bluuebunny/crossref_metadata_2025_split huggingface dataset:
Error characterization in iQuam SSTs using triple collocations with satellite measurements
Authors: Xu Feng , Ignatov Alexander 
Published: September 2016

AbstractVarious types of in situ sea surface temperature (SST) measurements have dominated during different periods of the satellite era. Their corresponding errors should be characterized to curtail the nonuniformities in calibration and validation of reprocessed historical satellite SST data. SSTs from several major in situ platform types reported in the NOAA in situ Quality Monitor (iQuam) system have been collocated with NOAA‐17 Advanced Very High Resolution Radiometer (AVHRR) and Envisat Advanced Along Track Scanning Radiometer (AATSR) satellite SSTs from 2003 to 2009, produced by the European Space Agency (ESA) Climate Change Initiative (CCI) program. The standard deviations of errors in iQuam in situ and nighttime satellite CCI SSTs estimated using triple‐collocation analyses are 0.75 K for ships, 0.21–0.22 K for drifters and Argo floats, 0.17 K and 0.40 K for tropical and coastal moorings, 0.35–0.38 K for AVHRR, and 0.15–0.30 K for AATSR. The distribution of in situ and satellite errors in space and time is also analyzed, along with their single‐sensor error distributions.
The 2013 Wyoming upper mantle earthquakes: Tomography and tectonic implications
Authors: Wang Xinyang , Zhao Dapeng , Li Jiabiao 
Published: September 2016

AbstractOn 21 September 2013 two earthquakes (M 4.8 and 3.0, focal depths >70 km) occurred in the lithospheric mantle beneath central Wyoming, which provide a rare opportunity to investigate the lithosphere rheology and dynamics. We determined a detailed 3‐D P wave tomography in the source area of the Wyoming earthquakes using a large number of high‐quality traveltime data of local earthquakes and teleseismic events. Our results show that the 2013 Wyoming earthquakes occurred in an isolated high‐velocity (high‐V) anomaly which extends down to a depth of ~160 km. We propose two possible scenarios about the cause of the 2013 Wyoming earthquakes. One is that the high‐V anomaly reflects a remnant of the subducted Farallon slab which fractured under long‐term negative buoyancy and heating by the infilling asthenosphere. The other is removing of a dense mantle lithospheric root. The present results shed new light on the rheology and seismotectonics of the continental lithosphere.
Impacts of mesoscale activity on the water masses and circulation in the Coral Sea
Authors: Rousselet L. , Doglioli A. M. , Maes C. , Blanke B. , Petrenko A. A. 
Published: September 2016

AbstractThe climatological vision of the circulation within the Coral Sea is today well established with the westward circulation of two main jets, the North Caledonian Jet (NCJ) and the North Vanuatu Jet (NVJ) as a consequence of the separation of the South Equatorial Current (SEC) on the islands of New Caledonia, Vanuatu, and Fiji. Each jet has its own dynamic and transports different water masses across the Coral Sea. The influence of mesoscale activity on mean flow and on water mass exchanges is not yet fully explored in this region of intense activity. Our study relies on the analysis of in situ, satellite, and numerical data. Indeed, we first use in situ data from the Bifurcation cruise and from an Argo float, jointly with satellite‐derived velocities, to study the eddy influence on the Coral Sea dynamics. We identify an anticyclonic eddy as participating in the transport of NVJ‐like water masses into the theoretical pathway of NCJ waters. This transfer from the NVJ to the NCJ is confirmed over the long term by a Lagrangian analysis. In particular, this numerical analysis shows that anticyclonic eddies can contribute up to 70–90% of the overall eddy transfer between those seemingly independent jets. Finally, transports calculated using S‐ADCP measurements (0–500 m) show an eddy‐induced sensitivity that can reach up to 15 Sv, i.e., the order of the transport of the jets.
Red Algae
Authors: Fredericq Suzanne , Schmidt William E 
Published: September 2016

Abstract

Red algae are a phylum of about 7100 mostly marine, unicellular and multicellular photosynthetic eukaryotes that belong to the Supergroup Plantae. Multicellular taxa consist exclusively of a filamentous construction lacking true tissues despite their often superficially complex plant body. This group is unique in the Tree of Life in lacking both flagella and centrioles with a 9 + 2 microtubule arrangement in all stages of the life history.
They include species with elaborate life cycles, significant ecological importance and extensive economical applications. The oldest known taxonomically resolved eukaryotic fossil, ca. 1250–1100 million years ago, is a red alga.

