bluuebunny/crossref_metadata_2025_split huggingface dataset:
The modulation of the seasonal cross‐shelf sea level variation by the cold pool in the Middle Atlantic Bight
Authors: Sha Jin , Jo Young‐Heon , Yan Xiao‐Hai , Liu W. T. 
Published: October 2015

AbstractThis study explores the influence of the cold pool in the Middle Atlantic Bight (MAB) to cross‐shelf sea surface slope by fitting an annual harmonic to temperature and salinity profiles from 1993 to 2012 and compares to the 20 year averaged altimetry sea level anomaly (SLA). The consistency within the bottom temperature, thermal steric height, total steric height, and altimetry observation validates that the cold pool induces a depressed sea level in the middle shelf overlapping with the dominant surface seasonal cycles. Temporally, the cold pool pattern is most apparent in July and August as a result of magnitude competition between the thermal and haline steric height. In addition, Ensemble Empirical Mode Decomposition (EEMD) is employed to reconstruct the altimetry SLA and reveals the middle‐shelf depression pattern from single year's SLA data. The locations of the SLA depression from 1993 to 2012 agree with the cold pool locations identified from in situ measurements, suggesting a promising application of altimetry SLA in the cold pool study. Conclusively, this study reveals the modulation of the cross‐shelf sea level variation by the cold pool, and contributes to the understanding of the sea level response to water masses on the continental shelf.
The impact of immobile zones on the transport and retention of nanoparticles in porous media
Authors: Molnar Ian L. , Gerhard Jason I. , Willson Clinton S. , O'Carroll Denis M. 
Published: October 2015

AbstractNanoparticle transport and retention within porous media is treated by conceptualizing the porous media as a series of independent collectors (e.g., Colloid Filtration Theory). This conceptualization assumes that flow phenomena near grain‐grain contacts, such as immobile zones (areas of low flow), exert a negligible influence on nanoparticle transport and assumes that retention and release of particles depends only on surface chemistry. This study investigated the impact of immobile zones on nanoparticle transport and retention by employing synchrotron X‐ray computed microtomography (SXCMT) to examine pore‐scale silver nanoparticle distributions during transport through three sand columns: uniform iron oxide, uniform quartz, and well‐graded quartz. Extended tailing was observed during the elution phase of all experiments suggesting that hydraulic retention in immobile zones, not detachment from grains, was the source of tailing. A numerical simulation of fluid flow through an SXCMT data set predicted the presence of immobile zones near grain‐grain contacts. SXCMT‐determined silver nanoparticle concentrations observed that significantly lower nanoparticle concentrations existed near grain‐grain contacts throughout the duration of all experiments. In addition, the SXCMT‐determined pore‐scale concentration gradients were found to be independent of surface chemistry and grain size distribution, suggesting that immobile zones limit the diffusive transport of nanoparticles toward the collectors. These results suggest that the well‐known overprediction of nanoparticle retention by traditional CFT may be due to ignoring the influences of grain‐grain contacts and immobile zones. As such, accurate prediction of nanoparticle transport requires consideration of immobile zones and their influence on both hydraulic and surface retention.
Evaluating an unconfined aquifer by analysis of age‐dating tracers in stream water
Authors: Solomon D. K. , Gilmore T. E. , Solder J. E. , Kimball B. , Genereux D. P. 
Published: October 2015

