickett Steward T. A. , Walker Lawrence R.
Published: December 2014

Succession has been a focus of extensive ecological study for well over a century. Despite this sustained interest, succession remains a central theme in ecological research and is positioned to continue that prominence in this era of expanding human impacts. Community ecology is currently experiencing a profound conceptual expansion, providing many new insights into succession.

Here we present an existing conceptual framework of successional drivers that includes variation in site conditions, species availability and species performance, and expand it to include both evolutionary and geographic sources of variation. This framework is useful because it specifies relationships among individual drivers and is causally complete. While we generally think about succession as a within‐site process, the inclusion of phylogenetic and geographic processes allows integration across broader scales.

We use the conceptual framework to highlight several opportunities for successional research that have developed within community ecology, but have not been fully integrated into succession work. These ideas represent not only individual drivers of succession, but also potential synergistic processes operating through interaction with other drivers. The complexity of drivers in succession strongly argues for the need to move away from single factor studies towards combinatorial studies that incorporate multiple drivers.

Utilizing a trait‐based approach should allow researchers to address successional drivers at multiple ecological scales and lead to new insights that integrate ecological systems. Our ability to do this will depend on the availability of equivalent data across multiple systems, suggesting the need for more standardization in successional studies.

Addressing the research opportunities highlighted here will not only produce insights into successional systems, but also expand our understanding of fundamental questions in community ecology as a whole. Of particular importance is the ability to address broader scale questions that go beyond the idiosyncrasies of individual sites and systems. Understanding the dynamics of successional systems will remain critical to understanding, managing and predicting anthropogenic impacts on natural systems.
Usual interstitial pneumonia following resolution of cavitated pulmonary masses in a patient with ANCA‐associated vasculitis
Authors: Fukui Shoichi , Kobayashi Satomi , Kamei Satoshi , Takizawa Yasunobu , Setoguchi Keigo , Hishima Tsunekazu
Published: December 2014

A 72‐year‐old woman with slight pulmonary interstitial reticular markings was initially diagnosed with microscopic polyangiitis (MPA). Two years later, cavitated pulmonary masses appeared, and a biopsy specimen revealed granulomas. Granulomatosis with polyangiitis (GPA) was diagnosed. The masses resolved with treatment. Ten years later, the usual interstitial pneumonia (UIP) pattern appeared on chest computed tomography (CT). The diagnosis of lung toxicity from methotrexate (MTX) or cyclophosphamide (CYC) was precluded by the clinical course. Despite treatment with prednisolone (PSL), the UIP progressed. The change of pulmonary pathology from masses to UIP is rare in patients with GPA.
A novel histone deacetylase 6‐selective inhibitor suppresses synovial inflammation and joint destruction in a collagen antibody‐induced arthritis mouse model
Authors: Lee Jaejoon , Hong Eun Chung , Jeong Hyemin , Hwang Ji Won , Kim Hyungjin , Bae Eun‐Kyung , Ahn Joong Kyong , Choi Yoon‐La , Han Jungho , Cha Hoon‐Suk , Koh Eun‐Mi
Published: December 2014

Aim

To investigate the effects of Tubastatin A, a selective histone deacetylase‐6 inhibitor, on synovial inflammation and joint destruction in a collagen antibody‐induced arthritis (CAIA) mouse model.

Methods

Collagen antibody‐induced arthritis mice were given daily intraperitoneal injections of various concentrations of Tubastatin A (0, 10, 50, 100 mg/kg). The clinical score and paw thickness were measured. Mice were sacrificed on day 15, and the expression of tumor necrosis factor (TNF)‐α, interleukin (IL)‐1 and IL‐6 in the serum were analyzed using enyme‐linked immunosorbent assay (ELISA). Two pathologists independently measured the synovitis score. Micro‐computed tomography (CT) scans of the joints were performed to quantify joint destruction. The expression of IL‐6 from human fibroblast‐like synoviocytes (FLSs) after incubation with various doses of Tubastatin A (0, 0.75, 1.5, 3 μmol/L) was measured using ELISA.

