bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modulation of Wnt signaling is essential for the differentiation of ciliated epithelial cells in human airways
Authors: Schmid Andreas , Sailland Juliette , Novak Lisa , Baumlin Nathalie , Fregien Nevis , Salathe Matthias 
Published: September 2017

Wnt signaling is essential for the differentiation of airway epithelial cells during development. Here, we examined the role of Wnt signaling during redifferentiation of ciliated airway epithelial cells in vitro at the air liquid interface as a model of airway epithelial repair. Phases of proliferation and differentiation were defined. Markers of squamous metaplasia and epithelial ciliation were followed while enhancing β‐catenin signaling by blocking glycogen synthase kinase 3β with SB216763 and shRNA as well as inhibiting canonical WNT signaling with apical application of Dickkopf 1 (Dkk1). Our findings indicate that enhanced β‐catenin signaling decreases the number of ciliated cells and causes squamous changes in the epithelium, whereas treatment with DDk1 leads to an increased number of ciliated cells.
Flow Dependence of Suspended Sediment Gradations
Authors: Gibson S. A. , Cai C. 
Published: September 2017

AbstractSuspended sediment loads can coarsen or fine as a function of flow. The flow‐load gradation relationships can also vary nonmonotonically. This complex relationship between flow and load gradation complicates sediment model boundary condition selection and sediment rating curve analysis. This study analyzed flow‐gradation data from 78 gages in the continental United States, exploring trends and tendencies in the flow‐gradation relationships. Results were then compared to the flow‐gradation trends generated by sediment capacity equations and a meta‐analysis of sediment model data. Several systems, with abundant sediment supply fined with flow. However, most gage data and calibrated model inputs coarsened with flow. When nonmonotonic models were considered, one‐third to one‐half of the gages fit a second‐order curve, coarsening over low‐to‐moderate flows (up to an average annual exceedance probability of ∼30%) and fining over higher flows. The low‐flow‐coarsening trend was generally stronger than high‐flow‐fining trends. Many of these second‐order trends demonstrated behavior more like “asymptotic coarsening.” They coarsened until they reached a maximum physical grain size limit and gradation fined slightly or remained constant beyond the threshold flow. The dominance of flow‐coarsening suggests most of the rivers surveyed (which included a bias toward large, regulated rivers) are supply limited. Supply limited (bed regulated) rivers tend to coarsen with flow, while capacity limited, high supply systems tend to fine with flow. Sediment capacity equations computed a variety of flow‐gradation trends. Using transport functions to compute load‐gradation model boundary conditions will often diverge from (or even invert) observed trends, especially in supply limited systems.
Directivity Functions of Neutron Monitors
Authors: Karapetyan G. G. 
Published: September 2017

AbstractWe derive directivity function (DF) of neutron monitor (NM). It represents the distribution of count rate by asymptotic directions of primary cosmic ray protons, providing the detailed and accurate description of directional sensitivity of a NM. We present the DFs of several NM stations, located at high and low geographical latitudes, clarifying the features of their acceptance cones. The knowledge of DFs will help in research of galactic and solar cosmic rays based on neutron monitors. Particularly, using DFs, we estimated the times of maximum for diurnal variations of several stations and showed that they are consistent with the observed data.
Equatorial Ionospheric Response to Different Estimated Disturbed Electric Fields as Investigated Using Sheffield University Plasmasphere Ionosphere Model at INPE
Authors: Bravo M. A. , Batista I. S. , Souza J. R. , Foppiano A. J. 
Published: September 2017

