bluuebunny/crossref_metadata_2025_split huggingface dataset:
Software Tools for Systems Biology: Visualizing the Outcomes of
N
Experiments on
M
Entities
Authors: Poultney Chris , Shasha Dennis 
Published: June 2017

Abstract
Systems biology deals with genes, proteins, ions and other molecular entities. It involves the integrated analysis of these molecular entities from many experiments conducted under different conditions. This common feature – many treatment conditions and thousands or more entities – poses a challenge to finding the answers to natural questions such as: Which subsets of conditions yield similar outcomes? Which entities respond similarly in many conditions? and Which functional groupings of entities are most affected by which conditions? In this chapter, we describe a visualization tool to help answer these questions, complementary informatic tools to support alternate visualizations, and explore the lessons learned in constructing that tool both from the software designer's and biologist's perspective.
The
RNA
World: Identifying
miRNA
‐Target
RNA
Pairs as Possible Missing Links in Multi‐Network Models
Authors: Green Pamela J. , Meyers Blake C. 
Published: June 2017

Abstract
Plant cells contain highly complex and abundant populations of small RNAs that regulate gene expression at many levels, in diverse tissues, and show evidence of regulation under different growth conditions. These molecules have been recognized as important components of signalling networks, but investigations of their contributions to plant signalling pathways have only taken place within the past few years. As sequencing methods have improved, many new microRNAs (miRNAs) have been identified in the most well‐studied species; the discovery of miRNAs in less‐studied species is just beginning but has been greatly enabled by these new methods. Studies to compile and experimentally validate lists of miRNAs combined with high‐throughput expression profiling of small RNAs will better define the extent of small RNA regulation in plant cellular processes. Validation of miRNAs often includes the prediction and verification of their mRNA targets and the identification of these targets can provide insight into the biological role of individual miRNAs and miRNA families. However, the power of this information could be farther reaching if it can be interpreted with other interaction data. The incorporation of pairs of miRNAs and their targets into multi‐network models would accomplish this and would likely to provide the missing links in many regulatory pathways. Since approaches to address the function of individual miRNAs in mutants and transgenic plants are labour‐intensive, the hypotheses resulting from the models could focus attention on the miRNAs that play pivotal roles in a number of key regulatory pathways.
Perspectives on Ecological and Evolutionary Systems Biology
Authors: Richards Christina L. , Hanzawa Yoshie , Katari Manpreet S. , Ehrenreich Ian M. , Engelmann Kathleen E. , Purugganan Michael D. 
Published: June 2017

AbstractUnderstanding the emergent properties inherent to genome function requires an integrated approach of data from all levels of biology. Molecular biology data alone does not describe the complex interacting functions of organisms, while studies at the level of ecological communities and ecosystems have provided little insight into the molecular underpinnings of adaptation. Merging ecology and evolution into systems biology allows researchers to exploit a wealth of genomic information by incorporating the natural phenotypic, genetic and epigenetic diversity of model systems as well as their diverse ecologies and evolutionary histories. Here, we suggest that systems biology could more fully address the question of how organisms respond to environment if studies incorporated real field settings or experimental manipulation of relevant environmental factors. In addition, although the application of genomic approaches to non‐model systems has been slow, we highlight some of the significant progress that has been made. Ecological and evolutionary systems biology will lead to a much more sophisticated understanding of the origins and functions of biological diversity, and serve as a critical component in deciphering how organisms respond to complex environments.
Effect of Nutrient Availability on Root System Development
Authors: Cruz‐Ramírez Alfredo , Calderón‐Vázquez Carlos , Herrera‐Estrella Luis 
Published: June 2017

AbstractModern‐day plant root systems have been modeled from distinct ancestors and by different evolutionary pathways influenced by environmental cues, leading to varied root system architectures. Availability of mineral nutrients has played a major role in evolution and development of the diverse root system architectures. In this chapter, we review the importance of the study of mineral nutrition on root development and describe the physiological, morphological and molecular responses of plant roots to diverse nutrient deficiencies and how the different hormone signaling pathways participate in these responses.
Biosynthesis of Plant Cell Wall and Related Polysaccharides by Enzymes of theGT2andGT48Families
Authors: Stone Bruce A. , Jacobs Andrew K. , Hrmova Maria , Burton Rachel A. , Fincher Geoffrey B. 
Published: June 2017

