bluuebunny/crossref_metadata_2025 huggingface dataset:
Downstream Effects of Recent Reservoir Development on the Morphodynamics of a Meandering Channel: Savery Creek, Wyoming, USA
Authors: Legleiter C. J.
Published: August 2014

Recent reservoir construction on Savery Creek provided an opportunity to examine the downstream effects of a dam on a small, meandering channel. The new dam, completed in 2005, modified the flow regime by reducing the magnitude of spring peaks and increasing baseflows, including a second period of high discharge in the fall. A time series of remotely sensed data spanning 1980–2011 was used to measure lateral migration rates, quantify areas of erosion and deposition, and map spatial patterns of channel change. Both migration rates, and gross erosion and deposition increased during the post‐dam era, although 2 years of exceptionally large snowmelt runoff also occurred during this time. Net sediment flux inferred from the image time series was negative for both the upper and lower reaches for the first photo pair after the dam's completion but became positive for the most recent photos. Detailed topographic surveys of five individual meander bends were used to produce digital elevation models of difference and infer bed material transport rates. For three sites located in the upper reach, downstream increases in transport rate implied a sediment deficit satisfied through channel incision and/or bank erosion. For two sites in the lower reach where sediment supply was greater, larger values of gross erosion were balanced by enhanced deposition and transport rates stabilized or increased along each bend. Together, these results suggest that Savery Creek has entered a period of adjustment as the channel adapts to altered, dam‐regulated supplies of water and sediment. Copyright © 2014 John Wiley & Sons, Ltd.
Ar cluster ion beam sputtering of InSb investigated by ToF‐SIMS
Authors: Miyasaka Toyomitsu , Yamauchi Takeshi , Nagatomi Takaharu , Kono Teiichiro
Published: August 2014

Ar gas cluster ion beam (GCIB) sputtering of InSb was investigated, and the sputtering rate and depth resolution of time‐of‐flight secondary ion mass spectrometry sputter depth profiling were examined. The practical sputtering rate for InSb using 20 keV Ar2500+ irradiation was confirmed at the incident angles of 0°, 40°, and 60°, and the sputtering rate was too low to perform sputtering at 80°. The preferential sputtering and surface roughness observed under GCIB irradiation was lower than that observed under 3 keV Ar+ irradiation. Characteristic ripple formation was confirmed under 20 keV Ar2500+ irradiation and had a strong influence on the depth resolution. The highest depth resolution was obtained at the incident angle of 0° because no ripple formation occurred and the level of surface roughness was low among the irradiation of GCIB at incident angles of 0°, 40°, and 60°. The present results revealed that GCIB sputtering is an effective method for sputter depth profiling of InSb. Copyright © 2014 John Wiley & Sons, Ltd.
Dynamically vulcanized polypropylene/ethylene‐propylene diene monomer/organoclay nanocomposites: Effect of mixing sequence on structural, rheological, and mechanical properties
Authors: Naderi Ghasem , Khosrokhavar Ramin , Shokoohi Shirin , Bakhshandeh Gholam Reza , Ghoreishy Mir Hamid Reza
Published: August 2014

Dynamically vulcanized thermoplastic elastomer (TPE) nanocomposites based on polypropylene (PP), ethylene‐propylene diene monomer (EPDM) and cloisite 15A were prepared via direct melt mixing in a co‐rotating twin‐screw extruder. The mixing process was carried out with optimized processing parameters (barrel temperature = 180°C; screw speed = 150 rpm; and feeding rate = 0.2 kg/hr). The formulation used to prepare the nanocomposites was fixed to 75/20/5 (PP/EPDM/Cloisite©15A), expressed in mass fraction. Effect of mixing sequence on the properties of vulcanized and unvulcanized (TPE) nanocomposites prepared under similar conditions was investigated using X‐ray diffraction (XRD) and a tensile testing machine. Results showed that the sequence of mixing does affect the properties of final TPE nanocomposites. Accordingly, nanocomposite samples prepared through mixing the preblended PP/clay masterbatch with EPDM phase, show better clay dispersion within the polymer matrix. J. VINYL ADDIT. TECHNOL., 22:320–325, 2016. © 2014 Society of Plastics Engineers
Combined anterior and rotational laxity measurements allow characterizing personal knee laxity profiles in healthy individuals
Authors: Mouton Caroline , Seil Romain , Meyer Tim , Agostinis Hélène , Theisen Daniel
Published: August 2014

Purpose

The aim of this study was to quantify sagittal and rotational knee laxity profiles taking into account individual influencing factors.

Methods

Linear regression models were used to determine which individual characteristics (age, height, body mass and sex) influenced the outcome in a group of 104 healthy subjects. The standardized residuals were used as individualized (corrected) laxity scores and were combined to determine knee laxity profiles.

Results

Anterior knee laxity was not influenced by individual characteristics. Rotational knee laxity was higher in females and inversely related to body mass. The correlation between anterior laxity and internal rotation scores was weak (r = 0.24, p = 0.02). The proportion of knees concerned by increased laxity scores (scores >1) was similar for anterior displacement, internal and external rotation (15 %). Only 32 % of the tested subjects showed a normal profile (score >−1 and <1) for all three directions, 33 % were concerned by hyperlaxity, 40 % by hypolaxity and 5 % by both.

