bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of varying upper ocean stratification on coastal near‐inertial currents
Authors: Kim Sung Yong , Kurapov Alexander L. , Kosro P. Michael 
Published: November 2015

AbstractThe influence of varying horizontal and vertical stratification in the upper layer (
m) associated with riverine waters and seasonal atmospheric fluxes on coastal near‐inertial currents is investigated with remotely sensed and in situ observations of surface and subsurface currents and realistic numerical model outputs off the coast of Oregon. Based on numerical simulations with and without the Columbia River (CR) during summer, the directly wind‐forced near‐inertial surface currents are enhanced by 30%–60% when the near‐surface layer has a stratified condition due to riverine water inputs from the CR. Comparing model results without the CR for summer and winter conditions indicates that the directly wind‐forced near‐inertial surface current response to a unit wind forcing during summer are 20%–70% stronger than those during winter depending on the cross‐shore location, which is in contrast to the seasonal patterns of both mixed‐layer depth and amplitudes of near‐inertial currents. The model simulations are used to examine aspects of coastal inhibition of near‐inertial currents, manifested in their spatial coherence in the cross‐shore direction, where the phase propagates upward over the continental shelf, bounces at the coast, and continues increasing upward offshore (toward surface) and then downward offshore at the surface, with magnitudes and length scales in the near‐surface layer increasing offshore. This pattern exhibits a particularly well‐organized structure during winter. Similarly, the raypaths of clockwise near‐inertial internal waves are consistent with the phase propagation of coherence, showing the influence of upper layer stratification and coastal inhibition.
Immunology of Fish
Authors: Fletcher Thelma C , Secombes Christopher J 
Published: November 2015

Abstract

Innate immunity provides some form of defence against pathogens in all multicellular organisms but with cartilaginous and bony fish, although the lowest group of jawed vertebrates, the addition of a classic adaptive immune response becomes apparent. This provides the refinements of specificity for antigen recognition and memory. The T and B lymphocytes are the effector leucocytes, acquiring their antigen‐specific receptors (immunoglobulin for B cells and T‐cell receptor for T cells) in the anterior kidney (bone marrow being absent) and thymus. The B cells are responsible for the production of antibodies that function as different immunoglobulin classes, whereas subsets of T lymphocytes are capable of killing target cells or helping with B‐ and other T‐cell functions. Knowledge of these mechanisms is important for the use and design of vaccines, now so essential for the aquaculture industry, whereas studies of fish immunology contribute to the understanding of the evolution of adaptive immunity.

Key Concepts

Fish possess innate and adaptive immune responses, with classical adaptive immunity present only in jawed vertebrates.

Adaptive immunity allows memory of prior exposure to foreign molecules (antigens), so that on subsequent contact protective mechanisms are more rapidly mobilised: the basis of vaccination.

Lymphocytes mediate adaptive immunity and have surface receptors that recognise antigens, initiating the production of circulating antibodies and the activation of cell‐mediated responses.

The functions of the immune system are similar in fish and mammals although there are differences owing to the aquatic physiology and ectothermic nature of fish that provide evolutionary interest.

Leucocyte–antigen interactions take place in immune sites, such as the kidneys, spleen, gills and intestine. Bone marrow and lymph nodes are lacking.

Knowledge of fish immunology is proving essential for the development of vaccines for the expanding aquaculture industry.
Tombusviridae
Authors: Sit Tim L , Lommel Steven A 
Published: November 2015

Abstract

The
Tombusviridae
is a relatively large and diverse family of plant viruses that have small single‐stranded, positive‐sense,
RNA
(ribonucleic acid) genomes which have been grouped together owing to the high degree of sequence identity displayed by their
RNA
‐dependent
RNA
polymerases. Tombusvirid virion structures, gene expression strategies, replication,
RNA
recombination, virus movement and the support of satellite viruses/defective‐interfering
RNAs
have been particularly well characterised. All genera (with the exception of the
Umbraviruses
) produce spherical virions with capsid proteins that can be subdivided by the presence (or absence) of a
C
‐terminal protruding domain. Transmission of several members by fungal zoospores in a species‐specific manner has been reported while aphid transmission of
Umbraviruses
is completely dependent on a helper virus from the
Luteoviridae
. The virions of several members have been utilised for biotechnology purposes.

