bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography
Authors: Wan Qun , Parks Jerry M. , Hanson B. Leif , Fisher Suzanne Zoe , Ostermann Andreas , Schrader Tobias E. , Graham David E. , Coates Leighton , Langan Paul , Kovalevsky Andrey
Published: September 2015

Significance

Most enzymatic reactions involve hydrogen or proton transfer among the enzyme, substrate, and water at physiological pH. Thus, enzyme catalysis cannot be fully understood without accurate mapping of hydrogen atom positions in these macromolecular catalysts. Direct information on the location of hydrogen atoms can be obtained using neutron crystallography. We used neutron crystallography and biomolecular simulation to characterize the initial stage of the glycoside hydrolysis reaction catalyzed by a family 11 glycoside hydrolase. We provide evidence that the catalytic glutamate residue alternates between two conformations bearing different basicities, first to obtain a proton from the bulk solvent, and then to deliver it to the glycosidic oxygen to initiate the hydrolysis reaction.
Do hedges always hedge?
Authors: Adamczyk Magdalena
Published: September 2015

One of the canonical uses of jakby in Polish is that of the Lakoffian hedge, which modifies the propositional content of an utterance by pointing to its fuzziness, inexactitude or approximation. In conversational speech the word is frequently put to excessive use, which appears to significantly deviate from the prescribed one, and as such deserves closer attention. The aim of the present study, which makes use of corpus linguistics tools to collect naturally-occurring data and discourse analysis framework to manually examine them, is twofold. Initially, it sets out to examine the linguistic contexts of jakby, which are assumed to furnish valuable guidelines for sifting out the prototypical uses of the word from the innovative ones. Next, the focus shifts onto indentifying context-sensitive functions of the latter in highly diversified stretches of discourse. The research findings demonstrate that the cotextual settings of the non-canonical jakby exhibit a number of distinctive characteristics, such as frequent co-occurrence of the word with pragmatic markers, reflexive discourse and unfilled pauses, all indicative of its relatively tenuous link with the neighbouring portions of text. As regards the functions of the unconventional jakby, the word emerges as a pragmatically multifunctional yet no longer hedging device, capable of, among others, facilitating floor-holding/-grabbing, helping to plan discourse, marking register clash and introducing elaboration on prior thought. Rich in pragmatic functions and syntactically more detached from the adjacent textual material than its canonical base, the investigated jakby appears to fit into the category of propositionally empty yet strategically salient pragmatic markers.
The Consequences of Claw Removal on Stone Crabs Menippe spp. and the Ecological and Fishery Implications
Authors: Duermit Elizabeth , Kingsley-Smith Peter R. , Wilber Dara H.
Published: September 2015

The practice of claw removal in the fishery for stone crab Menippe spp. can affect fished populations in an atypical way because harvested individuals are not necessarily killed. In all stone crab fisheries, crabs are returned to the water after their claws are harvested with the expectation that claws may be regenerated, thus “renewing” the fishery. The number of legal-sized claws that can be removed from an individual differs (with local regulations) throughout the stone crabs' range. We examined the direct and indirect consequences of removing one and two claws by monitoring mortality and prey consumption in the short term (14 d) and mortality and growth over the long term (11 months). Claw removal induced mortality within days when wound widths were greater than 7 mm, regardless of the number of claws removed. Wound widths created by autotomy were similar to those created by a clean, forced break along the natural fracture plane. These results suggest that direct mortality following claw removal may be low in a two-claw fishery for stone crabs that do not incur large wounds; however, indirect effects that result from altered feeding abilities may be substantial. Stone crabs with one claw removed (the crusher) consumed fewer bivalves than control (intact) crabs, whereas stone crabs with two claws removed did not consume any bivalves but ate fish flesh. Consequently, bivalves, an important prey resource throughout the stone crabs' geographical range, are eliminated from a clawless crab's diet until its claws are regenerated. No stone crabs regenerated a legal-sized claw on the first molt after claw removal, and no stone crabs larger than 104 mm carapace width molted within 11 months. Thus, the long intermolt duration of legal-sized stone crabs and the reduced prey consumption for stone crabs that lost claws indicate that the return to the fishery of previously harvested stone crabs is probably an uncommon occurrence.

Received December 17, 2014; accepted June 15, 2015
Ubiquitin plays an atypical role in GPCR-induced p38 MAP kinase activation on endosomes
Authors: Grimsey Neil J. , Aguilar Berenice , Smith Thomas H. , Le Phillip , Soohoo Amanda L. , Puthenveedu Manojkumar A. , Nizet Victor , Trejo JoAnn
Published: September 2015

Protease-activated receptor 1 (PAR1) is a G protein–coupled receptor (GPCR) for thrombin and promotes inflammatory responses through multiple pathways including p38 mitogen-activated protein kinase signaling. The mechanisms that govern PAR1-induced p38 activation remain unclear. Here, we define an atypical ubiquitin-dependent pathway for p38 activation used by PAR1 that regulates endothelial barrier permeability. Activated PAR1 K63-linked ubiquitination is mediated by the NEDD4-2 E3 ubiquitin ligase and initiated recruitment of transforming growth factor-β–activated protein kinase-1 binding protein-2 (TAB2). The ubiquitin-binding domain of TAB2 was essential for recruitment to PAR1-containing endosomes. TAB2 associated with TAB1, which induced p38 activation independent of MKK3 and MKK6. The P2Y1 purinergic GPCR also stimulated p38 activation via NEDD4-2–mediated ubiquitination and TAB1–TAB2. TAB1–TAB2-dependent p38 activation was critical for PAR1-promoted endothelial barrier permeability in vitro, and p38 signaling was required for PAR1-induced vascular leakage in vivo. These studies define an atypical ubiquitin-mediated signaling pathway used by a subset of GPCRs that regulates endosomal p38 signaling and endothelial barrier disruption.
TRPC6 is the endothelial calcium channel that regulates leukocyte transendothelial migration during the inflammatory response
Authors: Weber Evan W. , Han Fei , Tauseef Mohammad , Birnbaumer Lutz , Mehta Dolly , Muller William A.
Published: September 2015

