Finding a Box Representation for a Graph in $O(n^2\Delta^2\ln n)$ time

An axis-parallel box in $b$-dimensional space is a Cartesian product $R_1 \times R_2 \times \cdots \times R_b$ where $R_i$ (for $1 \leq i \leq b$) is a closed interval of the form $[a_i, b_i]$ on the real line. For a graph $G$, its boxicity is the minimum dimension $b$, such that $G$ is representable as the intersection graph of (axis-parallel) boxes in $b$-dimensional space. The concept of boxicity finds application in various areas of research like ecology, operation research etc. Chandran, Francis and Sivadasan gave an $O(\Delta n^2 \ln^2 n)$ randomized algorithm to construct a box representation for any graph $G$ on $n$ vertices in $\lceil (\Delta + 2)\ln n \rceil$ dimensions, where $\Delta$ is the maximum degree of the graph. They also came up with a deterministic algorithm that runs in $O(n^4 \Delta )$ time. Here, we present an $O(n^2 \Delta^2 \ln n)$ deterministic algorithm that constructs the box representation for any graph in $\lceil (\Delta + 2)\ln n \rceil$ dimensions.

Propensity to Form Amyloid Fibrils Is Encoded as Excitations in the Free Energy Landscape of Monomeric Proteins

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation-prone (N*) states, which are rarely populated under force free native conditions but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration (C]), mechanical force (f), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive N* states. Interestingly, the phase boundaries separating the folded and unfolded states at all C] and f fall on a master curve, which can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension (R), which are accessible in pulling experiments, (R), reveal the presence of a native-like N* with a disordered solvent-exposed amino-terminal beta-strand. The structure of the N* state is identical with that found in Fyn SH3 by NMR dispersion experiments. We show that the timescale for fibril formation can be estimated from the population of the N* state, determined by the free energy gap separating the native structure and the N* state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the N* state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain. (C) 2014 Elsevier Ltd. All rights reserved.

Finding space to mental health : promoting mental health in adolescents (12 to 14 year olds): preliminary results of the intervention's effectiveness

Resumen: La salud mental y el bienestar son fundamentales para nuestra capacidad colectiva y individual como seres humanos de pensar, de exteriorizar los sentimientos, de establecer y mantener relaciones, para estudiar, para perseguir las actividades de ocio, para tomar decisiones diarias y para disfrutar de una vida plena. Una adolescencia saludable es un prerrequisito para una vida adulta saludable. Sin embargo, la realidad actual presenta un panorama preocupante. La formación del capital mental individual y colectivo - especialmente en las primeras etapas de la vida - está siendo retenida por una serie de riesgos evitables para la salud mental (World Health Organization [WHO], 2013). Los adolescentes del sur de Europa (región que ha sido más severamente afectada por la crisis financiera; e.g., Portugal) son señalados como un grupo extremadamente vulnerable, ya que su salud mental fácilmente podría ser influenciada por las dificultades económicas de sus padres y la escasez de solidaridad social (European Parliament, 2012). La promoción de la salud mental de los adolescentes es considerada como una preocupación fundamental (WHO, 2005a, 2013). En este ámbito, las intervenciones centradas en la promoción de la literacía de la salud mental han revelado importantes ventajas en la prevención, reconocimiento, intervención precoz y la reducción del estigma (Pinfold, Stuart, Thornicroft & Arboleda-Florez, 2005; Pinfold, Toulmin, Thornicroft, Huxley, Farmer & Graham, 2003; Schulze, Richter-Werling, Matschinger & Angermeyer, 2003; Stuart, 2006). En consonancia con los marcos de promoción de la salud mentales propuestos por la Organización Mundial de la Salud (2005a), tenemos que involucrar a jóvenes en los ambientes donde interactúan (Burns, 2011). Las escuelas son implícitamente uno de los locales más importantes para la promoción de la salud mental de los adolescentes (Barry, Clarke, Jenkins & Patel, 2013; WHO, 2001). El proyecto “Abrir Espacio para la Salud Mental – Promoción de la salud mental en adolescentes (12-14 años)” tiene como objetivo incrementar literacía de la salud mental en los jóvenes. En el primer año se ha desarrollado un instrumento de evaluación - Mental Health Literacy questionnaire (MHLq) - y la intervención para la promoción de la salud mental. La intervención consiste en 2 sesiones, 90 minutos cada una, implementadas con intervalo de una semana. Siguen una metodología interactiva, utilizando dinámicas de grupo, videos, música y discusión. El estudio de la eficacia de la intervención se lleva a cabo mediante un análisis pre y pos-test con el MHLq, utilizando un grupo experimental y un grupo de control. Este artículo presenta los resultados preliminares de la eficacia de la intervención de promoción de la salud mental en una muestra de 100 adolescentes portugueses (12-14 años). El pos-test mostró un incremento de los niveles de conocimientos de salud mental y estrategias de autoayuda. Los resultados sugieren que la intervención desarrollada parece ser adecuada al objetivo propuesto y refuerzan la creencia de que intervenciones escolares, sistemáticas y sostenibles, para la promoción de la salud mental con jóvenes, es un enfoque prometedor para la promoción de la literacía de la salud mental (Schulze et al., 2003; Rickwood et al., 2005; Corrigan et al., 2007; WHO, 2010).

