bluuebunny/crossref_metadata_2025_split huggingface dataset:
Storm‐induced changes in coastal geomorphology control estuarine secondary productivity
Authors: Filgueira Ramón , Guyondet Thomas , Comeau Luc A. , Grant Jon 
Published: December 2013

AbstractEstuarine ecosystems are highly sensitive not only to projected effects of climate change such as ocean warming, acidification, and sea‐level rise but also to the incidence of nor'easter storms and hurricanes. The effects of storms and hurricanes can be extreme, with immediate impact on coastal geomorphology and water circulation, which is integral to estuarine function and consequently to provision of ecosystem services. In this article, we present the results of a natural estuarine‐scale experiment on the effects of changes in coastal geomorphology on hydrodynamics and aquaculture production. A bay in Prince Edward Island, Canada, was altered when a nor'easter storm eroded a second tidal inlet through a barrier island. Previous field and modeling studies allowed a comparison of prestorm and post‐storm circulation, food limitation by cultured mussels, and aquaculture harvest. Dramatic increases in mussel production occurred in the year following the opening of the new inlet. Model studies showed that post‐storm circulation reduced food limitation for cultured mussels, allowing greater growth. Climate change is expected to have severe effects on the delivery of marine ecosystem services to human populations by changing the underlying physical‐biological coupling inherent to their functioning.
Geochemical diversity in first rocks examined by the Curiosity Rover in Gale Crater: Evidence for and significance of an alkali and volatile‐rich igneous source
Authors: Schmidt M. E. , Campbell J. L. , Gellert R. , Perrett G. M. , Treiman A. H. , Blaney D. L. , Olilla A. , Calef F. J. , Edgar L. , Elliott B. E. , Grotzinger J. , Hurowitz J. , King P. L. , Minitti M. E. , Sautter V. , Stack K. , Berger J. A. , Bridges J. C. , Ehlmann B. L. , Forni O. , Leshin L. A. , Lewis K. W. , McLennan S. M. , Ming D. W. , Newsom H. , Pradler I. , Squyres S. W. , Stolper E. M. , Thompson L. , VanBommel S. , Wiens R. C. 
Published: December 2013

AbstractThe first four rocks examined by the Mars Science Laboratory Alpha Particle X‐ray Spectrometer indicate that Curiosity landed in a lithologically diverse region of Mars. These rocks, collectively dubbed the Bradbury assemblage, were studied along an eastward traverse (sols 46–102). Compositions range from Na‐ and Al‐rich mugearite Jake_Matijevic to Fe‐, Mg‐, and Zn‐rich alkali‐rich basalt/hawaiite Bathurst_Inlet and span nearly the entire range in FeO* and MnO of the data sets from previous Martian missions and Martian meteorites. The Bradbury assemblage is also enriched in K and moderately volatile metals (Zn and Ge). These elements do not correlate with Cl or S, suggesting that they are associated with the rocks themselves and not with salt‐rich coatings. Three out of the four Bradbury rocks plot along a line in elemental variation diagrams, suggesting mixing between Al‐rich and Fe‐rich components. ChemCam analyses give insight to their degree of chemical heterogeneity and grain size. Variations in trace elements detected by ChemCam suggest chemical weathering (Li) and concentration in mineral phases (e.g., Rb and Sr in feldspars). We interpret the Bradbury assemblage to be broadly volcanic and/or volcaniclastic, derived either from near the Gale crater rim and transported by the Peace Vallis fan network, or from a local volcanic source within Gale Crater. High Fe and Fe/Mn in Et_Then likely reflect secondary precipitation of Fe3+ oxides as a cement or rind. The K‐rich signature of the Bradbury assemblage, if igneous in origin, may have formed by small degrees of partial melting of metasomatized mantle.
U.S. Government shutdown degrades aviation radiation monitoring during solar radiation storm
Authors: Tobiska W. Kent , Gersey Brad , Wilkins Richard , Mertens Chris , Atwell William , Bailey Justin 
Published: December 2013

