bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling transport of energetic particles in corotating interaction regions: A case study
Authors: Zhao Lulu , Li Gang , Ebert R. W. , Dayeh M. A. , Desai M. I. , Mason G. M. , Wu Z. , Chen Y. 
Published: December 2015

AbstractWe investigate energetic particle transport in corotating interaction regions (CIRs) through a case study. The CIR event we study occurred on 8 February 2008 and was observed by both the Advanced Composition Explorer (ACE) and the twin Solar TErrestrial RElations Observatory (STEREO) B spacecraft. An in situ reverse shock was observed by STEREO B (1.0 AU) but not ACE (0.98 AU). Using STEREO B observations and assuming the CIR structure does not vary significantly in the corotating frame, we estimate the shock location at later times for both the STEREO B and ACE observations. Further assuming the accelerated particle spectral shape at the shock does not vary with shock location, we calculate the particle differential intensities as observed by ACE and STEREO B at two different times by solving the focused transport equation using a Monte Carlo simulation. We assume that particles move along Parker's field and experience no cross‐field diffusion. We find that the modulation of sub‐MeV/nucleon particles is significant. To obtain reasonable comparisons between the simulations and the observations by both ACE and STEREO B, one has to assume that the CIR shock can accelerate more particles at a larger heliocentric distance than at a smaller heliocentric distance.
Small‐scale fluctuations in barium drifts at high latitudes and associated Joule heating effects
Authors: Hurd L. D. , Larsen M. F. 
Published: December 2015

AbstractMost previous estimates of Joule heating rates, especially the contribution of small‐scale structure in the high‐latitude ionosphere, have been based on incoherent scatter or coherent scatter radar measurements. An alternative estimate can be found from the plasma drifts obtained from ionized barium clouds released from sounding rockets. We have used barium drift data from three experiments to estimate Joule heating rates in the high‐latitude E region for different magnetic activity levels. In particular, we are interested in the contribution of small‐scale plasma drift fluctuations, corresponding to equivalent electric field fluctuations, to the local Joule heating rate on scales smaller than those typically resolved by radar or other measurements. Since Joule heating is a Lagrangian quantity, the inherently Lagrangian estimates provided by the chemical tracer measurements are a full description of the effects of electric field variance and neutral winds on the heating, differing from the Eulerian estimates of the type provided by ground‐based measurements. Results suggest that the small‐scale contributions to the heating can be more than a factor of 2 greater than the mean field contribution regardless of geomagnetic conditions, and at times the small‐scale contribution is even larger. The high‐resolution barium drift measurements, moreover, show that the fine structure in the electric field can be more variable than previous studies have reported for similar conditions. The neutral winds also affect the heating, altering the height‐integrated Joule heating rates by as much as 12%, for the cases studied here, and modifying the height distribution of the heating profile as well.
Stress‐induced seismic azimuthal anisotropy in the upper crust across the North West Shelf, Australia
Authors: Gavin Lisa J. , Lumley David 
Published: December 2015

AbstractSeismic azimuthal anisotropy (SAA) is observed in many areas of the Earth, and fast polarized directions (ϕ) have been mapped using earthquake surface waves and teleseismic S wave splitting over large regional and tectonic scales. Higher‐resolution petroleum exploration data, including 3‐D seismic surveys and dipole shear logs, often exhibit azimuthal anisotropy; however, we are unaware of any published studies mapping SAA from exploration‐scale data to study large‐scale regional and tectonic SAA trends. The physical mechanisms causing SAA in earthquake data are a subject of great interest; comparing regional ϕ trends to the higher‐resolution exploration trends may help understand these mechanisms. We present a SAA analysis using seismic exploration data across the North West Shelf (NWS) of Australia. We map the fast polarization directions ϕ from 34 dipole shear logs and two 3‐D seismic surveys and compare them to in situ maximum horizontal stress orientations (σH). Our results show that the ϕ and σH trends correlate across a geographical area spanning almost 2000 km and are similar to published results in the region from earthquake seismology. These results suggest that differential horizontal stress is the likely mechanism causing SAA at a wide range of spatial scales on the NWS of Australia. We also show that SAA is not observed at exploration scales in some areas of the NWS and propose a lithology‐dependent stress sensitivity model in which SAA is strongest in clean, unconsolidated quartz‐dominated sandstones and weaker or nonexistent in well‐consolidated cemented rocks and shale‐dominated sediments.
A multiscale climate emulator for long‐term morphodynamics (MUSCLE‐morpho)
Authors: Antolínez José Antonio A. , Méndez Fernando J. , Camus Paula , Vitousek Sean , González E. Mauricio , Ruggiero Peter , Barnard Patrick 
Published: December 2015

