bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new climate index controlling winter wave activity along the Atlantic coast of Europe: The West Europe Pressure Anomaly
Authors: Castelle Bruno , Dodet Guillaume , Masselink Gerd , Scott Tim 
Published: January 2017

AbstractA pioneering and replicable method based on a 66‐year numerical weather and wave hindcast is developed to optimize a climate index based on the sea level pressure (SLP) that best explains winter wave height variability along the coast of western Europe, from Portugal to UK (36–52°N). The resulting so‐called Western Europe Pressure Anomaly (WEPA) is based on the sea level pressure gradient between the stations Valentia (Ireland) and Santa Cruz de Tenerife (Canary Islands). The WEPA positive phase reflects an intensified and southward shifted SLP difference between the Icelandic low and the Azores high, driving severe storms that funnel high‐energy waves toward western Europe southward of 52°N. WEPA outscores by 25–150% the other leading atmospheric modes in explaining winter‐averaged significant wave height, and even by a largest amount the winter‐averaged extreme wave heights. WEPA is also the only index capturing the 2013/2014 extreme winter that caused widespread coastal erosion and flooding in western Europe.
Comment on “Sandbox modeling of evolving thrust wedges with different preexisting topographic relief: Implications for the longmen Shan thrust belt, eastern Tibet” by C. Sun et al.
Authors: Tan Xibin , Xu Xiwei , Lu Renqi 
Published: January 2017

AbstractSun et al.'s (2016) sandbox modeling takes preexisting topographic relief into account for faulting activity at the compressional orogenic belt, which promotes better understanding of Longmenshan thrust belt's (LTB) orogenic process and faulting behavior. However, topographic relief in sandbox modeling is contradictory to central LTB's actual topographic relief, and as a result, both the comparison between sandbox modeling and actual tectonics and topography and the conclusion that Xiaoyudong Fault is a tear fault should be reconsidered. Actually, based on Sun et al.'s (2016) sandbox modeling, the Xiaoyudong Fault cannot be treated as a tear fault.
Percolation blockage: A process that enables melt pond formation on first year Arctic sea ice
Authors: Polashenski Chris , Golden Kenneth M. , Perovich Donald K. , Skyllingstad Eric , Arnsten Alexandra , Stwertka Carolyn , Wright Nicholas 
Published: January 2017

AbstractMelt pond formation atop Arctic sea ice is a primary control of shortwave energy balance in the Arctic Ocean. During late spring and summer, the ponds determine sea ice albedo and how much solar radiation is transmitted into the upper ocean through the sea ice. The initial formation of ponds requires that melt water be retained above sea level on the ice surface. Both theory and observations, however, show that first year sea ice is so highly porous prior to the formation of melt ponds that multiday retention of water above hydraulic equilibrium should not be possible. Here we present results of percolation experiments that identify and directly demonstrate a mechanism allowing melt pond formation. The infiltration of fresh water into the pore structure of sea ice is responsible for blocking percolation pathways with ice, sealing the ice against water percolation, and allowing water to pool above sea level. We demonstrate that this mechanism is dependent on fresh water availability, known to be predominantly from snowmelt, and ice temperature at melt onset. We argue that the blockage process has the potential to exert significant control over interannual variability in ice albedo. Finally, we suggest that incorporating the mechanism into models would enhance their physical realism. Full treatment would be complex. We provide a simple temperature threshold‐based scheme that may be used to incorporate percolation blockage behavior into existing model frameworks.
Horizontal propagation of large‐amplitude mountain waves into the polar night jet
Authors: Ehard Benedikt , Kaifler Bernd , Dörnbrack Andreas , Preusse Peter , Eckermann Stephen D. , Bramberger Martina , Gisinger Sonja , Kaifler Natalie , Liley Ben , Wagner Johannes , Rapp Markus 
Published: January 2017