AbstractGood ionospheric modeling is important to understand anomalous effects, mainly during geomagnetic storm events. Ionospheric electric fields, thermospheric winds, and neutral composition are affected at different degrees, depending on the intensity of the magnetic disturbance which, in turns, affects the electron density distribution at all latitudes. The most important disturbed parameter for the equatorial ionosphere is the electric field, which is responsible for the equatorial ionization anomaly. Here various electric field measurements and models are analyzed: (1) measured by the Jicamarca incoherent scatter radar (ISR), (2) from Jicamarca Unattended Long‐Term studies of the Ionosphere and Atmosphere (JULIA) radar, (3) deduced from magnetometers, (4) calculated from the time variations of the F layer height (dh′F/dt), and (5) deduced from interplanetary electric field determinations. The response of ionospheric parameters foF2 and hmF2 to the electric fields simulated using the Sheffield University Plasmasphere Ionosphere Model version available at Instituto Nacional de Pesquisas Espaciais is compared with observations for two locations, during the geomagnetic storm events of 17–18 April 2002 and 7–10 November 2004. Results are found to be consistent with the observations in such a way that a hierarchy among the different types of drifts used can be established. When no ISR measurements are available, the drifts deduced from magnetometers or measured by the JULIA are best when including the contribution derived from dh′F/dt for the 18–24 LT time interval. However, when none of these drifts are available, drifts inferred from the interplanetary electric field seem to be a good alternative for some purposes.
Automated River Reach Definition Strategies: Applications for the Surface Water and Ocean Topography Mission
Authors: Frasson Renato Prata de Moraes , Wei Rui , Durand Michael , Minear J. Toby , Domeneghetti Alessio , Schumann Guy , Williams Brent A. , Rodriguez Ernesto , Picamilh Christophe , Lion Christine , Pavelsky Tamlin , Garambois Pierre‐André 
Published: September 2017

AbstractThe upcoming Surface Water and Ocean Topography (SWOT) mission will measure water surface heights and widths for rivers wider than 100 m. At its native resolution, SWOT height errors are expected to be on the order of meters, which prevent the calculation of water surface slopes and the use of slope‐dependent discharge equations. To mitigate height and width errors, the high‐resolution measurements will be grouped into reaches (∼5 to 15 km), where slope and discharge are estimated. We describe three automated river segmentation strategies for defining optimum reaches for discharge estimation: (1) arbitrary lengths, (2) identification of hydraulic controls, and (3) sinuosity. We test our methodologies on 9 and 14 simulated SWOT overpasses over the Sacramento and the Po Rivers, respectively, which we compare against hydraulic models of each river. Our results show that generally, height, width, and slope errors decrease with increasing reach length. However, the hydraulic controls and the sinuosity methods led to better slopes and often height errors that were either smaller or comparable to those of arbitrary reaches of compatible sizes. Estimated discharge errors caused by the propagation of height, width, and slope errors through the discharge equation were often smaller for sinuosity (on average 8.5% for the Sacramento and 6.9% for the Po) and hydraulic control (Sacramento: 7.3% and Po: 5.9%) reaches than for arbitrary reaches of comparable lengths (Sacramento: 8.6% and Po: 7.8%). This analysis suggests that reach definition methods that preserve the hydraulic properties of the river network may lead to better discharge estimates.
Flow and Residence Times of Dynamic River Bank Storage and Sinuosity‐Driven Hyporheic Exchange
Authors: Gomez‐Velez J. D. , Wilson J. L. , Cardenas M. B. , Harvey J. W. 
Published: September 2017

AbstractHydrologic exchange fluxes (HEFs) vary significantly along river corridors due to spatiotemporal changes in discharge and geomorphology. This variability results in the emergence of biogeochemical hot‐spots and hot‐moments that ultimately control solute and energy transport and ecosystem services from the local to the watershed scales. In this work, we use a reduced‐order model to gain mechanistic understanding of river bank storage and sinuosity‐driven hyporheic exchange induced by transient river discharge. This is the first time that a systematic analysis of both processes is presented and serves as an initial step to propose parsimonious, physics‐based models for better predictions of water quality at the large watershed scale. The effects of channel sinuosity, alluvial valley slope, hydraulic conductivity, and river stage forcing intensity and duration are encapsulated in dimensionless variables that can be easily estimated or constrained. We find that the importance of perturbations in the hyporheic zone's flux, residence times, and geometry is mainly explained by two‐dimensionless variables representing the ratio of the hydraulic time constant of the aquifer and the duration of the event (Γd) and the importance of the ambient groundwater flow (). Our model additionally shows that even systems with small sensitivity, resulting in small changes in the hyporheic zone extent, are characterized by highly variable exchange fluxes and residence times. These findings highlight the importance of including dynamic changes in hyporheic zones for typical HEF models such as the transient storage model.
Ribosomal Proteins: Their Role in the Assembly, Structure and Function of the Ribosome
Authors: Razi Aida , Ortega Joaquin 
Published: September 2017

