bluuebunny/crossref_metadata_2025 huggingface dataset:
Tuning the hybridization bandgap by meta-molecules with in-unit interaction
Authors: Chen Yongqiang , Li Yunhui , Wu Qian , Jiang Haitao , Zhang Yewen , Chen Hong
Published: September 2015

In this paper, we demonstrate that the hybridization bandgap (HBG) can be tuned conveniently by deep subwavelength meta-molecules with in-unit interaction. Spontaneous-emission-cancellation-like (SEC-like) effect is realized in a meta-molecule by introducing the destructive interference of two detuned meta-atoms. The meta-atoms consisting of subwavelength zero-index-metamaterial-based resonators are side-coupled to a microstrip. Compared to conventional HBG configurations, the presence of in-unit interaction between meta-atoms provides more flexibility in tuning the bandgap properties, keeping the device volume almost unchanged. Both numerical simulations and microwave experiments confirm that the width, depth, and spectrum shape of HBG can be tuned by simply introducing SEC-like interaction into the meta-molecule. Due to these features, our design may be promising to be applied in microwave or optics communications systems with strict limitation of device volume and flexible bandgap properties.
Nonpolar resistive memory switching with all four possible resistive switching modes in amorphous LaHoO3 thin films
Authors: Sharma Yogesh , Pavunny Shojan P. , Fachini Esteban , Scott James F. , Katiyar Ram S.
Published: September 2015

We studied the resistive memory switching in pulsed laser deposited amorphous LaHoO3 (a-LHO) thin films for non-volatile resistive random access memory applications. Nonpolar resistive switching (RS) was achieved in Pt/a-LHO/Pt memory cells with all four possible RS modes (i.e., positive unipolar, positive bipolar, negative unipolar, and negative bipolar) having high RON/ROFF ratios (in the range of ∼104–105) and non-overlapping switching voltages (set voltage, VON ∼ ±3.6–4.2 V and reset voltage, VOFF ∼ ±1.3–1.6 V) with a small variation of about ±5–8%. Temperature dependent current-voltage (I–V) characteristics indicated the metallic conduction in low resistance states (LRS). We believe that the formation (set) and rupture (reset) of mixed conducting filaments formed out of oxygen vacancies and metallic Ho atoms could be responsible for the change in the resistance states of the memory cell. Detailed analysis of I–V characteristics further corroborated the formation of conductive nanofilaments based on metal-like (Ohmic) conduction in LRS. Simmons-Schottky emission was found to be the dominant charge transport mechanism in the high resistance state.
Plasmonic Fano interference produced by gold nano-disks on a dielectric Bragg stack
Authors: Hajebifard Akram , Berini Pierre
Published: September 2015

Fano interference is predicted in a structure consisting of a periodic array of uncoupled gold nano-disks (AuNDs) supported by a Bragg stack. The phenomenon occurs due to resonant interference between the reflection spectrum of the Bragg stack and localized surface plasmon resonances (LSPRs) on the AuNDs. Fitting the computational results to the Fano lineshape formula yields the Fano parameters of the resonances including their linewidth. One of the most important advantages of the structure is that the linewidth of the Fano resonances (∼9 nm) is much narrower than the bandwidth of the LSPR nano-disks (∼80 nm) and the reflection bandwidth of the Bragg stack on which the disks are supported (∼100 nm). The narrow Fano linewidth and the ease with which they can be interrogated using perpendicularly incident light makes the structure attractive for biosensing applications. The bulk sensitivities and figure of merit of Fano resonances in a proposed design are 44 nm/RIU (redshift) and −52 nm/RIU (blueshift), and ∼4 RIU−1, respectively.
Suppression of dark current through barrier engineer for solution-processed colloidal quantum-dots infrared photodetectors
Authors: Jiang Zhenyu , Hu Wenjia , Liu Yan , Zhang Wenjun , Mo Chen , You Guanjun , Wang Li , Atalla Mahmoud R. M. , Zhang Yu , Liu Jie , Kurhade Kandhar K. , Xu Jian
Published: September 2015

In an attempt to suppress the dark current, the barrier layer engineer for solution-processed PbSe colloidal quantum-dot (CQD) photodetectors has been investigated in the present study. It was found that the dark current can be significantly suppressed by implementing two types of carrier blocking layers, namely, hole blocking layer and electron blocking layer, sandwiched in between two active PbSe CQD layers. Meanwhile no adverse impact has been observed for the photo current. Our study suggests that this improvement resides on the transport pathway created via carrier recombination at intermediate layer, which provides wide implications for the suppression of dark current for infrared photodetectors.
Do price premiums for wool characteristics vary for different end products, processing routes and fibre diameter categories?
Authors: Cottle David , Fleming Euan
Published: September 2015