Leukocyte transendothelial migration (TEM) is a tightly regulated, multistep process that is critical to the inflammatory response. A transient increase in endothelial cytosolic free calcium ion concentration (↑[Ca2+]i) is required for TEM. However, the mechanism by which endothelial ↑[Ca2+]i regulates TEM and the channels mediating this ↑[Ca2+]i are unknown. Buffering ↑[Ca2+]i in endothelial cells does not affect leukocyte adhesion or locomotion but selectively blocks TEM, suggesting a role for ↑[Ca2+]i specifically for this step. Transient receptor potential canonical 6 (TRPC6), a Ca2+ channel expressed in endothelial cells, colocalizes with platelet/endothelial cell adhesion molecule-1 (PECAM) to surround leukocytes during TEM and clusters when endothelial PECAM is engaged. Expression of dominant-negative TRPC6 or shRNA knockdown in endothelial cells arrests neutrophils apically over the junction, similar to when PECAM is blocked. Selectively activating endothelial TRPC6 rescues TEM during an ongoing PECAM blockade, indicating that TRPC6 functions downstream of PECAM. Furthermore, endothelial TRPC6 is required for trafficking of lateral border recycling compartment membrane, which facilitates TEM. Finally, mice lacking TRPC6 in the nonmyeloid compartment (i.e., endothelium) exhibit a profound defect in neutrophil TEM with no effect on leukocyte trafficking. Our findings identify endothelial TRPC6 as the calcium channel mediating the ↑[Ca2+]i required for TEM at a step downstream of PECAM homophilic interactions.
Feynman's Operational Calculus and Beyond
Authors: Johnson Gerald W , Lapidus Michel L. , Nielsen Lance
Published: September 2015

This book provides an abstract theory of Feynman’s operational calculus for functions of (typically) noncommuting operators. Although it is inspired by Feynman’s original heuristic suggestions and time-ordering (or disentangling) rules in his seminal 1951 paper, as is made clear in the introduction (Chapter 1) and elsewhere in the text, the theory developed in this book also goes well beyond them in a number of directions which were not anticipated in Feynman’s work. In particular, the work presented in this volume is oriented towards dealing with abstract and (typically) noncommuting linear operators acting on some Banach space, rather than operators arising from some variety of path integration. Some of the key structures developed in this volume enable us to obtain, in some sense, an appropriate abstract substitute for a generalized functional integral associated with the Feynman operational calculus attached to a given n-tuple of pairs {(Aj,μj)}j=1n of typically noncommuting bounded operators Aj and probability measures μj, for j = 1, …, n and n ≥ 2.
The fossil record and evolution of avian egg nesting and incubation
Authors: Deeming D.C.
Published: September 2015

The fossil record of avian reproduction is relatively sparse. Despite the long history of birds since the Jurassic there are few examples of intact fossilised eggs and other signs of reproduction, such as nests, are extremely rare. This chapter reviews the fossil history of avian reproduction and appraises the validity of interpretation of fossil remains. In some instances, our understanding of the evolutionary history of bird reproduction can be considered as quite robust but in many cases the existing interpretation of material is over ambitious and so not necessarily very helpful. The chapter examines the fossil record particularly in light of reproductive physiology, morphology and behaviour. There is particular emphasis on how the nest environment has been investigated using fossilised materials. The evolution of reproduction is considered and the chapter concludes with a discussion of the reasons why avian reproduction is so poorly represented in the fossil record.
The influence of predation on the location and design of nests
Authors: Mainwaring M.C. , Reynolds S.J. , Weidinger K.
Published: September 2015

The risk of predation is ubiquitous for birds and natural selection favours those individuals with effective anti-predator responses. Accordingly, breeding birds employ a wide range of defences including the location and design of their nests. Birds preferentially locate their nests in positions that minimise the risk of predation, but as there are a diversity of nest types, locations range from those providing background matching to those where aggressive heterospecifics provide protection. Meanwhile, the design of nests also minimises the risk of predation and species alter the shape, size and building materials in relation to the risk of predation. Nevertheless, the chapter concludes that birds’ nests are multi-functional structures and that whilst their location and design are strongly influenced by the requirement to minimise predation risk, other factors such as the creation of suitable microclimates for offspring development also determine their location and design.
Nest construction and incubation in a changing climate
Authors: Mainwaring M.C.
Published: September 2015

