bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Evolution in Yeasts
Authors: Dujon Bernard 
Published: April 2015

Abstract

Used empirically over millennia for a variety of fermentation processes, the microscopic yeasts representing unicellular forms of modern fungi adapted to a large diversity of habitats have become powerful model organisms to understand eukaryotic genome evolution. Their broad evolutionary range offers unique views on both short‐ and long‐term genomic changes, with the possibility to confront observations with experimental results. Processes of duplications, gene loss and
de novo
gene creation form the bases of genome evolution, along with horizontal acquisitions and an unexpectedly high frequency of interspecies hybridisations. This short review summarises our present knowledge about genome evolution focussing on the subphylum of budding yeasts or
Saccharomycotina
, by far the most extensively studied lineage, without ignoring the multiphyletic origin of yeasts.

Key Concepts

Yeasts represent long‐evolved unicellular forms of modern fungi, adapted to rapid clonal expansions under favourable conditions, not primitive eukaryotes.

Over 1600 yeast species are presently described in the different subphyla of
Ascomycota
and
Basidiomycota
, within which the budding yeasts (
Saccharomycotina)
represent the largest deep‐branching lineage useful for genome evolution studies.

The different genome architectures of well‐circumscribed subgroups of
Saccharomycotina
indicate major evolutionary divides within which ancient events can be inferred.

Important modifications of the role of RNA occurred at the origin of
Saccharomycotina
(massive loss of spliceosomal introns and loss of RNAi control) and continued during their evolution (fixation of 5S RNA gene, change of deciphering mode and significance for synonymous codons).

All yeast genomes exhibit significant levels of redundancy, reflecting small‐scale duplications and, in one lineage, a whole‐genome duplication followed by extensive gene loss.

The balance between gene gains and losses accelerated yeast genome evolution beyond sequence divergence and chromosomal dynamics.

Novel genes regularly appeared during yeast genome evolution, resulting from duplication followed by sequence divergence, horizontal acquisition and
de novo
gene creation.

Interspecies hybridisation is a common phenomenon.

Resolution of hybrid genomes suggests an important role for interspecific exchanges in evolution.
Methodologies for Phylogenetic Inference
Authors: Gil Manuel , Anisimova Maria 
Published: April 2015

AbstractPhylogenetic inference from homologous molecular sequences is key to hypothesis testing and problem solving not only in evolutionary biology but also in a wide variety of other fields – from medicine to ecology. Model‐based phylogenetic methods rely on Markov substitution models to describe the molecular evolution as a stochastic process of character substitution over time on a phylogenetic tree relating the sequences. Model parameters are estimated with standard statistical inference methods, namely, Bayesian and maximum likelihood approaches. A typical phylogenetic analysis first infers a multiple sequence alignment. Given this alignment, a phylogenetic tree is then estimated together with branch lengths and model parameters. Ideally, the alignment and phylogeny should be estimated simultaneously, amongst others to take alignment uncertainty into account.Key ConceptsSequence Alignmentestimates an assignment of homologous molecular characters, that is, nucleotides, amino acids or codons related by common ancestry.Phylogenetic Treeis the hierarchical representation of evolutionary relationships between homologous molecular sequences. The leaves of the tree usually represent the present day sequences, while the internal nodes represent the common ancestors.Model of Molecular Evolutionis the mathematical description of the process of sequence change through time, such as character substitutions, insertions and deletions.Phylogenetic Likelihoodis the probability function of observing the sequence data given the model of molecular evolution and phylogenetic tree.Frequentist Phylogenetic Inferencerelies on optimised phylogenetic likelihood to estimate parameters of a model of molecular evolution and a phylogenetic tree.Bayesian Phylogenetic Inferencerelies on phylogenetic likelihood and a prior probability distribution of parameters to obtain a posterior probability distribution of parameters of a model of molecular evolution and a phylogenetic tree.Branch Supportquantifies the uncertainty of phylogenetic inference by assigning statistical confidence to the inferred partitions (i.e. clades) on a phylogenetic tree.Alignment Uncertaintyquantifies the statistical confidence of sequence alignment, which compounds the uncertainty of phylogenetic inference.
Nuclear Membranes
Authors: Zuela Noam , Gruenbaum Yosef 
Published: April 2015