No Australian wool price hedonic studies have separated auction data into different end product-processing groups (PPR) on the basis of all fibre attributes that affect the suitability of wool sale lots for PPR. This study was conducted to assess: (1) whether including information about PPR groupings is more useful in understanding price than clustering by broad fibre diameter (FD) categories, and (2) if the ‘noise’ of macroeconomic effects on price can be reduced by using a clean price relative to the market indicator (RelPrice) formula or a log RelPrice formula compared with log price or clean price. Hedonic models using data derived from 369 918 Australian auction sale lots in 2010–2011 were estimated for these four dependent price variables. Linear FD models predicted less of price’s variance than quadratic or exponential models. Segmenting wool sale lots into 10 PPR before wool price analyses was found to increase the proportion of price variance explained and thus be worthwhile. The change in price with a change in FD, staple length and staple strength differs significantly between PPR. Calculating RelPrice or log RelPrice appears a better price parameter than clean price or log price. Comparing the RelPrice and clean price models, the mean absolute percentage errors were 6.3% and 16.2%, respectively. The differences in price sensitivity to FD, staple length and staple strength across PPR implies a complex set of price-setting mechanisms for wool as different users place different values on these wool properties. These price-setting mechanisms need to be incorporated in hedonic models for agricultural products that possess this characteristic. The wool price premiums can be used to estimate relative economic values when constructing sheep breeding selection indexes and can help determine the most profitable wool clip preparation strategies.
Effect of fermentation of soybean meal with varying protein solubility on ileal digestibility of nutrients in growing pigs
Authors: Upadhaya Santi D. , Ryu Je-hoon , Kang Kyung-il , Cho Seong-Jun , Kim In Ho
Published: September 2015

Apparent ileal digestibility and standardised ileal digestibility of energy, dry matter, nitrogen and amino acids were evaluated in five cannulated [(Landrace × Yorkshire) × Duroc)] barrows with an initial bodyweight of 27.1 ± 0.58 kg in a 5 × 5 Latin square design. Pigs were fed unfermented soybean meal (USM) as control and fermented soybean meal A, B and C (FSMA, FSMB and FSMC, respectively), with 52.4%, 62.0% and 71.8% protein solubility, respectively, and a nitrogen-free diet. The nitrogen-free diet was used to determine basal endogenous losses of crude protein and amino acids. The apparent ileal digestibility of dry matter and nitrogen was greater (P < 0.05) in FMSC and tended to improve in FSMA and FSMB compared with the control. The apparent ileal digestibility of isoleucine, phenylalanine and valine was greater in all fermented soybean meal whereas that of lysine was greater (P < 0.05) in FSMC compared with USM. Likewise, the apparent ileal digestibility of aspartic acid and proline was greater (P < 0.05) in FSMA and FSMC. The standardised ileal digestibility of crude protein and lysine was higher (P < 0.05) in FSMC and tended to improve in FSMA and FSMB whereas the standardised ileal digestibility of isoleucine was higher (P < 0.05) in FSMA, FSMB and FSMC compared with USM. In conclusion, fermentation of soybean meal showed better digestibility compared with USM regardless of its protein solubility values.
Effect of feeding semi-moist diets and highly digestible carbohydrate and protein sources in the prestarter phase on performance of broiler chicks
Authors: Tabeidian Sayed Ali , Sadeghi Ghorbanali , Toghyani Majid , Habibian Mahmood
Published: September 2015