AbstractThe U.S. Government shutdown from 1 to 17 October 2013 significantly affected U.S. and global aviation radiation monitoring. The closure occurred just as a S2 radiation storm was in progress with an average dose rate of 20 μSv h‐1. We estimate that during the radiation event period, one‐half million passengers were flying in the affected zone and, of this population, four would have received sufficient dose to contract fatal cancer in their lifetimes. The radiation environment can be treated like any other risk‐prone weather event, e.g., rain, snow, icing, clear air turbulence, convective weather, or volcanic ash, and should be made available to flight crews in a timely way across the entire air traffic management system. The shutdown highlighted the need for active operational monitoring of the global radiation environment. Aviation radiation risk mitigation steps are simple and straightforward, i.e., fly at a lower altitude and/or use a more equatorward route. Public tools and media methods are also needed from the space weather scientific and operational communities to provide this information in a timely and accessible manner to the flying public.
Neurons and Neural Networks: Computational Models
Authors: Rotstein Horacio G , Nadim Farzan 
Published: December 2013

Abstract

Neural networks produce electrical activity that is generated by the biophysical properties of the constituent neurons and synapses. Individual neurons produce electrical signals through processes that are highly nonlinear and communicate these signals to one another through synaptic interactions, resulting in emergent network outputs. The output of neural networks underlies behaviours in all higher animals. Mathematical equations can be used to describe the electrical activity of neurons and neural networks and the underlying biophysical properties. These equations give rise to computational models of neurons and networks that can be analysed using mathematical techniques or numerically simulated with computers. This article briefly reviews the current mathematical and computational techniques involved in modelling neurons and neural networks.

Key Concepts:

An action potential is a brief nonlinear rise and fall of the membrane voltage of a cell and is the primary signal used for neural communication.

Excitability is the ability of neurons and other cell types to produce action potentials when the transmembrane voltage crosses a threshold.

The Hodgkin–Huxley model is a mathematical description of how action potentials are generated in neurons and propagate along their axons.

The integrate‐and‐fire neuron is a simplified mathematical model of excitability in neurons, is useful for the ability to do mathematical analysis and is used primarily in network models.

Bifurcation is a mathematical term for a change in the qualitative structure of a dynamical system when a parameter value is changed.

Neural oscillations are repetitive or rhythmic changes in the voltage activity of a neuron or a network of neurons. Neural oscillations may arise in individual neurons or through network synchrony.

Bursting is the ability of some neurons and networks to produce periodic spiking activity followed by an interval of no activity.

A half‐centre oscillator is a network of two neurons that probursting activity out of phase with one another and is a key subnetwork of central pattern generators.
Bacterial Reproduction and Growth
Authors: Scheffers Dirk‐Jan 
Published: December 2013

Abstract

Bacteria growing in a suitable medium increase in number by having each cell increase in size, and then each cell divides to produce two daughter cells. The increase in cell number in a culture is, therefore, a result of the activity of the cell during the division cycle, between the period of birth by division and the subsequent division. There is a close relation between the composition of the growth medium and the bacterial growth rate and
Deoxyribonucleic acid (DNA)
replication. The exponential growth of bacteria can be understood from the increase of cellular material, such as
ribonucleic acid
and protein, which, in turn, generate more cellular components. Recent studies have revealed a relation between the cell cycle and the control of initiation of DNA replication, cell division and cell surface synthesis.

Key Concepts:

Bacterial growth rate is a function of the growth conditions.

Fast‐growing rod‐shaped bacterial cells are larger than slow‐growing cells.

A key regulatory event in the bacterial cell cycle is the initiation of DNA replication.

Bacterial cells age over time.

Multiple rounds of chromosome replication can be accommodated within one bacterial cell cycle.