AbstractIn this chapter we outline the evolution of our understanding of the biological functions, genetics and regulation of enzymes of the GT2 and GT48 families of glycosyl transferases. The GT2 family is very large and includes enzymes encoded by the cellulose synthase gene superfamily, together with many other transferases with diverse substrate specificities that are distributed from the Archaea to humans. On the other hand, there are relatively few known members of the GT48 family, in which activities are limited to putative (1,3)‐β‐d‐glucan synthases of embryophytes, fungi and yeasts. The review is focused on a number of individual case studies, which have been chosen on the basis of their biological and economical importance in plant biology. The history of our knowledge of (1,4)‐β‐d‐glucan (cellulose) synthases and (1,3;1,4)‐β‐d‐glucan synthases in plants will be reviewed as representatives of the GT2 family, while the (1,3)‐β‐d‐glucan (or callose) synthases will be compared with these, as representatives of the GT48 family. These synthases have been extensively studied using biochemical techniques, but they are associated with membranes and are not easily purified. Emerging functional genomics technologies have been used to identify the genes encoding the cellulose synthases of the GT2 family, while new proteomics procedures have provided amino acid sequence that has in turn been applied to the identification of the GT48 (1,3)‐β‐d‐glucan synthases of plants. The enzymes are involved in the synthesis of structurally similar polysaccharides, but appear to have evolved independently.
Adaptive backstepping neural control of state‐delayed nonlinear systems with full‐state constraints and unmodeled dynamics
Authors: Zhang Tianping , Xia Meizhen , Zhu Jiaming 
Published: June 2017

SummaryIn this paper, the problem of adaptive neural control is discussed for a class of strict‐feedback time‐varying delays nonlinear systems with full‐state constraints and unmodeled dynamics, as well as distributed time‐varying delays. The considered nonlinear system with full‐state constraints is transformed into a nonlinear system without state constraints by introducing a one‐to‐one asymmetric nonlinear mapping. Based on modified backstepping design and using radial basis function neural networks to approximate the unknown smooth nonlinear function and using a dynamic signal to handle dynamic uncertainties, a novel adaptive backstepping control is developed for the transformed system without state constraints. The uncertain terms produced by state time delays and distributed time delays are compensated for by constructing appropriate Lyapunov‐Krasovskii functionals. All signals in the closed‐loop system are proved to be semiglobally uniformly ultimately bounded. A numerical example is provided to illustrate the effectiveness of the proposed design scheme.
Making Copper(0) Nanoparticles in Glycerol: A Straightforward Synthesis for a Multipurpose Catalyst
Authors: Dang‐Bao Trung , Pradel Christian , Favier Isabelle , Gómez Montserrat 
Published: June 2017

AbstractSmall zero‐valent copper nanoparticles (CuNPs) have been straightforwardly prepared from Cu(I) and Cu(II) precursors in glycerol and in the presence of polyvinylpyrrolidone as stabilizer. Thanks to the negligible vapor pressure of the solvent, these original nano‐systems could be directly characterized in glycerol as well as in the solid state, exhibiting relevantly homogeneous colloidal dispersions, also even after catalysis. CuNPs coming from the well‐defined coordination complex di‐μ‐hydroxobis[(N,N,N′,N′‐tetramethylethylenediamine)copper(II)] chloride {[Cu(κ2‐N,N‐TMEDA)(μ‐OH)]2Cl2} have been highly efficient in C–C and C–heteroatom bond formation processes. This new catalytic system has proved its performance in C–N couplings and in the synthesis of differently substituted propargylic amines through cross‐dehydrogenative couplings, multi‐component reactions such as A3 (aldehyde‐alkyne‐amine) and KA2 (ketone‐alkyne‐amine) couplings, as well as in the formation of heterocycles such as benzofurans, indolizines, and quinolines under smooth conditions. No significant copper amount was detected in the extracted organic compounds from the catalytic phase by inductively coupled plasma‐atomic emission spectroscopic (ICP‐AES) analyses, proving a highly efficient immobilization of copper nanoparticles in glycerol. From a mechanistic point of view, spectroscopic data (infrared and ultraviolet‐visible spectra) agree with a surface‐like catalytic reactivity.magnified image
Comparative performance of deciduous and permanent dental morphology in detecting biological relatives
Authors: Paul Kathleen S. , Stojanowski Christopher M. 
Published: June 2017

AbstractObjectivesDental morphology plays a key role in reconstructing population history and evolutionary relationships at global, regional, and intracemetery scales. At the inter‐individual level, it is assumed that close biological kin exhibit greater phenotypic similarity than non‐relatives. Heritability estimates provide one measure of phenotypic resemblance but are not easily incorporated into analyses of archaeological samples. In this study we evaluate the assumption that relatives are more similar phenotypically than non‐relatives. We compare results for permanent dental morphology to those obtained using deciduous dental morphology in a matched dataset (Paul & Stojanowski,).Materials and MethodsPermanent trait expression was scored from dental casts representing 69 sibling pairs, curated as part of the longitudinal Burlington Growth Study. Simulating a biodistance approach, 22 morphological traits of permanent tooth crowns were used to generate 69 inter‐relative and 2,076 non‐relative Euclidean distances. Following distance ordination, family‐specific dispersion values were calculated from multidimensional scaling coordinates. Output was compared to that of a previous study that focused on deciduous crown variation in the same set of individuals (Paul & Stojanowski,). Mantel tests were used to evaluate the correlation of a proxy genetic distance matrix to both the permanent and deciduous dental distance matrices.ResultsOn average, inter‐relative distances generated from morphological traits of permanent tooth crowns were smaller than expected by chance based on resampling (p < 0.001). While family‐specific dispersion varied greatly for both permanent and deciduous datasets, over 75% of the families exhibited greater dispersion with permanent traits. This suggests that morphological traits of the permanent dentition provide a less faithful reflection of biological relatedness than morphological traits of the deciduous dentition. Mantel tests indicate that both the deciduous and permanent distance matrices are significantly correlated with a matrix of genetic relatedness coefficients; however, the magnitude of the correlations was low.DiscussionOverall, morphological traits of permanent tooth crowns perform moderately well in distinguishing relatives from non‐relatives, but deciduous crown variations may provide a more direct reflection of the underlying genetic structure of intra‐site or intra‐cemetery samples. These findings have implications for bioarchaeological research and biodistance practices. In particular, morphological traits of the deciduous dentition should be incorporated into standard data collection protocols because of their stronger signal of relatedness.
Gene therapy decreases seizures in a model of Incontinentia pigmenti
Authors: Dogbevia Godwin K. , Töllner Kathrin , Körbelin Jakob , Bröer Sonja , Ridder Dirk A. , Grasshoff Hanna , Brandt Claudia , Wenzel Jan , Straub Beate K. , Trepel Martin , Löscher Wolfgang , Schwaninger Markus 
Published: June 2017

ObjectiveIncontinentia pigmenti (IP) is a genetic disease leading to severe neurological symptoms, such as epileptic seizures, but no specific treatment is available. IP is caused by pathogenic variants that inactivate the Nemo gene. Replacing Nemo through gene therapy might provide therapeutic benefits.MethodsIn a mouse model of IP, we administered a single intravenous dose of the adeno‐associated virus (AAV) vector, AAV‐BR1‐CAG‐NEMO, delivering the Nemo gene to the brain endothelium. Spontaneous epileptic seizures and the integrity of the blood–brain barrier (BBB) were monitored.ResultsThe endothelium‐targeted gene therapy improved the integrity of the BBB. In parallel, it reduced the incidence of seizures and delayed their occurrence. Neonate mice intravenously injected with the AAV‐BR1‐CAG‐NEMO vector developed no hepatocellular carcinoma or other major adverse effects 11 months after vector injection, demonstrating that the vector has a favorable safety profile.InterpretationThe data show that the BBB is a target of antiepileptic treatment and, more specifically, provide evidence for the therapeutic benefit of a brain endothelial‐targeted gene therapy in IP. Ann Neurol 2017;82:93–104
A novel cause of chronic viral meningoencephalitis: Cache Valley virus
Authors: Wilson Michael R. , Suan Dan , Duggins Andrew , Schubert Ryan D. , Khan Lillian M. , Sample Hannah A. , Zorn Kelsey C. , Rodrigues Hoffman Aline , Blick Anna , Shingde Meena , DeRisi Joseph L. 
Published: June 2017