AbstractThe nuclear envelope (NE) is a double membrane barrier that separates the nuclear content from the cytoplasm. The outer nuclear membrane is contiguous with the endoplasmic reticulum (ER). The perinuclear space or lumen separates the nuclear membranes. Both nuclear membranes contain numerous nuclear envelope transmembrane proteins (NETs), many of them are expressed in a tissue‐ and developmental‐specific manner. These proteins are responsible for the majority of the recently discovered NE functions, which include cell migration, chromatin organisation, cell signalling, gene silencing and transcriptional regulation. NETs are also implicated in diseases, collectively known as nuclear envelopathies, affecting bones, skin, muscles, neurons and systemic disorders. The mechanisms leading to these diseases are largely unknown and are major research goals for future studies. Further studies of the nuclear membranes, their proteins and novel functions will help us expand our understanding of their vast array of cellular functions and gain insights into numerous diseases.Key ConceptsThe nuclear envelope separates the nucleus from the cytoplasm.It is composed of an outer nuclear membrane (ONM), an inner nuclear membrane (INM), nuclear pore complexes (NPCs) and nuclear lamina.The INM is fused to the ONM at the NPC sites.The INM contains a unique set of nuclear envelope transmembrane proteins (NETs), many of which are expressed in a tissue‐specific manner.Many NETs share common protein domains with other NETs including the LEM, SUN and KASH domains.NETs are involved in regulating signalling pathways and gene positioning.Most NETs interact either directly or indirectly with nuclear lamins.SUN‐domain proteins interact in the perinuclear space with KASH‐domain proteins to make the LINC (linker of nucleoplasm and cytoplasm) complexes that physically link the nuclear interior with the cytoplasmic filament networks and organelles.Mutations in several human NETs cause heritable diseases.
Structural Revision and Elucidation of the Biosynthesis of Hypodoratoxide by 13C,13C COSY NMR Spectroscopy
Authors: Barra Lena , Ibrom Kerstin , Dickschat Jeroen S. 
Published: April 2015

AbstractFeeding of (2,3,4,5,6‐13C5)mevalonolactone to the fungus Hypomyces odoratus resulted in a completely labeled sesquiterpene ether. The connectivity of the carbon atoms was easily deduced from a 13C,13C COSY spectrum, revealing a structure that was different from the previously reported structure of hypodoratoxide, even though the reported 13C NMR data matched. A structural revision of hypodoratoxide is thus presented. Its absolute configuration was tentatively assigned from its co‐metabolite cis‐dihydroagarofuran. Its biosynthesis was investigated by feeding of (3‐13C)‐ and (4,6‐13C2)mevalonolactone, which gave insights into the complex rearrangement of the carbon skeleton during terpene cyclization by analysis of the 13C,13C couplings.
Role of processing history on the mechanical and electrical behavior of melt‐compounded polycarbonate‐multiwalled carbon nanotube nanocomposites
Authors: Choong Gabriel Yew Hong , Lew Chun Yee , De Focatiis Davide Stefano Antonio 
Published: April 2015

ABSTRACTThis work investigates the effects of primary compounding temperature and secondary melt processes on the mechanical response and electrical resistivity of polycarbonate filled with 3 wt % multiwalled carbon nanotubes (CNT). Nanocomposites were melt compounded in an industrial setting at a range of temperatures, and subsequently either injection molded or compression molded to produce specimens for the measurement of electrical resistivity, surface hardness, and uniaxial tensile properties. Secondary melt processing was found to be the dominant process in determining the final properties. The effects observed have been attributed to structural arrangements of the CNT network as suggested by morphological evidence of optical microscopy and resistivity measurements. Properties were found to be relatively insensitive to compounding temperature. The measured elastic moduli were consistent with existing micromechanical models. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42277.
Economic Structure, Social Risks and the Challenges to Social Policy in Macau, China
Authors: Li Bingqin , Zeng Zhonglu 
Published: April 2015