Conclusions

The diversity of laxity profiles found here highlights that the interpretation of multidirectional knee laxity is complex and suggests the necessity for individualized care of knee diseases and injuries. These results contribute to the understanding of knee laxity and throw the basis for prevention strategies and improvement of treatment outcomes in injuries and diseases.

Level of evidence

Case series with no comparison groups, Level IV.
Tree diversity patterns in successive vegetation types along an elevation gradient in the Mountains of Eastern Mexico
Authors: Toledo‐Garibaldi María , Williams‐Linera Guadalupe
Published: August 2014

Tree species richness changes along elevation gradients in response to underlying environmental conditions. Our hypothesis was that richness is associated with climatic variables and decreases with elevation. The objective was to identify trends in species, genus and family richness, diversity and vegetation structure in relation to climate variables along an elevation gradient with successive types of forest in Veracruz, Mexico. Trees were identified and measured in 0.1 ha at 15 sites located from 140 to 4000 m a.s.l. Generalized linear models were used to fit richness, diversity, basal area and density as a function of elevation; the best model was selected using Akaike's Information Criterion. Multivariate analyses were used to explore climatic variables associated to composition of groups of sites along the gradient. Along the entire elevation gradient, species, genus and family richness decreased unimodally, and diversity decreased monotonically. Richness was positively correlated with temperature but not with precipitation. Basal area increased monotonically and highest basal area was associated with high humidity and certain tree species (Quercus and Abies). Ordinations indicated three groups of sites: lower elevation dry forest associated with temperature seasonality, mid‐elevation cloud forest associated with precipitation‐related variables, and coniferous forest at the top of the gradient associated with elevation. Our study shows that different plant communities are associated with certain climatic conditions and harbour different tree species, genera and families. The results support the hypothesis that species richness is associated with climate, and decreases with elevation.
Effects of a classroom‐based educational resource on adolescent mental health literacy: A cluster randomised controlled trial
Authors: Perry Yael , Petrie Katherine , Buckley Hannah , Cavanagh Lindy , Clarke Deborah , Winslade Matthew , Hadzi‐Pavlovic Dusan , Manicavasagar Vijaya , Christensen Helen
Published: August 2014

Evidence suggests that poor mental health literacy is a key barrier to help‐seeking for mental health difficulties in adolescence. Educational programs have shown positive effects on literacy, however, the evidence base remains limited and available studies have many methodological limitations. Using cluster Randomised Control Trial (RCT) methodology, the current study examines the impact of ‘HeadStrong’, a school‐based educational intervention, on mental health literacy, stigma, help‐seeking, psychological distress and suicidal ideation. A total of 380 students in 22 classes (clusters) from 10 non‐government secondary schools was randomised to receive either HeadStrong or Personal Development, Health and Physical Education (PDHPE) classes. Participants were assessed pre‐ and post‐intervention, and at 6‐month follow‐up. Literacy improved and stigma reduced in both groups at post‐intervention and follow‐up, relative to baseline. However, these effects were significantly greater in the HeadStrong condition. The study demonstrates the potential of HeadStrong to improve mental health literacy and reduce stigma.
Wastewater micropollutants as tracers of sewage contamination: analysis of combined sewer overflow and stream sediments
Authors: Hajj-Mohamad M. , Aboulfadl K. , Darwano H. , Madoux-Humery A.-S. , Guérineau H. , Sauvé S. , Prévost M. , Dorner S.
Published: August 2014

This work presents the first measurement of wastewater micropollutants in combined sewer sediments and compares with measurements from water and sediments in natural streams.
The dynamics and pH-dependence of Ag43 adhesins’ self-association probed by atomic force spectroscopy
Authors: Jacquot Adrien , Sakamoto Chizuko , Razafitianamarahavo Angelina , Caillet Céline , Merlin Jenny , Fahs Ahmad , Ghigo Jean-Marc , Duval Jérôme F. L. , Beloin Christophe , Francius Grégory
Published: August 2014

Self-associating auto-transporter (SAAT) adhesins are two-domain cell surface proteins involved in bacteria auto-aggregation and biofilm formation.
Toward highly radiative white light emitting nanostructures: a new approach to dislocation-eliminated GaN/InGaN core–shell nanostructures with a negligible polarization field
Authors: Kim Je-Hyung , Ko Young-Ho , Cho Jong-Hoi , Gong Su-Hyun , Ko Suk-Min , Cho Yong-Hoon
Published: August 2014

Broadband visible-light emitting GaN/InGaN core–shell nanostructures were demonstrated by a dislocation-eliminating chemical vapor-phase etching technique followed by metal–organic chemical vapor deposition.
Reductive decyanation of malononitriles and cyanoacetates using photoactivated neutral organic super-electron-donors
Authors: Doni Eswararao , Murphy John A.
Published: August 2014

A metal-free reductive procedure for decyanation of malononitriles and cyanoacetates, using photoactivated organic electron donors, is described.
Dopamine 02 receptor plays a critical role in cell proliferation and proopiomelanocortin expression in the pituitary
Authors: Yamaguchi Hiroo , Aiba Atsu , Nakamura Kenji , Nakao Kazuki , Sakagami Hiroyuki , Goto Kaoru , Kondo Hisatake , Katsuki Motoya
Published: August 2014

Background:  It has been suggested that the dopaminergic system is involved in the inhibitory control of secretion of pituitary hormones and in the regulation of motor function in the striatum. To elucidate the specific role of the dopamine D2 receptor (D2R) in the pituitary and brain, we generated D2R deficient (D2R mutant) mice using the gene targeting method.