Optimal embryonic and offspring development only occurs within relatively narrow thermal limits and prolonged periods of time spent outside of these limits result in sub-optimal development and, sometimes, mortality. Therefore, climate change may negatively influence birds during nest construction and incubation in a number of ways. The most serious direct threats to nest-building birds are from inundation of seabirds’ nests and sub-optimal sex allocation in megapodes, whilst the most serious indirect threats include the reduced availability of nest sites and building materials and changes in host-parasite interactions. Meanwhile, the most serious threat to incubating birds is the reduced viability of eggs. However, nest construction and incubation are relatively plastic parental behaviours that may enable birds to adapt to climate change. During nest construction, birds can change their nesting phenology, nest-site selection and nest design and during incubation, birds can make behavioural changes to keep their eggs at the optimum temperature.
Control of invertebrate occupants of nests
Authors: López-Rull I. , Macías Garcia C.
Published: September 2015

Avian nests are built to provide a secure, insulated environment for the developing chicks. This, inevitably, also provides a convenient habitat for their ectoparasites—bugs, mites, ticks, flies and lice—which, in addition to warmth and refuge, find in them a predictable source of food in the form of blood and other tissues of chicks and parents. First the chapter describes the different ectoparasites that afflict birds in their nests, their life cycles, and the damage they can cause to chicks and/or parents, either because of the resources they take from the growing chicks or from the diseases such as bird malaria that they transmit. Then the chapter describes the physiological, immunological and behavioural defences that birds have evolved to reduce the risk or the severity of the nest ectoparasites’ attacks. The chapter describes how grooming, appropriate nest-site selection, nest maintenance and selection of nest materials can all contribute to stave off ectoparasites.
Improvements in our understanding of behaviour during incubation
Authors: Marasco V. , Spencer K.A.
Published: September 2015

The importance of incubation behaviour in driving breeding success and ultimately individual fitness has been the focus of a great deal of work over the last few decades. Here, the chapter reviews the current empirical evidence for the many biotic and abiotic factors that can influence both parental and embryonic behaviour during the incubation period. The chapter shows that although studying individual behaviour is important, understanding how parents interact with each other and with their developing offspring can give further insights into how incubation behaviours can drive breeding success and the long-term success of their offspring. Importantly the chapter also describes the latest work on our understanding of what physiological mechanisms underlie these differing patterns of behaviour, including oxidative stress and endocrine mechanisms. The chapter also highlights the fact that there are many questions that remain unanswered in this field and it urges an integrative approach to solve these remaining puzzles.
Advances in techniques to study incubation
Authors: Smith J.A. , Cooper C.B. , Reynolds S.J.
Published: September 2015

Knowledge of incubation is vital for conservation and management of birds that provide ecosystem services. However, incubation is problematic to study because this is when many species are at their most secretive and sensitive to disturbance. Direct observations at nests permit quantification of a wide range of incubation behaviours. However, they are time-consuming, labour-intensive and can disturb breeding birds. Therefore, under most circumstances we must rely on other methods. Over the last century numerous methods have been developed to investigate incubation that automate direct observations. This chapter provides an account of various methods used to monitor incubation remotely. In particular, it critically appraises the advantages and disadvantages of an automated device that is widely used in studies of captive and free-living species. In so doing the chapter provides practical and theoretical advice that can be employed to adopt the most appropriate method to study incubation within various contexts.
Function Spaces and Partial Differential Equations
Authors: Taheri Ali
Published: September 2015

This book, which is the first volume of two, presents a comprehensive treatment of aspects of classical and modern analysis relating to theory of ‘partial differential equations’ and the associated ‘function spaces’. It begins with a quick review of basic properties of harmonic functions and Poisson integrals and then moves into a detailed study of Hardy spaces. The classical Dirichlet problem is considered and a variety of methods for its resolution ranging from potential theoretic (Perron’s method of sub-harmonic functions and Wiener’s criterion, Green’s functions and Poisson integrals, the method of layered potentials or integral equations) to variational (Dirichlet principle) are presented. Parallel to this is the development of the necessary function spaces: Lorentz and Marcinkiewicz spaces, Sobolev spaces (integer as well as fractional order), Hardy spaces, the John-Nirenberg space BMO, Morrey and Campanato spaces, Besov spaces and Triebel-Lizorkin spaces. Harmonic analysis is deeply intertwined with the topics covered and the subjects of summability methods, Tauberian theorems, convolution algebras, Calderon-Zygmund theory of singular integrals and Littlewood-Paley theory that on the one hand connect to various PDE estimates (Calderon-Zygmund inequality, Strichartz estimates, Mihlin-Hormander multipliers, etc.) and on the other lead to a unified characterisation of various function spaces are discussed in great depth. The book ends by a discussion of regularity theory for second order elliptic equations in divergence form— first with continuous and next with measurable coefficients—and covers, in particular, De Giorgi’s theorem, Moser iteration, Harnack inequality and local boundedness of solutions. (The case of elliptic systems and related topics is discussed in the exercises.)
Convergence of Fourier Series: Dinivs. Dirichlet-Jordon
Authors: Taheri Ali
Published: September 2015

This chapter presents a discussion of various criterions on pointwise and almost everywhere convergence of Fourier series. Introduction of Hilbert-Sobolev spaces on the circle and it also presents some of their basic properties.
Perron’s Method of Sub-Harmonic Functions
Authors: Taheri Ali
Published: September 2015

The solvability of the classical Dirichlet problem via the method of sub-harmonic functions (or Perron’s method) is presented in this chapter. Boundary regularity via existence of barriers and various sufficient conditions: exterior cone, exterior sphere conditions are discussed in detail. Wiener’s remarkable criterion is presented and various applications including existence of Green’s functions and the Riemann mapping theorem are discussed.
Harmonic-Hardy Spaces hp(ℍ)
Authors: Taheri Ali
Published: September 2015