Benthic invertebrates that form habitat on deep banks off southern California, with special reference to deep sea coral

There is increasing interest in the potential impacts that fishing activities have on megafaunal benthic invertebrates occurring in continental shelf and slope ecosystems. We examined how the structure, size, and high-density aggregations of invertebrates provided structural relief for fishes in continental shelf and slope ecosystems off southern California. We made 112 dives in a submersible at 32−320 m water depth, surveying a variety of habitats from high-relief rock to flat sand and mud. Using quantitative video transect methods, we made 12,360 observations of 15 structure-form-ing invertebrate taxa and 521,898 individuals. We estimated size and incidence of epizoic animals on 9105 sponges, black corals, and gorgonians. Size variation among structure-form-ing invertebrates was significant and 90% of the individuals were <0.5 m high. Less than 1% of the observations of organisms actually sheltering in or located on invertebrates involved fishes. From the analysis of spatial associations between fishes and large invertebrates, six of 108 fish species were found more often adjacent to invertebrate colonies than the number of fish predicted by the fish-density data from transects. This finding indicates that there may be spatial associations that do not necessarily include physical contact with the sponges and corals. However, the median distances between these six fish species and the invertebrates were not particularly small (1.0−5.5 m). Thus, it is likely that these fishes and invertebrates are present together in the same habitats but that there is not necessarily a functional relationship between these groups of organisms. Regardless of their associations with fishes, these invertebrates provide structure and diversity for continental shelf ecosystems off southern California and certainly deserve the attention of scientists undertaking future conservation efforts.

Gene structure and transcription of IRF-2 in the mandarin fish Siniperca chuatsi with the finding of alternative transcripts and microsatellite in the coding region

The gene of interferon regulatory factor-2 (IRF-2) has been cloned from the mandarin fish (Siniperca chuatsi). The IRF-2 gene has 6,418 nucleotides (nt) and contains eight exons and seven introns, encoding two mRNAs. The two IRF-2 mRNAs each contained an open reading frame of 873 nt, which both translate into the same 291 amino acids but differed in their 5' untranslated region: one mRNA was transcribed initially from the exon 1 bypassing exon 2, while the other was transcribed from the exon 2. The microsatellites (CA repeats) could be found in the carboxyl terminal region of mandarin fish IRF-2, which result in the truncated form molecules. The microsatellites' polymorphism was investigated, and eight alleles were found in 16 individuals. The microsatellites were also examined in IRF-2 of several freshwater perciform fishes. The transcription of the IRF-2 in different tissues with or without poly inosine-cytidine stimulation was analyzed by real-time PCR, and the constitutive transcription of both molecules could be detected in all the tissues examined.

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

Novel bioassays to examine the host-finding ability of plant-parasitic nematodes

We present two novel bioassays to be used in the examination of plant-parasitic nematode host-finding ability. The host-finding 'pipette-bulb assay' was constructed from modelled Pasteur pipette bulbs and connecting barrels using parafilm fastenings. This assay examines the direction of second-stage juvenile (J2) migration in response to a host seedling, through a moistened sand substrate, which underlies terminal upward-facing 'seedling bulbs', one containing a host seedling in potting compost, the other with only potting compost. An equal watering regime through both upward-facing seedling bulbs creates a directional concentration gradient of host diffusate chemotactic factors. Positive chemotactic stimuli cause the J2 to orientate and migrate towards the host plant. We present validation data collected from assays of the root-knot nematode, Meloidogyne incognita, and the potato cyst nematode, Globodera pallida, which indicate a highly significant positive attraction of J2 of both species to respective host plants. This represents a simple, quick and inexpensive method of assessing host-finding behaviour in the laboratory. We consider that the pipette-bulb assay improves on previous host-finding/chemo-attraction assays through creating a more biologically relevant environment for experimental J2; analysis is quick and easy, allowing the straightforward interpretation of results. In addition, we have developed an 'agar trough' sensory assay variant which we believe can be used rapidly to ratify nematode responses to chemical gustatory or olfactory cues. This was constructed from a water agar substrate such that two counting wells were connected by a raised central trough, all flooded with water. Two small water agar plugs were dehydrated briefly in an oven and then hydrated in either an attractant, repellent or water control; these plugs were then placed in the terminal counting wells and subsequently leached the attractant or repellent to form a concentration gradient along the central trough, which contained the initial J2 innoculum. Our data show that both M. incognita and G. pallida J2 are positively attracted to host diffusates. In addition, they displayed a strong repulsion in response to 1 M NaCl2. J2 of M. incognita displayed a mild aversion to a non-host oak root diffusate, whereas G. pallida J2 displayed a strong aversion to the same non-host diffusate; neither species responded to a compost leachate. We believe that the agar trough assay improves on previous methods by facilitating rapid diffusion of attractant or repellents. Both of the aforementioned assays were designed as tools to assess the impact of RNAi-based reverse genetics screens for gene targets involved in chemosensory orientation.

