bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrification
Authors: Stein Lisa Y , Nicol Graeme W 
Published: April 2018

Abstract

The global nitrogen cycle is initiated by the fixation of atmospheric N
2
, by either natural or chemical processes, to bioavailable ammonium (NH
4
+
). Nitrification is the oxidative process that transforms this ammonium to nitrate, via a nitrite intermediate. Nitrification is performed solely by microorganisms: ammonia‐oxidising bacteria and archaea oxidise ammonia to nitrite, nitrite‐oxidising bacteria oxidise nitrite to nitrate and comammox bacteria oxidise ammonia to nitrate. Nitrifiers (and anammox) are distinguished from other microorganisms as they can grow solely from the oxidation of inorganic nitrogenous molecules and fix carbon dioxide as their sole carbon source, although many can also grow using alternative catabolic processes, by cross‐feeding, and/or by mixotrophy. Key enzymes to the nitrification process include ammonia monooxygenase, hydroxylamine dehydrogenase and nitrite oxidoreductase. A putative enzyme catalysing nitric oxide oxidation to nitrite is currently uncharacterised. Essential intermediates to nitrification include hydroxylamine, nitric oxide and nitrite. As well as performing a required component of the global nitrogen cycle, nitrifying microorganisms are also responsible for the loss of nitrogen‐based fertilisers in soil and play a critical role in emission of the potent greenhouse gas, nitrous oxide, as mediated by production and consumption of nitric oxide in their metabolism.

Key Concepts

Nitrification is an oxidative process that transforms reduced nitrogen, primarily ammonia, to nitrate.

Fluxes in nitrogen transformations associated with nitrification activity have accelerated greatly over the past century owing to the production and application of inorganic ammonium‐based fertilisers.

Microorganisms involved in nitrification are ubiquitously distributed in nature and found virtually everywhere that ammonia and oxygen are present.

Nitrification is mediated by bacteria and archaea and is performed by either two (ammonia and nitrite oxidisers) or one (comammox) canonical functional group.

Autotrophic pathways of ammonia‐ and nitrite‐oxidising bacteria are the Calvin cycle or reverse TCA cycle; ammonia‐oxidising archaea assimilate carbon dioxide via the 3‐hydroxypropionate/4‐hydroxybutyrate pathway.

Key enzymes of nitrification are ammonia monooxygenase, hydroxylamine dehydrogenase, nitric oxide oxidase (putative) and nitrite oxidoreductase.

Methanotrophic and heterotrophic microorganisms can carry out parts of nitrification but cannot grow from oxidising reduced nitrogen compounds.

Mechanisms for the production of nitric oxide and nitrous oxide are distinct among nitrifying microorganisms.

Comparative genome analysis and the use of differential inhibitors can assist in determining differences in physiology and niche preference among nitrifying microorganisms.

There is substantial physiological diversity within individual functional groups (e.g. ammonia oxidisers) which results in niche differentiation both within and between taxonomic groups of nitrifiers.
Family‐Based Association Test (
FBAT
)
Authors: Laird Nan M , Lange Christoph 
Published: April 2018

Abstract

Statistical tests of association are commonly used to confirm or exclude a relationship between disease and selected genetic variants. Tests based on data from unrelated individuals are popular, but can be invalid in the presence of genetic confounding, for example the sample contains individuals with different genetic ancestries. Family designs that use affected individuals and their relatives can limit the problem of validity using within‐family comparisons. The transmission disequilibrium test (TDT) is the original family test for association proposed for affected offspring and their parents. The test is simple and intuitive, is totally robust and the most powerful against an alternative that assumes an additive mode of inheritance. The family‐based association test (FBAT) is a generalisation of the TDT suitable for other family designs; other modes of inheritance; dichotomous, measured and time‐to‐onset phenotypes and haplotypes of tightly linked markers. FBATs are generally less powerful than tests based on a sample of equivalent size of unrelated individuals, but special settings exist, for example testing for rare variants with affected offspring and their parents, where the family design has a power advantage.

Key Concepts

Genetic tests based on population or cohort samples can be invalid owing to differing genetic ancestries.

Association designs using family members can reduce or avoid bias using within‐family comparison.

The simplest family test is the TDT which uses affected offspring and their parents.

FBAT refers to a class of tests for family designs that can accommodate any type of genetic model, any phenotype and any family configuration, for example parents and their offspring, sibships or even general pedigrees.

FBATs are based on the distribution of Mendelian transmissions from parents to offspring and thus only require that Mendel's Laws hold under the null hypothesis of no linkage and no association.

FBAT tests can accommodate missing parents or founders by conditioning on the observed genotype configuration in the family, or technically, on the sufficient statistics for the missing parents/founders.

Other methods for testing with family designs that are based on the distribution of genotypes, rather than transmissions, are not completely robust to population substructure in the presence of admixture.

In general, FBATs are less powerful than their population‐based counterparts, given the same amount of genotyping required, but in some circumstances, for example for rare variants, and in testing for gene–environment interactions, they can be more powerful.

With rare variants, it is generally considered desirable to consider jointly all rare variants in a specific region. This may require dealing with transmissions of multiple correlated variants that leads to using a number of different approximations.
Regulation of Mitochondrial Energy Metabolism
Authors: Lalou Claude , Bellance Nadège 
Published: April 2018

Abstract

Mitochondria are organelles that play various roles in the physiology processes such as energy production, calcium signalling and apoptosis. Mitochondria are continually solicited to reply to the cell's energy demand. Thus, impairments in mitochondrial function can lead to diseases, because of its implication into cells homeostasis and its essential role in ATP (adenosine triphosphate) production. The energy metabolism is regulated by mTOR (mechanistic target of rapamycin) and AMPK (AMP‐activated protein kinase) signalling pathways. In addition, the mitochondrial biogenesis is controlled by a triad of transcription factors, PGC1α (PPARγ coactivator 1 alpha)–NRF1 (nuclear respiratory factor 1)–TFAM (mitochondrial transcription factor A). Once the regulations behind the energy synthesis are altered, the organelle will adapt accordingly. Overall, the deficiencies that characterised mitochondria in pathologies are not just about structural defaults. Impairments can target regulation processes. In other words, the energy remodelling or worse, the mitochondrial energy crisis, results from upstream factors. Then, the mechanisms behind regulations of mitochondrial energy metabolism appear to impact cell physiology, as can be deduced from remodelling reported in neurodegenerative diseases or even cancer.

Key Concepts

ROS are involved in energy homeostasis by activating AMPK.

PGC1á is not only related to mitochondrial biogenesis. It stimulates gluconeogenesis.

MFN2 may have opposite functions in neurodegenerative disease and cancer.

Mitochondrial deficiencies that induce impairments in energy production, lead to neurodegeneration.

Bioenergetics characterization of tumours is essential for specific targeting in chemotherapy treatment.

LONP1, involved in mitochondrial quality control and energy metabolism, may be consider as a bioenergetic biomarker in cancer.

AMPK induces mitochondrial biogenesis and catabolism; while mTORC1 induces anabolism.
Plant Lipid Droplets
Authors: McLachlan Deirdre H 
Published: April 2018

Abstract

Plant lipid droplets are small, lipid‐rich organelles found in most cell types. Their function as an energy store for postgerminative seedling establishment has been well documented in seeds; however, their function in other tissue types is not so obvious. There is now a growing body of evidence to suggest that lipid droplets are important for biotic and abiotic stress responses in vegetative tissues, and recent work has shown that they are also used as energy stores in those tissues. Biogenesis and degradation of these organelles is currently of great interest to the biotechnology sector, as engineering of these processes can be used to enhance and alter lipid production for applications such as human and animal nutrition, drug delivery and recombinant protein production.

Key Concepts

Lipid droplets are found in all plant organs.

Lipid droplet coat proteins are involved in the biogenesis, degradation and function of plant lipid droplets.

Both seed and nonseed tissues use lipid droplets as an energy store.

Lipid droplets are important for plant stress signalling in vegetative tissues.

Plant lipid metabolism is of key interest to the biotechnology industry.
Heat Shock Protein 47 (
HSP47
)
Authors: Ibrahim Fatin Hazwani , Abd Latip Normala , Abdul‐Wahab Mohd Firdaus 
Published: April 2018

Abstract

Heat shock protein 47 (HSP47), a noninhibitory serine protease inhibitor (SERPIN, clade H1) family member, is a unique collagen‐specific molecular chaperone. The binding of HSP47 to collagen has been the subject of intense investigation, as it binds to and only to collagen. This binding specificity presents a relatively unexplored potential of using HSP47 as a target for treatment of collagen‐related diseases and abnormalities. Homology model studies and structural determination have revealed the important amino acid residues for HSP47‐collagen binding interaction. HSP47‐knockout experiment in mice proved the importance of HSP47 for correct folding of collagen triple helices, thus critical for normal development. Various diagnostic and treatment strategies based on the unique HSP47 functions are now being investigated and proposed.

Key Concepts

Many heat shock proteins (HSPs) act as molecular chaperones to counter the damaging effects of heat, for example unfolding, aggregation and degradation.

HSP47 is a collagen‐specific chaperone, essential for collagen biosynthesis.

HSP47 binding and release is pH‐dependent, with the involvement of His residues that governs the release.

HSP47 has the potential to be used as diagnostic and therapeutic targets in various diseases and abnormalities.

HSP47 modulators and inhibitors are under extensive investigation due to its therapeutic potential in many types of diseases.
Two novel PRNP truncating mutations broaden the spectrum of prion amyloidosis
Authors: Capellari Sabina , Baiardi Simone , Rinaldi Rita , Bartoletti‐Stella Anna , Graziano Claudio , Piras Silvia , Calandra‐Buonaura Giovanna , D'Angelo Roberto , Terziotti Camilla , Lodi Raffaele , Donadio Vincenzo , Pironi Loris , Cortelli Pietro , Parchi Piero 
Published: April 2018

AbstractTruncating mutations in PRNP have been associated with heterogeneous phenotypes ranging from chronic diarrhea and neuropathy to dementia, either rapidly or slowly progressive. We identified novel PRNP stop‐codon mutations (p.Y163X, p.Y169X) in two Italian kindreds. Disease typically presented in the third or fourth decade with progressive autonomic failure and diarrhea. Moreover, one proband (p.Y163X) developed late cognitive decline, whereas some of his relatives presented with isolated cognitive and psychiatric symptoms. Our results strengthen the link between PRNP truncating mutations and systemic abnormal PrP deposition and support a wider application of PRNP screening to include unsolved cases of familial autonomic neuropathy.
Adaptive formation control of autonomous underwater vehicles with model uncertainties
Authors: Gao Zhenyu , Guo Ge 
Published: April 2018

SummaryThis paper investigates the formation control problem of underactuated autonomous underwater vehicles (AUVs). What makes this problem different and challenging is that, in the AUV model, the mass and damping matrices are not diagonal with nonzero off‐diagonal terms and unknown hydrodynamic damping terms. To address the effect of nonzero off‐diagonal terms, we introduce a coordinate transformation, while the unknown hydrodynamic damping terms are approximated adaptively by a neural network. Then, a leader‐follower control strategy is presented, where each follower needs to track a virtual vehicle. This strategy translates the formation control problem into a set of position (including heading) tracking problems for the following AUVs. The position and heading tracking controller is designed based on Lyapunov direct method and backstepping technique, taking into account the effect of the nonzero off‐diagonal terms in the mass matrix and the unknown hydrodynamic damping terms. Simulations are given to demonstrate the effectiveness of the control method proposed.
Hydrogen‐Bonded Liquid Crystals in Confined Spaces—Toward Photonic Hybrid Materials
Authors: Spengler Matthias , Dong Ronald Y. , Michal Carl A. , Hamad Wadood Y. , MacLachlan Mark J. , Giese Michael 
Published: April 2018

AbstractA series of hybrid materials based on chiral nematic mesoporous organosilica (CNMO) films infiltrated with liquid crystalline hydrogen‐bonded assemblies is prepared and characterized with respect to the mutual manipulation of the photonic properties of the host and the liquid‐crystalline behavior of the guest. Detailed differential scanning calorimetry studies reveal the impact of confinement on the mesomorphic behavior of the liquid crystalline assemblies in the pores of the CNMO films. The photonic properties of the chiral nematic mesoporous host can be controlled by changing the temperature or irradiating the films with UV light. These stimuli‐induced phase transitions are accompanied by changes in the orientational order of the mesogens as revealed by 19F NMR spectroscopy. The combination of confinement and changes in the molecular orientation in a unique hybrid material based on hydrogen‐bonded liquid crystals and a porous host with a chiral nematic mesostructure is an interesting concept for the design of optical sensors, reflectors, or filters.
Engineering Micropatterned Dry Adhesives: From Contact Theory to Handling Applications
Authors: Hensel René , Moh Karsten , Arzt Eduard 
Published: April 2018