Harmonic-Hardy spaces and Poisson integrals in the upper half-space are discussed in this chapter. Convergence to boundary function in vertical and non-tangential manners is also presented. Kelvin transform and various properties of harmonic functions are studied and then Hardy spaces of holomorphic functions in the upper half-plane are discussed at some length at the end.
Littlewood-Paley Theory, Lp-Multipliers and Function Spaces
Authors: Taheri Ali
Published: September 2015

In this chapter, Littlewood-Paley theory is developed using the theory of vector-valued singular integral operators. Various applications including multiplier theorem and Strichartz estimates for the wave operator are then discussed. Characterisation of various function spaces on ℝn via Littlewood-Paley theory is also presented.
Layered Potentials, Jump Relations and Existence Theorems
Authors: Taheri Ali
Published: September 2015

This chapter includes a thorough and detailed discussion of existence theorems for the four basic boundary-value problems associated with the Laplace operator, i.e., the interior and exterior Dirichlet problems and the interior and exterior Neumann problems. The theory of integral equations and compact operators play a pivotal role.
Recognizing the Non-religious
Authors: Lee Lois
Published: September 2015

In recent years, the extent to which contemporary societies are secular has come under scrutiny. At the same time, many countries have increasingly large non-affiliate, ‘subjectively secular’ populations, and actively non-religious cultural movements such as the New Atheism and the Sunday Assembly have come to prominence. Making sense of secularity and irreligion, and the relationship between them, has therefore emerged as a crucial task for those seeking to understand contemporary societies and the nature of ‘modern’ life. Drawing on ethnographic fieldwork in southeast England, this book develops a new vocabulary, theory, and methodology for thinking about the secular. It distinguishes between separate and incommensurable aspects of so-called secularity as insubstantial and substantial. Recognizing the cultural forms that present themselves as non-religious—as distinct from secularity as the irrelevance or religious and religious-like cultural forms—opens up new, more egalitarian, and more theoretically coherent ways of thinking about people who are ‘not religious’ alongside those who are traditionally religious or alternatively spiritual. Identifying the non-religious in this way not only gives rise to new research questions and theoretical possibilities about how non-religious people sense and perform their difference from religious others, but allows us to reimagine the secular itself, in new and productive ways.
Introduction Revisiting the Secular
Authors: Lee Lois
Published: September 2015

This book’s core question is whether ‘not religious’ people are characterized and identifiable by their lack of engagement with religion or whether they are influenced by sensing or performing their difference from religious others. Are they meaningfully non-religious or are they largely indifferent to matters of religion? To what extent should unreligious rituals and practices be understood independently of religion if they have religious equivalents or antecedents? If they are developed in contradistinction to religious cultures, is it sufficient to understand them as insubstantially areligious, post-religious, or secular, rather than as substantively non-religious? This chapter sets out the distinction between the ‘secular’ and the ‘non-religious’ upon which these questions rely, and explores how it might be possible to move from an overly inclusive and therefore slippery notion of secularity to a more specific set of concepts.
Contradistinctions in Terms
Authors: Lee Lois
Published: September 2015

This chapter clarifies the core conceptual argument of the book, and presents the wider, relational vocabulary in which it is embedded. The vocabulary also provides one way of distinguishing and managing the multiple relationships with religion that terms like ‘secularity’, ‘non-religion’, ‘secularism’, ‘atheism’, and ‘non-theism’ are supposed to describe. This terminological work is useful in its own right, but it is also bound up with the theoretical problems that the book investigates, in which the insubstantial, purely analytical notions of secularity are confused or conflated with concrete non-religious forms. The relational vocabulary developed provides a solution to those problems, facilitating the ways of recognizing the non-religious and reimagining the secular that the book proposes.
Effect of Moderate Exercise on Mitochondrial Proteome in Heart Tissue of
Spontaneous Hypertensive Rats
Authors: Rocha Luiz Antonio de Oliveira , Oliveira Kleber Souza , Migliolo Ludovico , Franco Octavio Luiz
Published: September 2015

BACKGROUND

Hypertension is a multifactorial disease and an important independent risk factor for cardiovascular diseases. Exercise training is one of the most important non-pharmacological therapeutic strategies for treating hypertension; however, mitochondrial adaptations in the hypertensive heart as a result of exercise remain obscure.

METHODS

Aiming to explore the effects of exercise training of moderate intensity on the mitochondrial proteome in hypertensive animal models before and after the pathology developed, 20 isogenic male spontaneous hypertensive rats (SHRs) were randomly divided into 2 groups, 1 with animals of 6 and 40 weeks of age. Animals were submitted to exercise training on a treadmill for 30 minutes, 5 days per week for 4 weeks at 90% of the anaerobic threshold (AT). A mitochondrial sample extract from the left ventricle was prepared and further analyzed using LC-MS/MS.

RESULTS

Proteomics analyses led to the identification of 143 proteins in all groups. The data showed a considerable and clear increase in the abundance of NADH dehydrogenase and ATP synthase, as well as voltage-dependent anion channel (VDAC) type 1 decrease in exercise groups. When exercise effects were compared, differential proteins expressed only in exercise increased, such as cytochrome c oxidase, alcohol dehydrogenase, and NADH dehydrogenase [ubiquinone] 1 alpha subcomplex.

CONCLUSIONS

The results support the proposition that moderate exercise induces a beneficial adaptation in left ventricle myocardial mitochondria in order to attenuate the decrease in ATP production in hypertensive models.
Stx-Producing Shigella Species From Patients in Haiti: An Emerging Pathogen With the Potential for Global Spread
Authors: Gray Miranda D. , Leonard Susan R. , Lacher David W. , Lampel Keith A. , Alam Meer T. , Morris J. Glenn , Ali Afsar , LaBreck Patrick T. , Maurelli Anthony T.
Published: September 2015

Shiga toxins (Stx) are commonly produced by Shigella dysenteriae serotype 1 and Stx-producing Escherichia coli. However, the toxin genes have been detected in additional Shigella species. We recently reported the emergence of Stx-producing Shigella in travelers in the United States and France who had recently visited Hispaniola (Haiti and the Dominican Republic). In this study, we confirm this epidemiological link by identifying Stx-producing Shigella from Haitian patients attending clinics near Port-au-Prince. We also demonstrate that the bacteriophage encoding Stx is capable of dissemination to stx-negative Shigella species found in Haiti, suggesting that Stx-producing Shigella may become more widespread within that region.
In-Hospital Pneumococcal Polysaccharide Vaccination Is Associated With Detection of Pneumococcal Vaccine Serotypes in Adults Hospitalized for Community-Acquired Pneumonia
Authors: Grijalva Carlos G. , Wunderink Richard G. , Zhu Yuwei , Williams Derek J. , Balk Robert , Fakhran Sherene , Courtney D. Mark , Anderson Evan J. , Qi Chao , Trabue Christopher , Pavia Andrew T. , Moore Matthew R. , Jain Seema , Edwards Kathryn M. , Self Wesley H.
Published: September 2015

During an etiology study of adults hospitalized for pneumonia, in which urine specimens were examined for serotype-specific pneumococcal antigen detection, we observed that some patients received 23-valent pneumococcal polysaccharide vaccine before urine collection. Some urine samples became positive for specific vaccine pneumococcal serotypes shortly after vaccination, suggesting false-positive test results.
The Association of Tibia Femur Ratio and Degenerative Disease of the Spine, Hips, and Knees
Authors: Weinberg Douglas S. , Liu Raymond W.
Published: September 2015

Background:

When individuals with asymmetric lower extremities present for evaluation of limb-length inequality, correction can occur at the tibia, femur, or in both bones; however, there are limited data available to justify either technique. The aim of this study is to examine the normal ratio of tibia length/femur length (T/F), and to explore the relationship between T/F ratio and osteoarthritis of the spine, hips, and knees.

Methods:

Bone lengths of 1152 cadaveric femora and tibiae from the Hamann-Todd osteological collection were measured. Degenerative joint disease was graded in the hip, knee, and spine. Correlations between the ratio of T/F and osteoarthritis were evaluated with multiple regression analysis.

Results:

The average ratio of T/F was 0.80±0.03. There was a strong correlation between age and arthritis at all sites, with standardized β ranging from 0.44 to 0.57 (P<0.0005 for all). There was a significant correlation between increasing T/F and hip arthritis (standardized β=0.08, P=0.006), and knee arthritis (standardized β=0.08, P=0.008).

Discussion:

Increasing tibia length relative to femur length was found to be a significant predictor of ipsilateral hip and knee arthritis. Therefore, we recommend that when performing limb lengthening, surgical planning should lean toward recreating the normal ratio of 0.80. In circumstances where one bone is to be overlengthened relative to the other, bias should be toward overlengthening the femur. This same principle can be applied to limb-reduction surgery, where in certain circumstances, one may choose to preferentially shorten the tibia.

Clinical Relevance:

This is the first study to report long-term consequences of lower extremity segment disproportion.
Evolution of tsunami warning systems and products
Authors: Bernard Eddie , Titov Vasily
Published: September 2015

Each year, about 60 000 people and $4 billion (US$) in assets are exposed to the global tsunami hazard. Accurate and reliable tsunami warning systems have been shown to provide a significant defence for this flooding hazard. However, the evolution of warning systems has been influenced by two processes: deadly tsunamis and available technology. In this paper, we explore the evolution of science and technology used in tsunami warning systems, the evolution of their products using warning technologies, and offer suggestions for a new generation of warning products, aimed at the flooding nature of the hazard, to reduce future tsunami impacts on society. We conclude that coastal communities would be well served by receiving three
standardized, accurate
, real-time tsunami warning products, namely (i) tsunami energy estimate, (ii) flooding maps and (iii) tsunami-induced harbour current maps to minimize the impact of tsunamis. Such information would arm communities with vital flooding guidance for evacuations and port operations. The advantage of global standardized flooding products delivered in a common format is efficiency and accuracy, which leads to effectiveness in promoting tsunami resilience at the community level.
Tsunami currents in ports
Authors: Borrero Jose C. , Lynett Patrick J. , Kalligeris Nikos
Published: September 2015

Tsunami-induced currents present an obvious hazard to maritime activities and ports in particular. The historical record is replete with accounts from ship captains and harbour masters describing their fateful encounters with currents and surges caused by these destructive waves. Despite the well-known hazard, only since the trans-oceanic tsunamis of the early twenty-first century (2004, 2010 and 2011) have coastal and port engineering practitioners begun to develop port-specific warning and response products that accurately assess the effects of tsunami-induced currents in addition to overland flooding and inundation. The hazard from strong currents induced by far-field tsunami remains an underappreciated risk in the port and maritime community. In this paper, we will discuss the history of tsunami current observations in ports, look into the current state of the art in port tsunami hazard assessment and discuss future research trends.
Resilience from coastal protection
Authors: Ewing Lesley C.
Published: September 2015

Coastal areas are important residential, commercial and industrial areas; but coastal hazards can pose significant threats to these areas. Shoreline/coastal protection elements, both built structures such as breakwaters, seawalls and revetments, as well as natural features such as beaches, reefs and wetlands, are regular features of a coastal community and are important for community safety and development. These protection structures provide a range of resilience to coastal communities. During and after disasters, they help to minimize damages and support recovery; during non-disaster times, the values from shoreline elements shift from the narrow focus on protection. Most coastal communities have limited land and resources and few can dedicate scarce resources solely for protection. Values from shore protection can and should expand to include environmental, economic and social/cultural values. This paper discusses the key aspects of shoreline protection that influence effective community resilience and protection from disasters. This paper also presents ways that the economic, environmental and social/cultural values of shore protection can be evaluated and quantified. It presents the Coastal Community Hazard Protection Resilience (CCHPR) Index for evaluating the resilience capacity to coastal communities from various protection schemes and demonstrates the use of this Index for an urban beach in San Francisco, CA, USA.
Spatially Resolved Plant Metabolomics: Some Potentials and Limitations of Laser-Ablation Electrospray Ionization Mass Spectrometry Metabolite Imaging
Authors: Etalo Desalegn W. , De Vos Ric C.H. , Joosten Matthieu H.A.J. , Hall Robert D.
Published: September 2015

Laser-ablation electrospray ionization (LAESI)-mass spectrometry imaging has been applied to contrasting plant organs to assess its potential as a procedure for performing in vivo metabolomics in plants. In a proof-of-concept experiment, purple/white segmented Phalaenopsis spp. petals were first analyzed using standard liquid chromatography-mass spectrometry analyses of separate extracts made specifically from the purple and white regions. Discriminatory compounds were defined and putatively annotated. LAESI analyses were then performed on living tissues, and these metabolites were then relocalized within the LAESI-generated data sets of similar tissues. Maps were made to illustrate their locations across the petals. Results revealed that, as expected, anthocyanins always mapped to the purple regions. Certain other (nonvisible) polyphenols were observed to colocalize with the anthocyanins, whereas others were found specifically within the white tissues. In a contrasting example, control and Cladosporium fulvum-infected tomato (Solanum lycopersicum) leaves were subjected to the same procedures, and it could be observed that the alkaloid tomatine has clear heterogeneous distribution across the tomato leaf lamina. Furthermore, LAESI analyses revealed perturbations in alkaloid content following pathogen infection. These results show the clear potential of LAESI-based imaging approaches as a convenient and rapid way to perform metabolomics analyses on living tissues. However, a range of limitations and factors have also been identified that must be taken into consideration when interpreting LAESI-derived data. Such aspects deserve further evaluation before this approach can be applied in a routine manner.
Complex modeling: a strategy and software program for combining multiple information sources to solve ill posed structure and nanostructure inverse problems
Authors: Juhás Pavol , Farrow Christopher L. , Yang Xiaohao , Knox Kevin R. , Billinge Simon J. L.
Published: September 2015

A strategy is described for regularizing ill posed structure and nanostructure scattering inverse problems (i.e.structure solution) from complex material structures. This paper describes both the philosophy and strategy of the approach, and a software implementation, DiffPy Complex Modeling Infrastructure (DiffPy-CMI).
Orbits of crystallographic embedding of non-crystallographic groups and applications to virology
Authors: Twarock Reidun , Valiunas Motiejus , Zappa Emilio
Published: September 2015

The architecture of infinite structures with non-crystallographic symmetries can be modelledviaaperiodic tilings, but a systematic construction method for finite structures with non-crystallographic symmetry at different radial levels is still lacking. This paper presents a group theoretical method for the construction of finite nested point sets with non-crystallographic symmetry. Akin to the construction of quasicrystals, a non-crystallographic groupGis embedded into the point group {\cal P} of a higher-dimensional lattice and the chains of allG-containing subgroups are constructed. The orbits of lattice points under such subgroups are determined, and it is shown that their projection into a lower-dimensionalG-invariant subspace consists of nested point sets withG-symmetry at each radial level. The number of different radial levels is bounded by the index ofGin the subgroup of {\cal P}. In the case of icosahedral symmetry, all subgroup chains are determined explicitly and it is illustrated that these point sets in projection provide blueprints that approximate the organization of simple viral capsids, encoding information on the structural organization of capsid proteins and the genomic material collectively, based on two case studies. Contrary to the affine extensions previously introduced, these orbits endow virus architecture with an underlying finite group structure, which lends itself better to the modelling of dynamic properties than its infinite-dimensional counterpart.
Etude structurale et vibrationnelle d'un nouveau composé complexe de cobalt: [Co(imidazole)4Cl]Cl
Authors: Derbel Amira , Mhiri Tahar , Graia Mohsen
Published: September 2015