AbstractWe analyze a large‐amplitude mountain wave event, which was observed by a ground‐based lidar above New Zealand between 31 July and 1 August 2014. Besides the lidar observations, European Centre for Medium‐Range Weather Forecasts (ECMWF) data, satellite observations, and ray tracing simulations are utilized in this study. It is found that the propagation of mountain waves into the middle atmosphere is influenced by two different processes at different stages of the event. At the beginning of the event, instabilities in a weak wind layer cause wave breaking in the lower stratosphere. During the course of the event the mountain waves propagate to higher altitudes and are refracted southward toward the polar night jet due to the strong meridional shear of the zonal wind. As the waves propagate out of the observational volume, the ground‐based lidar observes no mountain waves in the mesosphere. Ray tracing simulations indicate that the mountain waves propagated to mesospheric altitudes south of New Zealand where the polar night jet advected the waves eastward. These results underline the importance of considering horizontal propagation of gravity waves, e.g., when analyzing locally confined observations of gravity waves.
An approach to secure weather and climate models against hardware faults
Authors: Düben Peter D. , Dawson Andrew 
Published: January 2017

AbstractEnabling Earth System models to run efficiently on future supercomputers is a serious challenge for model development. Many publications study efficient parallelization to allow better scaling of performance on an increasing number of computing cores. However, one of the most alarming threats for weather and climate predictions on future high performance computing architectures is widely ignored: the presence of hardware faults that will frequently hit large applications as we approach exascale supercomputing. Changes in the structure of weather and climate models that would allow them to be resilient against hardware faults are hardly discussed in the model development community. In this paper, we present an approach to secure the dynamical core of weather and climate models against hardware faults using a backup system that stores coarse resolution copies of prognostic variables. Frequent checks of the model fields on the backup grid allow the detection of severe hardware faults, and prognostic variables that are changed by hardware faults on the model grid can be restored from the backup grid to continue model simulations with no significant delay. To justify the approach, we perform model simulations with a C‐grid shallow water model in the presence of frequent hardware faults. As long as the backup system is used, simulations do not crash and a high level of model quality can be maintained. The overhead due to the backup system is reasonable and additional storage requirements are small. Runtime is increased by only 13 % for the shallow water model.
Heavy Metal Adaptation
Authors: Guevara‐García Ángel A , Lara F Paloma , Juárez L Katy , Herrera‐Estrella Luis R 
Published: January 2017

AbstractFifty‐three chemical elements, those with densities higher than 5 g cm−3, are categorized as heavy metals. Ecologically speaking, any element that is not used in basic metabolism or biodegradable should be regarded as a heavy metal. Heavy metals are natural components of the biosphere and as such are part of biogeochemical cycles; however, as a consequence of human activities, heavy metal concentrations have reached toxic levels in the soils and water bodies of many ecosystems around the world. Actually, using multidisciplinary approaches, including ‘omics’ strategies, several factors involved in heavy metal adaptation have been identified. In the coming years, the detailed study of the contribution of these factors to the heavy metal tolerance mechanism, as well as the crosstalk between them, should produce the necessary knowledge for the development of heavy metal‐tolerant crops that would improve agricultural productivity to meet growing food demand.Key ConceptsHeavy metals are the group of chemical elements with densities higher than 5 g cm−3.Any chemical element that causes environmental pollution could be considered as heavy metal.Heavy metal concentrations increase to toxic levels through human activities.Biogeochemical cycles are considered to have an important role in maintaining environmental equilibrium of heavy metals.All heavy metals reaching a concentration higher than 0.1% generate a polluted and toxic environment.Metallophytes can be used as biomarkers of heavy metal‐polluted soils.Hyperaccumulator plants are those that actively take up and translocate heavy metals from the soil, accumulating them in aboveground organs.Some plant exudates (named phytosiderophores) are known to take part in the uptake and mobilisation of heavy metals.
Turgor Pressure
Authors: Fricke Wieland 
Published: January 2017