Key Concepts

Various genera most likely arose through RNA recombination.

Tombusviridae
species replicate to high titres within their host cells.

RNA genomes are small with a limited number of gene products that serve multiple functions.

RNA–RNA interactions control gene expression in several genera.

Viral‐encoded suppressors of RNA silencing act at several different stages in the response cascade.

Virions (if present) are non‐enveloped and extremely stable.

Several members are transmitted through soil by specific fungal zoospores.
B
Lymphocytes: Receptors
Authors: DeFranco Anthony L 
Published: November 2015

Abstract

B lymphocytes can synthesise Ig heavy chains that are either secreted or membrane‐bound, the latter having a transmembrane domain and a short cytoplasmic domain. Membrane‐bound Ig heavy chains and Ig light chains assemble in the ER with each other and with a heterodimer of Igα and Igβ, which mediate signalling and internalisation functions. The complex of these four polypeptides is called the B cell antigen receptor (BCR). BCR signalling occurs via three types of tyrosine kinases. Src‐family kinases phosphorylate the two tyrosine‐containing motif in the cytoplasmic domains of Igα and Igβ (the ITAMs), which recruits a second type of tyrosine kinase Syk. Syk is responsible for most downstream signalling, although calcium and diacylglycerol also require a third tyrosine kinase Btk. BCR signalling pathways are central to virtually all aspects of B cell biology, as they are required for B cell development, tolerance induction, survival and activation.

Key Concepts

Naïve B cells express their immunoglobulin as a cell surface receptor for antigen, called the BCR (B cell receptor for antigen).

In developing precursors of B cells, the successful generation of an immunoglobulin heavy chain is sensed by the incorporation of that heavy chain into pre‐BCR molecules, which exhibit constitutive signalling.

Signalling by the BCR controls development, survival and activation of B cells in a manner that is dependent on the developmental stage or activation state of the B cell. This signalling is important both for tolerisation of self‐reactive B cells and for activation of B cells recognising foreign antigen.

Co‐receptors that recognise complement components, sialic acid residues, or IgG bound to antigens strongly enhance or inhibit signalling by the BCR to aid in self‐non‐self‐discrimination.

The BCR is also an endocytic receptor that delivers antigen to internal compartments where protein antigens are processed into peptides and loaded onto MHC class II molecules to facilitate interactions with T cells, which are essential for production of high‐affinity antibodies.

Defects in generation of BCRs or signalling components of the BCR result in B cell immunodeficiencies, the most common of which is due to loss‐of‐function mutations of the intracellular protein tyrosine kinase Btk, referred to as X‐linked agammaglobulinemia.

B cell malignancies often have activated BCR signalling as a driver of their proliferation and/or survival, and selective Btk inhibitors are now approved therapeutics for some types of B cell malignancies.
Leishmania
Authors: Bates Paul A 
Published: November 2015

Abstract

Leishmania
are vector‐borne parasitic protozoa that cause the human tropical disease leishmaniasis. Over 30 species have been described, with 11 of these being important pathogens. The disease has three main forms: cutaneous, mucocutaneous and visceral leishmaniasis. The parasites undergo a complex developmental cycle in their phlebotomine sand fly vectors leading to the differentiation of infectious metacyclic promastigote forms, and are transmitted by bite. Many species are zoonotic, being maintained in domestic or wild animal reservoir hosts, and the others are anthroponotic and transmitted from human to human. In their mammalian hosts they live as intracellular amastigote forms inside macrophages. There are relatively few drugs available to treat leishmaniasis, and control of the sand fly vectors or reservoir hosts is difficult. The best long‐term solution to the public health challenge of leishmaniasis will be vaccines, and progress is being made, but an effective vaccine for human usage has not been developed yet.

Key Concepts

Leishmania
are intracellular parasites that live in the phagolysosomes of macrophages, a unique location for a eukaryotic pathogen.

The different forms of leishmaniasis result from infection of differently located populations of macrophages and the human response to infection.

Leishmaniasis is a chronic infection that can be treated, but limited drugs are available and no prophylactic vaccine is yet available for human use.

There are many species of
Leishmania
but all share a common set of molecular, biochemical and cell biological features along with species‐specific properties.

There are more sand fly vectors than
Leishmania
species, but they exist in specific pairs, each parasite being transmitted by one or more particular species of sand fly.
Plant Breeding and Crop Improvement
Authors: Caligari Peter DS , Forster Brian P 
Published: November 2015

Abstract

To respond to the increasing need to feed the world's population, standing at 7.1–7.2 billion in 2013 and predicted to reach over 9 billion by 2050, as well as an ever greater demand for a balanced and healthy diet, there is a continuing need to produce improved new cultivated varieties of crop plants. Land available for crop production is limited and has stayed at 660 million hectares for the past 50 years. Much of the world's best soils are already in use and others are protected, for example, for environmental concerns. The demand for food brings marginal lands into play for which stress‐tolerant crops need to be developed. Climate variation is yet another challenge breeders have to respond to. In short, more food, fibre, fuel and forage need to be produced per unit of land, and time is of the essence. The strategies used to meet these demands are increasingly based on our knowledge of relevant science, particularly genetics and reproductive biology. Success is gained by a multidisciplinary understanding and the deployment of relevant science and technology.

Key Concepts

Plant breeders must have access to genetic variation in crop species.

Plant breeders must be equipped with the tools to respond quickly to new demands by developing accelerated breeding techniques and the ability to screen for traits of interest rapidly among progeny.

Yield and yield stability remain the top priorities for breeders.

Increasing production of plant products is essential for food, feed and fibre for the increasing World population.

Breeders must be visionary in planning for requirements in the future, at least 7–20 years ahead, as this is the timescale from initiating the breeding programme to release cultivars.
Chromosomal Instability (
CIN
) in Cancer
Authors: Horne Steven D , Ye Christine J , Heng Henry HQ 
Published: November 2015

Abstract

Chromosomal instability (
CIN
) represents a common feature in the majority of cancers. Despite that the search for specific molecular mechanisms linked to the causation or consequences of cancer has become very popular in cancer research, there is no general conceptual framework that unifies the observed diverse molecular findings. By applying the genome theory of cancer evolution, we briefly define and clarify
CIN
, synthesise its importance in macro‐cellular evolutionary selection, unify diverse molecular mechanisms under the evolutionary mechanism of cancer and discuss its potential implications. Understanding the relationship of stress,
CIN
and genome‐mediated cancer evolution offers clarity and direction to researchers, and monitoring
CIN
within an evolutionary context can provide valuable clinical information for determining treatment administration and patient prognosis.

Key Concepts

Chromosomal aberrations exist in the majority of cancers, suggesting the importance of understanding CIN in cancer.

Cancer genome evolution exists in two cyclical phases: a genome replacement mediated punctuated (macro‐cellular) phase and a gene/epigene‐mediated stepwise (micro‐cellular) phase; triggering CIN is the key to entering the macro‐cellular evolutionary phase.

CIN represents the key driver of cancer, as high levels rapidly produce wide varieties of new genome systems, providing necessary heterogeneity (and ample opportunity) for evolutionary selection.

Understanding the relationship among CIN, different genetic level dynamics and macro‐cellular evolution can be accomplished using multiple level landscape models.

Application of the evolutionary mechanism of cancer in understanding CIN offers clarity by unifying the wide variety of involved genetic and non‐genetic mechanisms and factors.

The consequences of high stress‐induced CIN (e.g. genome chaos, adaptation and accelerated macro‐cellular evolution) hold high implications in cancer treatment and drug resistance.

Fuzzy inheritance, which also reflects as elevated CIN at the genome level, represents a major mechanism of cancer evolution.