AbstractInterest in understanding long‐term coastal morphodynamics has recently increased as climate change impacts become perceptible and accelerated. Multiscale, behavior‐oriented and process‐based models, or hybrids of the two, are typically applied with deterministic approaches which require considerable computational effort. In order to reduce the computational cost of modeling large spatial and temporal scales, input reduction and morphological acceleration techniques have been developed. Here we introduce a general framework for reducing dimensionality of wave‐driver inputs to morphodynamic models. The proposed framework seeks to account for dependencies with global atmospheric circulation fields and deals simultaneously with seasonality, interannual variability, long‐term trends, and autocorrelation of wave height, wave period, and wave direction. The model is also able to reproduce future wave climate time series accounting for possible changes in the global climate system. An application of long‐term shoreline evolution is presented by comparing the performance of the real and the simulated wave climate using a one‐line model.
Intermittency of gravity wave momentum flux in the mesopause region observed with an all‐sky airglow imager
Authors: Cao Bing , Liu Alan Z. 
Published: December 2015

AbstractThe intermittency of gravity wave momentum flux (MF) near the OH airglow layer (∼87 km) in the mesopause region is investigated for the first time using observation of all‐sky airglow imager over Maui, Hawaii (20.7°N, 156.3°W), and Cerro Pachón, Chile (30.3°S, 70.7°W). At both sites, the probability density function (pdf) of gravity wave MF shows two distinct distributions depending on the magnitude of the MF. For MF smaller (larger) than ∼16 m2 s−2 (0.091 mPa), the pdf follows a lognormal (power law) distribution. The intermittency represented by the Bernoulli proxy and the percentile ratio shows that gravity waves have higher intermittency at Maui than at Cerro Pachón, suggesting more intermittent background variation above Maui. It is found that most of the MF is contributed by waves that occur very infrequently. But waves that individually contribute little MF are also important because of their higher occurrence frequencies. The peak contribution is from waves with MF around ∼2.2 m2 s−2 at Cerro Pachón and ∼5.5 m2 s−2 at Maui. Seasonal variations of the pdf and intermittency imply that the background atmosphere has larger influence on the observed intermittency in the mesopause region.
Intestinal removal of free fatty acids from hosts by Lactobacilli for the treatment of obesity
Authors: Chung Hea‐Jong , Yu Jae G. , Lee In‐Ah , Liu Ming‐Jie , Shen Yan‐Fei , Sharma Satya P. , Jamal Mohammad A. H. M. , Yoo Jun‐Hyun , Kim Hyeon‐Jin , Hong Seong‐Tshool 
Published: December 2015

Recent findings on the association of gut microbiota with various diseases, including obesity, prompted us to investigate the possibility of using a certain type of gut bacteria as a safe therapeutic for obesity. Lactobacillus mutants with enhanced capacity in absorption of free fatty acids (FFAs) were isolated to show reduced absorption of FFAs by the administered host, attributing to inhibition of body weight gain and body fat accumulation as well as amelioration of blood profiles. Consequently, high throughput screening of natural FFAs‐absorbing intestinal microbes led to the isolation of Lactobacillus reuteri JBD30 l. The administration of Lactobacillus JBD30l lowered the concentration of FFAs in the gut fluid content of small intestine, thus reducing intestinal absorption of FFAs whereas promoting fecal excretion of FFAs. Animal data also confirmed that the efficacy of Lactobacillus JBD30l on body weight similar to that of orlistat, an FDA‐approved pharmaceutical for long‐term use to treat obesity. In a subsequent random, double‐blind, placebo‐controlled clinical trial (KCT0000452 at Clinical Research Information Service of Korea), there was a statistically significant difference in the percentage change in body weight between the Lactobacillus JBD301 and the placebo group (P = 0.026) as well as in the BMI (P = 0.036) from the 0‐week assessment to the 12‐week assessment. Our results show that FFA‐absorbing Lactobacillus JBD301 effectively reduces dietary fat absorption, providing an ideal treatment for obesity with inherent safety.
Dendritic Cells
Authors: See Peter , Ginhoux Florent 
Published: December 2015