Bacteria use their nutritional state as a cue for the start of cell division.
Porifera (Sponges): Recent Knowledge and New Perspectives
Authors: Renard Emmanuelle , Gazave Eve , Fierro‐Constain Laura , Schenkelaars Quentin , Ereskovsky Alexander , Vacelet Jean , Borchiellini Carole 
Published: December 2013

Abstract

Porifera, commonly named sponges, are true animals or metazoan despite their anatomical and morphological simplicity that had led to a long‐time debate about their nature (animal versus vegetal) and constitution (colonies of unicellular organisms versus multicellular organisms). Sponges are a successful group of mostly marine filter feeder organisms that represent a major life form of several ecosystems. Devoid of organs, the main characteristics of their body plan are the presence of a network of pores (at the origin of their name), choanocyte chambers and canals devoted to water filtration and spicules (when present) allowing tissue physical support. Currently considered as the sister group to all the other animals, these organisms have a key phylogenetic position. Recent studies have shown that they possess an unexpected molecular complexity raising exciting questions about early animal evolution.

Key Concepts:

As adults, sponges are sedentary filter feeder animals.

The water flow is canalised in an aquiferous system composed of pores (ostia), canals and choanocyte chambers.

At present, the number of formally described sponge species is comprised between 8000 and 9000.

Sponges are divided into four clades […] Hexactinellida, Demospongiae, Calcarea and Homoscleromorpha.

As sponges are devoid of organs, their individual cells or cell layers ensure vital functions.

One cell type may have several functions.

In addition to cell plurifunctionality, the functional plasticity of sponges also relies on a high capacity of cell transdifferentiation.

Sponges often use both asexual and sexual reproduction.

Most of key transcription families and main signalling pathways required for eumetazoan development and body patterning are present in sponges.

The recent rising interest for Porifera is expected to lead to a better understanding of animal evolution.
MitochondrialDNA: Fate of the Paternal Mitochondrial Genome
Authors: St. John Justin C 
Published: December 2013

AbstractThe mitochondrial genome encodes key proteins of the electron transfer chain, which generates the vast majority of cellularadenosine triphosphatethrough oxidative phosphorylation. This genome is normally transmitted to subsequent generations through the oocyte and is maternally inherited. Sperm mitochondrialdeoxyribonucleic acid (DNA)is normally eliminated early during embryonic development, but this tends to be species specific. There are several mechanisms that could account for its elimination. The elimination of sperm mitochondrial DNA is essential for the functional integrity of the offspring, as sperm mitochondrial DNA appears to harbour a large number of mitochondrial DNA defects, whereas maternally inherited mitochondrial DNA rearrangements appear to be transmitted at a very low frequency. However, there are an increasing number of assisted reproductive technologies that could lead to the transmission of sperm mitochondrial DNA and this requires significant investigation.Key Concepts:Mitochondrial DNA is predominantly maternally inherited.In some species, there is either leakage or directed transmission of sperm mitochondrial DNA.Elimination of sperm mitochondrial DNA is essential for maintaining the health of the individual.It still remains to be determined how sperm mitochondrial DNA is eliminated and whether this is truly a targeted process.The role of sperm mtDNA requires determination.
Cold Acclimation and Freezing Tolerance in Plants
Authors: Ouellet Francois , Charron Jean‐Benoit 
Published: December 2013

Abstract

The capacity to survive winter conditions varies greatly in the plant kingdom. Cold acclimation is the process leading to the development of freezing tolerance in plants. It is a complex multigenic process that requires a programmed and integrated genetic capacity to activate the appropriate mechanisms needed to withstand harsh winter conditions. Hardy plants have evolved complex mechanisms to tightly regulate gene expression, including events at the transcriptional and post‐transcriptional levels. Hundreds of cold‐induced genes encoding structural and regulatory proteins have been identified. These proteins have been found in many species, but in most cases, they had been first identified in model species. Most of the studies in the field are still performed with the model dicotyledonous plant
Arabidopsis
, but
Brachypodium
distachyon
is emerging as a model for monocotyledonous species.

Key Concepts:

Plants must possess the genetic makeup to develop tolerance to harsh winter conditions.

Low temperature induces the expression of many genes in plants.

The C‐repeat binding factor (CBF) pathway is still the only identified pathway that regulates gene expression at low temperature.

The existence of the CBF components in a species does not ensure the capacity to cold acclimate.

Although microRNAs associated with cold response have been discovered, few have been assigned to specific physiological events in the cold acclimation process.

Few links between the regulation of cold stress response and chromatin dynamics have been identified in plants thus far.