In total, 1400 1-day-old male Ross 308 broiler chicks were used to examine the effects of inclusion of alternative carbohydrate and protein sources in prestarter diets and the form of diet on subsequent performance, physiological development and carcass characteristics of broilers. The experimental diets were offered from 1 to 7 days of age and were as follows: control maize–soybean–fish meal diet (CON); maize–soybean meal–casein–dextrose diet (CD); maize–soybean meal–casein-maize starch diet (CS); maize–soybean meal–maize gluten–dextrose diet (GD); and maize–soybean meal–maize gluten–maize starch diet (GS). Each diet was provided in either solid or semi-moist (30% moisture) form, resulting in 10 dietary treatments in a 5 × 2 factorial arrangement. During the first week, a significant (P < 0.05) decrease in feed intake and weight gain was observed in the chicks receiving the CD or the CS diets compared with the chicks receiving the CON diet. Chicks receiving the CON diet also exhibited lower (P < 0.05) feed conversion ratio than did those receiving the CD or the CS diets. The adverse effect of feeding the CD and CS diets on liveweight of the birds was still evident at 21 and 42 days of age (P < 0.05). Chicks on the semi-moist diets consumed less (P < 0.05) feed than those on the solid diets during the first week. Nevertheless, chicks fed the semi-moist diets had higher (P < 0.05) weight gain and exhibited lower (P < 0.05) feed conversion ratio than did those fed solid diets. During the entire period, the highest weight gain and feed intake were observed in chicks receiving the CON prestarter diet in semi-moist form. During the first week, chicks receiving the CD or the CS diet exhibited the lowest (P < 0.05) small intestine weight and length. Conversely, at the age of 21 days, these chicks had higher (P < 0.05) small intestine weight than did the other chicks. It can be concluded that using a maize–soybean–fish meal-based prestarter diet in semi-moist form improves chick development and positively affects growth performance.
Synthesis, Structures, and Properties of Polynuclear Silver(I) Complexes Containing Tetra-Phosphine Ligand with Ag⋅⋅⋅C Interactions
Authors: Huang Ting-Hong , Yan Jie , Yang Hu , Tan Changbin , Yang Yan
Published: September 2015

Reaction of AgNO3 and N,N,N′,N′-tetrakis((diphenylphosphino)methyl)benzene-1,4-diamine (pbaa) with sodium N-ethyldithiocarbamate (Na(Etdtc)) in CH3CN/toluene and CH3CN/DMF solvents produced two Ag4S4-based coordination complexes [Ag4(pbaa)(µ-κ1S,κ2S-Etdtc)4] (1) and [Ag4(pbaa)(µ-κ1S,κ2S-Etdtc)2(µ-κ1S,κ1S-Etdtc)2] (2). Structural analysis shows that the Ag4S4 cores in 1 are interconnected by one pbaa ligand in a tetradentate mode and four Etdtc– anions in a µ-κ1S,κ2S mode to form a three-layer conformation, whereas the Ag4S4 cores in 2 are linked by ligands pbaa (the tetradentate mode) and Etdtc– (the µ-κ1S,κ1S and µ-κ1S,κ2S modes) to yield the other type of three-layer conformation. In addition, in different solvent systems, the Ag atoms also form different types of weak Ag···C interactions with Ag···C distances of 3.297–3.344 Å in 1 and 3.237–3.416 Å in 2. The emission spectrum of complex 1 in DMF solution displays a broad orange–red emission peak at 518 nm, which may be assigned to the ligand-to-metal charge transfer transition.
Seasonal copepod lipid pump promotes carbon sequestration in the deep North Atlantic
Authors: Jónasdóttir Sigrún Huld , Visser André W. , Richardson Katherine , Heath Michael R.
Published: September 2015

Significance

Every autumn across the North Atlantic, large numbers of zooplankton copepods migrate from the surface waters into the ocean's interior to hibernate at depths of 600–1,400 m. Through this migration, they actively transport lipid carbon to below the permanent thermocline, where it is metabolized at a rate comparable to the carbon delivered by sinking detritus. This “lipid pump” has not been included in previous estimates of the deep-ocean carbon sequestration, which are based on either measurements of sinking fluxes of detritus, or estimates of new primary production. Unlike other components of the biological pump, the lipid pump does not strip the surface ocean of nutrients, and decouples carbon sequestration from nutrient replenishment, a process we term the “lipid shunt.”
Do handwritten words magnify lexical effects in visual word recognition?
Authors: Perea Manuel , Gil-López Cristina , Beléndez Victoria , Carreiras Manuel
Published: September 2015

An examination of how the word recognition system is able to process handwritten words is fundamental to formulate a comprehensive model of visual word recognition. Previous research has revealed that the magnitude of lexical effects (e.g., the word-frequency effect) is greater with handwritten words than with printed words. In the present lexical decision experiments, we examined whether the quality of handwritten words moderates the recruitment of top-down feedback, as reflected in word-frequency effects. Results showed a reading cost for difficult-to-read and easy-to-read handwritten words relative to printed words. But the critical finding was that difficult-to-read handwritten words, but not easy-to-read handwritten words, showed a greater word-frequency effect than printed words. Therefore, the inherent physical variability of handwritten words does not necessarily boost the magnitude of lexical effects.
Topology through the centuries: Low dimensional manifolds
Authors: Milnor John
Published: September 2015

This note will provide a lightning tour through the centuries, concentrating on the study of manifolds of dimension 2, 3, and 4. Further comments and more technical details about many of the sections may be found in the Appendix.
Large-scale extraction of gene interactions from full-text literature using DeepDive
Authors: Mallory Emily K. , Zhang Ce , Ré Christopher , Altman Russ B.
Published: September 2015

Motivation: A complete repository of gene–gene interactions is key for understanding cellular processes, human disease and drug response. These gene–gene interactions include both protein–protein interactions and transcription factor interactions. The majority of known interactions are found in the biomedical literature. Interaction databases, such as BioGRID and ChEA, annotate these gene–gene interactions; however, curation becomes difficult as the literature grows exponentially. DeepDive is a trained system for extracting information from a variety of sources, including text. In this work, we used DeepDive to extract both protein–protein and transcription factor interactions from over 100 000 full-text PLOS articles.