Abstract

Turgor pressure is the hydrostatic pressure in excess of ambient atmospheric pressure which can build up in living, walled cells. Turgor is generated through osmotically driven inflow of water into cells across a selectively permeable membrane; this membrane is typically the plasma membrane. The maintenance of turgor in cells requires energy. Turgor pressures can be as small as 0.1–0.4 MPa yet can also exceed 2–3 MPa. Cells of many organisms can build up turgor pressure. In plants, turgor pressure plays an important role in key processes such as growth, development, mechanical support, signalling, organ movement, flowering and responses to stress. The ability to build up significant turgor pressure in cells has been key to the evolutionary success of terrestrial plants to pursue a sessile life strategy.

Key Concepts

Turgor pressure refers to the hydrostatic pressure in cells in excess of ambient (normal) atmospheric pressure.

Turgor pressure is best known in plant cells but also occurs in walled cells of other organismal kingdoms.

The build‐up and maintenance of turgor pressure requires five key components: water, solutes, a selectively permeable membrane, a wall and metabolic energy.

Values of turgor pressures cover a wide range; they can be as small as 0.1–0.4 MPa yet also exceed 2–3 MPa.

Turgor pressure in plants plays a key role in processes such as growth, development, mechanical support, signalling, flowering and stress response.

Turgor pressure is an ideal means in plant cells through which the energy content of water molecules (water potential) can be adjusted quickly, within seconds.

The ability of plants to establish significant cell turgor pressure was key to their evolutionary success to colonise land while pursuing a sessile life strategy.

The best‐known example of rapid changes in cell turgor causing microscopic movements is the reversible opening and closing of stomatal pores in leaves.

As plant cells are generally very small (picolitre‐range volumes), eating a fruit such as an apple which contains highly pressurised cells does not hurt.
Evolution of Photosynthesis
Authors: Cardona Tanai 
Published: January 2017

Abstract

Photosynthesis originated once during the early Archaean due to the emergence of photochemical reaction centres, the biological nanomachines that convert the energy of light into chemical energy. The evolution of the photosynthetic machinery is consistent with a single origin of photosynthesis followed by an early diversification event that resulted in the rapid evolution of distinct reaction centre types and pigment forms. One of these reaction centres specialised in highly oxidising photochemistry, which facilitated the oxidation of Mn and the evolution of the water‐oxidising cluster of Photosystem
II
. In addition, the last common ancestor of all photosynthetic organisms can be traced back to a period of time near the root or at the root of the tree of life of bacteria, with the current distribution of photosynthesis being the result of widespread loss of photosynthetic capacity and horizontal gene transfer.

Key Concepts

Photosynthesis originated at least 3.5 billion years ago, but it could be much older.

Photosynthesis evolved only once in ancestral forms of bacteria.

Type I and Type II reaction centres originated from an ancestral gene duplication event.

The last common ancestor of photosynthetic bacteria had type I and type II reaction centres.

Photosystem II originated from the close interaction of a Type I and Type II reaction centre.

The ancestral homodimeric Photosystem II was able to catalyse the oxidation of water.

The last common ancestor of photosynthetic bacteria had protochlorophyllide and chlorophyllide reductase and could make pigments similar to chlorophyll
a
and bacteriochlorophyll
g
.

Nitrogenase and the chlorophyll synthesis enzymes originated from an ancient gene duplication event predating the diversification of bacteria.

The current distribution of photosynthesis in bacteria is explained by widespread loss of photosynthesis and horizontal gene transfer.
Xylem: Differentiation, Water Transport and Ecology
Authors: Fricke Wieland 
Published: January 2017

