bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative semiempirical, ab initio, and DFT study on the thermodynamic properties of linear and branched PFSA/Fs, PFCA/Fs, and perhydroalkyl sulfonic acids, alkanes, and alcohols
Authors: Rayne Sierra , Forest Kaya 
Published: July 2019

AbstractA systematic and comprehensive semiempirical, Hartree-Fock (HF) ab initio, and B3LYP density functional theory (DFT) study was conducted on the relative thermodynamic properties of various linear and branched perfluorinated and perhydrogenated alkyl compounds. The semiempirical AM1, PM3, and PM6 methods all consistently and accurately predict that branched alkyl compounds will generally be more thermodynamically stable than their linear counterparts. In contrast, HF and B3LYP calculations with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets predict that linear isomers will be more stable than branched analogs. These different linear versus branched perfluoroalkyl/perhydroalkyl thermodynamic property trends between semiempirical and ab initio/DFT methods were evident in both gas and aqueous phase calculations. Comparison of experimentally determined thermodynamic properties for several classes of linear and branched alkanes and alcohols with values calculated at the PM6 and B3LYP/6-311++G(d,p) levels of theory supported the well known findings that such DFT and HF approaches incorrectly predict branched alkyl compounds will be less thermodynamically stable than linear isomers. Calculations at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) and M05-2X/6-311++G(d,p) levels of theory on a representative subset of the linear and branched perfluorinated compounds supported the thermodynamic conclusions from the PM6 method. Strong agreement between PM6 estimated thermodynamic properties and available experimental data supports use of this computational method for accurately calculating the well established higher thermodynamic stability of branched alkyl compounds. Branched perfluoroalkyl compounds are thus expected to be more thermodynamically stable than their linear analogs.
PSA Dynamics traditionally evaluated with an inadequate formula
Authors: Gerber Hans-Jürg 
Published: July 2019

AbstractThe PSA doubling time is usually calculated from measured PSA values with an inadequate formula that tacitly assumes the absence of that process, which it is supposed to reveal. We present a modified calculational procedure which is optimized to unveil a weak second exponential process in the presence of a strong first one, using early screening data. The notion of Break Even Time (BET) indicates the stages of the processes.
The NCBO OBOF to OWL Mapping
Authors: Moreira Dilvan , Mungall Christopher , Shah Nigam , Aitken Stuart , Richter John-Day , Redmond Timothy , Musen Mark 
Published: July 2019

AbstractTwo of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL. Availability: This mapping functionality can be embedded into OBO-Edit and Protégé-OWL ontology editors. This software is available at: http://bioontology.org/wiki/index.php/OboInOwl:Main_Page
High energy-charged cell factory for heterologous protein synthesis
Authors: Kim Pil , Kim Hye Jung , Kwon Yeong Deok , Lee Sang Yup 
Published: July 2019

AbstractOverexpression of gluconeogenic phosphoenolpyruvate carboxykinase (PCK) under glycolytic conditions enables Escherichia coli to maintain a greater intracellular ATP concentration and, consequently, to up-regulate genes for amino acid and nucleotide biosynthesis. To investigate the effect of a high intracellular ATP concentration on heterologous protein synthesis, we studied the expression of a foreign gene product, enhanced green fluorescence protein (eGFP), under control of the T7 promoter in E. coli BL21(DE3) strain overexpressing PCK. This strain was able to maintain twice as much intracellular ATP and to express two times more foreign protein than the control strain. These results indicate that a high energy-charged cell can be beneficial as a protein-synthesizing cell factory. The potential uses of such a cell factory are discussed.
Rsp5 promotes Gene Activation mediated by 9aaTAD Transcription Factors Oaf1 and Gal4
Authors: Lipp Joachim , Koranda Manfred , Piskacek Martin 
Published: July 2019

AbstractNine-amino-acid transactivation domain, 9aaTAD, defines a large superfamily of yeast and mammals transcription factors. The transactivation of the 9aaTAD has been addressed to multiple general co-activators TAF9, MED15, CBP and p300. We demonstrate for the 9aaTAD transcription factors Oaf1 and Gal4 functional and physical interaction with E3-Ubiquitin Ligase Rsp5. The Rsp5-associations with RNA polymerase II and TFIID were reported previously.
An apparent medieval stereogram incorporating a symbol for optical illusion
Authors: Cisne John 
Published: July 2019