Abstract

Dendritic cells (DCs) are distributed in almost all tissues body, acting as sentinels of the immune system. They serve as specialised pathogen‐sensing and antigen‐presenting cells that initiate and regulate the immune response. DCs are derived from unique progenitors present in the bone marrow, which seed the tissues where they differentiate into mature DCs. Transcriptomic, phenotypic and functional analyses indicate that human and murine DCs can be divided into three subsets: two subsets of conventional DCs (cDC) named cDC1 and cDC2, and a third lineage of plasmacytoid DCs (pDCs). Each subset is unique and has distinct functional specialisations to control specific T‐cell responses. DCs form a complex cellular network capable of integrating multiple environmental signals and can induce either immunity or tolerance. As a consequence, DCs are suitable candidates for therapeutic intervention in immune‐mediated conditions.

Key Concepts

Dendritic cells are a heterogeneous group of specialised pathogen‐sensing and antigen‐presenting cells.

They are distributed in almost all tissues and organs, and act as sentinels of the immune system.

They are derived from DC‐restricted progenitors present in the bone marrow and arise from a dedicated lineage.

They can be grouped into three subsets based on ontogeny and transcription factor dependency: two lineages of conventional DCs named cDC1 and cDC2, as well as a third lineage of plasmacytoid DCs (pDCs).

Each subset is unique and has distinct functional specialisations.

The cDC1 subset is efficient at cross‐presentation, and elicits Th1 responses.

The cDC2 subset is capable of eliciting Th2 and Th17 responses.

pDCs produce large amounts of type I interferons to combat viral infections.
Natural Antibodies
Authors: Zouali Moncef 
Published: December 2015

AbstractNatural antibodies are essentially antibodies of the immunoglobulin M (IgM) isotype present in the circulation of normal humans and other mammalian species. They are detectable in the serum of healthy individuals before deliberate immunisation. They are often directed against highly conserved epitopes and often bind to ligands of varying chemical composition with low affinity. This antibody subset contrasts with immune antibodies, which are produced in response to the introduction of antigens to the immune system. Natural antibodies are frequently directed to intracellular structures, rather than to cell‐surface antigens. They have been found to play an innate‐like role in protection against infectious agents and to exert homeostatic functions in a variety of experimental models. Other investigations suggest that natural antibodies can play a pathogenic role in autoinflammatory diseases.Key ConceptsA natural antibody is an antibody present in the circulation of an animal or a subject that had not been previously exposed to the corresponding antigen.Certain B‐lymphocyte subsets, such as B‐1a cells, are committed to natural antibody production.The antibody repertoire expressed in B‐cell malignancies exhibits several features in common with those of the natural antibody repertoire of healthy subjects.It is possible that natural antibody production is driven by microorganisms indigenous to the organism, such as bacteria living in the intestine.Natural antibodies play a role in shaping the B‐cell repertoire and may represent the precursors of antibodies to pathogens.Natural antibodies could serve as innate recognition receptors, recognising various bacterial cell‐wall components or parasites.Studies of rodents rendered deficient in natural antibodies suggest that this antibody subset is endowed with a homeostatic potential and housekeeping functions, such as recognition and removal of senescent cells and other self‐antigens.Circumstantial evidence suggests that natural antibodies can be associated with protection against Alzheimer disease, atherosclerosis or cancer development.B lymphocytes secreting natural antibodies could represent a reservoir capable of mutating their immunoglobulin variable region genes to give rise to high‐affinity pathogenic autoantibodies.
W
arburg,
O
tto
H
einrich
Authors: Nickelsen Kärin 
Published: December 2015

Abstract
Otto Heinrich Warburg (1883–1970) was a German biochemist and Director of the Kaiser Wilhelm Institute for Cell Physiology in Berlin‐Dahlem. Warburg is noted for eminent studies of central metabolic processes, such as respiration, cancer and photosynthesis. He revolutionised cell physiological and biochemical research through the introduction of physical methods and techniques (manometry, spectrophotometry and others) and he was able to identify and crystallise a number of important (co‐)enzymes. For his work in cellular respiration, Warburg was awarded the Nobel Prize in Medicine or Physiology in 1931.
Clostridia
Authors: Dürre Peter 
Published: December 2015