AbstractWelfare state is often perceived as a response to help people coping with shocks caused by economic down turn. However, as argued by Hamnett, welfare state can directly assist economic restructuring. Thus, social policies can be responses to unsatisfied social needs or be proactive measures to push for economic changes.Macau is in a somewhat special position in that policy‐makers are aware that the economy has been excessively dependent on the gaming industry. The government prevent it from being hit by recess through economic restructuring.In this paper, we examine the current social spending pattern and the nature of the social security system in Macau and establish that social policy in Macau is largely reactive. To achieve economic restructuring, there needs to be more proactive measures to facilitate human development and more stress on social investment.
Topiramate: a review of analytical approaches for biological matrices
Authors: Pinto Eduardo Costa , Dolzan Maressa Danielli , Cabral Lucio Mendes , Armstrong Daniel W. , de Sousa Valéria Pereira 
Published: April 2015

AbstractTopiramate is an anticonvulsant drug and it has been used worldwide for a wide range of applications. It is mainly indicated for the treatment of partial and generalized seizures, including Lennox Gastant Syndrome and generalized tonic–clonic seizures, and prophylactic treatment of migraine. Different analytical approaches by high‐performance liquid chromatography have been described to analyze topiramate because of its lack of chromophore groups, including derivatization with UV‐absorbing moieties, derivatization with fluorescent moieties, refractive index detection, conductivity detection, chemiluminescent nitrogen detection, evaporative light scattering detection and MS detection. In addition, some methods for determination of topiramate by capillary electrophoresis have been published as well as by gas chromatography. Thus, it is beneficial to evaluate and compare these papers before selecting the most suitable method/detector to analyze this drug. This systematic review provides a description of the main analytical methods available for the analysis of topiramate in biological matrices. Each of these methods is briefly discussed considering the detector used with HPLC. HPLC coupled with MS is the main technique used for topiramate analysis in biological matrices, mainly in the electrospray ionization‐negative mode. Copyright © 2015 John Wiley & Sons, Ltd.
Determination of trimethylamine‐N‐oxide in combination with l‐carnitine and γ‐butyrobetaine in human plasma by UPLC/MS/MS
Authors: Grinberga Solveiga , Dambrova Maija , Latkovskis Gustavs , Strele Ieva , Konrade Ilze , Hartmane Dace , Sevostjanovs Eduards , Liepinsh Edgars , Pugovics Osvalds 
Published: April 2015

AbstractAn ultra‐high‐performance liquid chromatography–mass spectrometry (UPLC/MS/MS) method was developed and validated for the quantification of trimethylamine‐N‐oxide (TMAO) simultaneously with TMAO‐related molecules l‐carnitine and γ‐butyrobetaine (GBB) in human blood plasma. The separation of analytes was achieved using a Hydrophilic interaction liquid chromatography (HILIC)‐type column with ammonium acetate–acetonitrile as the mobile phase. TMAO determination was validated according to valid US Food and Drug Administration guidelines. The developed method was successfully applied to plasma samples from healthy volunteers. Copyright © 2015 John Wiley & Sons, Ltd.
Tungsten Carbide and CNT–Graphene‐Supported Pd Electrocatalyst toward Electrooxidation of Hydrogen
Authors: Han Suenghoon , Youn Duck Hyun , Lee Min Hee , Lee Jae Sung 
Published: April 2015

AbstractDevelopment of platinum‐free catalysts is urgently needed to make fuel cells a competitive technology for power generation in various fields. Here we report that combination of palladium and tungsten carbides supported on carbon nanotubes (CNT) graphene (GR) composite exhibits high activity for electrochemical hydrogen oxidation reaction. In the cyclic voltammetry, the electrochemical active surface area of Pd/WC/CNT–GR is much larger than that of other synthesized catalysts and even commercial Pt/C catalyst. In single cell operation, Pd/WC/CNT–GR shows 65 % of the maximum power density of the state‐of‐the‐art Pt/C catalyst and loses only 5 % of maximum power density after 50 h. Beneficial roles of WC and CNT–GR are discussed for the improved performance of palladium catalysts.
Off‐Stoichiometry in Alluaudite‐Type Sodium Iron Sulfate Na2+2xFe2−x(SO4)3 as an Advanced Sodium Battery Cathode Material
Authors: Oyama Gosuke , Nishimura Shin‐ichi , Suzuki Yuya , Okubo Masashi , Yamada Atsuo 
Published: April 2015