Results:  Electrophysiological studies as well as ligand binding assays show no functional D2R in mutant mice. The D2R mutant mice display a hypoactivity and a slow, creeping movement. The expression of enkephalin mRNA in the striatum is increased in the mutant mice, but not that of dynorphin and substance P. D2R mutant mice have significantly darker coat colour than their wild‐type littermates and show an elevation of plasma alpha‐melanocyte stimulating hormone (a‐MSH) levels. We found corresponding hyperplastic changes of intermediate lobe of the pituitary and the increased expression of proopiomelanocortin (POMC) in the pituitary in D2R mutant mice.

Conclusion:  D2R plays a critical role in the inhibitory regulation of endocrine cell proliferition and the transcription of POMC mRNA, and consequently in the regulation of a‐MSH in plasma. D2R might be involved in the regulation of enkephalin expression in the striatum, and hence might affect the movement and the behaviour.
Nitrogen timing and rate effects on growth and grain yield of delayed permanent-water rice in south-eastern Australia
Authors: Dunn B. W. , Dunn T. S. , Beecher H. G.
Published: August 2014

The need for continual improvement in water productivity of rice farming has led to the development of delayed permanent (continuous) water (DPW) irrigation practice for drill-sown rice in south-eastern Australia. Current rice-growing practices have the crop flooded for most, or all, of its growing period, whereas DPW has reduced the period of flooding during the vegetative phase, resulting in significant water savings. The changed water-management practice required nitrogen (N) management practices to be investigated, because traditional N application timings and rates may no longer be suitable. Six experiments were conducted over three rice-growing seasons, 2010–11, 2011–12 and 2012–13, on two soil types in south-eastern Australia. Nitrogen applications at sowing, early tillering, mid-tillering and pre-PW were investigated at different rates and split-timing combinations. In the third season, three current commercial semi-dwarf rice varieties, Reiziq, Sherpa and Langi, were investigated for their growth and grain yield using different N treatments under DPW management.
Nitrogen applied with the seed at sowing increased vegetative plant growth but did not increase grain yield, whereas N applied at early tillering had no significant impact on plant growth or grain yield. Nitrogen applied at mid-tillering often increased plant growth but did not lead to increased grain yield over treatments that received all N before PW application at 18–22 days before panicle initiation. When rice is managed under DPW, all N should be applied in one application, before the application of PW. The results from this research show that applying 100 kg N ha–1 before PW for rice grown under DPW was the best N-management option for the experimental fields. All three varieties grew and yielded well under the practice of DPW and responded similarly to N application rates and timings.
In situ characterisation of physicochemical state and concentration of nanoparticles in soil ecotoxicity studies using environmental scanning electron microscopy
Authors: Tuoriniemi Jani , Gustafsson Stefan , Olsson Eva , Hassellöv Martin
Published: August 2014

Environmental context Characterisation of nanoparticles in terms of number concentration and aggregation state is essential for interpreting data from toxicological tests. These parameters have never been measured in situ in tests carried out in soil matrices. Here, environmental scanning electron microscopy imaging is evaluated for particles in soil, and a method for determining the number concentrations by counting the particles in the images is developed. Abstract The interpretation of nanoparticle toxicity data in soils is currently impeded by the lack of methods capable of characterising particles in situ. To draw relevant and accurate conclusions it would be desirable to characterise particle sizes, agglomeration state and number concentrations. In this article, methodologies for imaging nanoparticles in soils are evaluated for conventional scanning electron microscopy (SEM) and environmental or variable pressure scanning electron microscopy (ESEM). A protocol for dispersing Au particles (~25 to ~450nm) into soil without causing aggregation was developed. The number of particles observed per imaged area of soil correlated linearly with concentration. To determine the number of particles per volume of soil it was also necessary to know how deep in the sample the particles can be visualised. The depth was estimated by both using the Kanaya Okayama model, and spiking the soil with dispersions of known number concentration. These concentrations were determined with a range of methods to ensure their accuracy. Because larger particles can be detected deeper in the matrix, such a calibration should be performed over a range of particle sizes.
The persistence and transformation of silver nanoparticles in littoral lake mesocosms monitored using various analytical techniques
Authors: Furtado Lindsay M. , Hoque Md Ehsanul , Mitrano Denise M. , Ranville James F. , Cheever Beth , Frost Paul C. , Xenopoulos Marguerite A. , Hintelmann Holger , Metcalfe Chris D.
Published: August 2014

Environmental context
Silver nanoparticles discharged with municipal wastewater may contaminate surface waters and harm aquatic ecosystems. We applied several analytical techniques to investigate the persistence and transformation of silver nanoparticles in a natural lake environment, and show, through multiple lines of evidence, that they persisted in lake water for several weeks after addition. The nanoparticles were releasing silver ions through dissolution, but these toxic ions were likely binding with natural organic matter in the lake water.

Abstract
Silver nanoparticles (AgNPs) may be released into surface waters, where they can affect aquatic organisms. However, agglomeration, dissolution, surface modifications and chemical speciation are important processes that control the toxicity of AgNPs. The purpose of the study was to apply various methods for monitoring the persistence and transformation of AgNPs added to littoral lake mesocosms. Analysis of total Ag showed that the levels in the mesocosms declined rapidly in the first 12h after addition, followed by a slower rate of dissipation with a half-life (t1/2) of ~20 days. Analysis using single particle ICP-MS (spICP-MS) showed no evidence of extensive homo-agglomeration of AgNPs. The stability of AgNPs was likely due to the low ionic strength and high concentrations of humic-rich dissolved organic carbon (DOC) in the lake water. Analyses by spICP-MS, cloud point extraction (CPE) and asymmetric flow field flow fractionation coupled to ICP-MS (AF4-ICP-MS) all indicated that the concentrations of AgNP decreased over time, and the nanoparticles underwent dissolution. However, the concentrations of dissolved silver, which includes Ag+, were generally below detection limits when analysed by centrifugal ultrafiltration and spICP-MS. It is likely that the majority of free ions released by dissolution were complexing with natural organic material, such as DOC. An association with DOC would be expected to reduce the toxicity of Ag+ in natural waters. Overall, we were able to characterise AgNP transformations in natural waters at toxicologically relevant concentrations through the use of multiple analytical techniques that compensate for the limitations of the individual methods.
Successional stage after land abandonment modulates fire severity and post-fire recovery in a Mediterranean mountain landscape
Authors: López-Poma Rosario , Orr Barron J. , Bautista Susana
Published: August 2014

This study analyses the effect of successional stage after farmland terrace abandonment on post-fire plant recovery in a Mediterranean landscape. Specific objectives of the study were to (1) compare fuel characteristics and fire severity in three successional stages after farmland abandonment – dry grassland, dense shrubland and pine stands; (2) analyse the effect of pre-fire successional stage and fire severity on vegetation recovery and (3) analyse the relative vulnerability (i.e. potential for ecosystem shift and soil degradation) to wildfires of the successional stages. We assessed 30 abandoned terraces (15 unburned and 15 burned), with diverse successional stages, on the Xortà Range (south-east Spain). Post-fire recovery was measured 1, 4 and 7 years after fire. The successional stages varied in aboveground biomass, litter amount, vertical structure and continuity of plant cover, and flammability. Dry grassland showed the lowest fire severity, whereas no differences in severity were found between shrubland and pine stands. One year after fire, plant cover was inversely related to fire severity; this relationship attenuated with time after fire. Post-fire recovery of pine stands and shrubland led in both cases to shrublands, contributing to landscape homogenisation. The pine stands showed the largest changes in composition due to fire and the lowest post-fire plant recovery – a sign of high vulnerability to fire.
“The sheikh of the translators”
Authors: Osman Ghada
Published: August 2014

With the ascension to power of the Abbasid dynasty in 750 CE and the transfer of the capital of the Muslim Empire to the newly-created city of Baghdad, the middle of the eighth century heralded an era that in Islamic history is referred to as the “Golden Age,” during which period the Muslim world became an unrivaled intellectual center for science, philosophy, medicine, and education. Approximately eighty years after the dynasty’s rise to power, the Abbasid Caliph (ruler) al-Ma’mun (d. 833 CE) established in Baghdad Bayt al-Hikma (the House of Wisdom), an educational institution where Muslim and non-Muslim scholars together sought to gather the world’s knowledge not only via original writing but also through translation. Probably the most well-known and industrious translator of the era was Hunayn ibn Ishaq (d. 873 CE), known in the West by the Latinized name “Joannitius.” Referred to as “the sheikh of the translators,” he is reported to have mastered the four principal languages of his time: Greek, Syriac, Persian, and Arabic. Hunayn is credited with an immense number of translations, ranging from works on medicine, philosophy, astronomy, and mathematics, to magic and oneiromancy. This article looks at Hunayn’s work, briefly places this key figure within the translatorial habitus, discusses his methodology towards translation, as described in his own works, and examines that methodology in light of the sociological and sociolinguistic factors of the time.
Translators in international organizations
Authors: Dam Helle V. , Zethsen Karen Korning
Published: August 2014

This article focuses on the occupational status of translators in international organizations. It reports on an empirical study on the job status of Danish staff translators working in the European Union as compared to that of Danish staff translators working in the national market. The study is based on data from questionnaires completed by 63 EU translators and 113 national-market translators, i.e., a total of 176 respondents. The translators’ perceptions of their occupational status were studied and compared through their responses to questions revolving around four parameters of occupational prestige: (1) remuneration, (2) education/expertise, (3) power/influence, and (4) visibility. Based on the literature, we hypothesized that the EU translators would enjoy a higher status than the national-market translators — a hypothesis which the study failed to confirm. In the article, the analyses and findings of the study are discussed, along with the possible reasons for the lack of alignment between the hypothesis and the results.
Subordination in a dynamic account of grammar
Authors: Langacker Ronald W.
Published: August 2014