ObjectiveImmunodeficient patients are particularly vulnerable to neuroinvasive infections that can be challenging to diagnose. Metagenomic next generation sequencing can identify unusual or novel microbes and is therefore well suited for investigating the etiology of chronic meningoencephalitis in immunodeficient patients.MethodsWe present the case of a 34‐year‐old man with X‐linked agammaglobulinemia from Australia suffering from 3 years of meningoencephalitis that defied an etiologic diagnosis despite extensive conventional testing, including a brain biopsy. Metagenomic next generation sequencing of his cerebrospinal fluid and brain biopsy tissue was performed to identify a causative pathogen.ResultsSequences aligning to multiple Cache Valley virus genes were identified via metagenomic next generation sequencing. Reverse transcription polymerase chain reaction and immunohistochemistry subsequently confirmed the presence of Cache Valley virus in the brain biopsy tissue.InterpretationCache Valley virus, a mosquito‐borne orthobunyavirus, has only been identified in 3 immunocompetent North American patients with acute neuroinvasive disease. The reported severity ranges from a self‐limiting meningitis to a rapidly fatal meningoencephalitis with multiorgan failure. The virus has never been known to cause a chronic systemic or neurologic infection in humans. Cache Valley virus has also never previously been detected on the Australian continent. Our research subject traveled to North and South Carolina and Michigan in the weeks prior to the onset of his illness. This report demonstrates that metagenomic next generation sequencing allows for unbiased pathogen identification, the early detection of emerging viruses as they spread to new locales, and the discovery of novel disease phenotypes. Ann Neurol 2017;82:105–114
Optoelektrochemische In‐situ‐Beobachtung der kathodischen Abscheidung einzelner Cobaltnanopartikel
Authors: Brasiliense Vitor , Clausmeyer Jan , Dauphin Alice L. , Noël Jean‐Marc , Berto Pascal , Tessier Gilles , Schuhmann Wolfgang , Kanoufi Fréderic 
Published: June 2017

AbstractDie Elektrochemie einzelner Partikel auf einer Nanoelektrode wird mittels optischer Dunkelfeldmikroskopie untersucht. Die Betrachtung des gestreuten Lichts macht es möglich, die elektrochemische Abscheidung einzelner Cobaltnanopartikel mit Radien bis hinunter zu 65 nm in situ zu verfolgen. Die Dimensionen von größeren Submikropartikeln können durch Superlokalisierung der Partikelgrenzen bestimmt werden. Zusätzlich enthält das gestreute Licht ergänzende Informationen über die komplexe Redoxchemie. Mit der optoelektrochemischen Technik werden wertvolle Einblicke in elektrokatalytische Prozesse während der Abscheidung gewonnen, die durch elektrochemische Messungen an einzelnen Partikeln allein nicht zugänglich wären.
Protonierung von Nitraminen: Bildung des O‐ oder N‐protonierten Kations
Authors: Saal Thomas , Rahm Martin , Christe Karl O. , Haiges Ralf 
Published: June 2017

AbstractDie Reaktionen von Nitramin, N‐Methylnitramin und N,N‐Dimethylnitramin mit wasserfreiem HF und den binären supersauren Systemen HF/MF5 (M=As, Sb) wurden bei Temperaturen unterhalb von −40 °C untersucht. Mittels multinuklearer NMR‐Spektroskopie konnte in Lösung ausschließlich die O‐Protonierung beobachtet werden, wobei aus reiner HF‐Lösung selbst bei −78 °C kein Feststoff isoliert werden konnte. Im HF/MF5‐System konnte jedoch protoniertes Nitramin zum ersten Mal in Form feuchtigkeitsempfindlicher MF6−‐Salze isoliert werden, die sich bei Temperaturen oberhalb von −40 °C zersetzen. Im Feststoff resultiert abhängig vom Gegenion ein O‐protoniertes oder N‐protoniertes Kation. Dies ist in Einklang mit Rechnungen, die einen nur minimalen Energieunterschied zwischen O‐Protonierung und N‐Protonierung aufzeigen. Die Salze [H2N‐NO2H][AsF6], [H3N‐NO2][SbF6], [MeHNNO2H][SbF6] und [Me2NNO2H][SbF6] wurden durch ihre Röntgenkristallstrukturen charakterisiert.
From Lithium‐Ion to Sodium‐Ion Batteries: Advantages, Challenges, and Surprises
Authors: Nayak Prasant Kumar , Yang Liangtao , Brehm Wolfgang , Adelhelm Philipp 
Published: June 2017