Brachypodium distachyon
is a potential model for the study of cold acclimation.
Molecular Genetics of Saethre–Chotzen Syndrome
Authors: Mathijssen Irene MJ 
Published: December 2013

AbstractSaethre–Chotzen syndrome is caused by mutations and large deletions in theTWIST1gene. It is a congenital disorder characterised by coronal suture synostosis, upper eyelid ptosis and mild anomalies of the hand and feet, amongst others.TWIST1and other genes that can cause craniosynostosis closely interact during embryogenesis of the vault and in the establishment of the coronal sutures in particular. This involves a delicate process of progressive expansion of the frontal and parietal bones, inhibiting their osteogenic fronts when the cranial bones meet, and starting a balance between proliferation of mesenchymal cells within the sutural area and differentiation of osteoprogenitor cells towards the bony rims to allow expansion of the cranial bones.TWIST1is particularly required for inhibition of the osteogenic fronts from the frontal and parietal bones when they get into close contact. The changes inTWIST1that cause Saethre–Chotzen syndrome result in a loss of function and thus fusion of the bones, taking place at 16 weeks of gestation.Key Concepts:Saethre–Chotzen syndrome is caused by mutations and large deletions in theTWIST1gene that result in a loss of function.Coronal suture synostosis is a consistent feature of Saethre–Chotzen syndrome.Mutations inFGFR2are another frequent cause for syndromic craniosynostosis with coronal suture synostosis (Apert and Crouzon syndromes). TheFGFR2mutations result in a gain of function.TWIST1is required for establishment of the coronal sutures during embryogenesis.TWIST1inhibits the progression of the osteogenic fronts of the expanding frontal and parietal bones during embryogenesis and is mainly expressed by mesenchymal cells in the centre of the developing coronal suture.TWIST1interacts withMSX2,EPHNA4andEphA4in preventing osteoprogenitor cells from invading the coronal suture.TWIST1 and TCF12 form heterodimers, whose dosage is critical for normal coronal suture development.FGFR2is particularly expressed at the osteogenic fronts of the frontal and parietal bones.FGFR2expression is regulated byTWIST1.
Consent‐in‐Interaction
Authors: Shipman Hannah E 
Published: December 2013

AbstractInformed consent is the ethical and legal bedrock of much clinical practice and research involving humans. A paradigm of consent focusing on individual autonomy and self‐determination is dominant and underpins much of the empirical work undertaken. Alongside a focus on seeking to ‘improve’ consent within this framework are alternative perspectives, considering consent in the context of human interaction and communication. Such perspectives highlight the roles and relationships of all involved parties and the complexity of the unfolding discourse. They call for a redefinition of what a successful consent encounter is and for a review of understandings of professional practice and persuasion. Though these issues are touched on by other sociological work, discursive studies highlight the achievement of consent as a proceeding interaction and the involvement and influences of all involved, with implications for professional practice.Key Concepts:Informed consent has become central to much clinical practice and research involving humans.There are limitations to addressing the challenges of achieving informed consent in practice from within its own frame of reference.Sociological work has emphasised the significance of social contexts and processes in how consent proceeds.Discursive and interactional approaches give further emphasis to the performative and contextual nature of consent interactions, highlighting the roles of all interlocutors.Professionals involved in seeking consent could use insights from discursive work in selecting communicative strategies that best go on to enable their patients and research participants.
Genetic Variants Involved in Intracellular Mechanisms of Chemoresistance to Anticancer Drugs Due to Changes in the Effect on Their Molecular Targets
Authors: Marin Jose JG , Blazquez Alba G , Serrano Maria A , Briz Oscar , Monte Maria J , Macias Rocio IR 
Published: December 2013

Abstract

Modern anticancer pharmacological treatment is challenged by the important limitation of the refractoriness of many tumours to anticancer drugs. This is due to different combinations of a complex and yet poorly understood variety of mechanisms of chemoresistance, which account for a reduction in the intracellular concentrations of active agents or poor response to their action. The present article focusses on changes in the expression and appearance of the genetic variants affecting genes involved in a weaker activity of the intracellular active agents, which may be accounted for by: (1) changes in the molecular targets of these drugs, either by directly reducing or enhancing the expression of the target or by modifying its ability to respond to the drug; (2) enhanced repair of drug‐induced
deoxyribonucleic acid
damage; and finally, because the activation of apoptosis is a final goal of many pharmacological regimes; (3) the stimulation of antiapoptotic mechanisms and/or the inhibition of proapoptotic ones.

Key Concepts:

Changes in the expression levels of molecular targets strongly determine the efficacy of anticancer drugs.

Chemoresistance may be due to the appearance of genetic variants accounting for changes in the ability of molecular targets to respond to anticancer drugs.

Antitumour drugs, whose mechanism of action is based on DNA damage, are less efficient in tumour cells with enhanced DNA‐repairing activity.

The presence of genetic variants accounting for an impaired function of proapoptotic genes favour tumour chemoresistance.

The presence of genetic variants accounting for a constitutive activation of survival pathways reduces the efficacy of anticancer drugs.
Genetics of Birth Weight
Authors: Timpson Nicholas J 
Published: December 2013

Abstract

Possibly the most ubiquitously measured early life health feature, birth weight is a staple of predelivery consultations and is the perennial statement of the health of the new born. Birth weight as a measurement is simple, fixed in time and recorded with relative stability in comparison to other more labile and less precise measures immediately after birth. However, birth weight can be thought of as a distal snapshot of a collection of complex biological events marking the interplay between endogenous foetal genetics and the in‐uterine experience of the new child. Although birth weight is convenient and often well measured, it imperfectly summarises a swathe of biology along with important markers of the environment in which a new life has developed. This article will consider the genetic contributions to birth weight and how these may help to further our understanding of this naturally complex phenotype.

Key Concepts:

Birth weight as an epidemiological measurement – This article considers the merits and limitations of birth weight as an epidemiological measurement and the implications of using a cross sectional measure to summarise a complex biological event.

Epidemiology of birth weight – This article considers the importance of birth weight as an epidemiological outcome and potential risk factor for later life health.

Genomewide genetics association studies – This article summarises and explains the results of genomewide association studies for birth weight.

Indirect genetic association or gene–environment interaction – This article considers how apparently indirect genetic associations may be operating through gene–environment interaction and how they may be important for the interpretation of genetic effects.

Mendelian randomisation – This article considers applied epidemiological analyses where genetic proxies for hypothetical risk factors are used to deliver improved inference.
Understanding Tumour Metabolic Reprogramming with Metabolomics
Authors: Stirdivant Steven , Milburn Michael , Eckhart Andrea , Beebe Kirk 
Published: December 2013

Abstract

Although cancer is well recognised as a genetic disease, there is an emerging awareness that many of these genetic mutations promote an established hallmark of tumour cells – metabolic reprogramming. And while the connection between oncogenic signalling and the metabolic reprogramming of tumour cells (in hindsight) is highly intuitive, how to expand on this knowledge and capitalise on it for therapeutic gain is yet to be fully actualised. An emerging opportunity to expand this possibility involves taking advantage of the fact that diverse genetic alterations in tumour cells converge to the shared features of metabolic reprogramming. Therefore, these features could offer a common means to target the tumour irrespective of the mutational status. However, in all likelihood, the most selective and efficacious treatments will emerge from combining data to specifically define the genetic and metabolic features of a tumour with modern genomic and metabolomic technologies. Conceptually, genotyping and metabotyping can be combined in an effort to define efficacious first line dual‐targeted combinations. Although there are many practical considerations and challenges to achieve this end, the premise will be described through a number of preclinical examples that begin to offer an illustration of this possibility.

Key Concepts:

Oncogenes and tumour suppressors directly regulate metabolic reprogramming.

Metabolic reprogramming supports tumour energetics, biosynthesis and survival.

Metabolic targets present viable options for therapeutic development.

Global metabolite profiling provides knowledge into tumour signalling pathway dysregulation.

Metabolic reprogramming contributes to therapeutic resistance/sensitivity.

Understanding malignant cell metabolism affords greater insight into optimal drug combination strategies.

Metabolomics combined with genotyping offers an opportunity to advance personalised cancer medicine.