Finding exoplanets orbiting young active stars - I. Technique

Stellar activity, such as starspots, can induce radial velocity (RV) variations that can mask or even mimic the RV signature of orbiting exoplanets. For this reason RV exoplanet surveys have been unsuccessful when searching for planets around young, active stars and are therefore failing to explore an important regime which can help to reveal how planets form and migrate. This paper describes a new technique to remove spot signatures from the stellar line-profiles of moderately rotating, active stars (v sin i ranging from 10 to 50 km s(-1)). By doing so it allows planetary RV signals to be uncovered. We used simulated models of a G5V type star with differing dark spots on its surface along with archive data of the known active star HD 49933 to validate our method. The results showed that starspots could be effectively cleaned from the line-profiles so that the stellar RV jitter was reduced by more than 80 per cent. Applying this procedure to the same models and HD 49933 data, but with fake planets injected, enabled the effective removal of starspots so that Jupiter mass planets on short orbital periods were successfully recovered. These results show that this approach can be useful in the search for hot-Jupiter planets that orbit around young, active stars with a v sin i of similar to 10-50 km/s.

Finding Your Feet in the Field: Critical Reflections of Early Career Researchers on Field Research in Transitional Societies

Fieldwork that takes place in conflict or transitional regions is becoming increasingly popular amongst early-career and more seasoned researchers, but is an area that retains an air of mystery and remains an exotic form of knowledge gathering. There exists a paucity of personal reflection on the challenges associated with conducting fieldwork in conflicted or transitional regions and a limited amount of insight into the practical steps taken in advance of and when immersed in the field. Such reticence to share honest fieldwork experiences, particularly the more challenging research that takes place in conflict or transitional settings aids in creating a culture of silence. This paper attempts to counteract this silence by drawing on the challenges experienced by two early career researchers conducting fieldwork in Uganda and Palestine, focusing on the practical steps taken in advance of entering the field, and the challenges faced whilst engaged in fieldwork. Specific challenges are highlighted throughout, including: physical access to areas in conflict; engaging with reluctant research participants; the emotional impact of fieldwork on the researcher; maintaining confidentiality; researching with vulnerable victims; and ensuring appropriate knowledge exchange between researchers and participants. The paper concludes by emphasising the requirement for greater reflection on the inherently personal challenges associated with conducting fieldwork in conflicted or transitional settings and highlights the view that fieldwork is a privileged position that carries great responsibilities which must be upheld to ensure the sustainability of future research. This paper hopes to contribute to the wider debate on conducting fieldwork and the challenges associated with working in conflicted or transitional regions.

Finding Spaces for Urban Food Production – Matching Spatial and Stakeholder Analysis with Urban Agriculture Approaches in the Urban Renewal Area of Dortmund-Hörde, Germany

Using the case of an economically declined neighbourhood in the post-industrial German Ruhr Area (sometimes characterized as Germany’s “Rust Belt”), we analyse, describe and conclude how urban agriculture can be used as a catalyst to stimulate and support urban renewal and regeneration, especially from a socio-cultural perspective. Using the methodological framework of participatory action research, and linking bottom-up and top-down planning approaches, a project path was developed to include the population affected and foster individual responsibility for their district, as well as to strengthen inhabitants and stakeholder groups in a permanent collective stewardship for the individual forms of urban agriculture developed and implemented. On a more abstract level, the research carried out can be characterized as a form of action research with an intended transgression of the boundaries between research, planning, design, and implementation. We conclude that by synchronously combining those four domains with intense feedback loops, synergies for the academic knowledge on the potential performance of urban agriculture in terms of sustainable development, as well as the benefits for the case-study area and the interests of individual urban gardeners can be achieved.