Subordination is no exception to the rule that basic and general notions are the hardest to characterize. There is in fact no guarantee that it represents a single or unified phenomenon. Rather than a definition, my immediate goal is thus to elucidate and clarify the numerous factors involved. I believe they are best understood in terms of an integrated account of meaning, grammar, processing, and discourse being developed in Cognitive Grammar (CG). Relative, complement, and adverbial clauses will be examined here by way of presenting and supporting this approach.
Utterances ending in the conjunction että
Authors: Koivisto Aino
Published: August 2014

This article presents an analysis of Finnish utterances that end in the conjunction että during conversational talk. Traditionally known as a complementizer, että is the equivalent to the English subordinating conjunction that. Thus, a linguistic unit that ends in että could be interpreted as being incomplete or as projecting a complement clause to follow. However, this study argues that some että-final utterances can be analyzed as being complete. Several arguments will be offered to support this claim. For example, syntactically, these utterances contain neither complement-taking predicates nor other complement-taking constructions that are associated with the conjunction että. This can be assumed to indicate that että does not function as a complementizer, but rather as a syntactically more independent particle that does not project a specific type of continuation. This claim is supported by the fact that other languages have conjunctions that are also developing uses as final particles. This analysis adopts the methodology and theoretical insights of conversation analysis and interactional linguistics.
French and Finnish converbal constructions and their translation from French into Finnish
Authors: Havu Eva
Published: August 2014

The term ‘subordination’ is often associated with clause combining by conjunctions marking the linkage, but subordination can also be expressed by other means. Both French and Finnish have nonfinite constructions which can be regarded as subordinate clauses with an “operational dependency” towards the main clause. This is because their temporal, aspectual and modal implication is dependent on the semantics of the main clause. However, “traditional” subordinate clauses have a more explicit syntactic structure, whereas nonfinite constructions are constructionally more complex, different types of information being embedded in the construction. This paper first discusses French and Finnish converbs and their eventual correspondence, and then proceeds to examine six Finnish translations of French literary texts in order to see how translators have interpreted and translated the original French converbs.
Letters of Artisans and the Labouring Poor (England, c. 1750–1835)
Authors: Laitinen Mikko , Auer Anita
Published: August 2014

Histories of linguistic variability and language standardization in Late Modern England have predominantly focused on the well-educated layers of society. This paper aims at providing a more complete overview of language use during that period by focusing on the lower social ranks. The discussion will be based on the corpus Letters of Artisans and the Labouring Poor (LALP), which contains more than 2,000 letters of application for poor relief from the period c.1750−1835. The first part of the paper describes the corpus in some detail. The second part discusses new research questions that the lower-class material raises; this will be illustrated by two case studies. In the first study, the material will be viewed from the point of view of spelling acquisition and fossilization. The second case study focuses on providing diachronic time depth to some of the current issues discussed in the sociolinguistics of globalization (Blommaert 2010), such as mobility and developing literacies.
Vida PURA: A Cultural Adaptation of Screening and Brief Intervention to Reduce Unhealthy Drinking Among Latino Day Laborers
Authors: Ornelas India J. , Allen Claire , Vaughan Catalina , Williams Emily C. , Negi Nalini
Published: August 2014

Background

Brief intervention is known to reduce drinking in primary care; however, because health care access is limited for Latino immigrants, traditional brief interventions are unlikely to reach this population.

Methods

Using Barrera and Castro's framework, our study aims to culturally adapt a screening and brief intervention program to reduce unhealthy alcohol use among Latino day laborers, a particularly vulnerable group of Latino immigrant men. We conducted 18 interviews with Latino day laborers and 13 interviews with mental health and substance use providers that serve Latino immigrant men. Interviews were conducted until saturation of themes was reached. Themes from interviews were used to identify sources of mismatch between traditional screening and brief intervention in our target population.

Results

Unhealthy alcohol use was common, culturally accepted, and helped relieve immigration-related stressors. Men had limited knowledge about how to change their behavior. Men preferred to receive information from trusted providers in Spanish. Men faced significant barriers to accessing health and social services but were open to receiving brief interventions in community settings. Findings were used to design Vida PURA, a preliminary adaptation design of brief intervention for Latino day laborers. Key adaptations include brief intervention at a day labor worker center provided by promotores trained to incorporate the social and cultural context of drinking for Latino immigrant men.

Conclusions

Culturally adapted brief intervention may help reduce unhealthy drinking in this underserved population.
Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets
Authors: Hormoz Sahand , Bhanot Gyan , Biehl Michael , Bilal Erhan , Meyer Pablo , Norel Raquel , Rhrissorrakrai Kahn , Dayarian Adel
Published: August 2014

Motivation: Translating findings in rodent models to human models has been a cornerstone of modern biology and drug development. However, in many cases, a naive ‘extrapolation’ between the two species has not succeeded. As a result, clinical trials of new drugs sometimes fail even after considerable success in the mouse or rat stage of development. In addition to in vitro studies, inter-species translation requires analytical tools that can predict the enriched gene sets in human cells under various stimuli from corresponding measurements in animals. Such tools can improve our understanding of the underlying biology and optimize the allocation of resources for drug development.

Results: We developed an algorithm to predict differential gene set enrichment as part of the sbv IMPROVER (systems biology verification in Industrial Methodology for Process Verification in Research) Species Translation Challenge, which focused on phosphoproteomic and transcriptomic measurements of normal human bronchial epithelial (NHBE) primary cells under various stimuli and corresponding measurements in rat (NRBE) primary cells. We find that gene sets exhibit a higher inter-species correlation compared with individual genes, and are potentially more suited for direct prediction. Furthermore, in contrast to a similar cross-species response in protein phosphorylation states 5 and 25 min after exposure to stimuli, gene set enrichment 6 h after exposure is significantly different in NHBE cells compared with NRBE cells. In spite of this difference, we were able to develop a robust algorithm to predict gene set activation in NHBE with high accuracy using simple analytical methods.

Availability and implementation: Implementation of all algorithms is available as source code (in Matlab) at http://bhanot.biomaps.rutgers.edu/wiki/codes_SC3_Predicting_GeneSets.zip, along with the relevant data used in the analysis. Gene sets, gene expression and protein phosphorylation data are available on request.

Contact:  hormoz@kitp.ucsb.edu
PHOXTRACK–a tool for interpreting comprehensive datasets of post-translational modifications of proteins
Authors: Weidner Christopher , Fischer Cornelius , Sauer Sascha
Published: August 2014

Summary: We introduce PHOXTRACK (PHOsphosite-X-TRacing Analysis of Causal Kinases), a user-friendly freely available software tool for analyzing large datasets of post-translational modifications of proteins, such as phosphorylation, which are commonly gained by mass spectrometry detection. In contrast to other currently applied data analysis approaches, PHOXTRACK uses full sets of quantitative proteomics data and applies non-parametric statistics to calculate whether defined kinase-specific sets of phosphosite sequences indicate statistically significant concordant differences between various biological conditions. PHOXTRACK is an efficient tool for extracting post-translational information of comprehensive proteomics datasets to decipher key regulatory proteins and to infer biologically relevant molecular pathways.

Availability: PHOXTRACK will be maintained over the next years and is freely available as an online tool for non-commercial use at http://phoxtrack.molgen.mpg.de. Users will also find a tutorial at this Web site and can additionally give feedback at https://groups.google.com/d/forum/phoxtrack-discuss.

Contact:  sauer@molgen.mpg.de.

Supplementary information:  Supplementary data are available at Bioinformatics online.
Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction
Authors: Heymann Michael , Opthalage Achini , Wierman Jennifer L. , Akella Sathish , Szebenyi Doletha M. E. , Gruner Sol M. , Fraden Seth
Published: August 2014

An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.
Case of tick‐associated rash illness caused by Amblyomma testudinarium
Authors: Natsuaki Masaru , Takada Nobuhiro , Kawabata Hiroki , Ando Shuji , Yamanishi Kiyofumi
Published: August 2014

We report a case of tick‐associated rash illness (TARI), a new clinical entity of erythema migrans associated with a tick bite without infection of Lyme borreliosis agent. The patient, a 53‐year‐old man, went hiking in a mountainous area of Minoh City, Osaka Prefecture in October 2012. An erythematous macule with itching and a biting tick was found on his left thigh 2 days later, which gradually expanded. On the first visit to our department at the fifth day after hiking, an erythematous macule of 10 cm was recognized around the bite site. He had no systemic symptoms, and laboratory data were within normal limits. The tick was identified as a nymph of Amblyomma testudinarium. Histopathologically, perivascular infiltrates, mainly consisting of T lymphocytes, were seen in the dermis. The skin rash disappeared within 2 weeks with no treatment. Serum antibody titers against Lyme disease borrelial and rickettsial agents on the first visit and 2 weeks later were negative. These results indicate that the skin lesion of TARI was not associated with borrelial or rickettsial infection but a T‐cell‐mediated allergic reaction to salivary gland substances of the tick.
Axillary giant lipoma: A report of two cases and published work review
Authors: Nakamura Yasuhiro , Teramoto Yukiko , Sato Sayuri , Yamada Katsuhiro , Nakamura Yoshiyuki , Fujisawa Yasuhiro , Fujimoto Manabu , Otsuka Fujio , Yamamoto Akifumi
Published: August 2014