AbstractReversible adhesion is the key functionality to grip, place, and release objects nondestructively. Inspired by nature, micropatterned dry adhesives are promising candidates for this purpose and have attracted the attention of research groups worldwide. Their enhanced adhesion compared to nonpatterned surfaces is frequently demonstrated. An important conclusion is that the contact mechanics involved is at least as important as the surface energy and chemistry. In this paper, the roles of the contact geometry and mechanical properties are reviewed. With a focus on applications, the effects of substrate roughness and of temperature variations, and the long‐term performance of micropatterned adhesives are discussed. The paper provides a link between the current, detailed understanding of micropatterned adhesives and emerging applications.
Cobalt Boron Imidazolate Framework Derived Cobalt Nanoparticles Encapsulated in B/N Codoped Nanocarbon as Efficient Bifunctional Electrocatalysts for Overall Water Splitting
Authors: Liu Mei‐Rong , Hong Qin‐Long , Li Qiao‐Hong , Du Yonghua , Zhang Hai‐Xia , Chen Shumei , Zhou Tianhua , Zhang Jian 
Published: April 2018

AbstractThe development of efficient and low‐cost bifunctional electrocatalysts for oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) is highly desirable for electrochemical energy conversion. Herein, this study puts forward a new Co decorated N,B‐codoped interconnected graphitic carbon and carbon nanotube materials (Co/NBC) synthesized by direct carbonization of a cobalt‐based boron imidazolate framework. It is demonstrated that the carbonization temperature can tune the surface structure and component of the resultant materials and optimize the electrochemically active surface area to expose more accessible active sites, effectively boosting the electrocatalytic activity. As a result, the optimized Co/NBC shows superior bifunctional catalytic activity and stability toward OER and HER in 1.0 m KOH solution. Furthermore, the catalyst can serve as both the anode and cathode for water splitting to achieve a current density of 10 mA cm−2 at a cell voltage of 1.68 V. Experimental results and theoretical calculations indicate that the excellent activity of Co/NBC catalyst benefits from the synergistic effect of partial oxidation of metallic cobalt, conductive N,B‐codoped graphitic carbon and carbon nanotube, and the coupled interactions among these components. This work opens a promising avenue toward the exploration of boron imidazolate frameworks as efficient heteroatom‐doped catalysts for electrocatalysis.
Hydrophobic Patterning‐Based 3D Microfluidic Cell Culture Assay
Authors: Han Sewoon , Kim Junghyun , Li Rui , Ma Alice , Kwan Vincent , Luong Kevin , Sohn Lydia L. 
Published: April 2018

AbstractEngineering physiologically relevant in vitro models of human organs remains a fundamental challenge. Despite significant strides made within the field, many promising organ‐on‐a‐chip models fall short in recapitulating cellular interactions with neighboring cell types, surrounding extracellular matrix (ECM), and exposure to soluble cues due, in part, to the formation of artificial structures that obstruct >50% of the surface area of the ECM. Here, a 3D cell culture platform based upon hydrophobic patterning of hydrogels that is capable of precisely generating a 3D ECM within a microfluidic channel with an interaction area >95% is reported. In this study, for demonstrative purposes, type I collagen (COL1), Matrigel (MAT), COL1/MAT mixture, hyaluronic acid, and cell‐laden MAT are formed in the device. Three potential applications are demonstrated, including creating a 3D endothelium model, studying the interstitial migration of cancer cells, and analyzing stem cell differentiation in a 3D environment. The hydrophobic patterned‐based 3D cell culture device provides the ease‐of‐fabrication and flexibility necessary for broad potential applications in organ‐on‐a‐chip platforms.
Contact Lenses for Color Blindness
Authors: Badawy Abdel‐Rahman , Hassan Muhammad Umair , Elsherif Mohamed , Ahmed Zubair , Yetisen Ali K. , Butt Haider 
Published: April 2018

