bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical Ecology
Authors: Lundberg Per 
Published: October 2014

Abstract

Theoretical ecology is the study of the fundamental forces and processes determining the course of evolution and how ecological systems are assembled and maintained. Theoretical ecology therefore typically encompasses almost all levels of biological organisation (from genes to ecosystems). Behavioural ecology, life history evolution and demography, population ecology, and the ecology of communities and ecosystems are the typical domains. Theoretical ecology usually, but not always, uses mathematics for modelling and building of theories. Some models of ecological systems are deterministic, that is, assuming that there is no or little environmental variability; others are stochastic and take into account that the environment is (randomly) variable in space and time. Theoretical ecology progresses under the common scientific attitude that we indeed are able to reveal generalities and law‐like behaviours of nature despite the overwhelming diversity of life on Earth.

Key Concepts:

Theoretical ecology is simplifying complex problems and using mathematical models to reach general insights.

Theoretical ecology has close and natural ties to evolutionary biology.

Synthesis and bringing research disciplines together (e.g. behaviour ecology and population dynamics), hallmarks of good theory.

Theoretical ecology is an important part of applied ecology, for example, in conservation biology and in fisheries management.

Theory and data are naturally inseparable.
Shotgun Proteomics
Authors: Banks Charles AS , Lakshminarasimhan Mahadevan , Washburn Michael P 
Published: October 2014

Abstract

Investigating how the protein machinery in cells functions is fundamental to biological enquiry. Technology that can identify and quantitate a multitude of unknown proteins can facilitate such investigations. Although techniques such as Western blotting are able to provide limited but useful information about a known protein if a suitable antibody is available, mass spectrometry provides a platform for the large‐scale identification and quantitation of the many unknown proteins in a typical sample. In particular, shotgun proteomics techniques have been used for studying global changes in whole proteomes, probing the subunit composition of protein complexes, and for mapping post‐translational modifications. The advent of whole genome sequencing has enabled recent advances in shotgun proteomics technology. Multidimensional protein identification technology (MudPIT), which couples mass spectrometry and multidimensional chromatography, achieves exquisitely sensitive protein detection. There are a variety of methods used to quantify the identified proteins, from isotopic labelling to ‘label free’ spectral counting.

Key Concepts:

‘Shotgun proteomics’ aims to identify all proteins present in a sample using mass spectrometry to make measurements that depend on a protein's mass.

Before mass spectrometry, proteins in a sample are digested with a protease to create a complex peptide mixture for analysis.

Peptides between approximately 10 and 30 amino acids long can generate characteristic fragmentation patterns that can be used to identify their sequences.

Chromatography is used to enrich peptides of the same kind; if enough of these enter the mass spectrometer concurrently, they can be characterised.

These homogeneous populations of peptides are isolated and fragmented inside the mass spectrometer; as these fragments are detected, MS/MS spectra are generated.

The patterns described by these MS/MS spectra are peptide ‘fingerprints’ which can be matched to predicted spectral patterns; genomic nucleic acid sequences are used to predict these spectral patterns.

Protein quantitation is possible; strategies used include counting the number of MS/MS spectra per protein obtained during the analysis (label free), or labelling proteins/peptides from two samples with different isotopes.
Insect Viruses
Authors: Possee Robert D , King Linda A 
Published: October 2014

Abstract

Viruses from over 16 families have been isolated from insects to date and show as much variation in structural and organisational paradigms as viruses from most other animal classes. Unique to the insect viruses is the ability of several families to produce a large pseudocrystalline occlusion body that protects the mature virus particles in the environment. Such occlusion bodies have led to these viruses evolving a complex array of associations with their insect host and in many cases causing large‐scale disease epizootics. Some of these viruses have been used for the purposes of biocontrol of insect pests in agriculture. Among the remaining nonoccluded insect viruses all of the basic structural and organisational paradigms are present in different families. Many insect viruses seem able to coexist in a single host without causing obvious disease. However, the life history strategies of their insect hosts has led the insect viruses to evolve some intriguing replicative strategies of their own that have few, if any, counterparts among the other animal viruses.

Key Concepts:

Insect viruses have genomes that may comprise double‐ or single‐stranded DNA or RNA.

Insect viruses exhibit as much structural diversity as viruses that infect any other form of life.

