bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Analysis of Free-Text Alcohol Use Documentation in the Electronic Health Record
Authors: Garcia-Webb M. , Chen ES 
Published: April 2014

SummaryBackground: Alcohol use is a significant part of a patient’s history, but details about consumption are not always documented. Electronic Health Record (EHR) systems have the potential to improve assessment of alcohol use and misuse; however, a challenge is that critical information may be documented primarily in free-text rather than in a structured and standardized format, thereby limiting its use.Objective: To characterize the use and contents of free-text documentation for alcohol use in the social history module of an EHR.Methods: This study involved a retrospective analysis of 500 alcohol use entries that include structured fields as well as a free-text comment field. Two coding schemes were developed and used to analyze these entries for: (1) quantifying the reasons for using free-text comments and (2) categorizing information in the free-text into separate elements. In addition, for entries indicating possible alcohol misuse, a preliminary review of other structured parts of the EHR was conducted to determine if this was also documented elsewhere.Results: The top three reasons for using free-text were limited ability to describe alcohol use frequency (75%), amount (22%), and status (18%) with available structured fields. Within the free-text, descriptions of frequency were most common (79%) using words or phrases conveying occasional (61%), daily (13%), or weekly (12%) use. Of the 36 cases suggesting alcohol misuse, 44% had mention of alcohol problems in the problem list or past medical history.Conclusions: Based on the early findings, implications for improving the structured collection and use of alcohol use information in the EHR are provided in four areas: (1) system enhancements, (2) user training, (3) decision support, and (4) standards. Next steps include examining how alcohol use is documented in other parts of the EHR (e.g., clinical notes) and how documentation practices vary based on patient, provider, and clinic characteristics.Citation: Chen ES, M. Garcia-Webb M. An analysis of free-text alcohol use documentation in the electronic health record: Early findings and implications. Appl Clin Inf 2014; 5: 402–415 http://dx.doi.org/10.4338/ACI-2013-12-RA-0101
Messenger RNA- Versus Retrovirus-Based Induced Pluripotent Stem Cell Reprogramming Strategies: Analysis of Genomic Integrity
Authors: Steichen Clara , Luce Eléanor , Maluenda Jérôme , Tosca Lucie , Moreno-Gimeno Inmaculada , Desterke Christophe , Dianat Noushin , Goulinet-Mainot Sylvie , Awan-Toor Sarah , Burks Deborah , Marie Joëlle , Weber Anne , Tachdjian Gérard , Melki Judith , Dubart-Kupperschmitt Anne 
Published: April 2014

Abstract

The use of synthetic messenger RNAs to generate human induced pluripotent stem cells (iPSCs) is particularly appealing for potential regenerative medicine applications, because it overcomes the common drawbacks of DNA-based or virus-based reprogramming strategies, including transgene integration in particular. We compared the genomic integrity of mRNA-derived iPSCs with that of retrovirus-derived iPSCs generated in strictly comparable conditions, by single-nucleotide polymorphism (SNP) and copy number variation (CNV) analyses. We showed that mRNA-derived iPSCs do not differ significantly from the parental fibroblasts in SNP analysis, whereas retrovirus-derived iPSCs do. We found that the number of CNVs seemed independent of the reprogramming method, instead appearing to be clone-dependent. Furthermore, differentiation studies indicated that mRNA-derived iPSCs differentiated efficiently into hepatoblasts and that these cells did not load additional CNVs during differentiation. The integration-free hepatoblasts that were generated constitute a new tool for the study of diseased hepatocytes derived from patients' iPSCs and their use in the context of stem cell-derived hepatocyte transplantation. Our findings also highlight the need to conduct careful studies on genome integrity for the selection of iPSC lines before using them for further applications.
Reconsidering Ampere’s Double Layer Representation for Magnetic Field, Evaluation in a NDE Dection of a zero volume crack
Authors: Poloujadoff M. , Bettaieb L. , Kokabi H. 
Published: April 2014