Monitoring CIN within an evolutionary context can provide valuable information for both cancer research and treatment.
Plant Responses to Phosphorus Availability
Authors: Hodge Angela 
Published: November 2015

Abstract

Phosphorus (P) is an essential macronutrient for normal plant growth and function. However, acquisition of sufficient P from the soil environment is often problematic for the plant owing to the tendency for P to react with the principal cations in most soils and its low rates of diffusive supply. Thus, a marked P depletion zone forms around the root. Plants can enhance their P acquisition by modifying their root system architecture through increasing the number and length of lateral roots and root hairs. Plants can also chemically modify the soil environment close to their roots through the release of protons and organic acids. These chemical modifications are particularly well developed in ‘cluster‐rooted’ plant species and help these plants extract P from otherwise poorly available sources. Finally, plants can form symbiotic associations with mycorrhizal fungi, an ancient symbiosis that likely evolved to help solve the P problem for plants.

Key Concepts

Phosphorus (P) is an essential macronutrient for healthy plant growth and development.

Phosphorus ions react with a number of charged surfaces in the soil environment and phosphate ions are poorly mobile in soils.

Small, but sharply defined, phosphate depletion zones rapidly develop at the root surface.

Mycorrhizal hyphae and/or root hairs can extend outside these depletion zones to explore a larger soil volume for P uptake.

Mycorrhizal fungi can also down‐regulate the root (i.e. direct) P uptake pathway.

In extremely nutrient impoverished soils, some plant species have developed cluster roots to aid P acquisition.

Cluster roots release compounds, notably citrate, into the soil to help chemically extract P from charged surfaces and their large surface area further aids uptake of the P forms released.
Drosophila
as a Model to Study Intestinal Stem Cells
Authors: Takashima Shigeo 
Published: November 2015

Abstract

Although there were several old reports described proliferating stem‐like cells in adult intestinal tissue of insects,
Drosophila
digestive tract has not been drawing attention from intestinal stem cell (ISC) scientists. In 2006, two studies (Micchelli and Perrimon, 2006; Ohlstein and Spradling, 2006) revisited this issue. As they clearly pointed out active stem cell population in this organ and evidenced the usefulness of
Drosophila
digestive tract as an ideal model system to study ISCs, the fly intestine was finally brought into the light of stem cell science. Fly ISCs require multiple signals to maintain their proper function similar to their mammalian counterparts do. Notch, Wnt, JAK/STAT and EGFR signals are initially reported as the key players but many other genes and signals are also listed up to date. In this article, a landscape of the network comprised with a variety of signals and genes controlling ISC behaviour (i.e. self‐renewal, proliferation and differentiation) is observed.

Key Concepts

Drosophila
intestinal stem cell (ISC) research provides essential ideas to understand how stem cells keep organ integrity throughout life.

Precision and robust regulation of ISC functions by a variety of signalling activities ensures constant tissue renewal and recovery from severe injury.

The functions of ISC include self‐renewal, proliferation, cell‐fate choice and differentiation into mature intestinal cells.

Each function is regulated by distinct molecular signals with multiple mutual interactions.

The aim of this article is to provide current knowledge about
Drosophila
ISCs and the idea how rapidly this research area expands using molecular genetics‐friendly
Drosophila
as a model organism.
E
duard
A
.
S
trasburger (1844–1912)
Authors: Nickelsen Kärin 
Published: November 2015

Abstract
Eduard A. Strasburger (1844–1912) was a German plant cytologist. From 1880, he was Director of the Botany Institute and the Botanical Garden at the University of Bonn. Strasburger is particularly noted for discovering the stages of nuclear and cellular division in algae and higher plants. He first observed how the pollen tube grows into the embryo sac, he explained the structure and function of plasmodesmata and contributed a great number of important elements to the cytological and histological knowledge of plants. Strasburger was the author of a seminal textbook in botany which, up to this day, is published in revised editions and still connected with his name.
RIG
‐
I
‐Like Receptors
Authors: Yong Hui Yee , Luo Dahai 
Published: November 2015