Methods: We built an extractor for gene–gene interactions that identified candidate gene–gene relations within an input sentence. For each candidate relation, DeepDive computed a probability that the relation was a correct interaction. We evaluated this system against the Database of Interacting Proteins and against randomly curated extractions.

Results: Our system achieved 76% precision and 49% recall in extracting direct and indirect interactions involving gene symbols co-occurring in a sentence. For randomly curated extractions, the system achieved between 62% and 83% precision based on direct or indirect interactions, as well as sentence-level and document-level precision. Overall, our system extracted 3356 unique gene pairs using 724 features from over 100 000 full-text articles.

Availability and implementation: Application source code is publicly available at https://github.com/edoughty/deepdive_genegene_app

Contact:  russ.altman@stanford.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Development of a three-dimensional growth prediction model for the Japanese scallop in Funka Bay, Japan, using OGCM and MODIS
Authors: Liu Yang , Saitoh Sei-Ichi , Ihara Yu , Nakada Satoshi , Kanamori Makoto , Zhang Xun , Baba Katsuhisa , Ishikawa Yoichi , Hirawake Toru
Published: September 2015

The Japanese scallop (Patinopecten (Mizuhopecten) yessoensis) is an important commercial species in Funka Bay, Japan, where it is farmed using the hanging culture method. Our study was based on 6 years (from 2006 to 2011) of monthly in situ observations of scallop growth at Yakumo station. To produce a basic spatial distribution dataset, we developed an interpolation solution for the shortage of Chl-a concentration data available from the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite. Additionally, we integrated four-dimensional variational (4D-VAR) assimilation water temperature data from ocean general circulation models (OGCMs), with four vertical levels (6, 10, 14, and 18 m) from the sea surface. Statistical models, including generalized additive models (GAMs) and generalized linear models, were applied to in situ observation data, satellite data, and 4D-VAR data to identify the influence of environment factors (interpolated Chl-a, temperature, and depth) on the growth of scallops, and to develop a three-dimensional growth prediction model for the Japanese scallops in Funka Bay. We considered three methods to simulate the growth process of scallops (accumulation, summation, and product), and used them to select the most suitable model. All the interpolated Chl-a concentrations and 4D-VAR temperature data were verified by shipboard data. The results revealed that GAM, using an accumulation method that was based on a combination of integrated temperature, integrated log Chl-a, depth, and number of days, was best able to predict the vertical and spatial growth of the Japanese scallop. The predictions were verified by in situ observations from different depths (R2 = 0.83–0.94). From the distribution of three-dimensional predicted scallop growth maps at each depth, it was suggested that the growth of the Japanese scallop was most favourable at 6 m and least favourable at 18 m, although variations occurred in each aquaculture region in different years. These variations were probably due to the ocean environment and climate variation.
Sexual dysfunctions
Authors: Hawton Keith
Published: September 2015

Chapter 11 discusses sexual dysfunctions. It outlines their nature, causes (including potential contributing psychological factors), assessment as well as sex therapy, and the treatment of individuals and couples with sexual dysfunction.
Anxiety Disorders in Adults
Authors: McLean Peter D. , Woody Sheila R.
Published: September 2015

In this title, the authors review psychosocial treatments for anxiety disorders, focusing on the scientific basis and demonstrated outcomes of the treatments. Cognitive-behavioral therapies are highlighted, as they have been the most frequently investigated approaches to treating anxiety disorders. Individual chapters feature specific phobias: social phobia, panic disorder, and generalized anxiety disorder. The book is rich in clinical material and integrates science and clinical practice in an effort to help practitioners to improve the effectiveness of their work with anxious clients. Recently developed psychosocial treatments for anxiety disorders reflect the systematic influence of scientifically generated knowledge, and these new treatments yield strong results. Research in such areas as information processing, cognition, behavioral avoidance, and the physiological components of anxious arousal has increased our knowledge of mediators that cause and maintain anxiety disorders.
Evidence-Based Practice
Authors: McLean Peter D. , Woody Sheila R.
Published: September 2015