AbstractColor vision deficiency (color blindness) is an inherited genetic ocular disorder. While no cure for this disorder currently exists, several methods can be used to increase the color perception of those affected. One such method is the use of color filtering glasses which are based on Bragg filters. While these glasses are effective, they are high cost, bulky, and incompatible with other vision correction eyeglasses. In this work, a rhodamine derivative is incorporated in commercial contact lenses to filter out the specific wavelength bands (≈545–575 nm) to correct color vision blindness. The biocompatibility assessment of the dyed contact lenses in human corneal fibroblasts and human corneal epithelial cells shows no toxicity and cell viability remains at 99% after 72 h. This study demonstrates the potential of the dyed contact lenses in wavelength filtering and color vision deficiency management.
Bioinspired Stimuli‐Responsive Color‐Changing Systems
Authors: Isapour Golnaz , Lattuada Marco 
Published: April 2018

AbstractStimuli‐responsive colors are a unique characteristic of certain animals, evolved as either a method to hide from enemies and prey or to communicate their presence to rivals or mates. From a material science perspective, the solutions developed by Mother Nature to achieve these effects are a source of inspiration to scientists for decades. Here, an updated overview of the literature on bioinspired stimuli‐responsive color‐changing systems is provided. Starting from natural systems, which are the source of inspiration, a classification of the different solutions proposed is given, based on the stimuli used to trigger the color‐changing effect.
Effect of Various Oxidants on Reaction Mechanisms, Self‐Limiting Natures and Structural Characteristics of Al2O3 Films Grown by Atomic Layer Deposition
Authors: Wang Haoran , Liu Yunfei , Liu Hui , Chen Zheng , Xiong Pengpeng , Xu Xiangchen , Chen Fangyi , Li Kun , Duan Yu 
Published: April 2018

AbstractThe present study investigates the Al2O3 films grown by low‐temperature atomic layer deposition (ALD) with water vapor (H2O), oxygen plasma (O2 plasma), and ozone gas (O3) serving as oxidants. The reaction processes with different oxidants are examined by in situ quadrupole mass spectrometry analysis of the gas phase species, which reveals a possible sequential reaction mechanism of trimethylaluminum and O2 plasma. The coefficient of standard deviation (CSD) of the oscillation frequency change of the in situ quartz crystal microbalance (Δf) to represent the self‐limiting nature of the films is used, and an obvious relationship is observed between the CSD of Δf values and the density of ALD films, which suggests the intrinsic relationship between the structural characteristics and the self‐limiting natures of the ALD processes outside the temperature window. Fourier transform infrared spectroscopy reveals a large number of OCO, CO, and CH bonds remaining in the H2O‐based Al2O3 films, and the smallest concentration of carbon species is found to remain in the O3‐based Al2O3 films, which explains the sources of the different self‐limiting natures and structural characteristics for the different oxidant‐based Al2O3 films.
Self‐Cleaning and Antibacterial Zeolitic Imidazolate Framework Coatings
Authors: Miao Weizhen , Wang Jing , Liu Jindun , Zhang Yatao 
Published: April 2018

AbstractSuperhydrophobic surface with self‐cleaning function like lotus leaf can inhibit bacterial adhesion to some extent; however, it cannot completely avoid bacterial contamination because it could not kill them. In this work, a facile modified sol–gel method to prepare self‐cleaning and antibacterial coating is proposed. Zeolitic imidazolate framework‐8 (ZIF‐8) nanoparticles with good hydrophobic and antibacterial properties are mixed with polyvinylidene fluoride (PVDF) colloidal particle suspension, then, the PVDF/ZIF‐8 nanocomposite is modified with 1H, 1H, 2H, 2H‐perfluorooctyltriethoxysilane (POTS) to prepare PVDF/ZIF‐8/POTS (PZP) coating solution. The resultant PZP nanocomposite coatings have a high contact angle (>160°) and a low sliding angle (<7°). Meanwhile, it is found that the dirt particles accumulated on the surface can be easily washed off by rolling water droplets, demonstrating its superb self‐cleaning function. Notably, the PZP nanocomposite coating shows excellent antibacterial activity against Gram‐negative Escherichia coli. These ZIF‐8‐based nanocomposite coatings with superb self‐cleaning function and high antibacterial activity denote their great potential in a wider range of practical applications.