Insect viruses may be enveloped or non‐enveloped.

Some insect viruses may form occlusion bodies comprising virions embedded within a protein matrix.

Insect viruses may have evolved 350–400 million years ago.

Many insect viruses share genetic and structural similarities with viruses of vertebrates.

Some insect viruses are unique to invertebrate species.

Insect viruses can be highly pathogenic to their hosts or cause little or no signs of infection.

Some insect viruses have been used as biopesticides to control insect pests.
Gene Inactivation Strategies: An Update
Authors: Guo Chang‐An , O'Neill Lucas M , Ntambi James M 
Published: October 2014

Abstract

The ability to manipulate gene expression levels has been essential to the study of gene function and biological processes. Classically, whole body deletions of genes were generated via homologous recombination. Over the past two decades, the development of Cre‐Lox and flippase/flippase recombinase target based gene inactivation technologies allowed researchers to closely regulate the location and timing of gene expression. However, these methods are costly and time consuming. The last few years have seen a revolution in the approaches scientists use to inactivate gene expression, such as the development of highly efficient
ribonucleic acid interference (RNAi)
delivery systems and the groundbreaking genome editing technologies. Here, the authors describe the recent updates on
small interfering RNA (siRNA)
in vivo
delivery as well as the methodologies and applications of zinc‐finger nucleases, transcription activator‐like effector nucleases and clustered regularly interspaced short palindromic repeats. Equipped with these powerful tools, scientists can now rapidly modulate the expression of genes of interest and precisely modify the genomic sequences in virtually any organisms.

Key Concepts:

RNA interference (RNAi) is an endogenous post‐transcriptional gene‐regulatory mechanism mediated by noncoding RNA molecules to regulate gene expression.

Chemical modification on siRNA reduces off‐target effect, improves RNAi efficiency and enhances the stability of siRNA for
in vivo
applications.

Genome editing is a genetic approach used to directly manipulate an organism's genome by inserting, replacing, or removing DNA sequences.

Engineered nucleases, such as zinc‐finger nucleases (ZFNs), transcription activator‐like effector nucleases (TALENs) and the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)/Cas (CRISPR‐associated) system enable targeted genetic modifications in cells, tissues and organisms.
Molecular Genetics of Myopathies Caused by β‐Tropomyosin Mutations
Authors: Pelin Katarina , Marttila Minttu , Wallgren‐Pettersson Carina 
Published: October 2014

Abstract

Mutations in the gene encoding β‐tropomyosin,
TPM2
, cause clinically and histologically overlapping congenital myopathies such as nemaline myopathy, cap myopathy and core‐rod myopathy, and often also a fibre size disproportion between type 1 and type 2 muscle fibres. In addition,
TPM2
mutations can cause distal arthrogryposis and Escobar syndrome, or unspecific myopathies with various combinations of clinical and histological features. The vast majority of the
TPM2
mutations are dominant, either
de novo
or familial. Missense mutations and in‐frame deletions or insertions of single amino acids are the most common types of mutation. Three dominant donor splice site mutations have also been described, predicted to cause exon skipping and subsequent loss of 42 amino acids. Only one recessive mutation has been identified in
TPM2
, that is, a nonsense mutation causing nemaline myopathy with Escobar syndrome. Of the 30 different
TPM2
mutations identified to date, six are gain‐of‐function mutations causing increased muscle contractility.

Key Concepts:

Dominant mutations in the
TPM2
gene cause a variety of congenital myopathies and distal arthrogryposis.

Recessive mutations in
TPM2
are rare.

Tropomyosin mutations alter actin‐tropomyosin interactions, tropomyosin dimer formation and muscle contraction.

Gain‐of‐function mutations cause increased muscle contractility.

Hypercontractile molecular phenotypes result in distal arthrogryposis and congenital myopathies with contractures.
Molecular Genetics of Inherited Glucocorticoid Deficiency
Authors: Meimaridou Eirini , Kowalczyk Julia , Metherell Louise A 
Published: October 2014

Abstract

Familial glucocorticoid deficiency (FGD) is a rare autosomal recessive disorder characterised by isolated glucocorticoid deficiency and resistance of the adrenal cortex to adrenocorticotropic hormone (ACTH) action. Technological advances in genetics have contributed to our better understanding of the disease.
Deoxyribonucleic acid (DNA)
sequencing technology has given insight into the genetic cause of more than 60% of FGD cases, and revealed intersecting phenotypes with other adrenal insufficiency disorders. Defects have been recognised in the ACTH receptor (
MC2R
) and its accessory protein (
MRAP
), in the mitochondrial cholesterol transfer protein STAR, in
MCM4
essential for DNA stability and repair and in
NNT
and
TXNRD2
, essential for redox homoeostasis/detoxification of ROS. The remaining causes are yet to be elucidated and using next generation sequencing tools could incriminate additional pathways responsible for the onset of the disease.