Abstract

The RIG‐I‐like receptors (RLRs), RIG‐I (retinoic acid inducible gene 1), MDA5 (melanoma differentiation‐associated gene 5) and LGP2 (laboratory of genetics and physiology 2) play an essential role in sensing viral infection and initiating interferon‐mediated antiviral immune response. RLRs share similar domain architecture to support specific detection of viral RNA (ribonucleic acid). RIG‐I has an auto‐inhibitory conformation and upon binding of RNA ligand undergoes conformational changes to expose
N
‐terminal CARDs (caspase activation and recruitment domains) for interaction with the adaptor protein MAVS (mitochondrial antiviral‐signalling protein) for signalling. MDA5 adopts an open but inactive conformation and is able to oligomerise on long RNA duplexes to bring its CARDs into close proximity to MAVS. The downstream signalling cascade up‐regulates the type I interferon expression. Post‐translational modifications, alternative splicing and translational variants as well as several regulatory proteins play important roles in the regulation of RLRs signalling. Although robust activation of RLRs is essential for clearance of viral infection, uncontrolled activation of RLR signalling could potentially trigger or exacerbate pre‐existing autoimmune conditions.

Key Concepts

RIG‐I‐like receptors (RLRs) are pattern recognition receptor (PRR) which specifically recognise viral RNAs

RLRs undergo conformational changes leading to activation when bound to viral RNA

RLRs relay signal to a common signalling adaptor MAVS (mitochondrial antiviral‐signalling protein) leading to activation of transcription factors promoting the expression of interferons and pro‐inflammatory cytokines which reduces initial viral replication and spread

RLRs are tightly regulated by various proteins and post‐translational modifications to prevent undesired auto‐activation
Covalently Attached Liquids: Instant Omniphobic Surfaces with Unprecedented Repellency
Authors: Wang Liming , McCarthy Thomas J. 
Published: November 2015

AbstractRecent strategies to prepare “omniphobic” surfaces have demonstrated that minimizing contact angle hysteresis (CAH) is the key criterion for effectiveness. CAH is affected by chemistry and topography defects at the molecular and higher levels, thus most surfaces exhibit significant CAH. Preparative methods for stable coatings on smooth substrates with negligible CAH (<2°) for a broad range of liquids have not been reported. In this work, we describe a simple and rapid procedure to prepare omniphobic surfaces that are stable under pressure and durable at elevated temperatures. Consistent with theory, they exhibit sliding angles that decrease with liquid surface tension. Slippery omniphobic covalently attached liquid (SOCAL) surfaces are obtained through acid‐catalyzed graft polycondensation of dimethyldimethoxysilane. The smooth, stable, and temperature‐resistant coatings show extremely low CAH (≤1°) and low sliding angles for liquids that span surface tensions from 78.2 to 18.4 mN m−1.
A Computational Method for Stochastic Optimal Control Problems in Financial Mathematics
Authors: Kafash Behzad , Delavarkhalafi Ali , Karbassi Seyed Mehdi 
Published: November 2015

AbstractPrinciple of optimality or dynamic programming leads to derivation of a partial differential equation (PDE) for solving optimal control problems, namely the Hamilton‐Jacobi‐Bellman (HJB) equation. In general, this equation cannot be solved analytically; thus many computing strategies have been developed for optimal control problems. Many problems in financial mathematics involve the solution of stochastic optimal control (SOC) problems. In this work, the variational iteration method (VIM) is applied for solving SOC problems. In fact, solutions for the value function and the corresponding optimal strategies are obtained numerically. We solve a stochastic linear regulator problem to investigate the applicability and simplicity of the presented method and prove its convergence. In particular, for Merton's portfolio selection model as a problem of portfolio optimization, the proposed numerical method is applied for the first time and its usefulness is demonstrated. For the nonlinear case, we investigate its convergence using Banach's fixed point theorem. The numerical results confirm the simplicity and efficiency of our method.