AbstractThe mean transit time (MTT) is a fundamental property of a groundwater flow system that is strongly related to the ratio of recharge rate to storage volume. However, obtaining samples for estimating the MTT using environmental tracers is problematic as flow‐weighted samples over the full spectrum of transit times are needed. Samples collected from the base flow of a gaining stream in the North Carolina Coastal Plain (West Bear Creek) that were corrected for exchange with the atmosphere yielded environmental tracer concentrations (SF6 and CFC‐11) very similar to flow‐weighted values from nine or ten streambed piezometers that directly sampled groundwater during low streamflow. At higher streamflow on the falling limb of the hydrograph, stream tracer concentrations (after correction for gas exchange) were significantly higher than the flow‐weighted mean from piezometers, consistent with dominance of the stream tracer signal by transient influx of surface water and/or younger subsurface water. The apparent MTT derived from SF6 in low flow stream water samples was 26 years, suggesting a groundwater recharge rate of about 210 mm/yr, that is consistent with vertical profiles obtained by sampling nested piezometers in the aquifer. When sampled under low flow conditions when streamflow consists of a high component of groundwater discharge, West Bear Creek appears to act as a flow‐weighted integrator of transit times and, streamflow samples can provide fundamental information regarding groundwater recharge rate and MTT. Our study suggests that watershed‐scale evaluation of some groundwater flow systems is possible without utilizing monitoring wells.
Dynein and Kinesin
Authors: Steele John W , Goldstein Lawrence SB 
Published: October 2015

Abstract

During the life cycle of a eukaryotic cell, chromosomes and other cellular materials must be distributed to daughter cells, proteins must be synthesised and delivered to their site of utilisation and cellular organelles must be delivered to, and retrieved from, appropriate places within the cell. In some cell types, such as neurons, essential cellular materials must be delivered across long distances from the cell body to distal axon terminals or dendrites. Because diffusion is incapable of accomplishing these tasks, eukaryotes have developed an active transport mechanism that relies on superfamilies of kinesin, dynein and myosin motor proteins that walk along microtubule or microfilament tracks. This article discusses how the microtubule‐based motors of the kinesin and dynein superfamilies mediate intracellular transport and cilia/flagella motility within eukaryotic cells.

Key Concepts

Microtubules have an intrinsic polarity that microtubule‐based motor proteins recognise to generate adenosine triphosphate (ATP)‐dependent unidirectional movement.

Both the kinesin and dynein catalytic polypeptides contain a stand‐alone motor domain, which is the actual microtubule‐dependent ATPase force‐generating unit of these motors.

Axonemal dyneins, which comprise the outer and inner dynein arms, power cilia and flagella beating by producing sliding movements between adjacent outer‐doublet microtubules.

Cytoplasmic dyneins are primarily transport motors driving retrograde transport through a minus‐end‐directed ATP‐dependent mechanism.

In neurons, dynein complexes with different intermediate chain isoforms have distinct roles, including cargo binding and transport, and phosphorylation of the intermediate chain may also specify binding to specific cargo.

Differences in the stalk and tail domains and various associated proteins (light chains) distinguish the multiple classes of kinesin superfamily members.

A key functional distinction between dyneins and kinesins is that, while kinesin family members can generate movement in the plus‐ or minus‐end direction, dynein motors generate only minus‐end‐directed movement.

To fill the numerous intracellular roles for plus‐end‐directed motility, eukaryotic cells have evolved a large array of kinesin superfamily members.

Microtubule‐based motors must be regulated on an individual and collective scale to facilitate the correct temporal and spatial intracellular placement of eukaryotic organelles.

Cytoplasmic dynein and its dynactin complex drive retrograde, minus‐end‐directed movement in neurons, whereas kinesins typically move towards the anterograde direction.
Epithelial Cells: Immunological Aspects
Authors: Pastore Saveria , Albanesi Cristina , Girolomoni Giampiero 
Published: October 2015

Abstract

Far from simply representing passive targets of environmental or immunological attack, epithelial cells play an active role in the generation and expression of protective immune responses. In response to physical, chemical or microbial perturbation of the epithelial barrier, these cells provide a valid defensive line by the expression of an array of soluble mediators with direct antimicrobial and/or chemotactic activities towards distinct immune cell populations and also towards cytokines and adhesion molecules that affect their functional activation. These epithelial cell‐driven molecular events are also involved in the pathogenesis of chronic inflammatory disorders, with the amplification of the inflammatory reactions because of a sustained crosstalk with infiltrating leucocytes. In particular, T‐cell‐derived cytokines have been identified as the most effective inducers of pro‐inflammatory signals in epithelial cells, in turn responsible for further recruitment and local activation of immune cells, leading to the eventual amplification of the inflammatory reaction.