The paper has two different objectives. The first one is to show that Ampere’s double layer method, which is equivalent to one of the Maxwell equations, leads to the integration of a simple closed form expression, thus avoiding the need to solve complicated partial differential equations. The second aim is to study the case of a zero volume defect in a NDE problem by a perturbation method and the introduction of a double layer. The combination of these two techniques leads to a very fast solution of the problem. A practical example including
Estado de Conservação da ictiofauna do rio Guandu, afluente do baixo rio Doce, ES
Authors: Silva Adriana Maria , Giongo Patricia , Belei Frederico , Sampaio Wagner Martins Santana 
Published: April 2014

<p class="Standard">A bacia do rio Doce possui uma parcela significativa da biodiversidade de peixes das bacias costeiras do Brasil. O rio Guandu é um dos principais tributários do baixo rio Doce e até hoje são carentes as informações sobre a ictiofauna nessa bacia. O presente trabalho teve por objetivo, inventariar e avaliar a ictiofauna do rio Guandu, tributário do baixo rio Doce. Foram capturados 202 indivíduos, distribuídos em seis ordens, 16 famílias e 29 espécies. Dentre as espécies encontradas, oito delas são exóticas e uma delas pode estar sob ameaça de extinção na região. Os resultados contribuem para o conhecimento da ictiofauna do rio Doce, na porção Baixo Guandu. Estudos científicos mais aprofundados na região são de extrema importância para se traçar estratégias de conservação adequadas.</p><p class="Standard"> </p><p class="Standard">DOI: 10.7902/ecb.v4i1.56</p>
The development of magmatism along the Cameroon Volcanic Line: Evidence from seismicity and seismic anisotropy
Authors: De Plaen R. S. M. , Bastow I. D. , Chambers E. L. , Keir D. , Gallacher R. J. , Keane J. 
Published: April 2014

AbstractThe Cameroon Volcanic Line (CVL) straddles the continent‐ocean boundary in West Africa but exhibits no clear age progression. This renders it difficult to explain by traditional plume/plate motion hypotheses; thus, there remains no consensus on the processes responsible for its development. To understand better the nature of asthenospheric flow beneath the CVL, and the effects of hotspot tectonism on the overlying lithosphere, we analyze mantle seismic anisotropy and seismicity. Cameroon is relatively aseismic compared to hotspots elsewhere, with little evidence for magmatism‐related crustal deformation away from Mount Cameroon, which last erupted in 2000. Low crustal Vp/Vs ratios (∼1.74) and a lack of evidence for seismically anisotropic aligned melt within the lithosphere both point toward a poorly developed magmatic plumbing system beneath the CVL. Null SKS splitting observations dominate the western continental portion of the CVL; elsewhere, anisotropic fast polarization directions parallel the strike of the Precambrian Central African Shear Zone (CASZ). The nulls may imply that the convecting upper mantle beneath the CVL is isotropic, or characterized by a vertically oriented olivine lattice preferred orientation fabric, perhaps due to a mantle plume or the upward limb of a small‐scale convection cell. Precambrian CASZ fossil lithospheric fabrics along the CVL may have been thermomechanically eroded during Gondwana breakup ∼130 Ma, with an isotropic lower lithosphere subsequently reforming due to cooling of the slow‐moving African plate. Small‐scale lithospheric delamination during the 30 Ma recent development of the line may also have contributed to the erosion of the CASZ lithospheric fossil anisotropy, at the same time as generating the low‐volume alkaline basaltic volcanism along the CVL.
Histones: Gene Organisation and Post‐translational Modification
Authors: Doenecke Detlef 
Published: April 2014

Abstract

Histones are highly conserved basic proteins that form the major part of the protein moiety of eukaryotic chromosomes. Together with
deoxyribonucleic acid (DNA)
, they organise the repeat unit of chromatin, the nucleosome, which consists of a deoxyribonucleoprotein core particle and linker DNA connecting these core units. The core particle is composed of 147 nucleotide pairs of DNA and two copies of each of the four core histones H2A, H2B, H3 and H4. The DNA linking core particles is associated with one copy of a fifth histone type termed H1. The basal organisation of chromatin as a histone–DNA complex implies that histones functionally participate in the regulation of chromatin‐bound processes, such as transcription, DNA repair or DNA replication. Post‐translational modification of histone amino acid side chains or replacement of canonical histones by nonallelic variants and recognition of such modified sites by regulatory factors are key processes in modulating the functional organisation of chromatin.