Chapter 1 discusses evidence-based practice, including recent developments in the scientist-practitioner movement (treatments that work, efficacy, treatment guidelines, and managed care), scientific literature, the transfer of technology, measurement of client progress, the components of good guidelines and standards of proof.
The Nature of Anxiety
Authors: McLean Peter D. , Woody Sheila R.
Published: September 2015

This chapter explores the extent of current knowledge on the general nature of anxiety. It begins with a discussion of categorical and dimensional views of anxiety, including issues of diagnosis, subtyping, and comorbidity. It reviews research findings into the presence of a negative affect common to anxiety states, and cognitive factors that distinguish anxiety syndromes, as well as a hierarchical model of anxiety that incorporates information from both perspectives. Finally, results from research examining distinct components of the anxiety response (behavior, cognition, and physiology) are outlined.
Work Stress and Coping in Organizations: Progress and Prospects
Authors: Burke Ronald J.
Published: September 2015

Chapter 5 discusses work stress and coping in organizations. It reviews the coping literature focusing on the workplace, presents a framework for the study of coping in organizations (including the organizational environment, cognitive appraisal, individual stress and coping behaviours). It discusses managerial health and well-being, the psychological effects of organizational change, and draws conclusions about coping with work stress.
Meeting Challenges in a Classroom Context
Authors: Boekaerts Monique
Published: September 2015

Chapter 7 focuses on the concept of positive educational psychology in the classroom context. It discusses learning according to the principles of positive psychology, goal setting and goal striving as part of the self-regulation process, the effects of a lack of self-regulation, self-regulation versus self-control, effort-management and volitional control.
Teaching Students How to Cope With Adversity: The Three Cs
Authors: Johnson David W. , Johnson Roger T.
Published: September 2015

This chapter explores adversity, and methods of teaching students how to cope with stress and adversity. It discusses the independent-self and the interdependent-self, the ‘Three Cs’ programme, which emphasizes cooperative community (social interdependence, interpersonal relationships, group skills), constructive conflict (the benefits of controversy, problem-solving training, peer mediation), and civic values.
Information processing by simple molecular motifs and susceptibility to noise
Authors: Mc Mahon Siobhan S. , Lenive Oleg , Filippi Sarah , Stumpf Michael P. H.
Published: September 2015

Biological organisms rely on their ability to sense and respond appropriately to their environment. The molecular mechanisms that facilitate these essential processes are however subject to a range of random effects and stochastic processes, which jointly affect the reliability of information transmission between receptors and, for example, the physiological downstream response. Information is mathematically defined in terms of the entropy; and the extent of information flowing across an information channel or signalling system is typically measured by the ‘mutual information’, or the reduction in the uncertainty about the output once the input signal is known. Here, we quantify how extrinsic and intrinsic noise affects the transmission of simple signals along simple motifs of molecular interaction networks. Even for very simple systems, the effects of the different sources of variability alone and in combination can give rise to bewildering complexity. In particular, extrinsic variability is apt to generate ‘apparent’ information that can, in extreme cases, mask the actual information that for a single system would flow between the different molecular components making up cellular signalling pathways. We show how this artificial inflation in apparent information arises and how the effects of different types of noise alone and in combination can be understood.
Evolutionary origins and development of saw-teeth on the sawfish and sawshark rostrum (Elasmobranchii; Chondrichthyes)
Authors: Welten Monique , Smith Moya Meredith , Underwood Charlie , Johanson Zerina
Published: September 2015

A well-known characteristic of chondrichthyans (e.g. sharks, rays) is their covering of external skin denticles (placoid scales), but less well understood is the wide morphological diversity that these skin denticles can show. Some of the more unusual of these are the tooth-like structures associated with the elongate cartilaginous rostrum ‘saw’ in three chondrichthyan groups: Pristiophoridae (sawsharks; Selachii), Pristidae (sawfish; Batoidea) and the fossil Sclerorhynchoidea (Batoidea). Comparative topographic and developmental studies of the ‘saw-teeth’ were undertaken in adults and embryos of these groups, by means of three-dimensional-rendered volumes from X-ray computed tomography. This provided data on development and relative arrangement in embryos, with regenerative replacement in adults. Saw-teeth are morphologically similar on the rostra of the Pristiophoridae and the Sclerorhynchoidea, with the same replacement modes, despite the lack of a close phylogenetic relationship. In both, tooth-like structures develop under the skin of the embryos, aligned with the rostrum surface, before rotating into lateral position and then attaching through a pedicel to the rostrum cartilage. As well, saw-teeth are replaced and added to as space becomes available. By contrast, saw-teeth in Pristidae insert into sockets in the rostrum cartilage, growing continuously and are not replaced. Despite superficial similarity to oral tooth developmental organization, saw-tooth spatial initiation arrangement is associated with rostrum growth. Replacement is space-dependent and more comparable to that of dermal skin denticles. We suggest these saw-teeth represent modified dermal denticles and lack the ‘many-for-one’ replacement characteristic of elasmobranch oral dentitions.
Extensions of d'Alembert's paradox for elongated bodies
Authors: Spalart Philippe R.
Published: September 2015