Key Concepts

Red algae are crucial organisms for understanding the evolution of sex and life cycles.

Red algae are crucial organisms to understand the evolution of multicellularity since the oldest eukaryote on record is a red alga.

Red algae are important in the evolution of photosynthetic eukaryotes since their ancestor hosted a cyanobacterium that became the plastid through the event of primary endosymbiosis.

Mitochondrial genomes among multicellular red algae are highly conserved, supporting the notion of a rapid radiation among the morphologically divergent multicellular lineages.

The calcifying coralline red algae are widespread, long‐lived barometers of ocean health and real‐time indicators of global warming and ocean acidification impacts.
Haeme Biosynthesis
Authors: Moghe Akshata , Phillips John D , Anderson Karl E 
Published: September 2016

AbstractHaeme is a cofactor required for the function of many key haemoproteins in living organisms. The pathway for haeme synthesis consists of eight enzymes and their substrates and products. Pathway intermediates include an amino acid, a pyrrole and a series of porphyrins that undergo decarboxylations followed by insertion of iron to form haeme (iron protoporphyrinIX). When activities of enzymes in the haeme biosynthetic pathway are altered by mutations or inhibitors, pathway intermediates may accumulate and cause skin photosensitivity and neurological dysfunction, as found in the porphyrias. Closely related pathways in plants and bacteria provide chlorophylls and other tetrapyrrolic pigments important for harvesting energy from light.Key ConceptsHaeme is essential as a cofactor for proteins involved in key biological processes such as oxidations, oxygen transport and storage and electron transport.The haeme biosynthetic pathway consists of eight enzymes, which have been characterised and their genes sequenced in many species including humans.Closely related pathways in plants and bacteria synthesise chlorophyll and other light‐harvesting pigments.Key stages in haeme biosynthesis are the synthesis of the precursor amino acid ALA, formation of the cyclic tetrapyrroles uroporphyrinogen III, decarboxylation to form protoporphyrinogen IX, oxidation to protoporphyrin IX and insertion of iron to complete haeme synthesis.ALA is synthesised from glycine and succinyl‐coenzyme A in animals, yeast and some bacteria, but from glutamate in plants, algae, archaea and some other bacteria.In mammals, the tissues that are most active in haeme synthesis are the bone marrow, where haeme is used primarily for haemoglobin; and the liver, which synthesises large amounts of cytochrome P450 enzymes and smaller amounts of many other haemoproteins.The initial enzyme ALAS1 is rate limiting for haeme biosynthesis in mammalian liver, and this enzyme is downregulated by the endproduct haeme.Synthesis of pathway enzymes in the marrow is coordinated by erythroid‐specific transcription factors and iron.
Immunotoxicology
Authors: Hartung Thomas 
Published: September 2016

Abstract

The immune system can be the target of many chemicals, with potentially adverse effects on the host's health. Over the past two decades, little has changed in the practice of immunotoxicity testing for regulatory purposes. Current guidelines still rely on animal tests, which include some immune endpoints in repeated dose tests and call for dedicated tests when alerts indicate a problem. At the same time, a wealth of
in vitro
approaches has been developed, but little has been adopted for routine testing. The extent to which immunotoxicity of chemicals represents a health problem at low levels of exposure is not clear: it appears that responses of healthy individuals to immunological challenges differ widely and most immunomodulators have little adverse effects, except when coinciding with an infectious or malignant challenge or when exposure early in life is expected, where the odds of progressing into infection and autoimmune diseases as well as cancer can be changed. The enormous overcapacity of immune defense, the presence of compensatory mechanisms and their fast restoration contribute to limiting health threats for the individual, although on a population base minor immunomodulations might also result in increased morbidities.
In vitro
alternative approaches might offer an opportunity to screen for problematic substances and prioritising them for
in vivo
testing.