Key Concepts:

The histone family of basic chromosome consists of five protein classes that organise together with DNA the nucleosome, the basic chromatin unit. Two copies of each of the four histones H2A, H2B, H3 and H4 form together with DNA the nucleosome core particle; linker DNA and histone H1 complete the nucleosome as the chromosomal repeat unit.

The five canonical histones are extremely conserved proteins, and the nucleosome structure is essentially the same from unicellular to vertebrate species.

Nonallelic variants of four of the five histones (the exception is H4) can replace the canonical isoforms, thereby mediating dynamic changes of chromatin structure and function.

Histones are post‐translationally modified by, for example, acetylation of lysine residues, methylation of lysine or arginine residues and phosphorylation of hydroxyl groups in side chains of serine, threonine or tyrosine. Such modified side chains (and combinations thereof) provide interaction sites for binding of factors involved in chromatin‐bound processes.

Histone H1 is also termed linker histones, because it interacts with the DNA linking nucleosome core particles. Yeast has just one type of H1‐like histones, whereas mammals have several nonallelic H1 variants. H1 is involved in the formation of higher order chromatin structures above the level of arrays of nucleosomes.
Peptide Mapping
Authors: Chen Gang 
Published: April 2014

Abstract

Proteomics is the large‐scale study of proteins, particularly their structures and functions. One of its most important tasks is to develop efficient and rapid approaches to identify various proteins. Peptide mapping is a commonly used strategy in protein identification. It involves the chemical or enzymatic treatment of proteins resulting in the formation of peptide fragments followed by separation and identification of the resultant fragments. Proteins are usually digested into peptides that are subsequently identified by mass spectrometry to obtain peptide mass fingerprints. Peptide mapping is an important technique for investigating protein primary structures and determining surface‐exposed sites or epitopes within proteins. It can be adapted to obtain internal protein sequences. Prior to identification, the proteins and peptides usually need to be separated by a variety of separation approaches, such as gel electrophoresis, liquid chromatograph, capillary electrophoresis, etc.

Key Concepts:

Sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS‐PAGE) is a commonly used approach for the separation of proteins and peptides.

Two‐dimensional gel electrophoresis (2‐DE) can separate a great many of proteins in two separation modes.

Proteolysis is a process where proteins are broken down into smaller peptides by proteases.

Proteases are enzymes that conduct proteolysis by hydrolysis of some specific peptide bonds.

Mass spectroscopy (MS) is an analytical technique to separate the components of a sample by their mass‐to‐charge ratios.

Peptide mass fingerprinting is the most popular analytical application of matrix‐assisted laser desorption/ionisation‐time of flight MS (MALDI‐TOF MS) and electrospray MS.

Electrospray became widely used as ionisation source for the MS analysis of proteins and peptides.

Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases.

Sequence coverage is the percentage of the database protein sequence covered by matching peptides.

Proteolytic microchip bioreactors are microdevices in which proteases are immobilised for efficient peptide mapping.
Protein Quaternary Structure: Symmetry Patterns
Authors: Stenkamp Ronald E 
Published: April 2014

Abstract

Protein molecules can assemble into larger, multisubunit oligomers that possess unique quaternary structures and biological properties. The properties of the oligomeric protein can be quite different from those of the individual subunits. The noncovalent protein–protein interactions giving rise to oligomers often result in symmetric complexes containing identical monomers in identical environments. The symmetry properties of these complexes are described, in particular with respect to the types of subunit–subunit interactions giving rise to the oligomers. Because the symmetry of the macromolecular assemblies is based on the symmetric interactions between the subunits, understanding the symmetry provides further insight into the functioning of the oligomers. Specific examples presented include: dimers and heptamers with cyclic symmetry, tetrameric and octameric oligomers with dihedral symmetry, multienzyme complexes with tetrahedral and dodecahedral structures, and pilin helical oligomers.