Abstract

The ribosome is the macromolecular assembly dedicated to translating the genetic information into proteins. Ribosomes are made of several RNA molecules and between 50 and 80 proteins. The role played by these proteins has been the focus of investigations for over five decades. Initially, proteins were thought to be the only functional component of the ribosome, whereas the rRNA was considered merely a scaffold. This view has evolved and now is clear that both the RNA and protein components of the ribosome are functionally important. The r‐proteins play a role in the assembly process of the ribosome and are also essential for the structure and function of the ribosome. Their importance in the physiology of the ribosome is revealed by the fact that mutations in ribosomal proteins lead to ribosomopathies, a group of diseases that include developmental, haematological, metabolic and cardiovascular disorders, as well as cancers.

Key Concepts

The ribosome is a large macromolecular assembly dedicated to synthesising all proteins in all cells.

The ribosome in all domains of life is made of a small and a large subunit.

The small subunit decodes the genetic code and translate it into the sequence of amino acids that form a protein.

The large subunit is responsible for the peptide bond formation that links the amino acids in a functional protein.

The three core mechanisms of protein synthesis, including decoding and catalysis of peptide bond formation are performed by ribosomal ribonucleic acid (RNA).

The ribosome also contains 55–80 proteins.

During ribosomal assembly, the ribosomal proteins drive folding of ribosomal ribonucleic acid (rRNA).

In the mature ribosome, ribosomal proteins participate in the translation process, binding of translation factors and tuning ribosomal properties including translation fidelity.

Ribosomal proteins are also a useful tool to study how cellular proteins acquired their ability to fold over geological timescales.
Dispersal: Biogeography
Authors: Wilkinson David M 
Published: September 2017

AbstractDispersal is one of the fundamental processes in biogeography, crucial to understanding the distribution of organisms. The most basic distinction between different types of dispersal is between organisms that disperse using their own energy and those that use energy from the environment. Dispersal can lead to two main patterns of range expansion. Either a population can slowly expand from the margins of its geographical range or a small number of individuals can disperse to a new location some distance from the current edge of the species range, or a combination of both of these processes can occur. Dispersal is also of importance in applied ecology, for example, humans have assisted the dispersal of many organisms to new parts of the world – sometimes leading to problems when they become pests in their new range. Understanding dispersal is also important in attempting to predict how organisms will respond to climate change.Key ConceptsThere are three fundamental processes in biogeography: evolution, extinction and dispersal.The most basic distinction between types of dispersal is between organisms that disperse using their own power (active dispersal) and those that use energy from the environment (passive dispersal).Much of biodiversity is microscopic; organisms of this size can often be easily dispersed by air or water currents – the extent to which geographical barriers are important for such organisms is currently an active area of research.Many larger animals are capable of dispersal under their own power, especially ones that can fly such as birds and bats.Individual organisms can sometimes appear at a location well outside their normal range, and such individuals are referred to as vagrants.There are two main patterns of range expansion ‘diffusion’ and ‘jump dispersal’.Vicariance biogeography has been an alternative to dispersal biogeography, which downplays the importance of dispersal, replacing it with the idea that a taxon's range can be divided by the formation of physical barriers.A key applied question is whether organisms will be able to disperse at a speed that will allow them to track future climate change.Human influence has had a big role in reducing the effects of dispersal barriers by moving organisms around the world.When a species is dispersed to another part of the world by human actions, its main parasites and predators can be left behind; occasionally, this can cause a dramatic increase in its population at the new site, and the introduced organism can become a pest species.
Mutation Databases
Authors: Baux David , Sasorith Souphatta , Bergougnoux Anne , Claustres Mireille 
Published: September 2017