AbstractStereograms mark a threshold in understanding visual perception. Modern study of stereopsis began with Wheatstone's invention of the stereogram and stereoscope (~ 1832), important tools in vision research and technical imagery ever since. Stereoscopic images formed with frieze and wallpaper patterns in illuminated Insular manuscripts such as the Book of Durrow (~ 680 CE), Lindisfarne Gospels (~ 700-720), and Book of Kells (~ 800) show that, long before spectacle-quality magnifying lenses (~ 1286), illuminators somehow copied multicolored, microscopically detailed designs freehand with an accuracy unsurpassed in scientific instruments until the Renaissance (but well within the power of normally sighted humans' stereoscopic discrimination). If the artists accomplished this feat by free fusion using the unaided eyes as a magnifying stereocomparator, as suggested, they should have been able to create autostereograms. Did they? Here I report two examples of an apparent stereopair from the Book of Durrow, which gives a sharp, strongly three-dimensional image that includes, among other symbols, an eye-shaped sign identified with mirages (Fig. 1). Apparently, precocious empirical knowledge of stereopsis played more than a technical role in the creation of some of the world's more famous graphic art.
Water soluble carbon nanotubes affect growth of the common gram (Cicer arietinum)
Authors: Tripathi Shweta , Sonkar Sumit Kumar , Kumar Abhishek , Khan M.Y. , Sarkar Sabyasachi 
Published: July 2019

AbstractMulti-walled Carbon nanotube, its role and implications in biological systems are currently under evaluation and became interesting for many researchers primarily working on the interface of chemistry, physics and biology. However, concerns about the potential toxicity of multi-walled carbon nanotubes have been raised. To carry such affords, herein we investigate the effects of carboxylic acid functionalized water soluble carbon nanotube (wsCNT) on the growth of gram Cicer arietinum plant. The growth of gram plants was observed with and without the presence of wsCNT to demonstrate that carboxylated functionalized multi-walled carbon nanotubes showed better growth and under more wsCNT, the growth was enhanced without showing apparent toxicity. Although this is a preliminary study with a small group of plants, our results encourage further confirmation studies with larger groups of plants.
Soil Carbon in Agroforestry Systems: An Unexplored Treasure?
Authors: Nair P. K. Ramachandran , Nair Vimala , Gama-Rodrigues Emanuela , Garcia Rasmo , Haile Solomon , Howlett David , Kumar B. Mohan , Mosquera-Losada M.-Rosa , Saha Subhrajit , Takimoto Asako , Tonucci Rafael 
Published: July 2019

AbstractSoil organic matter (SOM), which contains more reactive organic carbon (C) than any other single terrestrial pool, plays a major role in determining C storage in ecosystems and regulating atmospheric concentrations of carbon dioxide (CO2)^1^. Agroforestry, the practice of growing trees and crops in interacting combinations on the same unit of land^2^, primarily by resource-poor smallholder farmers in developing countries, is recognized as a strategy for soil carbon sequestration (SCS) under the Clean Development Mechanism (CDM) of the Kyoto Protocol^3^. The understanding about C storage and dynamics under agroforestry systems (AFS), however, is minimal. Our studies under various AFS in diverse ecological conditions in five countries showed that tree-based agricultural systems, compared to treeless systems, stored more C in deeper soil layers up to 1 m depth under comparable conditions. More C is stored in soil near the tree than away from the tree; higher SOC content is associated with higher species richness and tree density; and C3 plants (trees) contribute to more C in the silt- + clay-sized (&lt;53 &x00B5;m) fractions that constitute more stable C, than C4 plants, in deeper soil profiles4 - 8. These results provide clear indications of the possibilities for climate change mitigation through SCS in AFS, and opportunities for economic benefit - through carbon trading - to millions of smallholder farmers in developing countries.
Phenex: Ontological Annotation of Phenotypic Diversity
Authors: Balhoff James , Dahdul Wasila , Kothari Cartik , Lapp Hilmar , Lundberg John , Mabee Paula , Midford Peter , Westerfield Monte , Vision Todd 
Published: July 2019

AbstractPhenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. Thus, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be be configured to load ontologies for different taxonomic groups. The graphical user interface was developed for, and tested by, evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to better leverage decades of work in systematics and comparative morphology and contribute to an ever more useful web of linked biological data.
Metabolic constraints on the evolution of genetic codes: Did multiple 'preaerobic' ecosystem transitions entrain richer dialects?
Authors: Wallace Rodrick 
Published: July 2019

AbstractA mathematical model based on Tlusty's topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the 'aerobic' transition, enabled a punctuated sequence of increasingly complex genetic codes. These evolved until the ancestor to the present narrow spectrum of nearly maximal codes became locked-in by path dependence.
Detection of Metabolites by Proton Ex Vivo NMR, in Vivo MR Spectroscopy Peaks and Tissue Content Analysis: Biochemical-Magnetic Resonance Correlation: Preliminary Results
Authors: Sharma Rakesh , Rehani Madan , Agrawala Arun 
Published: July 2019