Key Concepts:

Many proteins form large complexes made up of multiple copies of identical subunits.

Analysis of the quaternary structures of protein complexes in terms of symmetry can determine how equivalent the subunits are, in function as well as structure.

Subunits in dimeric proteins related by twofold rotation axes interact using the same functional groups on each subunit, that is, isologously.

Protein complexes showing cyclic and helical symmetries have subunits that do not interact with the same functional groups on each subunit; they interact heterologously.

Large protein complexes can take on the symmetries shown by the Platonic solids.

Helical symmetry is found in large rod‐like structures such as pili.

Protein complexes showing point group symmetry are constructed using all of the available subunit–subunit binding surfaces and are ‘closed’ to addition of further subunits.

Helical structures containing identical subunits have unoccupied binding surfaces at the termini of the helix that can bind additional subunits and grow into unlimited polymers.
Pollination by Animals
Authors: Waser Nickolas M , Forrest Jessica RK 
Published: April 2014

Abstract

Most species of flowering plants depend on animals, such as bees, to move their pollen and enable sexual reproduction, and most animal pollinators, in turn, depend on flowers as sources of food or other materials. Although the interaction is mutualistic, benefitting both plants and animals, it is not cooperation, because the best ‘interests’ of the two partners differ. Animal pollination is critical for crop and natural ecosystems and plays central roles in plant ecology and evolution. In particular, selection imposed by animal pollinators is thought to have driven the evolution of much of the floral diversity we see today. Most plant–pollinator relationships are not specialised, one‐to‐one mutualisms – a fact that should make pollination networks somewhat resilient to species extinctions. Nevertheless, recent pollinator declines have given rise to concerns about loss of pollination services to crops and wild plant populations.

Key Concepts:

Most flowering plant species depend on animals to transfer pollen from anthers (the male organs of flowers) to stigmas (the female organs) in order to produce seeds.

Pollinating animals visit flowers to obtain resources: usually nectar or pollen, but sometimes oils, fragrances, resins or oviposition sites.

The divergent ‘interests’ of plants and pollinators in the interaction explain such phenomena as unrewarding flowers and nectar‐robbing insects.

Recent pollinator declines are causing concern about the maintenance of pollination services to crops and wild plants.

Pollination webs illustrating the linkages among plants and pollinators within a community show that reciprocally specialised interactions are rare.

Numerous studies show that pollinators can exert selection on plant traits, but selection by plants on pollinator traits has been harder to demonstrate.

Pollinators play an important role in the process of reproductive isolation and speciation in flowering plants.
FASTA
Search Programs
Authors: Pearson William R 
Published: April 2014

Abstract

The FASTA programs search protein and
deoxyribonucleic acid (DNA)
databases for sequences with statistically significant similarity. The programs compare proteins, DNA and short peptides and oligonucleotides, and run on most popular computers. FASTA and BLAST both seek to identify homologous proteins or DNA sequences. BLAST is faster, but FASTA is more flexible, providing both rigorous (SSEARCH, LALIGN, GGSEARCH and GLSEARCH) and heuristic (FASTA, FASTX/Y, TFASTX/Y and FASTS/M/F) algorithms, a wider range of scoring matrices and different approaches for estimating statistical significance. In addition, the FASTA programs offer options to search a small, representative database, but then the report results from a larger sequence set linked to the initial significant hits. The FASTA programs can also annotate the alignments to include the conservation state of aligned functional residues, such as active sites, and subalignment scores associated with domain boundaries. The FASTA programs provide flexible and rigorous alternatives to BLAST for protein, translated‐DNA and DNA alignment.

Key Concepts:

The FASTA program uses a heuristic (approximate) strategy for finding similar sequences, but the FASTA package includes SSEARCH and GGSEARCH, which provide rigorous algorithms.

Homologs can be identified because they share excess (statistically significant) sequence similarity.

E()‐values (expect‐values) report the significance (expectation) of a sequence similarity score.