Abstract

Mutation databases were developed in the 1990s and since then being a hot topic in the field of human molecular genetics. They have been constantly evolving, from a single gene to whole genome, from a few patients to whole populations, bringing the community to face multiple challenges, from the ethical and technical aspects of data sharing to the new methods to be developed to bring precision medicine to the patient. The new sequencing technologies, generating worldwide an uninterrupted flow of variants from patients and from the general population, challenge the information technology capacities of genetic centres. Huge databases are now present in multiple copies inside the institutions in high‐performance computing environments and are used to filter, interpret and prioritise variants in disease studies in order to facilitate the work of thousands of geneticists overwhelmed with the big data.

Key Concepts

Mutation databases appeared in the 1990s and were designed to store, organise and share genetic data.

The main categories were central databases, which gathered all variants, and locus‐specific databases, which were focused on one gene/disease with an expert curator.

The advent of high‐throughput sequencing changed the paradigm: central databases are becoming more and more experts and locus‐specific databases more and more genomic.

High‐throughput sequencing also brought a new category of databases for fast variant interpretation.

The main current issue is data sharing: success is linked to data quality, availability and usability.
Genetic Disease: Prevalence
Authors: Zlotogora Joël 
Published: September 2017

Abstract

Although monogenic diseases are considered to be rare, some are relatively frequent either in large parts of the world or in more delineated regions. Often, the relative high frequency is limited to some sub‐populations or even small communities. Various processes influence the prevalence of genetic diseases in the population, in particular the mutation rate, selection and founder effect with genetic drift. In some genes, the rates of new mutations are high, and the disorder is frequent, often appearing as sporadic. A selective advantage to carrier of a genetic trait will lead to an increased frequency of the disease as it has been observed for sickle cell disease in which the carrier status protects from malaria. A relative isolation of a population that expands rapidly may lead to an increased frequency of genetic traits due to a founder effect.

Key Concepts

In general individual genetic diseases are rare, however, the total number of individuals affected with genetic diseases is large.

High mutation rate of a specific gene may be responsible for the high prevalence of the corresponding disease.

A genetic disease may be prevalent as a result of selection since the mutation increase the fitness of the carrier.

Genetic isolation of a population may lead to the high frequency of genetic diseases as a result of a founder effect with genetic drift.

The genetic isolation of a population may be caused by geographic conditions (in the past), religion or consanguinity.
Sickle Cell Disease as a Multi‐Factorial Condition
Authors: Steinberg Martin H , Verhovsek Madeleine M 
Published: September 2017

Abstract

The phenotype of sickle cell anaemia is heterogeneous. Although all patients have the identical sickle haemoglobin mutation, the type, severity and frequency of complications are variable. The products of epistatic modifying genes, along with environmental influences, interact to determine the disease phenotype. Haemoglobin F concentration and its distribution among erythrocytes are likely the most important genetic modulator of disease severity. Polymorphic variation in several genetic loci, including
BCL11A
in chromosome 2p, the
HBS1L‐MYB
locus in 6q23 and the C‐T polymorphism 5′ to
HBG2
on chromosome 11p, are associated with differences in haemoglobin F gene expression.
ZBTB7A
in chromosome 19p, along with
BCL11A,
is a major suppressor of haemoglobin F expression.
α
‐Thalassaemia is the other major modulator of sickle cell disease. In addition to haemoglobin F and
α
‐thalassaemia, some evidence exists that genes influencing endothelial activation, inflammation, red blood cell hydration and haemostasis might contribute to phenotypic diversity.

Key Concepts

Sickle cell anaemia is a single‐gene disorder with heterogeneous clinical features.

The phenotype of sickle cell anaemia is affected by epistatic modifier genes.