Abstract

Clostridia are strictly anaerobic or moderately aerotolerant bacteria, gaining adenosine triphosphate (ATP) mostly by substrate level phosphorylation. However, electron transport chains and membrane pumps for H
+
or Na
+
extrusion are also found. These ions are then used for energy conservation by respective ATPases. A variety of heterotrophic compounds can be degraded, and a number of different fermentation pathways are employed. Several clostridia are also able of autotrophic growth, using CO
2
and CO as carbon source. Sophisticated methods for culturing and genetic manipulation are established. Several pathogenic species belong to the genus, but even some of the toxins are meanwhile used in therapy, research and cosmetic industry. Biotechnologically important are clostridial enzymes, the clostridial solvent production and cancer therapy by recombinant clostridial endospores. A recent industrial application at large scale is the production of bulk and fine chemicals from waste gases, especially synthesis gas.

Key Concepts

Clostridia are composing a taxonomically diverse group, which undergoes frequent reclassification.

Clostridia are anaerobic (sometimes not strictly) and form endospores, which is the cause for their ubiquitous occurrence.

Members of the genus
Clostridium
are nutritionally extremely versatile, able to degrade a large variety of heterotrophic substrates and able to grow under autotrophic conditions.

Clostridia participate to a large extent in biogeochemical cycles (e.g. of carbon, nitrogen and metals).

Few clostridia produce one or several toxins, however, among these toxins are the most potent known (botulinum toxin).

Both, clostridial toxins and clostridial cells are already used as or being developed into medical applications for therapy.

Autotrophic clostridia gained industrial relevance and are being used for converting waste gases into bulk and fine chemicals.
Nitrogen Fixation in Cyanobacteria
Authors: Stal Lucas J 
Published: December 2015

Abstract

Cyanobacteria are oxygenic photosynthetic bacteria that are widespread in marine, freshwater and terrestrial environments, and many of them are capable of fixing atmospheric nitrogen. However, ironically, nitrogenase, the enzyme that is responsible for the reduction of N
2
, is extremely sensitive to O
2
. Therefore, oxygenic photosynthesis and N
2
fixation are not compatible. Hence, cyanobacteria had to evolve a variety of strategies circumventing this paradox, allowing them to grow at the expense of N
2
, a ubiquitous source of nitrogen. Some filamentous cyanobacteria differentiate heterocysts. These cells lack the oxygenic photosystem and possess a glycolipid cell wall that keeps the oxygen concentration sufficiently low for nitrogen fixation to take place. This strategy is known as spatial separation of oxygenic photosynthesis and nitrogen fixation. Nonheterocystous cyanobacteria may temporally separate these processes by fixing nitrogen during the night. Again others use a combination of these strategies.

Key Concepts

Cyanobacteria may fix the ubiquitously available CO
2
and N
2
, and therefore cover the demand of the two most important elements.

The fixation of N
2
comes at a high metabolic energy cost, but cyanobacteria are phototrophic organisms that use sunlight to cover their energy demand.

Nitrogenase, the enzyme complex responsible for the fixation of N
2
, is sensitive to oxygen and requires a near‐to‐anoxic environment.

Cyanobacteria are phototrophic organisms evolving oxygen and they developed various strategies to combine this with N
2
fixation.

In order to fix N
2
, cyanobacteria separate the incompatible processes of oxygenic photosynthesis and N
2
fixation spatially (in different cells) or temporally (during the night), or a combination of both.

N
2
fixation in the ocean is restricted to the (sub)tropics and carried out by free‐living nonheterocystous filamentous and unicellular cyanobacteria and by symbiotic cyanobacteria living with microalgae.

Heterocystous cyanobacteria are found in freshwater, brackish water, terrestrial environments and symbiotic in plants and algae.