Sequence alignments are more accurate when the scoring matrix matches the evolutionary distance of the aligned sequences.

The FASTA programs can align against sequences not included in the initial search using library expansion.

The FASTA programs can use external annotations to modify aligned sequences and to partition similarity scores.
High‐throughput ‘On Chip’ Protein and Nucleic Acid Transfection
Authors: Herrmann Frank , Isalan Mark 
Published: April 2014

Abstract

Transfection describes the nonviral introduction of exogenous molecules into eukaryotic cells. Numerous transfection methods have been developed to transfer nucleic acids, proteins and other macromolecules across the plasma membrane efficiently. These include physical methods, such as electroporation, magnetofection and microinjection, as well as a chemical or biological carrier‐mediated methods. Chemical transfection reagents such as cationic lipids or polymers are widely used, either alone or in combination with scaffolds. Biological methods include delivery with cell‐penetrating protein domain fusions such as trans‐activator of transcription protein from human immunodeficiency virus, VP22 or Antennapedia peptides. Certain proteins such as zinc‐finger nucleases, which are used for targeted genome modification, even appear to have intrinsic cell‐penetrating properties. To facilitate large‐scale genomic and proteomic studies there is an increasing need for automated high‐throughput transfection platforms. Several such platforms have been developed, including multiwell plates, transfection microarrays and microfluidic chip formats. Overall, the different advantages and applications of these diverse methods to deliver cargo into cells are discussed.

Key Concepts:

Cell membranes are a barrier to the delivery of proteins and nucleic acids into cells.

Mechanical, chemical and biological methods of transfection have been developed to cross the cell membrane barrier.

Positively charged molecules, such as cationic lipids, polymers or peptides, can help to penetrate the negatively‐charged surface of cell membranes.

Various automatable high‐throughput technologies have been developed, including transfection microarrays.

Reverse transfection is a scalable, potentially high‐throughput process where cells are added to transfectable molecules, preimmobilised on a scaffold.
Genetics of Nicotine Addiction
Authors: Bloom A Joseph , Goate Alison M 
Published: April 2014

AbstractDiseases associated with addiction to nicotine, the key reinforcing constituent of tobacco, remain the largest cause of preventable death worldwide. Although twin studies indicate a large genetic contribution to the variation in smoking‐related behaviours, the polymorphisms underlying this heritability remain largely unidentified. Candidate gene studies have investigated several pathways, but thus far only those few genetic loci identified in unbiased genome‐wide association studies have been consistently replicated; these are the direct targets of nicotine in the nervous system, the nicotinic acetylcholine receptor subunit genesCHRNA5–CHRNA3–CHRNB4and the primary nicotine metabolism geneCYP2A6. These variants may differ in their influences regarding different aspects of smoking behaviour, and their frequencies vary widely among different ethnic populations. Use of more‐targeted phenotypes including biomarkers of smoke exposure such as cotinine, nicotine's major metabolite, and exhaled carbon monoxide, may provide the key to detecting further genetic correlates of nicotine dependence and related diseases.Key Concepts:Variation in nicotine addiction‐related traits have large genetic components.Genetic studies of nicotine addiction seek to identify drug targets for smoking cessation treatment and to improve treatments using genotype‐based personalised medicine.Candidate gene studies have focussed on the nicotinic acetylcholine receptors and genes in the nicotine metabolism, dopaminergic, serotonergic, GABAergic, and opioid pathways, but few associations have been convincingly replicated.Unbiased genome‐wide studies have identified very few consistent genetic associations with smoking‐related phenotypes.A functional variant in theCHRNA5–CHRNA3–CHRNB4gene cluster is robustly associated with multiple smoking behaviours and related disease risk.Functional variation in theCYP2A6nicotine metabolism gene is associated with cigarette consumption and related disease risk.Genetic factors contributing to nicotine addiction vary by ethnic population.Genotype–environment and genotype–treatment interactions are important factors determining smoking initiation, dependence and cessation outcomes.Use of biomarkers and other endophenotypes may provide greater power to identify genetic correlates of nicotine dependence.