Haemoglobin F is the best‐known genetic modifier of sickle cell anaemia.

Polymorphisms in three established quantitative trait loci modulate haemoglobin F.

High haemoglobin F levels are associated with reduced mortality and the rate of viscosity–vaso‐occlusive complications.

The locus of the haemoglobin F effect is the sickle erythrocyte.

The distribution of concentrations of haemoglobin F among sickle erythrocytes is likely to be the critical determinant of its clinical effects.

Co‐inheritance of α‐thalassaemia is associated with reduced rates of haemolysis and vasculopathic complications, but an increased incidence of viscosity–vaso‐occlusive manifestations.

Candidate gene and genome‐wide association studies have identified genes that potentially affect sickle cell disease phenotype by modifying disease pathogenesis.

It is likely that many genes, each playing a small role, contribute to the phenotypic heterogeneity of disease.
Mismatch Repair Genes
Authors: Kansikas Minttu , Nyström Minna , Peltomäki Päivi 
Published: September 2017

Abstract

The mismatch repair (MMR) system is necessary for the maintenance of genomic stability. The primary role of MMR is to correct errors such as base/base mismatches and small insertions/deletions that arise during DNA (deoxyribonucleic acid) synthesis. Loss of functional MMR results in increased rates of point mutations and microsatellite instability. Post‐replicative MMR is strand‐specific and serves mutation avoidance. Outside replication, discrimination between old and newly synthesised DNA strands is no longer necessary, and the MMR system can be mutagenic. Such non‐canonical actions of MMR are required, for example, for the generation of immunoglobulin diversity. The anti‐mutator and mutator activities of MMR play important roles in human diseases. Notably, germline mutations in MMR genes cause predisposition to Lynch syndrome, whereas epigenetic inactivation of the MMR gene
MLH1
underlies 15% of sporadic colorectal and other cancers.

Key Concepts

Post‐replicative mismatch repair can counteract or promote mutations.

DNA mismatch repair genes are conserved in evolution.

DNA mismatch repair genes comply with Knudson's two‐hit paradigm for tumour suppressor genes.

Deficient DNA mismatch repair is responsible for microsatellite instability in tumours.

Inherited defects in DNA mismatch repair underlie Lynch syndrome, a dominant predisposition to colorectal, endometrial and other cancers.
Auxin
Authors: Kathare Praveen K , Cioffi Timothy J , Dharmasiri Nihal , Dharmasiri Sunethra 
Published: September 2017

Abstract

Auxin is an essential plant hormone that regulates growth and development of plants from embryo development to senescence. Auxin exerts its regulatory effects by controlling cell division, cell expansion and cell differentiation. According to the currently accepted model, auxin is mainly synthesised from tryptophan in the shoot apex and transported to other tissues, where auxin is perceived in the nucleus coordinately by two groups of co‐receptors, and controls growth and development by regulating the expression of auxin‐responsive genes. Auxin acts in association with many other growth regulatory factors and external cues to properly coordinate plant growth and development with its environment. While molecular mechanisms involved in auxin biosynthesis, transport and signalling have been unearthed to a great extent, a complete understanding of these intricate mechanisms is yet to be acquired.

Key Concepts

Auxins are small organic molecules with an essential aromatic ring structure and a carboxyl side group of variable length.

Auxin regulates almost every aspect of plant growth and development by affecting cell division, expansion and differentiation at all stages of life.

The predominant natural auxin in plants is indole‐3‐acetic acid, and many synthetic chemicals with auxinic activity are being widely used as plant growth regulators and selective herbicides.

Plants maintain the auxin homeostasis by coordinating biosynthesis, transport, conjugation/deconjugation and degradation of auxins.

Auxin is coordinately perceived by two groups of co‐receptor proteins in the nucleus, resulting in degradation of Aux/IAA repressors, thereby modulating the expression of auxin‐responsive genes.

There is evidence for additional auxin perception and signalling mechanisms, but further studies are necessary for a complete understanding of these pathways.