AbstractThe xylem constitutes the part of plant vascular system which is primarily concerned with the long‐distance transport of water, dissolved minerals and signalling molecules from root to shoot. The development of xylem during tissue differentiation and organ growth is governed in particular by auxins and cytokinins. The mode of transport in xylem is bulk flow, driven by hydrostatic pressure gradients between root and shoot. These gradients involve substantial negative pressures (xylem tensions) during daytime transpiration. As xylem tension increases, so does the possibility of embolism and xylem dysfunction, particularly when water supply is sparse, unless embolism is repaired. The evolution of xylem reflects a combination of demands: optimising the volume flow rate, optimising control over xylem sap composition and minimising the chance of xylem dysfunction through embolism. Strategies to meet these often conflicting demands are reflected through differences in xylem anatomy between species which differ in their ecology.Key ConceptsA key innovation during the evolution of plants was the development of a long‐distance, ‘vascular’, transport system.The mode of long‐distance transport of substances is bulk flow.Bulk flow is driven by gradients in hydrostatic pressure.The xylem constitutes the part of vascular system which is primarily concerned with the transport of substances, including water, between root and shoot.The xylem is made up of cells which are dead at full maturity and fulfil a transport (xylem vessels, tracheids) and mechanical support (fibres) role and cells which are alive and provide metabolic activity (xylem parenchyma).Development of xylem starts from procambial and cambial cells and is governed by auxin and also cytokinins.Daytime transpiration is associated with significant negative pressures (tensions) in xylem; this increases the chance of embolism and (partial) loss of function of xylem.The structural design of xylem of plant species, which differ in their taxonomy and ecology, often reflects differences in the transpirational demand (water flux rates), water availability (and associated likeliness of embolism formation) and soil solution composition (and need to control xylem sap composition) encountered by these species.
Cell Culture Contamination
Authors: Gollin Susanne M , Lewis Dale W 
Published: January 2017

Abstract

Cell cultures are valuable models of health and disease, especially in translational research. Cell culture is important for genome editing, stem cell technologies, cancer research, investigating the basic mechanisms involved in development and differentiation, elucidating the role of genetic alterations in normal and abnormal cellular behaviour and developing and testing therapeutics. The clinically important field of classical cytogenetics requires cell culture to obtain metaphase chromosomes from dividing cells at the mitotic stage of the cell cycle when the chromosomes are most compact and visible as distinct entities. Further, culture
in vitro
facilitates analysis of cells in a controlled environment; minimises morbidity and mortality of human, animal or plant subjects and enables replicate studies over long periods of time. Cell lines are essential models for testing therapeutic efficacy, including drug screening and sensitivity studies. The main difficulty with cell cultures in the clinical or research laboratory is their propensity to contamination, whether by microbes or stray cells from other cultures. It is imperative to verify the authenticity of (authenticate) cell lines and rule out microbial contamination of cell cultures before initiating a series of experiments, at regular intervals during each experimental study and at the end of the study to assure the quality and validity of experimental results.

Key Concepts

Cell cultures are valuable models in biomedical research.

Cell cultures have a propensity to become contaminated by microbes.

Intra‐ or interspecies cross‐contamination of cell lines by mislabelling or stray cells from other cell lines results in misidentified cell cultures.

High‐quality research results rely on (1) cell line authentication to rule out cross‐contamination and (2) testing cell cultures for and avoiding microbial contamination, at the beginning, at regular intervals during and at the end of a research study.

Contaminated or misidentified cell cultures waste both time and money and produce invalid research results.
Mitochondrial Genome
Authors: Saccone Cecilia , Gadaleta Gemma 
Published: January 2017

Abstract

Mitochondria are cytoplasmic organelles present in all eukaryotic cells that are able to respire. They possess their own genetic system whose size and organisation are quite variable in plants, protists and fungi. A certain degree of structural variability is observed also in Metazoa. In human and all vertebrates, mitochondrial deoxyribonucleic acid (mtDNA) is rather small (about 17 kb) but constant as genetic content and organisation. It consists of two ribosomal ribonucleic acid (RNA) genes, 13 protein‐coding genes and 22 transfer RNAs. All other mitochondrial products are coded by nuclear DNA and transported into the mitochondrion. Mitochondrial genetic system has a uniparental, usually maternal, way of inheritance, and it is present in cell in a multicopy state. mtDNA replication, transcription and translation are also very peculiar. Evolutionary origin of mitochondria has been described through the endosymbiotic theory.