The steady incompressible irrotational flow past a three-dimensional body of any shape generates no forces. The historic paradox refers only to drag, but lift is also zero, which has been known but not emphasized. The new material concerns a body with a long constant cross section, such as a train. The final results for forces and moments are very simple. With zero angle of attack, we show that the force vectors on the front and rear parts of the body are each (asymptotically) equal to zero, if the pressure is referred to the freestream pressure. The lift and drag coefficients, based on frontal area, vanish proportionally tod/land (d/l)2, respectively, whered/lis the diameter-to-length ratio. This applies to any shape of the cross section, and of the ends. With an angle of attack, the nose and tail forces are non-zero but depend only on the angle of attack and the cross section's added mass per unit length. The pitching moment is proportional to the total added mass and the sine of twice the angle of attack. The present results clarify slender-body theory results. The practical consequence is that, for a long body with constant cross section, the shape of the nose or the tail is irrelevant to its own ‘partial’ drag and lift, and to the pitching moment.
Perceptual expertise in forensic facial image comparison
Authors: White David , Phillips P. Jonathon , Hahn Carina A. , Hill Matthew , O'Toole Alice J.
Published: September 2015

Forensic facial identification examiners are required to match the identity of faces in images that vary substantially, owing to changes in viewing conditions and in a person's appearance. These identifications affect the course and outcome of criminal investigations and convictions. Despite calls for research on sources of human error in forensic examination, existing scientific knowledge of face matching accuracy is based, almost exclusively, on people without formal training. Here, we administered three challenging face matching tests to a group of forensic examiners with many years' experience of comparing face images for law enforcement and government agencies. Examiners outperformed untrained participants and computer algorithms, thereby providing the first evidence that these examiners are experts at this task. Notably, computationally fusing responses of multiple experts produced near-perfect performance. Results also revealed qualitative differences between expert and non-expert performance. First, examiners' superiority was greatest at longer exposure durations, suggestive of more entailed comparison in forensic examiners. Second, experts were less impaired by image inversion than non-expert students, contrasting with face memory studies that show larger face inversion effects in high performers. We conclude that expertise in matching identity across unfamiliar face images is supported by processes that differ qualitatively from those supporting memory for individual faces.
Early detection surveillance for an emerging plant pathogen: a rule of thumb to predict prevalence at first discovery
Authors: Parnell S. , Gottwald T. R. , Cunniffe N. J. , Alonso Chavez V. , van den Bosch F.
Published: September 2015

Emerging plant pathogens are a significant problem for conservation and food security. Surveillance is often instigated in an attempt to detect an invading epidemic before it gets out of control. Yet in practice many epidemics are not discovered until already at a high prevalence, partly due to a lack of quantitative understanding of how surveillance effort and the dynamics of an invading epidemic relate. We test a simple rule of thumb to determine, for a surveillance programme taking a fixed number of samples at regular intervals, the distribution of the prevalence an epidemic will have reached on first discovery (discovery-prevalence) and its expectation
E
(
q
*). We show that
E
(
q
*) =
r
/
(N
/Δ), i.e. simply the rate of epidemic growth divided by the rate of sampling; where
r
is the epidemic growth rate,
N
is the sample size and Δ is the time between sampling rounds. We demonstrate the robustness of this rule of thumb using spatio-temporal epidemic models as well as data from real epidemics. Our work supports the view that, for the purposes of early detection surveillance, simple models can provide useful insights in apparently complex systems. The insight can inform decisions on surveillance resource allocation in plant health and has potential applicability to invasive species generally.
Changing ideas about eukaryotic origins
Authors: Williams Tom A. , Embley T. Martin
Published: September 2015