Abstract*Aim*: Metabolite concentrations by in vivo magnetic resonance spectroscopy and ex vivo NMR spectroscopy were compared with excised normal human tissue relaxation times and tissue homogenate contents.*Hypothesis*: Biochemical analysis combined with NMR and MR spectroscopy defines better tissue analysis.
Materials and Methods:
Metabolites were measured using peak area, amplitude and molecular weights of metabolites in the reference solutions. In normal brain and heart autopsy, muscle and liver biopsy tissue ex vivo NMR peaks and spin-lattice (T1) and spin-spin (T2) relaxation times, were compared with diseased tissue NMR data in meningioma brain, myocardial infarct heart, duchene-muscular-dystrophy muscle and diffused-liver-injury liver after respective in vivo proton MR spectroscopy was done. NMR data was compared with tissue homogenate contents and serum levels of biochemical parameters.*Results*: The quantitation of smaller NMR visible metabolites was feasible for both ex vivo NMR and in vivo MR spectroscopy. Ex vivo H-1 NMR and in vivo MRS metabolite characteristic peaks (disease/normal data represented as fold change), T1 and T2, and metabolites in tissue homogenate and serum indicated muscle fibrosis in DMD, cardiac energy depletion in MI heart, neuronal dysfunction in meningioma brain and carbohydrate-lipid metabolic crisis in DLI liver tissues.*Conclusion*: This preliminary report highlights the biochemical-magnetic resonance correlation as basis of magnetic resonance spectroscopic imaging data interpretation of disease.
Prebiotic Organic Microstructures
Authors: BASSEZ Marie-Paule , TAKANO Yoshinori , KOBAYASHI Kensei 
Published: July 2019

AbstractMicro- and sub-micrometer spheres, tubules and fiber-filament soft structures have been synthesized in our experiments conducted with 3 MeV proton irradiations of a mixture of simple inorganic constituents, CO, N2 and H2O. We analysed the irradiation products, with scanning electron microscopy (SEM) and atomic force microscopy (AFM). These laboratory organic structures produced wide variety of proteinous and non-proteinous amino acids after HCl hydrolysis. The enantiomer analysis for D-, L- alanine confirmed that the amino acids were abiotically synthesized during the laboratory experiment. Considering hydrothermal activity, the presence of CO2 and H2, of a ferromagnesian silicate mineral environment, of an Earth magnetic field which was much less intense during Archean times than nowadays and consequently of a proton excitation source which was much more abundant, we propose that our laboratory organic microstructures might be synthesized during Archean times. We show similarities in morphology and in formation with some terrestrial Archean microstructures and we suggest that some of the observed Archean carbon spherical and filamentous microstructures might be composed of abiogenic organic molecules. We further propose a search for such prebiotic organic signatures on Mars. This article has been posted on Nature precedings on 21 July 2010 [1]. Extinct radionuclides as source of excitation have been replaced by cosmic radiations which were much more intense 3.5 Ga ago because of a much less intense Earth magnetic field. The new version of the article has been presented at the ORIGINS conference in Montpellier in july 2011 [2] and has since been published in Origins of Life and Evolution of Biospheres 42 (4) 307-316, 2012.DOI: 10.1007/s11084-012-9290-5
Effects of surface passivation on gliding motility assays
Authors: Maloney Andy , Herskowitz Lawrence , Koch Steven 
Published: July 2019

AbstractIn this study, we report differences in the observed gliding speed of microtubules dependent on the choice of bovine casein used as a surface passivator. We observed differences in both speed and support of microtubules in each of the assays. Whole casein, comprised of [alpha]~s1~, [alpha]~s2~, [beta], and [kappa] casein, supported motility and averaged speeds of 966 ± 7 nm/s. Alpha casein can be purchased as a combination of s1 and s2 and supported gliding motility and average speeds of 949 ± 4 nm/s. Beta casein did not support motility very well and averaged speeds of 870 ± 30 nm/s. Kappa casein supported motility very poorly and we were unable to obtain an average speed. Finally, we observed that mixing alpha, beta, and kappa casein with the proportions found in bovine whole casein supported motility and averaged speeds of 966 ± 7 nm/s.
Arbuscular mycorrhizal fungus spores host bacteria and their biofilm efficient in nutrient biodynamics and soil-borne plant pathogen suppression
Authors: Cruz Andre , Ishii Takaaki 
Published: July 2019