Results

The clinical arthritis score was significantly attenuated and paw thickness was lower in the group treated with 100 mg/kg Tubastatin A compared with those treated with vehicle alone. The synovitis score was significantly reduced in the 100 mg/kg Tubastatin A‐treated group compared with the control group. Micro‐CT showed that quantitative measures of joint destruction were significantly attenuated in the 100 mg/kg Tubastatin A‐treated group compared with the control. The expression of IL‐6 in the sera was lower in the mice treated with Tubastatin A compared with the control. The expression of IL‐6 in human FLSs decreased dose‐dependently after incubation with Tubastatin A without affecting cell viability.

Conclusions

Tubastatin A successfully ameliorated synovial inflammation and protected against joint destruction in CAIA mice, at least in part, by modulating IL‐6 expression.
Efficient abstracting of dive profiles using a broken‐stick model
Authors: Photopoulou Theoni , Lovell Philip , Fedak Michael A. , Thomas Len , Matthiopoulos Jason
Published: December 2014

For diving animals, animal‐borne sensors are used to collect time–depth information for studying behaviour, ranging patterns and foraging ecology. Often, this information needs to be compressed for storage or transmission. Widely used devices called conductivity‐temperature‐depth satellite relay data loggers (CTD‐SRDLs) sample time and depth at high resolution during a dive and then abstract the time–depth trajectory using a broken‐stick model (BSM). This approximation method can summarize efficiently the curvilinear shape of a dive, using a piecewise linear shape with a small, fixed number of vertices, or break points.

We present the process of abstracting dives using the BSM and quantify its performance, by measuring the uncertainty associated with the profiles it produces. We develop a method for obtaining a confidence zone and an index for the goodness‐of‐fit (dive zone index, DZI) for abstracted dive profiles. We validate our results with a case study using dives from elephant seals (Mirounga spp.). We use generalized additive models (GAMs) to determine whether the DZI can be used as a proxy for an absolute measure of fit and investigate the relationship between the DZI and the dive shape.

We found a strong correlation between the residual sum of squares (RSS) for the difference between the detailed and abstracted profiles, and the DZI and maximum residual (R4), for dives resulting from CTD‐SRDLs (69% deviance explained). On its own, the DZI explained a lower percentage of deviance which was variable for abstracted dives with different numbers of break points. We also found evidence for systematic differences in the DZI for different dive shapes (65% deviance explained).

Although the proportional loss of information in the abstraction of time–depth dive profiles by BSM is high, what remains is sufficient to infer goodness‐of‐fit of the abstracted profile by reversing the abstraction process. Our results suggest that together the DZI and R4 can be used as a proxy for the RSS, and we present the method for obtaining these metrics for BSM‐abstracted profiles.
Talanoa as empathic apprenticeship
Authors: Farrelly Trisia , Nabobo‐Baba Unaisi
Published: December 2014

Talanoa has been defined as ‘talking about nothing in particular’, ‘chat’ or ‘gossip’. It is within the cultural milieu of talanoa that knowledge and emotions are shared and new knowledge is generated. Talanoa has recently been taken up by development researchers and others as a culturally appropriate research method in Pacific contexts. However, talanoa is often treated as synonymous with ‘informal open‐ended interviews’ and tends to gloss over the deep empathic understanding required in such exchanges. Highlighting the connection between talanoa and empathy is vital in ensuring that development practitioners and researchers are implicitly aware of the political dimensions, cultural appropriacy and socio‐ecological impact of their research methods. This connection is also critical in illuminating how talanoa as a method may decolonise research in the Pacific, inform the decolonisation of research in other cultural contexts, and contribute to ethical and empowering development policy and practice. We will argue for the merits of what we refer to here as ‘empathic apprenticeship’: an intentional, embodied, emotional, and intersubjective methodology and process between the researcher and the participant. An empathic apprenticeship has the potential to enhance shared understandings between all human beings and is essential if talanoa is intended as a decolonising research methodology.
Assessing the ‘true impact’ of development assistance in the Gaza Strip and Tokelau: ‘Most Significant Change’ as an evaluation technique
Authors: Shah Ritesh
Published: December 2014