The origin of eukaryotic cells is one of the most fascinating challenges in biology, and has inspired decades of controversy and debate. Recent work has led to major upheavals in our understanding of eukaryotic origins and has catalysed new debates about the roles of endosymbiosis and gene flow across the tree of life. Improved methods of phylogenetic analysis support scenarios in which the host cell for the mitochondrial endosymbiont was a member of the Archaea, and new technologies for sampling the genomes of environmental prokaryotes have allowed investigators to home in on closer relatives of founding symbiotic partners. The inference and interpretation of phylogenetic trees from genomic data remains at the centre of many of these debates, and there is increasing recognition that trees built using inadequate methods can prove misleading, whether describing the relationship of eukaryotes to other cells or the root of the universal tree. New statistical approaches show promise for addressing these questions but they come with their own computational challenges. The papers in this theme issue discuss recent progress on the origin of eukaryotic cells and genomes, highlight some of the ongoing debates, and suggest possible routes to future progress.
Rooting the tree of life: the phylogenetic jury is still out
Authors: Gouy Richard , Baurain Denis , Philippe Hervé
Published: September 2015

This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.
Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis
Authors: Akanni Wasiu A. , Siu-Ting Karen , Creevey Christopher J. , McInerney James O. , Wilkinson Mark , Foster Peter G. , Pisani Davide
Published: September 2015

The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an
α
-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the host nucleus. A general framework allowing the conceptualization of eukaryogenesis from a genomic perspective has long been lacking. Recent studies suggest that the origins of several archaebacterial phyla were coincident with massive imports of eubacterial genes. Although this does not indicate that these phyla originated through the same process that led to the origin of Eukaryota, it suggests that Archaebacteria might have had a general propensity to integrate into their genomes large amounts of eubacterial DNA. We suggest that this propensity provides a framework in which eukaryogenesis can be understood and studied in the light of archaebacterial ecology. We applied a recently developed supertree method to a genomic dataset composed of 392 eubacterial and 51 archaebacterial genera to test whether large numbers of genes flowing from Eubacteria are indeed coincident with the origin of major archaebacterial clades. In addition, we identified two potential large-scale transfers of uncertain directionality at the base of the archaebacterial tree. Our results are consistent with previous findings and seem to indicate that eubacterial gene imports (particularly from
δ
-
Proteobacteria, Clostridia and Actinobacteria) were an important factor in archaebacterial history. Archaebacteria seem to have long relied on Eubacteria as a source of genetic diversity, and while the precise mechanism that allowed these imports is unknown, we suggest that our results support the view that processes comparable to those through which eukaryotes emerged might have been common in archaebacterial history.
Sphaerochaeta associata sp. nov., a spherical spirochaete isolated from cultures of Methanosarcina mazei JL01
Authors: Troshina Olga , Oshurkova Viktoria , Suzina Natalia , Machulin Andrei , Ariskina Elena , Vinokurova Natalia , Kopitsyn Dmitry , Novikov Andrei , Shcherbakova Viktoria
Published: September 2015

An anaerobic, saccharolytic bacterial strain designated GLS2T was isolated from aggregates of the psychrotolerant archaeon Methanosarcina mazei strain JL01 isolated from arctic permafrost. Bacterial cells were non-motile, spherical, ovoid and annular with diameter 0.2–4 μm. They were chemoorganoheterotrophs using a wide range of mono-, di- and trisaccharides as carbon and energy sources. The novel isolate required yeast extract and vitamins for growth. The bacteria exhibited resistance to a number of β-lactam antibiotics, rifampicin, streptomycin and vancomycin. Optimum growth was observed between 30 and 34 °C, at pH 6.8–7.5 and with 1–2 g NaCl l− 1. Isolate GLS2T was a strict anaerobe but it tolerated oxygen exposure. On the basis of 16S rRNA gene sequence similarity, strain GLS2T was shown to belong to the genus Sphaerochaeta within the family Spirochaetaceae. Its closest relatives were Sphaerochaeta globosa BuddyT (99.3 % 16S rRNA gene sequence similarity) and Sphaerochaeta pleomorpha GrapesT (95.4 % similarity). The G+C content of DNA was 47.2 mol%. The level of DNA–DNA hybridization between strains GLS2T and BuddyT was 34.7 ± 8.8 %. Major polar lipids were phosphoglycolipids, phospholipids and glycolipids; major fatty acids were C14 : 0, C16 : 0, C16 : 0 3-OH, C16 : 0 dimethyl acetal (DMA), C16 : 1n8 and C16 : 1 DMA; respiratory quinones were not detected. The results of DNA–DNA hybridization, physiological and biochemical tests demonstrated genotypic and phenotypic differentiation of strain GLS2T from the four species of the genus Sphaerochaeta with validly published names that allowed its separation into a new lineage at the species level. Strain GLS2T therefore represents a novel species, for which the name Sphaerochaeta associata sp. nov. is proposed, with the type strain GLS2T ( = DSM 26261T = VKM B-2742T).
Variovorax gossypii sp. nov., isolated from Gossypium hirsutum
Authors: Kämpfer Peter , Busse Hans-Jürgen , McInroy John A. , Glaeser Stefanie P.
Published: September 2015