In the title complex, chloridotetrakis(1H-imidazole-κN3)cobalt(II) chloride, [CoCl(C3H4N2)4]Cl, the CoIIcation has a distorted square-pyramidal coordination environment. It is coordinated by four N atoms of four imidazole (Im) groups in the basal plane, and by a Cl atom in the apical position. It is isostructural with [Cu(Im)4Cl]Cl [Morzyk-Ociepaet al.(2012).J. Mol. Struct.1028, 49–56] and [Cu(Im)4Br]Br [Hossaini Sadret al.(2004).Acta Cryst. E60, m1324–m1326]. In the crystal, the [CoCl(C3H4N2)4]+cations and Cl−anions are linkedviaN—H...Cl hydrogen bonds, forming layers parallel to (010). These layers are linkedviaC—H...Cl hydrogen bonds and C—H...π and π–π [inter-centroid distance = 3.794 (2) Å] interactions, forming a three-dimensional framework. The IR spectrum shows vibrational bands typical for imidazol groups. The monoclinic unit cell of the title compound emulates an orthorhombic cell as its β angle is close to 90°. The crystal is twinned, with the refined ratio of twin components being 0.569 (1):0.431 (1).
Structure and spectroscopic properties ofN,S-coordinating 2-methylsulfanyl-N-[(1H-pyrrol-2-yl)methylidene]aniline methanol monosolvate
Authors: Richards D. Douglas , Ang M. Trisha C. , McDonald Robert , Bierenstiel Matthias
Published: September 2015

The reaction of pyrrole-2-carboxaldehyde and 2-(methylsulfanyl)aniline in refluxing methanol gave an olive-green residue in which yellow crystals of the title compound, C12H12N2S·CH3OH, were grown from slow evaporation of methanol at 263 K. In the crystal, hydrogen-bonding interactions link the aniline molecule and a nearby methanol solvent molecule. These units are linked by a pair of weak C—H...Omethanolinteractions, forming inversion dimers consisting of two main molecules and two solvent molecules.
Crystal structure of 4-(methoxycarbonyl)phenylboronic acid
Authors: Flanagan Keith J. , Senge Mathias O.
Published: September 2015

In the title compound, C8H9BO4, the methoxycarbonyl group is rotated out of the plane of the benzene ring by 7.70 (6)°. In the crystal, molecules are linkedviapairs of O—H...O hydrogen bonds, involving the boronic acid OH groups, forming inversion dimers. The dimers are linkedviaO—H...O hydrogen bonds, involving a boronic acid OH group and the carbonyl O atom, forming undulating sheets parallel to (10-2). Within the sheets there are also C—H...O hydrogen bonds present, also involving the carbonyl O atom. The sheets are linkedviaC—H...π and offset face-to-face π-interactions between inversion-related molecules [inter-centroid distance = 3.7843 (16) Å, interplanar distance = 3.3427 (4) Å and offset = 1.744 Å], forming a three-dimensional structure.
Crystal structure of 2-methoxy-1-nitronaphthalene
Authors: Yassine Hasna , Khouili Mostafa , El Ammari Lahcen , Saadi Mohamed , Ketatni El Mostafa
Published: September 2015

The asymmetric unit of the title compound, C11H9NO3, contains two molecules,AandB. In moleculeA, the dihedral angle between the planes of the naphthalene ring system (r.m.s. deviation = 0.003 Å) and the nitro group is 89.9 (2)°, and the C atom of the methoxy group deviates from the naphthyl plane by 0.022 (2) Å. Equivalent data for moleculeBare 0.008 Å, 65.9 (2)° and −0.198 (2) Å, respectively. In the crystal, molecules are linked by weak C—H...O interactions, forming [100] chains of alternatingAandBmolecules. Weak aromatic π–π stacking contacts, with a range of centroid–centroid distances from 3.5863 (9) to 3.8048 (9) Å, are also observed.
Crystal structure of (E)-N′-(3,4-difluorobenzylidene)-4-methylbenzenesulfonohydrazide
Authors: Wang Yeming , Yan Hong
Published: September 2015

In the title compound, C14H12F2N2O2S, the dihedral angle between the aromatic rings is 70.23 (8)° and the S—N—N=C torsion angle is 172.11 (11)°. In the crystal, N—H...O hydrogen bonds link the molecules into [100]C(4) chains, with adjacent molecules in the chain related by translational symmetry. The chains are linked by weak C—H...F and C—H...O interactions, thereby forming a three-dimensional network.
Crystal structure of (E)-1-(3-chlorophenyl)-3-(furan-2-yl)prop-2-en-1-one
Authors: Zingales Sarah K. , Wallace Maya Z. , Padgett Clifford W.
Published: September 2015

The title compound, C13H9ClO2, exhibits a non-planar geometry; the furan ring being inclined to the benzene ring by 50.52 (16)°. In the crystal, molecules stack along theaaxis; however, there are no significant intermolecular interactions present.
Crystal structure of 5-diethylamino-2-({[4-(diethylamino)phenyl]imino}methyl)phenol
Authors: Rani C. Vidya , Chakkaravarthi G. , Gandhi N. Indra , Rajagopal G.
Published: September 2015

In the title compound, C21H29N3O, the dihedral angle between the planes of the aromatic rings is 8.1 (2)°. The ethyl groups at one terminal site of the compound are disordered over two sets of sites with occupancies of 0.775 (9) and 0.225 (9). The molecule has anEconformation about the N=C bond. The molecular structure features an intramolecular O—H...N hydrogen bond, which closes anS(6) loop. In the crystal, weak C—H...π interactions leads to the formation of a three-dimensional network.
Crystal structure of β-D,L-fructose
Authors: Ishii Tomohiko , Senoo Tatsuya , Yoshihara Akihide , Fukada Kazuhiro , Sakane Genta
Published: September 2015