Key Concepts:

Glucocorticoid deficiency is a feature of many adrenal disorders with overlapping clinical presentations.

In most adrenal insufficiency disorders glucocorticoid deficiency is accompanied by mineralocorticoid deficiency.

Technological advances in genetics have accelerated our understanding of the genetic causes of such diseases.

Defects in novel pathways including those responsible for DNA stability and repair and those essential for redox homoeostasis/detoxification of ROS have recently been implicated in the pathogenesis of glucocorticoid deficiency.

40% of isolated glucocorticoid deficiency remains of unknown aetiology.
Gene Therapy for Severe Haemoglobin Disorders
Authors: Villamizar Olga , Chambers Christopher B , Wilber Andrew 
Published: October 2014

Abstract

Sickle cell disease (SCD) and β‐thalassaemia result from inherited mutations that cause structural abnormality or deficient synthesis of adult haemoglobin. Palliative therapies improve the quality/duration of life for many, but side effects result from long‐term use. Bone marrow transplantation can be curative, but is limited to individuals with a matched donor. Thus, gene delivery into the patient's haematopoietic stem cells is a desirable therapy. Lentiviral vectors encoding for erythroid‐specific expression of either γ‐ or β‐globin genes have been developed for this purpose. These vectors have been used to cure SCD and β‐thalassaemia in mouse models with positive results emerging from clinical trials. Concurrently, innovative strategies intending to reactivate endogenous γ‐globin expression or correct β‐globin mutations at the genome level are showing promise for the future. Ultimately, clinical utility of all these approaches depend on safety and efficacy so that a cure can be consistently achieved.

Key Concepts:

Sickle cell disease (SCD) and β‐thalassaemia are the most common single gene disorders, and a worldwide health concern.

The switch from foetal to adult haemoglobin production after birth marks the onset of disease.

Haematopoietic stem cell transplant is curative, but available to only a limited number of patients making gene therapy a highly desirable alternative.

Lentiviral vectors made possible the delivery of complex, erythroid‐specific globin expression cassettes into haematopoietic stem cells.

Mouse models of SCD and β‐thalassaemia have been cured with lentiviral vectors encoding for high‐level, erythroid specific expression of γ‐ and β‐globin genes.

The first adult β‐thalassaemia major patient treated with a β‐globin lentiviral vector remains transfusion‐independent and in good health 6 years after therapy.
Metal–Organic Frameworks for Oxygen Storage
Authors: DeCoste Jared B. , Weston Mitchell H. , Fuller Patrick E. , Tovar Trenton M. , Peterson Gregory W. , LeVan M. Douglas , Farha Omar K. 
Published: October 2014

AbstractWe present a systematic study of metal–organic frameworks (MOFs) for the storage of oxygen. The study starts with grand canonical Monte Carlo simulations on a suite of 10 000 MOFs for the adsorption of oxygen. From these data, the MOFs were down selected to the prime candidates of HKUST‐1 (Cu‐BTC) and NU‐125, both with coordinatively unsaturated Cu sites. Oxygen isotherms up to 30 bar were measured at multiple temperatures to determine the isosteric heat of adsorption for oxygen on each MOF by fitting to a Toth isotherm model. High pressure (up to 140 bar) oxygen isotherms were measured for HKUST‐1 and NU‐125 to determine the working capacity of each MOF. Compared to the zeolite NaX and Norit activated carbon, NU‐125 has an increased excess capacity for oxygen of 237 % and 98 %, respectively. These materials could ultimately prove useful for oxygen storage in medical, military, and aerospace applications.
Size‐Controlled Synthesis of Conjugated Polymer Nanoparticles in Confined Nanoreactors
Authors: Deng Sheng , Zhi Jian , Zhang Xianmei , Wu Qingqing , Ding Yun , Hu Aiguo 
Published: October 2014