AbstractAn alluaudite‐type sodium iron sulfate has recently been discovered as a 3.8 V cathode material for low‐cost, high‐power, and efficient sodium‐ion batteries. To optimize the composition of the alluaudite phase and to explore further compounds, we have carefully surveyed the Na2SO4‐FeSO4 binary system. Solid‐state reactions at a moderate temperature of 623 K produce two stable phases: 1) vanthoffite‐structured Na6Fe(SO4)4 and 2) alluaudite‐type Na2+2xFe2−x(SO4)3 with a certain non‐stoichiometry. The possible compositional and structural flexibilities demonstrated in this work inspire further improvement of the alluaudite‐type sodium metal sulfates for advanced sodium‐ion batteries.
Hydroboration of Graphene Oxide: Towards Stoichiometric Graphol and Hydroxygraphane
Authors: Poh Hwee Ling , Sofer Zdeněk , Šimek Petr , Tomandl Ivo , Pumera Martin 
Published: April 2015

AbstractCovalently functionalized graphene materials with well‐defined stoichiometric composition are of a very high importance in the research of 2D carbon material family due to their well‐defined properties. Unfortunately, most of the contemporary graphene‐functionalized materials do not have this kind of defined composition and, usually, the amount of heteroatoms bonded to graphene framework is in the range of 1–10 at. %. Herein, we show that by a well‐established hydroboration reaction chain, which introduces BH2 groups into the graphene oxide structure, followed by H2O2 or CF3COOH treatment as source of OH or H, we can obtain highly hydroxylated compounds of precisely defined composition with a general formula (C1O0.78H0.75)n, which we named graphol and highly hydroxylated graphane (C1(OH)0.51H0.14)n, respectively. These highly functionalized materials with an accurately defined composition are highly important for the field of graphene derivatives. The enhanced electrochemical performance towards important biomarkers as well as hydrogen evolution reaction is demonstrated.
Creating Coordination‐Based Cavities in a Multiresponsive Supramolecular Gel
Authors: Wei Shi‐Chao , Pan Mei , Fan Yuan‐Zhong , Liu Haoliang , Zhang Jianyong , Su Cheng‐Yong 
Published: April 2015

AbstractCreating cavities in varying levels, from molecular containers to macroscopic materials of porosity, have long been motivated for biomimetic or practical applications. Herein, we report an assembly approach to multiresponsive supramolecular gels by integrating photochromic metal–organic cages as predefined building units into the supramolecular gel skeleton, providing a new approach to create cavities in gels. Formation of discrete O‐Pd2L4 cages is driven by coordination between Pd2+ and a photochromic dithienylethene bispyridine ligand (O‐PyFDTE). In the presence of suitable solvents (DMSO or MeCN/DMSO), the O‐Pd2L4 cage molecules aggregate to form nanoparticles, which are further interconnected through supramolecular interactions to form a three‐dimensional (3D) gel matrix to trap a large amount of solvent molecules. Light‐induced phase and structural transformations readily occur owing to the reversible photochromic open‐ring/closed‐ring isomeric conversion of the cage units upon UV/visible light radiation. Furthermore, such Pd2L4 cage‐based gels show multiple reversible gel–solution transitions when thermal‐, photo‐, or mechanical stimuli are applied. Such supramolecular gels consisting of porous molecules may be developed as a new type of porous materials with different features from porous solids.
Langmuir and Langmuir–Blodgett Films from Amphiphilic Pillar[5]arene‐Containing [2]Rotaxanes
Authors: Trinh Thi Minh Nguyet , Nierengarten Iwona , Holler Michel , Gallani Jean‐Louis , Nierengarten Jean‐François 
Published: April 2015

AbstractAmphiphilic pillar[5]arene‐containing [2]rotaxanes have been prepared and fully characterized. In the particular case of the [2]rotaxane incorporating a 1,4‐diethoxypillar[5]arene subunit, the structure of the compound was confirmed by X‐ray crystal structure analysis. Owing to a good hydrophilic/hydrophobic balance, stable Langmuir films have been obtained for these rotaxanes and the size of the peripheral alkyl chains on the pillar[5]arene subunit has a dramatic influence on the reversibility during compression–decompression cycles. Indeed, when these are small enough, molecular reorganization of the rotaxane by gliding motions are capable of preventing strong π–π interactions between neighboring macrocycles in the thin film.
Frontline rituximab monotherapy induction versus a watch and wait approach for asymptomatic advanced‐stage follicular lymphoma: A cost‐effectiveness analysis
Authors: Prica Anca , Chan Kelvin , Cheung Matthew 
Published: April 2015