Key Concepts

Epithelial cells organise the physical barriers of the body, the first defensive lines against environmental, physical, chemical and microbial insults.

In response to any damage to the physical barriers of the body, epithelial cells display their nature of resident components of the immune system and provide a second defensive line by the release of a plethora of active mediators.

In genetically predisposed individuals, a defective permeability of the skin early in life leads to the penetration of environmental allergens and to the initiation of the chronic inflammatory syndrome known as atopy.

Loss‐of‐function mutations in the filaggrin gene are the most significant and well‐replicated risk factor for the development of atopy.

To adequately defend against microbial colonisation and infection, epithelial cells are endowed with the complete armamentarium of innate immune defence.

The epidermal growth factor receptor and its endogenous ligands provide a formidable mechanism to enhance innate immunity, while they oppose activation of adaptive immunity in epithelial cells.

Patients with atopic dermatitis are more susceptible to cutaneous fungal, viral and bacterial pathogens because of an articulate defect in the innate immunity mechanisms of the epithelial cell.

Dysregulated expression of cytokines and chemokines in skin keratinocytes leads to sustained skin infiltration and local activation of a variety of immune cell populations in chronic skin inflammatory disorders including atopic dermatitis.

Epithelial cells possess a number of effective regulatory mechanisms to control intensity and duration of inflammatory events.
Lymphocytes: Gamma Delta
Authors: Chien Yueh‐hsiu , Chowdhury Roshni Roy 
Published: October 2015

Abstract

γδ T cells, together with αβ T cells and B cells, are the only cells that use somatic gene rearrangement to generate diverse receptors to recognise different antigens. All three types of cells are present together in all but the most primitive vertebrates, suggesting that each type of cell functions uniquely, and all are necessary to maintain host immune competence. Indeed, γδ T cells and αβ T cells differ in antigen recognition, the generation of antigen‐specific repertoire, activation requirement and effector function development. These aspects allow γδ T cells to occupy unique temporal and functional niches in host immune defence. In infections, γδ T cells respond earlier than αβ T cells; and also emerge late after pathogen numbers start to decline. Thus, these cells may be involved in both establishing and resolving the inflammatory response.

Key Concepts

γδ T cells are present together with αβ T cells and B cells in all but the most primitive vertebrates. These are the only cells using somatic gene rearrangement to generate diverse receptor for antigen recognition.

γδ T cells contribute uniquely to host immune competence and function differently from αβ T cells in host defence and immune surveillance.

γδ T cells are similar to B cells in antigen recognition, in that antigens of different size, shape and molecular nature are recognised directly, and γδ T cells and B cells can recognise the same antigens.

γδ T cells require thymic maturation process before coming out to the periphery, and this process does very little to determine what γδ T cells can recognise, but determine how they will function.

γδ T cells are the major initial responders in acute infections, especially in producing IL‐17 to initiate the inflammatory response.
Autoimmune Arthritis: Animal Models
Authors: McCann Fiona E , Wythe Sarah E 
Published: October 2015

Abstract

Animal models are used for the study of a number of human autoimmune diseases, including multiple sclerosis, diabetes, rheumatoid arthritis, systemic lupus erythematosis and spondyloarthropathies. Induced, spontaneous and genetically manipulated animal models can be described in terms of their parallels to human disease and as valuable tools for the development of potential therapies. Studies in animal models have led to a number of important discoveries, which have increased our understanding of the pathogenesis of autoimmune disease, including the roles played by regulatory T cells and T
H
17 cells. In addition, important therapeutic advances have emerged as a result of studies of immune intervention in animal models of autoimmunity. For example, tumour necrosis factor (TNF) blocking drugs, which are widely used for the treatment of rheumatic diseases, were developed following pre‐clinical testing in animal models.

Key Concepts

Animal models may be either spontaneously occurring or induced as a result of genetic manipulation, immunisation with a self‐antigen or triggered by pathogen‐associated molecular patterns (PAMPs) in genetically susceptible hosts.

No animal model completely mimics human disease.

Animal models can be used to delineate common mammalian immunological mechanisms, test novel therapeutic concepts and understand mechanisms of drug action, but therapeutic efficacy therein is not predictive of response in clinical trials.

The use of transgenic and knockout strains facilitates the identification of key genes that contribute to disease susceptibility and pathogenesis.
Immune Vasculitis
Authors: Gopaluni Seerapani , Jayne David 
Published: October 2015

Abstract

Vasculitides are a group of disorders characterised by inflammation and necrosis of the walls of blood vessels, resulting in narrowing or occlusion of the vessel lumen, leading to ischaemia and destruction of the tissues. They are usually classified according to the size of the vessels predominantly involved. The nomenclature of vasculitides was revised in 2012 at the second international Chapel Hill Consensus Conference (CHCC2012) to reflect the advances in our understanding of vasculitis. A wide range of immunopathological mechanisms have been implicated in the aetiology of vasculitis, and a subset of small‐vessel vasculitides are strongly associated with antineutrophil cytoplasmic antibodies (ANCA). The clinical presentation, often involving multiple organ systems, is heterogenous and depends on the size and site of the vessels involved. This makes both classification and diagnosis of these disorders challenging. Management of these conditions is fraught with the difficulty of balancing the benefits of immunosuppression with toxicity. However, with improved understanding of the immunopathogenesis, earlier diagnoses and newer targeted treatment options, improvements in morbidity and mortality have been reported.

Key Concepts

Vasculitis may be ‘idiopathic’ or ‘primary’ but it is important to rule out common mimics of vasculitis and the many underlying conditions that can induce a ‘secondary’ vasculitis.

Vasculitides are usually classified according to the predominant size of the vessels involved, but there is ongoing debate as to the most accurate and clinically useful way to classify the conditions.

Immunopathological mechanisms are diverse, with roles for both humoral and cellular immune mechanisms.

A subset of small‐vessel vasculitides are strongly associated with antineutrophil cytoplasmic antibody (ANCA), and this is often used as a biomarker to aid diagnosis.

There is strong evidence for a pathogenic role of ANCA in the ‘ANCA associated vasculitides’, but the extent of this continues to be debated.

Vasculitis is usually considered a ‘systemic’ disease with the propensity to affect blood vessels throughout the body, but individual clinical presentations may be limited to specific organ systems.

Many patients initially experience a prodrome of nonspecific symptoms such as malaise, fatigue, fever, night sweats or weight loss.

The prevalence of vasculitis is increasing. This may be due to the increased rates of diagnosis, due to clinical suspicion and use of biomarkers such as ANCA; increased survival postdiagnosis or a true increased incidence.

Further research into the underlying pathological processes is vital to identifying potential treatment targets.

Many trials are currently in progress and will contribute to the improving rates of morbidity and mortality in systemic vasculitis.
S
taudinger,
H
ermann
Authors: Furukawa Yasu 
Published: October 2015

Abstract
Hermann Staudinger (1881–1965) is a German organic chemist who made fundamental contributions to the foundation of macromolecular chemistry (or polymer chemistry), for which he was awarded the Nobel Prize in Chemistry in 1953. Trained as a classical organic chemist, Staudinger interpreted that polymers, such as rubber, cellulose, starches, plastics and proteins, are composed of almost arbitrarily big organic molecules or macromolecules. His theory provoked antipathy among his contemporaries, and the stormy macromolecular debate continued until his views were finally accepted in the chemical community in the 1930s. His extensive research on macromolecules provided the basis for the new discipline of macromolecular chemistry.
Developmental Systems Theory
Authors: Griffiths Paul E , Hochman Adam 
Published: October 2015