AbstractSoluble conjugated polymeric nanoparticles are synthesized by Suzuki‐type polycondensation of two monomers (Ax + By, x>2, y≥2) in the channel of ordered mesoporous silica‐supported carbon nanomembranes (nanoreactors). These synthesized soluble conjugated microporous polymers (SCMPs) exhibit uniform particle‐size distributions and well‐controlled particle sizes. The control of particle size stems from the fact that the polycondensations exclusively take place inside the mesochannels of the nanoreactors. Photoluminescence studies show that polymeric nanoparticles with tetraphenylethene and pyrene substructures are highly fluorescent. The combination of both physical stability and processability offered by the soluble polymeric nanoparticles makes them particularly attractive in light emitting and other optoelectronic applications.
Complementary Standoff Chemical Imaging to Map and Identify Artist Materials in an Early Italian Renaissance Panel Painting
Authors: Dooley Kathryn A. , Conover Damon M. , Glinsman Lisha Deming , Delaney John K. 
Published: October 2014

AbstractTwo imaging modalities based on molecular and elemental spectroscopy were used to characterize a painting by Cosimo Tura. Visible‐to‐near‐infrared (400–1680 nm) reflectance imaging spectroscopy (RIS) and X‐ray fluorescence (XRF) imaging spectroscopy were employed to identify pigments and determine their spatial distribution with higher confidence than from either technique alone. For example, Mary’s red robe was modeled through the distribution of an insect‐derived red lake (RIS map) and lead white (XRF lead map), rather than a layer of red lake on vermilion. The RIS image cube was also used to isolate the preparatory design by mapping the reflectance spectra associated with it. In conjunction with results from an earlier RIS study (1650–2500 nm) to map and identify the binding media, a more thorough understanding was gained of the materials and techniques used in the painting.
A Motif for Infinite Metal Atom Wires
Authors: Yin Xi , Warren Steven A. , Pan Yung‐Tin , Tsao Kai‐Chieh , Gray Danielle L. , Bertke Jeffery , Yang Hong 
Published: October 2014

AbstractA new motif for infinite metal atom wires with tunable compositions and properties is developed based on the connection between metal paddlewheel and square planar complex moieties. Two infinite Pd chain compounds, [Pd4(CO)4(OAc)4Pd(acac)2] 1 and [Pd4(CO)4(TFA)4Pd(acac)2] 2, and an infinite PdPt heterometallic chain compound, [Pd4(CO)4(OAc)4Pt(acac)2] 3, are identified by single‐crystal X‐ray diffraction analysis. In these new structures, the paddlewheel moiety is a Pd four‐membered ring coordinated by bridging carboxylic ligands and μ2 carbonyl ligands. The planar moiety is either Pd(acac)2 or Pt(acac)2 (acac=acetylacetonate). These moieties are connected by metallophilic interactions. The results showed that these one‐dimensional metal wire compounds have photoluminescent properties that are tunable by changing ligands and metal ions. 3 can also serve as a single source precursor for making Pd4Pt bimetallic nanostructures with precise control of metal composition.
Bulky Aryloxide Ligand Stabilizes a Heterogeneous Metathesis Catalyst
Authors: Conley Matthew P. , Forrest William P. , Mougel Victor , Copéret Christophe , Schrock Richard R. 
Published: October 2014

AbstractThe reaction of [W(O)(CHCMe2Ph)(dAdPO)2], containing bulky 2,6‐diadamantyl aryloxide ligands, with partially dehydroxylated silica selectively yields a well‐defined silica‐supported alkylidene complex, [(SiO)W(O)(CHCMe2Ph)(dAdPO)]. This fully characterized material is a very active and stable alkene metathesis catalyst, thus allowing loadings as low as 50 ppm in the metathesis of internal alkenes. [(SiO)W(O)(CHCMe2Ph)(dAdPO)] also efficiently catalyzes the homocoupling of terminal alkenes, with turnover numbers exceeding 75 000 when ethylene is constantly removed to avoid the formation of the less reactive square‐based pyramidal metallacycle resting state.
A Crown Ether Decorated Dibenzocoronene Tetracarboxdiimide Chromophore: Synthesis, Sensing, and Self‐Organization
Authors: Ma Yingjie , Marszalek Tomasz , Yuan Zhongyi , Stangenberg Rene , Pisula Wojciech , Chen Long , Müllen Klaus 
Published: October 2014