The title compound, C6H12O6, was crystallized from an aqueous solution of equimolar mixture of D- and L-fructose (1,3,4,5,6-pentahydroxyhexan-2-one,arabino-hexulose or levulose), and it was confirmed that D-fructose (or L-fructose) formed β-pyranose with a2C5(or5C2) conformation. In the crystal, two O—H...O hydrogen bonds between the hydroxy groups at the C-1 and C-3 positions, and at the C-4 and C-5 positions connect homochiral molecules into a column along theaaxis. The columns are linked by other O—H...O hydrogen bonds between D- and L-fructose molecules, forming a three-dimensional network.
Crystal structure of (S)-2-amino-2-methylsuccinic acid
Authors: Fujii Isao
Published: September 2015

The title compound, C5H9NO4, crystallized as a zwitterion. There is an intramolecular N—H...O hydrogen bond involving thetrans-succinic acid and the ammonium group, forming anS(6) ring motif. In the crystal, molecules are linked by O—H...O hydrogen bonds, formingC(7) chains along thec-axis direction. The chains are linked by N—H...O and C—H...O hydrogen bonds, forming sheets parallel to thebcplane. Further N—H...O hydrogen bonds link the sheets to form a three-dimensional framework.
Crystal structure of dichlorido[2-(diphenylphosphanyl)-3,4,5,6-tetrafluorobenzene-1-thiolato-κ2P,S]gold(III)
Authors: Corfield Peter W. R. , Bailey Mary
Published: September 2015

The title compound, [Au(C18H10F4PS)Cl2], crystallizes as neutral molecules, with the AuIIIatom coordinated by two Cl atoms and by the P and S atoms of the bidentate phosphanyl thiolate ligand, in a slightly distorted square-planar environment. The molecules are linked into centrosymmetric dimersvialong axial Au—Cl bonds of 3.393 (4) Å. This axial Au—Cl distance is longer than is usually seen, although one other example has been given. Dimer formation may explain the unexpectedly low solubility of the compound in common polar solvents. There is also a separate intermolecular Au—F contact of 3.561 (6) Å, but this distance seems too long to be regarded as a bond. Two putative C—H...F hydrogen bonds appear to link the dimers into sheets parallel to (110). There is a short intermolecular F...F contact of 2.695 (10) Å between two dimers related by the twofold axis.
Crystal structure of 4-nitro-N-[(pyridin-2-yl)methylidene]aniline
Authors: Saphu Watcharin , Chainok Kittipong
Published: September 2015

The title compound, C12H9N3O2, adopts anEconformation at the imine double bond. The pyridyl ring makes a dihedral angle of 47.78 (5)° with the benzene ring, indicating the molecule is twisted. In the crystal, molecules are π–π stacked into columns parallel to [100], with an interplanar separation of 3.8537 (8) Å, corresponding to the length of theaaxis. The chains are further linkedviaweak C—H...O and C—H...N hydrogen bonds, forming two-dimensional sheets parallel to (010). The sheets interact by van der Waals interactions.
Crystal structure of Boc-(S)-ABOC-(S)-Ala-(S)-ABOC-(S)-Phe-OBn chloroform monosolvate
Authors: Wenger Emmanuel , Moulat Laure , Legrand Baptiste , Amblard Muriel , Calmès Monique , Didierjean Claude
Published: September 2015

In the title compound, phenyl (S)-2-[(S)-(1-{2-[(S)-(1-{[(tert-butoxy)carbonyl]amino}bicyclo[2.2.2]octan-2-yl)formamido]propanamido}bicyclo[2.2.2]octan-2-yl)formamido]-3-phenylpropanoate chloroform monosolvate, C42H56N4O7·CHCl3, the α,β-hybrid peptide contains two non-proteinogenic amino acid residues of (S)-1-aminobicyclo[2.2.2]octane-2-carboxylic acid [(S)-ABOC], two amino acid residues of (S)-2-aminopropanoic acid [(S)-Ala] and (S)-2-amino-3-phenylpropanoic acid [(S)-Phe], and protecting groups oftert-butoxycarbonyl (Boc) and benzyl ester (OBn). The tetramer folds into a right-handed mixed 11/9 helix stabilized by intramoleculari,i + 3 andi,i − 1 C=O...H—N hydrogen bonds. In the crystal, the oligomers are linked by N—H...O=C hydrogen bonds into chains along thea-axis direction. The chloroform solvent molecules are intercalated between the folded chainsviaC—H...O=C interactions.
Crystal structure of (μ-4-hydroxybenzenethiolato-κ2S:S)bis(μ-phenylmethanethiolato-κ2S:S)bis[(η6-1-isopropyl-4-methylbenzene)ruthenium(II)] tetrafluoridoborate
Authors: Stíbal David , Süss-Fink Georg , Therrien Bruno
Published: September 2015

The crystal structure of the dinuclear arene ruthenium title complex, [Ru2(C6H5OS)(C7H7S)2(C10H14)2]BF4, shows the two RuIIatoms to be bridged by two benzylthiophenolate units and one 4-hydroxythiophenolate unit, with the remaining three coordination sites of each RuIIatom being occupied byp-cymene ligands, completing the typical piano-stool coordination geometry. The BF4−counter-anion is surrounded by four cationic dinuclear complexes, showing an O—H...F hydrogen bond and several weak C—H...F interactions. This is the first example of an X-ray analysis of a mixed dinuclear trithiolate arene ruthenium(II) complex.