AbstractDevelopmental systems theory (DST) is a wholeheartedly epigenetic approach to development, inheritance and evolution. The developmental system of an organism is the entire matrix of resources that are needed to reproduce the life cycle. The range of developmental resources that are properly described as being inherited, and which are subject to natural selection, is far wider than has traditionally been allowed. Evolution acts on this extended set of developmental resources. From a developmental systems perspective, development does not proceed according to a preformed plan; what is inherited is much more than DNA; and evolution is change not only in gene frequencies, but in entire developmental systems.Key ConceptsDevelopment has no single locus of controlDevelopmental outcomes are influenced by the contexts in which development unfoldsThe developmental system of an organism is the matrix of resources that are required to reproduce the life cycleThe genome is designed to function in a specific developmental niche which is itself the product of evolutionThe impact of any given cause is contingent upon the state of the system as a wholeThe roles played by causal factors in development do not fall neatly into two kinds, one exclusively played by genes, the other played by nongenetic causesDevelopment is a dynamic process: the products of early stages of development can become the interactants of later stagesThe notion of the ‘genetic program’ is of little heuristic valueThe study of heredity will benefit from a broad approach that includes features of the developmental niche which are often overlookedEvolution is change in developmental systems as a whole, and not only change in gene frequencies
Antibody Microarrays
Authors: Wingren Christer , Borrebaeck Carl 
Published: October 2015

Abstract

Antibody‐based microarray is a recently established proteomic technology, providing unique opportunities for multiplexed protein expression profiling of crude, non‐fractionated samples in a specific, sensitive and miniaturised manner. A microarray can be printed with a few up to several thousands of different antibodies carrying the desired specificities, the biological sample added (e.g. a serum sample) and any specifically bound analytes detected and quantified. The obtained microarray images are then transformed into protein expression profiles, or protein maps, revealing the composition of the sample at the molecular level. Bioinformatics is used to handle the often large‐scale data set(s) acquired. Protein expression profiling using this tool will provide new opportunities for biomarker discovery, drug target identification, (early) disease diagnostics and prognostics as well as insights into disease biology.

Key Concepts

Antibody microarrays are based on dispensing antibodies one‐by‐one in an ordered pattern, an array, onto a solid support.

Antibody‐based microarray is a miniaturised set‐up for simultaneously measuring numerous proteins in minute amount of sample.

Antibody microarrays can be used to perform multiplexed protein expression profiling of crude, complex samples.

Using antibody microarrays, less than a drop of blood is required in order to generate a protein map, or protein fingerprint, reflecting the protein content in the sample.

Multiplexed protein expression profiling using antibody microarrays provides novel opportunities for biomarker discovery, disease diagnosis and prognosis.
Epigenetic Regulation in Plants
Authors: Temel Aslihan , Janack Bianka , Humbeck Klaus 
Published: October 2015

Abstract

Environment‐sensitive plant development follows a program inscribed in the
DNA,
and differential expression of the genes is the prerequisite of this program. In the last decades, it was possible to unravel how genes are correctly transcribed in time and space by interaction of trans‐acting factors with cis elements often located in the promoter of a gene. However recently, we learned that, in addition, another level of control, called epigenetic regulation, acting via alterations in chromatin structure is involved.

In this review, we will first summarise the basic mechanisms underlying epigenetic control of gene expression in plants. In the following article, we will focus on some selected recent results showing epigenetic control of major steps in plant development. This review cannot cover all new results in the field and we want to apologise to all who are not mentioned.

Key Concepts

Plant development involves coordinated expression of genes.

Recent findings show that this is also under epigenetic control.

Epigenetic control is exerted by different mechanisms, including DNA methylation, histone modifications and chromatin remodelling.

These modifications alter chromatin state, and by this, it can induce or repress expression of genes.

Major developmental steps, including seed development, flowering, sexual reproduction and leaf senescence are controlled by epigenetic mechanisms.

Stress responses of plants are also regulated by epigenetic mechanisms.