AbstractA macrocyclic dibenzocoronene tetracarboxdiimide containing two benzo‐21‐crown‐7 groups has been synthesized. It shows liquid‐crystalline behavior and selectively binds Pb2+ or K+ to form 1:2 complexes in solution. The complexation leads to a significant increase of fluorescence; the surface organization of discotic columnar structures, in the solid‐state, can be controlled by selective ion binding.
Numerical solutions of the equation concerning small adiabatic oscillations of pulsating components in double star systems
Authors: Ulaş B. 
Published: October 2014

AbstractThe equation governing small adiabatic radial oscillations for pulsating components in close binary stars modelled by tidally and rotationally distorted Roche geometry is solved numerically. With assumed initial conditions, solutions for systems with different mass ratios are presented. The changes in relative wave amplitude with various parameters are shown. The variation of the ratio of the pulsation frequencies of distorted to undistorted stars for given mass ratio of the binary systems is also investigated. Observational evidence is examined by using two data sets that show the modelled effects, by taking into account likely practical factors. The results show that the measured frequencies and amplitudes of surface waves can vary slightly for distorted stars in comparison to undistorted ones (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
AGN jets under the microscope: A divide?
Authors: Karouzos M. , Britzen S. , Witzel A. , Zensus A.J. , Eckart A. 
Published: October 2014

AbstractA new paradigm for active galactic jet kinematics has emerged through detailed investigations of BL Lac objects using very long baseline radio interferometry. In this new scheme, most, if not all, jet components appear to remain stationary with respect to the core but show significant non‐radial motions. This paper presents results from our kinematic investigation of the jets of a statistically complete sample of radio‐loud flat‐spectrum active galaxies, focusing on the comparison between the jet kinematic properties of BL Lacs and flat‐spectrum radio‐quasars. It is shown that there is a statistically significant difference between the kinematics of the two AGN classes, with BL Lacs showing more bent jets, that are wider and show slower movement along the jet axis, compared to flat‐spectrum radio‐quasars. This is interpreted as evidence for helically structured jets (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A wider audience: Turning VLBI into a survey instrument
Authors: Middelberg E. , Deller A.T. , Brisken W.F. , Morgan J.S. , Norris R.P. 
Published: October 2014

AbstractRadio observations using the Very Long Baseline Interferometry (VLBI) technique typically have fields of view of only a few arcseconds, due to the computational problems inherent in imaging larger fields. Furthermore, sensitivity limitations restrict observations to very compact and bright objects, which are few and far between on the sky. Thus, while most branches of observational astronomy can carry out sensitive, wide‐field surveys, VLBI observations are limited to targeted observations of carefully selected objects. However, recent advances in technology have made it possible to carry out the computations required to target hundreds of sources simultaneously. Furthermore, sensitivity upgrades have dramatically increased the number of objects accessible to VLBI observations. The combination of these two developments have enhanced the survey capabilities of VLBI observations such that it is now possible to observe (almost) any point in the sky with milli‐arcsecond resolution. In this talk I review the development of wide‐field VLBI, which has made significant progress over the last three years (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Dwarf galaxies in observed and simulated galaxy clusters
Authors: Lisker T. 
Published: October 2014

AbstractGalaxy clusters are populated by thousands of low‐mass galaxies, with hundreds of them already within stellar masses of 108 < M* ≤ 109.5 M⊙ and magnitudes of –16 < Mr < –19 mag. While objects in this regime are commonly termed “dwarfs”, they are not as faint and diffuse as many of the known Milky Way satellites. Their observed complexity, particularly regarding the dominant early‐type dwarf population, is still poorly understood and requires models and simulations of environmental influence on dwarfs. Studying cluster dwarf galaxies at the current time is motivated by two facts: (i) for nearby clusters, multicolour observational samples exist that are complete in the above luminosity range and cover a substantial portion of the cluster; (ii) state‐of‐the‐art semi‐analytic models based on high‐resolution N‐body simulations, reaching down to dwarf masses, have recently become available. Here I show how comparisons of models and observations can serve as a tool for studying the evolutionary history of low‐mass galaxy populations in today's clusters (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)