Cyanobacteria have a circadian clock that synchronises metabolic processes and allow for the fixation of N
2
.
N
otch Signalling in Cancer
Authors: Aithal Madhuri GS , Narayanappa Rajeswari 
Published: December 2015

Abstract

The Notch pathway is an evolutionarily conserved signalling pathway involved in the development of diverse organisms from drosophila to humans. It plays a pivotal role in maintenance of stem cells and cell‐fate determination in both developing embryos and adult organisms. Aberrant Notch signalling is oncogenic and is documented in various cancers such as cervical, breast, skin, colon, pancreatic, leukaemia, brain tumour and so on. Genome defects including both genetic and epigenetic alterations contribute to cancer development. Both Notch gain‐of‐function and loss‐of‐function mutations have been reported in various cancers. On the basis of the type of tissue, Notch genes are found to function as both oncogenes and tumour‐suppressor genes. Epigenetic alterations of Notch genes including DNA (deoxyribonucleic acid) methylation and histone modifications contribute to cancer development through transcription regulation, resulting in inappropriate activation or silencing of genes. Thus, Notch pathway plays an important role in tumour development through genetic and epigenetic modifications in several different ways.

Key Concepts

Notch pathway is an evolutionarily conserved cell‐signalling pathway involved in the development of both vertebrate and invertebrate species.

It is responsible for communication between adjacent cells controlling multiple cell differentiation through regulation of gene expression during embryonic and adult life.

Aberrant Notch signalling is linked with various human diseases including cancers by modifying the developmental state of the cells and subsequently maintaining the cells in an undifferentiated or proliferative fate.

Abnormal Notch signalling is found to influence oncogenesis through genome defects involving both genetic and epigenetic alterations.

Depending on the cellular context, altered Notch pathway genes can act either as oncogenes or tumour‐suppressor genes.

The first reported Notch mutation was the chromosome translocation in T‐cell acute lymphoblastic leukaemia patients creating an active and oncogenic Notch1. Since then, Notch mutations, both gain‐of‐function and loss‐of‐function, have been identified in various cancers.

Promoter hypermethylation in Notch genes is more common in cancer compared to hypomethylation.

Histone modifications are covalent, and among various forms, lysine acetylation and lysine/arginine methylation are most common in cancer.
Mitochondrial Depletion Syndromes
Authors: Finsterer Josef , Wakil Salma M 
Published: December 2015

Abstract

Mitochondrial DNA (mtDNA) depletion syndromes (MDDSs) are a clinically and molecularly heterogeneous group of mitochondrial disorders characterised by severely reduced mtDNA copy number in affected tissues. Phenotypically, MDDSs manifest as Alpers‐Huttenlocher disease (AHD), mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), infantile‐onset spinocerebellar ataxia (IOSCA), hepatocerebral MDDS, encephalomyopathic MDDS or myopathic MDDS. Genotypically, MDDSs are due to mutations in nine genes (POLG1, C10orf2/PEO1, DGUOK, MPV17, TK2, RRM2B, SUCLA2, SUCLG1, TYMP). Except for AHD and IOSCA, MDDSs are genetically heterogeneous. The diagnosis is established upon clinical and instrumental investigations and demonstration of depleted mtDNA in affected tissues, such as muscle, liver, brain or intestines. Treatment is symptomatic in the vast majority of the cases and can substantially relief clinical manifestations. A causal therapeutic approach with allogeneic, hematopoietic stem‐cell transplantation is available for MNGIE. MDDSs have a poor prognosis in the majority of the cases. The outcome is usually better the later the onset of the MDDSs.

Key Concepts

Paediatric and adult neurologist must be aware of multisystem mitochondrial depletion syndromes (MDDSs).

MDDSs predominantly manifest in the brain, muscle, liver, kidneys and intestines.

In addition to mutations in one of the nine classical genes associated with MDDS, it may be caused by mutations in other genes as well.

MDDSs are diagnosed by demonstration of mtDNA depletion upon biopsy of the most affected tissues.

mtDNA copy number may be normal in tissues hardly phenotypically affected.

Clinical severity of MDDS depends on the amount of the residual mtDNA copy number.

MDDSs may rarely also occur in adults due to mutations in nuclear genes other than the nine classical ones.
The Concept of Consecutive Matching Stria (
CMS
) and the Philosophy Behind the Concept of Individuality in Striated Match Comparisons
Authors: Heard Brian J. 
Published: December 2015

Abstract
This article discusses concept of using consecutive matching stria (CMS) as a quantitative method of describing an observed pattern match, its philosophy, history, a discussion on the relevance of such a concept and its relevance in a court of law.