Key Concepts

Mitochondria are eukaryotic cell organelles with their own genome.

Mitochondrial genome shows great structural variability in most eukaryotic taxa but is quite stable for content and organisation in Metazoans.

mtDNA has a small size with a poor gene content.

Two types of genes are encoded by mtDNA: genes for protein synthesis machinery and genes for respiratory chain subunits, fundamental for cell energy production.

The mitochondrial genome has bacterial origin, with several peculiar features about its replication and expression.

mtDNA is a multicopy genome that is uniparentally, usually maternal, transmitted and does not undergo recombination.

Evolution of mtDNA (within Metazoa) is lineage specific.
Chromosome 8
Authors: Hilton Matthew J , Wells Dan E 
Published: January 2017

AbstractChromosome 8 is a submetacentric chromosome containing about 5% of the euchromatic human genome. The total length of the chromosome has been estimated at 145 138 636 bp. Sequence analysis and annotation indicated that the chromosome contains 677 protein coding genes and 1031 noncoding genes. There are multiple online resources that provide sequence and mapping information for chromosome 8. These include the NCBI (National Center for Biotechnology Information) Map Viewer, the Mitelman Map, the Marshall Map and the OMIM (Online Mendelian Inheritance in Man) Morbid Map. Compilations of these sources suggest that chromosome 8 contains approximately 223 phenotypes, diseases or syndromes. Of these, 45 have yet to be associated with specific genes. Notably, a region of the distal p‐arm on chromosome 8 has a strikingly high mutation rate. In this region, the majority of the genes are involved in development or signalling of the nervous system.Key ConceptsChromosomes contain gene clusters.Certain chromosomal regions contain high mutation rates.Many diseases and syndromes do not correspond to specific genes.A single gene can produce multiple phenotypes, disease and syndromes.Some syndromes are not directly linked to a specific gene or genes, but to chromosomal morphology.
Sex Chromosome Abnormalities
Authors: Pappas Kara B , Migeon Claude J 
Published: January 2017

AbstractIn human subjects, the sex chromosomes are the X and the Y chromosomes. Normally, a complement of two X chromosomes (46,XX) is seen in females and one X and one Y (46,XY) in males. The X‐chromosome includes about 1500 genes, only a few of which are involved in sex development. The Y‐chromosome contains very few genes, but one gene,SRY, is the most important gene in male sex development. Multiple autosomal genes are also involved in sex development. Abnormalities of sex chromosomes can involve errors in the number of sex chromosomes, such as 45,X0 (Turner syndrome), 47,XXX, 47,XXY (Klinefelter syndrome), 47,XYY or mosaicism. Sex chromosome abnormalities also include aberrations of a single gene of the sex chromosome, leading to a disorder of sex development (DSD). This can result in 46,XX DSD and 46,XY DSD.Key ConceptsTurner syndrome occurs when females have a missing sex chromosome (45,X0) or have a mosaic complement of cells with one or more lines missing a sex chromosome.Girls with Turner syndrome have a variety of congenital anomalies, the most striking being short stature and premature ovarian failure.Klinefelter syndrome boys (47,XXY) have tall stature, marfinoid habitus, and may have difficulty with language development and verbal IQ (intelligent quotient).46,XY complete gonadal dysgenesis, or Swyer syndrome, describes patients who have both external and internal female organs with a 46,XY chromosome complement.46,XY disorders of sex development encompass a wide range of disorders including androgen insensitivity, partial gonadal dysgenesis and many more.46,XX disorders of sex development can result from a multitude of virilising disorders or the presence of Y‐chromosome material.Patients with disorders of sex development and intra‐abdominal gonads may be at risk for gonadoblastoma, depending on their underlying disorder.Assignment of sex, timing of surgery and medical management of patients with disorders of sex development is controversial.