BACKGROUNDA watch and wait (WW) strategy is the standard of care for patients with asymptomatic advanced‐stage follicular lymphoma. Recent data have demonstrated an improvement in the time to progression with rituximab induction (RI) with or without rituximab maintenance (RM) in comparison with a WW strategy wait in such patients. It remains unclear whether this is a cost‐effective strategy.METHODSA Markov decision analysis model was developed to compare the clinical outcomes, costs, and cost‐effectiveness of RI (4 weekly doses) plus RM (12 doses every 2 months), RI (4 weekly doses), and a WW strategy for patients newly diagnosed with low‐burden, asymptomatic advanced‐stage follicular lymphoma over a lifetime horizon. Baseline probabilities and utilities were derived from a systematic review of published studies, and they were evaluated on a 6‐month cycle. A Canadian public health payer's perspective was adopted, and costs were presented in 2012 Canadian dollars.RESULTSRI was the cheapest strategy. It was less costly at $59,953 versus $67,489 for the RM arm and $75,895 for the WW arm. It was also associated with a slightly lower quality‐adjusted life expectancy at 6.16 quality‐adjusted life years (QALYs) versus 6.28 QALYs for the RM strategy but was superior to WW (5.71 QALYs). In sensitivity analyses of key variables, this effectiveness was sensitive to the probability of first and second progression in the RI arm, and this indicated relatively neutral effectiveness between the 2 rituximab arms.CONCLUSIONSRI without maintenance for asymptomatic advanced‐stage follicular lymphoma is the preferred strategy: it minimizes costs per patient over a lifetime horizon. Cancer 2015;121:2637–2645. © 2015 American Cancer Society.
Organization and detailed parcellation of human hippocampal head and body regions based on a combined analysis of Cyto‐ and chemoarchitecture
Authors: Ding Song‐Lin , Van Hoesen Gary W. 
Published: April 2015

ABSTRACTThe hippocampal formation (HF) is one of the hottest regions in neuroscience because it is critical to learning, memory, and cognition, while being vulnerable to many neurological and mental disorders. With increasing high‐resolution imaging techniques, many scientists have started to use distinct landmarks along the anterior–posterior axis of HF to allow segmentation into individual subfields in order to identify specific functions in both normal and diseased conditions. These studies urgently call for more reliable and accurate segmentation of the HF subfields DG, CA3, CA2, CA1, prosubiculum, subiculum, presubiculum, and parasubiculum. Unfortunately, very limited data are available on detailed parcellation of the HF subfields, especially in the complex, curved hippocampal head region. In this study we revealed detailed organization and parcellation of all subfields of the hippocampal head and body regions on the base of a combined analysis of multiple cyto‐ and chemoarchitectural stains and dense sequential section sampling. We also correlated these subfields to macro‐anatomical landmarks, which are visible on magnetic resonance imaging (MRI) scans. Furthermore, we created three versions of the detailed anatomic atlas for the hippocampal head region to account for brains with four, three, or two hippocampal digitations. These results will provide a fundamental basis for understanding the organization, parcellation, and anterior–posterior difference of human HF, facilitating accurate segmentation and measurement of HF subfields in the human brain on MRI scans. J. Comp. Neurol. 523:2233–2253, 2015. © 2015 Wiley Periodicals, Inc.
Is TiO2(B) the Future of Titanium‐Based Battery Materials?
Authors: Fehse Marcus , Ventosa Edgar 
Published: April 2015

AbstractTitania materials are gaining interest as negative electrode materials in Li‐ion batteries due to their high power capability and enhanced safety. Today, Li4Ti5O12 is the material of choice for commercial batteries, but other titania materials, namely polymorphs of TiO2, are being explored because of their similar electrochemical behavior and higher theoretical specific charge capacity. In practice, the specific charge capacity of TiO2 remains far below the theoretical value of 336 mA h g−1 due to poor electrical conductivity and slow Li‐ion mobility. This Minireview describes the main strategies developed to overcome the limitations of TiO2 polymorphs. Special attention is given to TiO2(B) since its outstanding Li‐ion mobility, the highest mobility among all TiO2 polymorphs, has led to superior electrochemical performance. Finally, the potential of titania materials in sodium‐ion batteries is also discussed.