The democratic evaluative tradition has sought to change evaluation practice towards approaches and techniques that generate diverse forms of knowledge and foster public deliberation over a programme's merit and worth. This paper locates one evaluation method, ‘Most Significant Change’ (MSC), within this tradition. Drawing on two different evaluations – one, of a comprehensive economic sector assistance package to the Government of Tokelau, and the other of a psychosocial and academic support intervention for pre‐adolescent children in conflict‐affected regions of the Gaza Strip – the paper provides evidence of how MSC can capture unexpected outcomes, act as a tool for real‐time formative learning, and expose the competing theories, logics and values behind programme activity. The examples within the paper also provide evidence of how MSC begins to redistribute traditional power relationships in assessing the merit and worth of observed impacts by increasing the legitimacy of local programme knowledge, and engaging all parties in evaluative decisions. By doing so, MSC, the paper argues, better serves the purposes of learning, improvement and mutual accountability which should sit at the core of good development practice.
The Bacterial Type III Secretion System as a Target for Developing New Antibiotics
Authors: McShan Andrew C. , De Guzman Roberto N.
Published: December 2014

Antibiotic resistance in pathogens requires new targets for developing novel antibacterials. The bacterial type III secretion system (T3SS) is an attractive target for developing antibacterials as it is essential in the pathogenesis of many Gram‐negative bacteria. The T3SS consists of structural proteins, effectors, and chaperones. Over 20 different structural proteins assemble into a complex nanoinjector that punctures a hole on the eukaryotic cell membrane to allow the delivery of effectors directly into the host cell cytoplasm. Defects in the assembly and function of the T3SS render bacteria non‐infective. Two major classes of small molecules, salicylidene acylhydrazides and thiazolidinones, have been shown to inhibit multiple genera of bacteria through the T3SS. Many additional chemically and structurally diverse classes of small molecule inhibitors of the T3SS have been identified as well. While specific targets within the T3SS of a few inhibitors have been suggested, the vast majority of specific protein targets within the T3SS remain to be identified or characterized. Other T3SS inhibitors include polymers, proteins, and polypeptides mimics. In addition, T3SS activity is regulated by its interaction with biologically relevant molecules, such as bile salts and sterols, which could serve as scaffolds for drug design.
Machine‐Learning Techniques Applied to Antibacterial Drug Discovery
Authors: Durrant Jacob D. , Amaro Rommie E.
Published: December 2014

The emergence of drug‐resistant bacteria threatens to revert humanity back to the preantibiotic era. Even now, multidrug‐resistant bacterial infections annually result in millions of hospital days, billions in healthcare costs, and, most importantly, tens of thousands of lives lost. As many pharmaceutical companies have abandoned antibiotic development in search of more lucrative therapeutics, academic researchers are uniquely positioned to fill the pipeline. Traditional high‐throughput screens and lead‐optimization efforts are expensive and labor intensive. Computer‐aided drug‐discovery techniques, which are cheaper and faster, can accelerate the identification of novel antibiotics, leading to improved hit rates and faster transitions to preclinical and clinical testing. The current review describes two machine‐learning techniques, neural networks and decision trees, that have been used to identify experimentally validated antibiotics. We conclude by describing the future directions of this exciting field.
Preschool children favor copying a successful individual over an unsuccessful group
Authors: Wilks Matti , Collier‐Baker Emma , Nielsen Mark
Published: December 2014

The human aptitude for imitation and social learning underpins our advanced cultural practices. While social learning is a valuable evolutionary survival strategy, blind copying does not necessarily facilitate survival. Copying from the majority allows individuals to make rapid judgments on the value of a trait, based on its frequency. This is known as the majority bias: an individual's tendency to copy the behavior elicited by the largest number of individuals in a population. An alternative approach is to follow those who are the most proficient. While there is evidence that children do show both processes, no study has directly pitted them against each other. To do this, in the current experiment 36 children aged between 4 and 5 years watched live actors demonstrate, as a group or individually, how to open novel puzzle boxes. Children exhibited a bias to the majority when group and individual methods were successful, but favored the individual if the group method was unsuccessful. Affiliating children with the unsuccessful majority group did not impact on this pattern.
Obesity interacts with infectious mononucleosis in risk of multiple sclerosis
Authors: Hedström A. K. , Lima Bomfim I. , Hillert J. , Olsson T. , Alfredsson L.
Published: December 2014

Background and purpose

The possible interaction between adolescent obesity and past infectious mononucleosis (IM) was investigated with regard to multiple sclerosis (MS) risk.

Methods

This report is based on two population‐based case–control studies, one with incident cases (1780 cases, 3885 controls) and one with prevalent cases (4502 cases, 4039 controls). Subjects were categorized based on adolescent body mass index (BMI) and past IM and compared with regard to occurrence of MS by calculating odds ratios with 95% confidence intervals (CIs) employing logistic regression. A potential interaction between adolescent BMI and past IM was evaluated by calculating the attributable proportion due to interaction.

Results

Regardless of human leukocyte antigen (HLA) status, a substantial interaction was observed between adolescent obesity and past IM with regard to MS risk. The interaction was most evident when IM after the age of 10 was considered (attributable proportion due to interaction 0.8, 95% CI 0.6–1.0 in the incident study, and attributable proportion due to interaction 0.7, 95% CI 0.5–1.0 in the prevalent study). In the incident study, the odds ratio of MS was 14.7 (95% CI 5.9–36.6) amongst subjects with adolescent obesity and past IM after the age of 10, compared with subjects with none of these exposures. The corresponding odds ratio in the prevalent study was 13.2 (95% CI 5.2–33.6).

Conclusions

An obese state both impacts the cellular immune response to infections and induces a state of chronic immune‐mediated inflammation which may contribute to explain our finding of an interaction between adolescent BMI and past IM. Measures taken against adolescent obesity may thus be a preventive strategy against MS.
Color Assimilation of Resin Composites with Adjacent Color According to the Distance
Authors: Lee Yong‐Keun , Yu Bin , Zhao Guang‐Feng , Lim Jin Ik
Published: December 2014

Statement of Problem

Color of esthetic restorative materials shifts toward color of adjacent material.

Purpose

The purposes were to determine the amount of distance‐dependent color shift in resin composites toward the color of adjacent materials and to define a color shift parameter (CSP) that can quantify this phenomenon.

Methods

Three brands of resin composites, two shades for each, were investigated. Specimens of 2 (thickness) × 4 (width) × 16 (length) mm3 were fixed in an adjustable XY stage in contact with black and white ceramic tiles at each end. Color was measured by a spectroradiometer at seven separated points in 2‐mm intervals, in which P1 was 2 mm away from the black tile. Mean value of the color differences (ΔE*ab) between P1 and each of the other measurement points (P2–P6) was defined as the CSP, in which higher CSP value indicated smaller color assimilation toward P1 color.

Results

The range of the CSP was 7.5–12.4, which was influenced by the brand and shade of resin composites (p < 0.05).

Conclusions

The CSP defined in this study provided the amount of color shift of esthetic materials toward adjacent color, which indicated the color assimilation effect of these materials.

Clinical Significance

The CSP investigated in the present study might be used to compare the tendency of color assimilation of esthetic restorative materials, and proper CSP ranges for optimal color assimilation or color blocking should be further determined.
The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants
Authors: Alaba Sylwia , Piszczalka Pawel , Pietrykowska Halina , Pacak Andrzej M. , Sierocka Izabela , Nuc Przemyslaw W. , Singh Kashmir , Plewka Patrycja , Sulkowska Aleksandra , Jarmolowski Artur , Karlowski Wojciech M. , Szweykowska‐Kulinska Zofia
Published: December 2014

Liverworts are the most basal group of extant land plants. Nonetheless, the molecular biology of liverworts is poorly understood. Gene expression has been studied in only one species, Marchantia polymorpha. In particular, no microRNA (miRNA) sequences from liverworts have been reported.

Here, Illumina‐based next‐generation sequencing was employed to identify small RNAs, and analyze the transcriptome and the degradome of Pellia endiviifolia.

Three hundred and eleven conserved miRNA plant families were identified, and 42 new liverwort‐specific miRNAs were discovered. The RNA degradome analysis revealed that target mRNAs of only three miRNAs (miR160, miR166, and miR408) have been conserved between liverworts and other land plants. New targets were identified for the remaining conserved miRNAs. Moreover, the analysis of the degradome permitted the identification of targets for 13 novel liverwort‐specific miRNAs. Interestingly, three of the liverwort microRNAs show high similarity to previously reported miRNAs from Chlamydomonas reinhardtii.

This is the first observation of miRNAs that exist both in a representative alga and in the liverwort P. endiviifolia but are not present in land plants. The results of the analysis of the P. endivifolia microtranscriptome support the conclusions of previous studies that placed liverworts at the root of the land plant evolutionary tree of life.