Key Concepts

Chemicals and drugs have been associated with various types of immune modulation including allergy/sensitisation, autoimmunity, inflammation and immunosuppression, mainly in high‐dose animal experiments.

The majority of substances has never been tested as to immune effects.

It is not clear to which extent immuntoxicity of environmental chemicals produces public health effects, especially for immunosuppression.

The guidance how to test is limited, mainly based on assessment of immune organs in repeated dose (chronic) animal tests.

A number of
in vitro
tests have become available but only few have been pre‐validated so far.

Immunotoxicity and inflammation should be part of future integrated testing strategies.
Sexual Conflict
Authors: Bonduriansky Russell 
Published: September 2016

Abstract

Although females and males share a common interest in successful reproduction, the sexes often maximise their reproductive success (fitness) in mutually incompatible ways. Two types of sexual conflict are recognised:
Interlocus sexual conflict
reflects a conflict of interest over the outcome of an interaction between sexes (e.g. to mate or not?), with some genetic loci evolving to enhance male fitness at females' expense and other loci evolving to promote female fitness by mitigating male‐imposed harm. This conflict drives the evolution of sexually antagonistic male strategies such as coercive behaviours and morphologies, toxic ejaculates and infanticide and female counteradaptations that confer resistance to males.
Intralocus sexual conflict
reflects divergent selection on a shared trait whose expression is influenced by the same loci in both sexes, such that selection on one sex can displace the other sex from its phenotypic optimum. Both forms of sexual conflict drive the evolution of sexual dimorphism.

Key Concepts

Sexual conflict arises because strategies that maximise the fitness of one sex can reduce the fitness of the other sex.

Two basic forms of sexual conflict are recognised:
interlocus
(between genetic loci) and
intralocus
(within a genetic locus).

Interlocus sexual conflict is a conflict of interest over the outcome of some interaction (e.g. to mate or not?), mediated by different genetic loci in each sex.

Interlocus sexual conflict can lead to sexual ‘arms races’, whereby adaptations that benefit males at females' expense select for counteradaptations in females that mitigate male‐imposed harm.

Interlocus sexual conflict is manifested in a variety of traits that increase male reproductive success but harm females in the process, including behavioural harassment and coercion, morphological traits such as genital spines and chemical manipulation via ejaculate components or pheromones.

Intralocus sexual conflict is a conflict of interest over the expression of a shared trait that is subject to sex‐specific selection but influenced by the same genetic loci in both sexes.

Intralocus sexual conflict selects for modifications to the genetic basis of trait expression that allow each sex to evolve towards its phenotypic optimum, resulting in sexual dimorphism.

Intralocus sexual conflict challenges the ‘good genes’ model of sexual selection because females that mate with high‐quality males may produce low‐quality daughters.

Sexual conflict may increase the costs of sexual reproduction, reduce mean fitness in populations and (in theory) even promote population extinction.

The study of sexual conflict has become one of the most important and dynamic areas in evolutionary biology.
Ecological Genetics
Authors: Urban Mark C 
Published: September 2016

Abstract

Ecological genetics is the study of how ecologically relevant traits evolve in natural populations. Early research in ecological genetics demonstrated that natural selection often is strong enough to generate rapid adaptive changes in nature. Current work has expanded our understanding of the temporal and spatial scales at which natural selection can operate in nature. Modern ecological geneticists combine field observations, laboratory experiments and rapidly improving laboratory techniques to further our understanding about how traits evolve in nature. Genomic techniques are rapidly providing tools to identify regions under selection or that have changed through evolution. Ecological geneticists increasingly explore how evolutionary dynamics shape ecological properties. Consequently, ecological genetics is highly relevant to practical questions that lie at the interface of ecology and evolution.