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).
Cervical spinal cord compression: a rare and serious complication of Actinomadura pelletieri actinomycetoma
Authors: Ezaldeen Eshraga A. , Mohamed Ahmed Raif , Wadella El Sammani , El Dawi Nadia , Hassan Fahal Ahmed
Published: September 2015

Introduction:

Mycetoma is a chronic granulomatous inflammatory disease predominantly affecting the foot and hand. The cervical region is an uncommon site for mycetoma and spinal cord compression is a rare complication.

Case presentation:

This communication reports on a 40-year-old male farmer from Western Sudan who presented with quadriparesis due to cervical spine cord compression caused by Actinomadura pelletieri actinomycetoma. His condition started with a small painless subcutaneous swelling in the right shoulder region that gradually increased in size to involve the right side of the neck and the cervical spinal cord ending in progressive quadriparesis. He made a good response to an extended course of antibiotics, but was left with mild disability.

Conclusions:

A. pelletieri is an uncommon cause of actinomycetoma, and the clinical presentation of the reported patient is a rare and serious sequela of mycetoma. The literature contains only a very few reports on such presentation, and our case report will add to the knowledge and experience in managing such a presentation.
A rare case of fungal keratitis: diagnosis and management
Authors: McElnea Elizabeth , Farrell Stephen , Lynch Breda , Bishop Ken , Mullen Dorinda , Borman Andrew , Higgins Gareth
Published: September 2015

Introduction:

We report a case of keratitis caused by a member of the Phoma species of fungi.

Case presentation:

A 59-year-old contact lens wearer developed a non-healing corneal ulcer. Microbiological culture and subsequent PCR analysis were performed using samples obtained from corneal scraping. A fungus, phenotypically identified as a member of the Phoma species of fungi, was cultured. PCR from infected tissue confirmed the diagnosis.

Conclusion:

Although rarely pathogenic to humans, members of the ubiquitous Phoma species of fungi can occasionally cause keratitis. Corneal microtrauma associated with contact lens wear is probably important in precipitating such infections.
ProtAnnot: an App for Integrated Genome Browser to displayhow alternative splicing and transcription affect proteins
Authors: Mall Tarun , Eckstein John , Norris David , Vora Hiral , Freese Nowlan , Loraine Ann E.
Published: September 2015

One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing, and 3’ end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists.

Availability and Implementation

ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available fromhttp://www.bioviz.org.

Contact

aloraine@uncc.edu
More than money: exploring the role of investment advisors for sustainable investing
Authors: Paetzold Falko , Busch Timo , Chesney Marc
Published: September 2015

Purpose

– Investment advisors play a significant role in financial markets, yet the determinants of their behavior have not been explored in detail. The purpose of this paper is to explore the determinants of how actively advisors communicate about sustainable investing with their clients, and differences in the preferences of advisors compared to investors.

Design/methodology/approach

– Based on a survey with 296 retail and private banking investment advisors, this study employs an ordinary least squares regression model to explore the determinants of advisors activity in communicating about sustainable investing (SI) with their clients, differences in the aspects that matter to advisors and investors, and the role of the complexity of sustainability.

Findings

– Advisors activity in communicating about SI relates to their expectation of SI regarding financial return, real-world impact, and the fuzziness and trustworthiness of SI. Advisors appear not to be influenced by expected risk and their personal values, which runs against prior research findings and the interest of investors.

Research limitations/implications

– Future research should assess cultural differences and explore asymmetries between advisors and investors in regard to the role of volatility, values, impact measurement, and complexity.

Practical implications

– Investment advisors underweighting aspects related to risk and self-transcendent values relative to their clients might limit the suitability of clients ' portfolios, skew capital allocation, and depress the role of SI in financial markets. Generalized to salespeople this behavior might depress the market success of products related to sustainability at large.

Social implications

– The findings and their generalization indicate that salespeople might systematically deviate from their clients’ interests in regard to social responsibility. Advisors and salespeople in their mediating role might be an important barrier to sustainable development.

Originality/value

– This is the first quantitative study that explores the decision-making by investment advisors in the context of SI, and as such answers to specific calls in literature to explore the micro-foundations of decision making in regard to SI and social responsibility, and on the relationship between private investors and investment advisors. This study is based on unique and original empirical data on advisors that work with retail and wealthy private investors.