AbstractMobile and stationary energy storage by rechargeable batteries is a topic of broad societal and economical relevance. Lithium‐ion battery (LIB) technology is at the forefront of the development, but a massively growing market will likely put severe pressure on resources and supply chains. Recently, sodium‐ion batteries (SIBs) have been reconsidered with the aim of providing a lower‐cost alternative that is less susceptible to resource and supply risks. On paper, the replacement of lithium by sodium in a battery seems straightforward at first, but unpredictable surprises are often found in practice. What happens when replacing lithium by sodium in electrode reactions? This review provides a state‐of‐the art overview on the redox behavior of materials when used as electrodes in lithium‐ion and sodium‐ion batteries, respectively. Advantages and challenges related to the use of sodium instead of lithium are discussed.
γ‐Functionalizations of Amines through Visible‐Light‐Mediated, Redox‐Neutral C−C Bond Cleavage
Authors: Shu Wei , Genoux Alexandre , Li Zhaodong , Nevado Cristina 
Published: June 2017

AbstractCleavage of unstrained C−C bonds under mild, redox‐neutral conditions represents a challenging endeavor which is accomplished here in the context of a flexible, visible‐light‐mediated, γ‐functionalization of amines. In situ generated C‐centered radicals are harvested in the presence of Michael acceptors, thiols and alkyl halides to efficiently form new C(sp3)−C(sp3), C(sp3)−H and C(sp3)−Br bonds, respectively.
A statistical approach to develop biocomposites from epoxy resin, poly(furfuryl alcohol), poly(propylene carbonate), and biochar
Authors: Mashouf Roudsari Ghodsieh , Mohanty Amar K. , Misra Manjusri 
Published: June 2017

ABSTRACTEpoxy composites are typically petroleum based and prone to fracture. Increasing concerns about climate change have motivated scientists to find green alternatives. To address both drawbacks, effect of addition of poly(propylene carbonate) polyol (PPC), a polyol derived from carbon dioxide, and biochar, a byproduct of pyrolysis in an epoxy/poly(furfuryl alcohol) (PFA) network was studied. It is hypothesized that addition of PPC will increase impact strength while addition of inexpensive biochar will offset cost of final product. In addition, incorporation of PFA, PPC, and biochar can increase biobased content of thermoset. A statistical approach was used to find a systematic correlation between constituent contents and mechanical properties of biocomposites. Mixture design of experiment and backward elimination regression were used to model mechanical properties of biocomposites. The fitted models showed a great ability to predict mechanical properties of new formulations. Addition of 10% biochar increased tensile strength and toughness by 13% and 34%, respectively. Biochar also increased modulus while it had adverse effect on impact strength. Promising effect of PPC on toughening of matrix was proved and it was found that addition of 30% of PPC increased impact strength by fivefolds. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45307.
Cranial Indicators Identified for Peak Incidence of Otitis Media
Authors: Pagano Anthony S. , Wang Eugene , Yuan Derek , Fischer Daniel , Bluestone Charles , Marquez Samuel , Laitman Jeffrey 
Published: June 2017

ABSTRACTAcute otitis media (AOM) is one of the most common pediatric conditions worldwide. Peak age of occurrence for AOM has been identified within the first postnatal year and it remains frequent until approximately six postnatal years. Morphological differences between adults and infants in the cartilaginous Eustachian tube (CET) and associated structures may be responsible for development of this disease yet few have investigated normal growth trajectories. We tested hypotheses on coincidence of skeletal growth changes and known ages of peak AOM occurrence. Growth was divided into five dental eruption stages ranging from edentulous neonates (Stage 1) to adults with erupted third maxillary molars (Stage 5). A total of 32 three‐dimensional landmarks were used and Generalized Procrustes Analysis was performed. Next, we performed principal components analysis and calculated univariate measures. It was found that growth change in Stage 1 was the most rapid and comprised the largest amount of overall growth in upper respiratory tract proportions (where time is represented by the natural logarithmic transformation of centroid size). The analysis of univariate measures showed that Stage 1 humans did indeed possess the relatively shortest and most horizontally oriented CET's with the greatest amount of growth change occurring at the transition to Stage 2 (eruption of deciduous dentition at five postnatal months, commencing peak AOM incidence) and ceasing by Stage 3 (approximately six postnatal years). Skeletal indicators appear related to peak ages of AOM incidence and may contribute to understanding of a nearly ubiquitous human disease. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:1721–1740, 2017. © 2017 Wiley Periodicals, Inc.