Key Concepts

Ecological genetics is concerned with how traits evolve in natural populations.

Ecological geneticists apply a combination of natural surveys and experiments in the laboratory and in the field to discern genetic from plastic phenotypic variation and the agents of natural selection that determine this variation.

The ecological geneticist seeks to determine the dominant agents of selection in an environment and associate genetic variation to these selective agents and random drift.

Ecological genetics is concerned both with the spatial and temporal scales over which evolution can occur in nature and the constraints that prevent it.

Genomic methods provide new tools to gain a more complete understanding of genetic variation in nature as well as the agents of natural selection; genomics has so permeated ecological genetics that ecological genomics increasingly is used in place of ecological genetics.

Recent research has revealed evidence for adaptations in natural populations over rapid timescales and fine spatial scales.

This evidence for rapid or microgeographic adaptation argues for an increasing understanding of how evolution in nature affects ecological dynamics and patterns.

Most natural populations exchange genes and many habitats undergo recurrent extinction and colonisation dynamics, arguing for a metapopulation approach that incorporates a spatial perspective.

Species interactions often create strong selection on traits, and when two or more species adapt reciprocally to the other's evolving traits, coevolution occurs.

Ecological genetics can inform applied questions such as when natural pests or pathogens interact with agriculture or adaptation determines the dynamics of fisheries, thus making it relevant to human economy and welfare.
Stable Isotopes as Tools in Ecological Research
Authors: Newton Jason 
Published: September 2016

Abstract

Stable isotope analysis has proved to be an extremely useful tool in elucidating many ecological problems, with stable isotope ecology comprising the theme of a series of international conferences (
http://www.isoecol.org
). Stable isotopes can be used as biological tracers in the following ways: (1) to identify sources, for instance in determining the identity of basal carbon in a food web; (2) to distinguish sources, for example to determine whether a breeding animal is using local resources or its own reserves, or when an animal migrates/disperses from one location to another and (3) to quantify relative inputs in a system, for example determining the proportions of different prey items to a consumer's diet. When utilised carefully, stable isotope analysis provides some advantages over conventional methods and an additional device for the ecologist.

Key Concepts

Stable isotopes are useful tracers of ecological processes.

Carbon stable isotopes are useful tools in plant physiology and for tracing carbon sources.

Nitrogen stable isotope ratios in animal tissues are useful indicators of trophic level.

Combined carbon, nitrogen and sulfur isotope ratios in animal tissues elucidate food webs and trophic niche.

Hydrogen and oxygen isotope ratios in animals reflect those of local precipitation.

Care is needed when planning isotope food web studies.
Molecular Genetics of Renal Cancer
Authors: Klasson Timothy D , Giles Rachel H 
Published: September 2016

Abstract

Renal cancer affects 300 000 people worldwide, with about 75% of those cases being of the clear cell phenotype, which is characterised by somatic mutations acquired in the Von Hippel–Lindau (
VHL
)
tumour suppressor gene
(
TSG
). Most approved therapies for renal cancers have stemmed from understanding the molecular genetics of clear cell renal cancer, the study of which has entirely focused on VHL biology until recently. The remaining 25% of renal cell carcinoma (RCC) has distinct, yet related, molecular mechanisms, which are just beginning to be understood. For example, Type 1 papillary RCC is associated with mutations in the
MET
protooncogene and therapies targeting this pathway in these patients appear to be effective. Personalised medicine aims to tailor treatments to suit patients based on individual molecular signatures. With the increased availability of next generation sequencing in the clinical setting, the molecular genetics of primary and metastasised RCC will help determine treatment options available.

Key Concepts

There are several subtypes of renal cell carcinoma (RCC), each associated with distinct molecular genetics.

The most common type of RCC is the clear cell subtype, which is typically associated with inactivating mutations of the von Hippel–Lindau tumour suppressor on chromosome 3p.

3p deletion can also affect other tumour suppressors commonly mutated in RCC: PBRM1, SETD2 and BAP1, all chromatin remodelling factors.

Type 1 and 2 papillary renal cell carcinoma are also associated with their own mutations in the genes
MET
and
FH
, respectively

Understanding the molecular genetics of RCC is essential for the development of targeted therapies.
Vertebrate Embryo: Development of the Skin and Its Appendages
Authors: Lei Mingxing , Inaba Masafumi , Chuong Cheng‐Ming 
Published: September 2016

Abstract

Vertebrate skin consists of epidermis and dermis, both of which are characterised as highly heterogeneous suborgan/tissues containing complex structures with diverse functions. Skin epidermis starts to stratify during embryogenesis. It plays pivotal barrier functions in protecting the organism from water loss and environmental insults during postnatal life. The dermis is a connective tissue that is separated with the epidermis by a deposition of extracellular matrix called the basement membrane. During skin development, many skin appendages are also induced. Those include epidermal appendages such as feather follicles, hair follicles, sebaceous glands and sweat glands and dermal appendages such as the arrector pili muscle. More and more stem cell populations are characterised in these appendages recently. In addition, considerable progress has been made in identifying molecules and pathways that regulate development and regeneration of skin and its appendages.

Key Concepts

During chick skin development, feathered areas are formed in the skin with high‐cell density of dermal cells and naked areas are formed in low‐cell density regions.

Feather and hair development begins from thickening of epidermis and condensation of dermal cells, which is associated with the interaction among morphogens such as FGFs and BMPs.

The mechanism by which feather buds are arranged in a periodic pattern on the skin and branching formation within each bud might be explained by reaction–diffusion model, one of the mathematical models.

Feather follicles are differentiated from feather buds with the invaginated epidermis and the feathers have an ability of regeneration throughout lifetime owing to feather stem cells.

Development and regeneration of hair follicle involve reciprocal epidermal and dermal cell interactions.

Sequential activation of molecules including Wnt‐Eda‐Shh et al. is required for hair follicle development.

Secondary hair germ cells first response, followed by bulge stem cell activation during hair regeneration.

Regenerative hair cycling is regulated by epigenetic, microenvironment and macroenvironment factors.
Loss of Heterozygosity
Authors: Gorringe Kylie L 
Published: September 2016

Abstract

Loss of heterozygosity (LOH) is a genetic event frequently observed in many cancer types. The loss of one allele of a genetic locus can have multiple possible functional effects including haploinsufficiency, loss of gene expression and being the second ‘hit’ that unmasks a recessive tumour suppressor gene. LOH can be caused by mitotic errors, chromothripsis, gene conversion and inappropriate repair of DNA (deoxyribonucleic acid) breaks. The methods for detecting LOH are evolving from single locus assays such as microsatellite analysis, to accurate and sensitive genome‐wide assays including single‐nucleotide polymorphism arrays and massively parallel DNA sequencing. LOH is an important tool to aid in the discovery of novel tumour suppressor genes and now is gaining importance as a biomarker for clinical decision making in certain contexts.

Key Concepts

Loss of heterozygosity is a common genetic event in cancer whereby one allele is lost, leading to part of the genome appearing homozygous in the tumour where heterozygous in matching normal DNA.

Allelic imbalance is different from LOH: both alleles are still present but are in different numbers of copies.

Regions of LOH can be copy number neutral or show copy number loss.

Whole‐chromosome LOH can be caused by mitotic nondisjunction.

Defects in homologous recombination repair lead to increased levels of LOH in cancer.

The two‐hit hypothesis describes the inactivation of both copies of a recessive tumour suppressor gene in cancer; LOH can be one such hit.

Haplo‐insufficiency is where a gene cannot perform its function normally when present as only one copy and is a likely reason for selection of some LOH events.