Lipomas are common, benign, small‐sized, soft‐tissue tumors. However, giant lipomas are uncommon and the tumor size can cause pain and nerve compression syndrome. The axilla is an extremely rare location for development of giant lipomas. We report two cases of axillary giant lipoma. A 47‐year‐old man (case 1) and a 42‐year‐old woman (case 2) presented with a large mass in the axillary region. Case 2 had tenderness in the shoulder and numbness in the upper arm. Magnetic resonance imaging of each tumor showed a homogenous soft‐tissue mass in the axillary region, suggestive of lipoma. In case 2, the tumor extended from the axilla to the supraclavicular region and split and compressed the neurovascular bundle. Each lesion was successfully excised surgically without serious complications and recurrence. In case 2, the tenderness and numbness disappeared. Histologically, each lesion was composed of multilobulated, mature adipose cells, which led to a diagnosis of benign lipoma. Axillary giant lipoma is preferably excised surgically to avoid damage caused by tumor compression to the major vessels or nerves, to offer better local control and to establish a correct final diagnosis.
A chalcone with potent inhibiting activity against biofilm formation by nontypeable Haemophilus influenzae
Authors: Kunthalert Duangkamol , Baothong Sudarat , Khetkam Pichit , Chokchaisiri Suwadee , Suksamrarn Apichart
Published: August 2014

Nontypeable Haemophilus influenzae (NTHi), an important human respiratory pathogen, frequently causes biofilm infections. Currently, resistance of bacteria within the biofilm to conventional antimicrobials poses a major obstacle to effective medical treatment on a global scale. Novel agents that are effective against NTHi biofilm are therefore urgently required. In this study, a series of natural and synthetic chalcones with various chemical substituents were evaluated in vitro for their antibiofilm activities against strong biofilm‐forming strains of NTHi. Of the test chalcones, 3‐hydroxychalcone (chalcone 8) exhibited the most potent inhibitory activity, its mean minimum biofilm inhibitory concentration (MBIC50) being 16 μg/mL (71.35 μM), or approximately sixfold more active than the reference drug, azithromycin (MBIC50 419.68 μM). The inhibitory activity of chalcone 8, which is a chemically modified chalcone, appeared to be superior to those of the natural chalcones tested. Significantly, chalcone 8 inhibited biofilm formation by all studied NTHi strains, indicating that the antibiofilm activities of this compound occur across multiple strong‐biofilm forming NTHi isolates of different clinical origins. According to antimicrobial and growth curve assays, chalcone 8 at concentrations that decreased biofilm formation did not affect growth of NTHi, suggesting the biofilm inhibitory effect of chalcone 8 is non‐antimicrobial. In terms of structure–activity relationship, the possible substituent on the chalcone backbone required for antibiofilm activity is discussed. These findings indicate that 3‐hydroxychalcone (chalcone 8) has powerful antibiofilm activity and suggest the potential application of chalcone 8 as a new therapeutic agent for control of NTHi biofilm‐associated infections.
Immunological basis of anti‐Candida vaccines focused on synthetically prepared cell wall mannan‐derived manno‐oligomers
Authors: Paulovičová Lucia , Paulovičová Ema , Bystrický Slavomír
Published: August 2014

The increasing incidence of diseases caused by Candida species and complications in individuals with impaired immunity require new strategies for candidiasis treatment and prevention. The available therapies are often of limited effectiveness in immunocompromised patients, resulting in treatment failures, chronic infections and high mortality rates. Research directed at identifying the composition of an effective vaccine is required. Mannan forms the outermost layer of the Candida cell wall and has an essential role in modulation of anti‐Candida host immune responses. Therefore, Candida cell wall mannan and synthetically prepared manno‐oligomer‐based glycoconjugates are the foci of attention in vaccine candidate development. Almost all of the existing human vaccines mediate protection through neutralizing antibodies. Th1‐based and/or Th17‐based cellular immune responses, rather than antibody‐mediated immunity, mediate protection against candidiasis. Findings of published studies indicate that analysis of cellular immune responses as well as antibody responses is necessary when assessing the immunomodulatory properties of manno‐oligomer‐based glycoconjugates that are potential anti‐Candida vaccine candidates.
The consistency of experts' evaluation of obstetric claims for compensation
Authors: Andreasen S , Backe B , Lydersen S , Øvrebø K , Øian P
Published: August 2014

Objective

The aim of this study was to investigate the consistency of experts' evaluation of different types of obstetric claims for compensation.

Design

Inter‐rater reliability study of obstetric claims for compensation.

Setting

Medical experts' evaluation in The Norwegian System of Compensation to Patients, a no‐blame system.

Sample

The 15 most frequently used medical experts were asked to evaluate 12 obstetric claims applied for compensation.

Methods

Inter‐rater agreement was assessed by absolute agreement, Fleiss' kappa statistic and Gwet's AC1.

Main outcome measures

Consistency in the evaluation of negligence (carelessness without intention to harm) and causality (relation between care and injury) between negligence and patient injury.

Results

The experts demonstrated moderate consistency in their evaluation of negligence (Fleiss' kappa = 0.53/AC1 = 0.54) and causality (Fleiss' kappa = 0.41/AC1 = 0.54). There was a higher level of agreement in clinical scenarios with well‐documented diagnostic criteria and guidelines, including shoulder dystocia and asphyxia with low Apgar score and metabolic acidosis.

Conclusion

We found a moderate level of agreement in experts' evaluation of negligence and causality between the injury and provided health care, the two most important questions to be answered in obstetric claims for compensation.
Hedgehog signaling pathway regulated the target genes for adipogenesis in silkworm Bombyx mori
Authors: Liang Shuang , Chen Rui‐Ting , Zhang Deng‐Pan , Xin Hu‐Hu , Lu Yan , Wang Mei‐Xian , Miao Yun‐Gen
Published: August 2014

Hedgehog (Hh) signals regulate invertebrate and vertebrate development, yet the role of the pathway in adipose development remains poorly understood. In this report, we found that Hh pathway components are expressed in the fat body of silkworm larvae. Functional analysis of these components in a BmN cell line model revealed that activation of the Hh gene stimulated transcription of Hh pathway components, but inhibited the expression of the adipose marker gene AP2. Conversely, specific RNA interference‐mediated knockdown of Hh resulted in increased AP2 expression. This further showed the regulation of Hh signal on the adipose marker gene. In silkworm larval models, enhanced adipocyte differentiation and an increase in adipocyte cell size were observed in silkworms that had been treated with a specific Hh signaling pathway antagonist, cyclopamine. The fat‐body‐specific Hh blockade tests were consistent with Hh signaling inhibiting silkworm adipogenesis. Our results indicate that the role of Hh signaling in inhibiting fat formation is conserved in vertebrates and invertebrates.
A missense mutation in melanocortin 1 receptor is associated with the red coat colour in donkeys
Authors: Abitbol M. , Legrand R. , Tiret L.
Published: August 2014

The seven donkey breeds recognised by the French studbook are characterised by few coat colours: black, bay and grey. Normand bay donkeys seldom give birth to red foals, a colour more commonly seen and recognised in American miniature donkeys. Red resembles the equine chestnut colour, previously attributed to a mutation in the melanocortin 1 receptor gene (MC1R). We used a panel of 124 donkeys to identify a recessive missense c.629T>C variant in MC1R that showed a perfect association with the red coat colour. This variant leads to a methionine to threonine substitution at position 210 in the protein. We showed that methionine 210 is highly conserved among vertebrate melanocortin receptors. Previous in silico and in vitro analyses predicted this residue to lie within a functional site. Our in vivo results emphasised the pivotal role played by this residue, the alteration of which yielded a phenotype fully compatible with a loss of function of MC1R. We thus propose to name the c.629T>C allele in donkeys the e allele, which further enlarges the panel of recessive MC1R loss‐of‐function alleles described in animals and humans.
Does Fear Spill Over?
Authors: Chen Cathy Yi‐Hsuan
Published: August 2014

This paper develops a new methodology for analyzing fear spillovers between four implied volatility indices (MVXinCanada,VXJinJapan,VDAXinGermany andVIXin theUnitedStates) using a copula‐based bivariateMarkov‐switching model. We consider a parameterization of theMarkov‐switching model that allows for four possible states (consisting of combinations of either low or high expected volatilities). This model also combines selected copulas to describe the dependence pattern between different markets. The results show that dependencies, contagions and causalities between the four implied volatility index levels are strongly supported by the data in all copulas. From the dynamic and asymmetric analysis, the results indicate that the linkages between implied volatility indices are more pronounced when the indices rise.
Regulation of Na+ excretion and arterial blood pressure by purinergic signalling intrinsic to the distal nephron: consequences and mechanisms
Authors: Mironova E. , Boiko N. , Bugaj V. , Kucher V. , Stockand J. D.
Published: August 2014

Discretionary control of Na+ excretion is a key component of the regulation of arterial blood pressure in mammals. Sodium excretion is fine‐tuned in the aldosterone‐sensitive distal nephron by the activity of the epithelial Na+ channel (ENaC). Here, ENaC functions as a final effector of the renin–angiotensin–aldosterone system (RAAS) during negative feedback control of blood pressure. Mutations affecting ENaC activity and abnormal regulation of this channel affect blood pressure through pathological changes to Na+ excretion. Recent evidence demonstrates that powerful signalling pathways function in parallel with the RAAS to modulate ENaC activity and blood pressure. An inclusive paradigm is emerging with respect to regulation of blood pressure where ENaC serves as a critical point of convergence for several important signalling systems that affect renal Na+ excretion. A robust inhibitory purinergic signalling system intrinsic to the distal nephron dynamically regulates ENaC through paracrine ATP signalling via the metabotropic P2Y2 purinergic receptor to properly match urinary Na+ excretion to dietary Na+ intake. This enables blood pressure to be maintained within a normal range despite broad changes in dietary Na+ consumption. Loss of purinergic inhibition of ENaC increases blood pressure by causing inappropriate Na+ excretion. In contrast, stimulation of the P2Y2 receptor promotes natriuresis and a decrease in blood pressure. Such observations identify purinergic signalling in the distal nephron as possibly causative, when dysfunctional, for certain forms of elevated blood pressure, and as a possible therapeutic target for the treatment of elevated blood pressure particularly that associated with salt sensitivity.
Acanthocephalan infection and sparganosis in a green tree snake (Dendrelaphis punctulata)
Authors: Hill AG , Ladds PW , Spratt DM
Published: August 2014

Acanthocephalan and spargana parasites were identified within a body wall mass during exploratory surgery in a wild green tree snake. Acanthocephalan parasites have not previously been reported in this species. Surgical excision, the treatment of choice, could not be achieved because of the extensive infiltration of the coelomic cavity.