Literary Love Making in Nicholas Sparks Novels: Finding the Balance Between the Writer's Life and Writer's Work in Bestselling Romantic Love

For almost a decade now Nicholas Sparks has been writing love stories. Not only has he been publishing his stories, but they have received high acclaim in each of their installments. Several of his novels have been made into major motion pictures and increased his popularity quite significantly. His status as a successful romantic fiction writer is undeniable, but the question is, why? What is it about Nicholas Sparks that makes his novels so engaging, and personally, what do I need to do as an aspiring novelist to try and acquire the same literary status? Sparks’s novels reach readers at a number of different levels, thus giving them appeal no matter the intellectual intent of the reader. Theoretically, Sparks engages reader response techniques as well as formalist processes such as “habitualization” and “defamiliarization,” while also developing engaging plot lines that represent many of the experiences from his own life. His writing is not only academically redeemable, but it is also creatively stimulating; between the two, Sparks represents the thunder and lightning combination all writers strive for while trying to achieve literary success. This project also offers a creative element in which I attempt to exemplify many of the traits discussed in the analytical sections of this document, by recreating them in a creative, fictitious fashion. Themes such as: motion versus stasis, life versus death, and the ordinary versus the extraordinary all exist within the narrative structure of my short story “Trip to Fall.” Besides these thematic elements, the creative section strives to represent the balance Sparks achieves between the experiences of his own life and the fictitious world he creates. Overall, this project delves into the life of Nicholas Sparks to better understand the inspiration for his writing at the level of form as well as content, while also paying tribute to Sparks’s style through a representation of his work in my own words.

Literary love making in Nicholas Sparks novels: Finding the balance between the writer’s life and the writer’s work in bestselling Romantic Literature

For almost a decade now Nicholas Sparks has been writing love stories. Not only has he been publishing his stories, but they have received high acclaim in each of their installments. Several of his novels have been made into major motion pictures and increased his popularity quite significantly. His status as a successful romantic fiction writer is undeniable, but the question is, why? What is it about Nicholas Sparks that makes his novels so engaging, and personally, what do I need to do as an aspiring novelist to try and acquire the same literary status? Sparks’s novels reach readers at a number of different levels, thus giving them appeal no matter the intellectual intent of the reader. Theoretically, Sparks engages reader response techniques as well as formalist processes such as “habitualization” and “defamiliarization,” while also developing engaging plot lines that represent many of the experiences from his own life. His writing is not only academically redeemable, but it is also creatively stimulating; between the two, Sparks represents the thunder and lightning combination all writers strive for while trying to achieve literary success. This project also offers a creative element in which I attempt to exemplify many of the traits discussed in the analytical sections of this document, by recreating them in a creative, fictitious fashion. Themes such as: motion versus stasis, life versus death, and the ordinary versus the extraordinary all exist within the narrative structure of my short story “Trip to Fall.” Besides these thematic elements, the creative section strives to represent the balance Sparks achieves between the experiences of his own life and the fictitious world he creates. Overall, this project delves into the life of Nicholas Sparks to better understand the inspiration for his writing at the level of form as well as content, while also paying tribute to Sparks’s style through a representation of his work in my own words.

A note on the integral trace form in cyclotomic fields

Let m >= 3 be an integer, zeta(m) is an element of C a primitive mth root of unity, and K-m the cyclotomic field Q(zeta(m)). An explicit description of the integral trace form Tr-Km/Q(x (x) over bar)vertical bar Z[zeta(m)] where (x) over bar is the complex conjugate of x is presented. In the case where m is prime, a procedure for finding the minimum of the form subject to x being a nonzero element of a certain Z- module in Z[zeta(m)] is presented.

Necklace fibers as histopathological marker in a patient with severe form of X-linked myotubular myopathy

X-linked myotubular myopathy due to mutations in the MTM1 gene is classically characterized by a severe neonatal phenotype and a typical muscle biopsy presenting globular and centrally located nuclei in muscle myofibers. Recently, four patients with mild late-onset form have been described, a male with a hemizygous mutation and three females with heterozygous mutations in the MTM1 gene. The muscle biopsies were performed at 13-35 years of age and a new histological marker, the necklace fibers, was described. Here, we report two siblings with the pathogenic c.664 C > T mutation in the MTM1 gene, presenting a severe muscle weakness and respiratory impairment requiring ventilatory support since the first months of life until death, at the age of 36 months and 5 months. In the older brother the muscle biopsy, performed at the age of 30 months, showed almost 100% of necklace fibers, which were not present in the younger one submitted to muscle biopsy at 5 months of age. Our findings confirm the necklace fibers can be a histopathological finding of MTM1 myopathies, even in the severe neonatal form, and suggest that the necklace fibers appear or increase in number over time. (C) 2012 Elsevier B.V. All rights reserved.

A Closed-Form Solution for the Optimal Time Evolution of an Exponentially Decaying Signal with Thermal Noise

The signal-to-noise ratio of a monoexponentially decaying signal exhibits a maximum at an evolution time of approximately 1.26 T-2. It has previously been thought that there is no closed-form solution to express this maximum. We report in this note that this maximum can be represented in a specific, analytical closed form in terms of the negative real branch of an inverse function known as the Lambert W function. The Lambert function is finding increasing use in the solution of problems in a variety of areas in the physical sciences. (C) 2014 Wiley Periodicals, Inc.