AbstractThe combination of bacteria and arbuscular mycorrhizal fungi (AMF) would be ideal for nutrient biodvnamics in soils and protection from soil-borne plant pathogens (SBPP). During the process of plant colonization AMF interact with bacteria where spores cytoplasm and hvphae provide specific niches for certain populations of bacteria. The clarification of the relationship AMF-bacteria has great potential for sustainable agriculture. The currently research aimed to isolate and characterize bacteria. Which we have designated most probable endobacteria (MPE) from an AMF spore. Three bacterial strains were taken from about 500 spores by using a 200 &x00B5;m diameter hvpodermic needle. These bacteria were identified by DNA and morphological methods. Antagonism to SBPP (Pythium ultimum NBRC 100123, Fusarium oxyxporum f. sp. lactucae MAFF 744088, Rhizoctonia solani MAFF 237426 and Roselinia necatrix - isolated from a Japanese apricot (Prunus mume) by Dr. Norihiko Kobayashi), P solubilization, ethylene production, nitrogenase activity and stimulation of AMF hyphal growth were evaluated. Here we show that the bacteria strongly functioned on nutrient biodynamics (P solubilization and Nitrogenase activity), ethylene production, protection from SBPP and stimulation of AMF hyphal growth. In addition, fresh samples of spores and hyphae were observed and photographed with a new type of scanning electronic microscope (SEM) (FEI Co., Quanta 250FEG), where the hyphae and spores with bacterial slime could be detected. Our results demonstrated the importance of bacteria associated to AMF for the soil ecology having a substantial mpact on sustainability. More specifically, the methods of extraction by ultra-thin needle reveled species associated to AMF, probably from inside spores. Moreover, the observation of bacterial biofilm showed a physical structure that the bacteria could form surround spores and hyphae to help AMF.
Optimal encoding of interval timing in expert percussionists
Authors: Burr David , Chicchini Guido , Arrighi Roberto , Giusti Marco , Cecchetti Luca 
Published: July 2019

AbstractWe measured temporal reproduction in expert drummers, string-musicians and non-musical subjects. While duration reproduction of the controls showed a characteristic regression to the mean, drummers responded veridically. This behavior is well explained by a model that combines optimally the sensory estimate for duration (more precise in drummers) with a prior, given by the average of the past few trials. These results highlight the efficiency and adaptability of sensori-motor mechanisms estimating temporal duration.
Allele-specific primer based identification of dimeric alpha-amylase inhibitor
Authors: Sharma Pradeep , Sharma Pooja , Saini Manoj , Singh S. S. 
Published: July 2019

AbstractWheat is one of the most important staple food crops cultivated over 200 mha in the range of environment throughout the world. Wheat production must continue to increase by 2% annually, more particularly in developing world including south-east Asia. Besides increasing the inherent productivity of wheat, it is important to minimize the losses caused to production by various abiotic and biotic factors. Alpha–amylase inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as the energy source. They play an important role in the carbohydrate metabolism of many heterotrophic and autotrophic organisms. In this study, we aimed to make sequence comparison and phylogenetic relationship among dimeric alpha-amylase inhibitor genes. These genes were clustered into two major groups based on phylogenetic analysis. Multiple alignments show at least 24 candidates single nucleotide polymorphisms in inhibitor genes, which could further be exploited for SNPs based haplotype diversity among Indian released wheat genotype. We have detected dimeric alpha-amylase inhibitor genes in cultivated and wild ancestors of wheat using genome specific primers. Genes encoding dimeric alpha-amylase belong to the family of 24 kDa alpha-amylase inhibitors. In this study, specific primer pairs were designed based on SNPs of these genes and chromosome locations of inhibitor genes confirmed by amplification in accession of T. urartu, A. tauschii, and A. speltoides. Results obtained under this study support that inhibitor genes amplified with primer PSWDAIAF1/PSWDAIAF2 and PSWDAIBF1/PSWDAIBF2 is present on genome B. These results further support evidence at molecular level that dimeric alpha-amylase inhibitor in cultivated wheat is encoded by a multigene family.
Attentional control and engagement with digital technology
Authors: Alloway Tracy , Alloway Ross 
Published: July 2019

AbstractMultiple demands comprise the efficiency of attentional control. There is abundant evidence that when an individual attempts two or more attentionally demanding activities at the same time, the allocation of attention to the tasks is limited and performance suffers as a result. Yet, recent technological innovations require many individuals to manage multiple digital technologies simultaneously or to switch attentional control between tasks. The ability to multitask with various digital technologies involves dividing attention, switching between tasks, and keeping track of multiple strands of information in working memory.
Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review
Authors: Csermely Peter , Sandhu Kuljeet Singh , Hazai Eszter , Hoksza Zsolt , Kiss Huba , Miozzo Federico , Veres Daniel , Piazza Francesco , Nussinov Ruth 
Published: July 2019

AbstractDuring the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into ‘cumulus-type’, i.e., those similar to puffy (white) clouds, and ‘stratus-type’, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an ‘energy transfer’ mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by ‘multi-trajectories’; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach ‘rarely visited’ but functionally-related states. We also show the role of disorder in ‘spatial games’ of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks.