bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core variability in substitution rates and the basal sequence characteristics of the human genome
Authors: Sahakyan Aleksandr B. , Balasubramanian Shankar 
Published: August 2015

AbstractAccurate knowledge on the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39894 retrotransposon remnants, we reveal germline sequence-dependent nucleotide substitution rates that can be assigned to each position in the human genome. Benefiting from the data made available in such detail, we show that a simulated genome, generated by equilibrating a random DNA sequence solely using our rate constants, exhibits nucleotide organisation close to that in the human genome. We next generate the germline basal substitution propensity (BSP) profile of the human genome and show a decreased tendency of moieties with low BSP to undergo somatic mutations in many cancer types.
Facing the heat: thermoregulation and behaviour of lowland species of a cold-dwelling butterfly genus,Erebia
Authors: Kleckova Irena , Klecka Jan 
Published: August 2015

AbstractUnderstanding the potential of animals to immediately respond to changing temperatures is imperative for predicting the effects of climate change on biodiversity. Ectothermic animals, such as insects, use behavioural thermoregulation to keep their body temperature within suitable limits. It may be particularly important at warm margins of species occurrence, where populations are sensitive to increasing air temperatures. In the field, we studied thermal requirements and behavioural thermoregulation in low-altitude populations of the Satyrinae butterfliesErebia aethiops,E. euryaleandE. medusa. We compared the relationship of individual body temperature with air and microhabitat temperatures for the low-altitudeErebiaspecies to our data on seven mountain species, including a high-altitude population ofE. euryale, studied in the Alps. We found that the grassland butterflyE. medusawas well adapted to the warm lowland climate and it was active under the highest air temperatures and kept the highest body temperature of all species. Contrarily, the woodland species,E. aethiopsand a low-altitude population ofE. euryale, kept lower body temperatures and did not search for warm microclimates as much as other species. Furthermore, temperature-dependence of daily activities also differed between the three low-altitude and the mountain species. Lastly, the different responses to ambient temperature between the low- and high-altitude populations ofE. euryalesuggest possible local adaptations to different climates. We highlight the importance of habitat heterogeneity for long-term species survival, because it is expected to buffer climate change consequences by providing a variety of microclimates, which can be actively explored by adults. Alpine species can take advantage of warm microclimates, while low-altitude grassland species may retreat to colder microhabitats to escape heat, if needed. However, we conclude that lowland populations of woodland species may be more severely threatened by climate warming because of the unavailability of relatively colder microclimates.
Endogenous human stem cell-associated retroviruses
Authors: Glinsky Gennadi V. 
Published: August 2015

AbstractRecent discoveries of endogenous human stem cell-associated retroviruses (SCARs) revealed consistent activation of specific endogenous retroviral elements in human preimplantation embryos and documented the essential role of the sustained retroviral activities in the maintenance of pluripotency, functional identity and integrity of naïve-state embryonic stem cells, and anti-viral resistance of the early-stage human embryos. SCARs activity have been implicated in seeding thousands’ human-specific regulatory sequences in the hESC genome. Activation of specific SCARs, namely LTR7/HERVH and LTR5_Hs/HERVK, has been demonstrated in patients diagnosed with multiple types of cancer, autoimmune diseases, neurodegenerative disorders and it is likely associated with the emergence of clinically lethal therapy resistant death-from-cancer phenotypes in a sub-set of cancer patients diagnosed with different types of malignant tumors.
Life history effects on the molecular clock of autosomes and sex chromosomes
Authors: Amster Guy , Sella Guy 
Published: August 2015

AbstractOne of the foundational results of molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic “molecular clock”. We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in extant hominines (i.e., human, chimpanzee and gorilla), considering a model that approximates features of the mutational process in most mammals and birds and some other vertebrates. As we show, this model helps explain and reconcile a number of seemingly puzzling observations. In hominines, it can explain the puzzlingly low X-to-autosome ratios of substitution rates and how the ratios and rates of autosomal substitutions differ among lineages. Importantly, it suggests how to translate pedigree-based estimates of human mutation rates into split times among apes, given sex-specific life histories. In so doing, it helps bridge the gap between estimates of split times of apes based on fossil and molecular evidence. Finally, considering these effects can help to reconcile recent evidence that changes in generation times should have small effects on mutation rates in humans with classic studies suggesting that they have had major effects on rates of evolution in the mammalian phylogeny.
Ancienttrans-acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response
Authors: Plavskin Yevgeniy , Nagashima Akitomo , Perroud Pierre-François , Hasebe Mitsuyasu , Quatrano Ralph S. , Atwal Gurinder S. , Timmermans Marja C.P. 
Published: August 2015

ABSTRACTNovel developmental programs often evolve via cooption of existing genetic networks. To understand this process, we explored cooption of theTAS3tasiRNA pathway in the mossPhyscomitrella patens. We find an ancestral function for this repeatedly redeployed pathway in the spatial regulation of a conserved set of Auxin Response Factors. In moss, this results in stochastic patterning of the filamentous protonemal tissue. Through modeling and experimentation, we demonstrate that tasiRNA regulation confers sensitivity and robustness onto the auxin response. Increased auxin sensitivity parallels increased developmental sensitivity to nitrogen, a key environmental signal. We propose that the properties lent to the auxin response network, along with the ability to stochastically modulate development in response to environmental cues, have contributed to the tasiRNA-ARF module’s repeated cooption during evolution. The signaling properties of a genetic network, and not just its developmental output, are thus critical to understanding the evolution of multicellular forms.
A conserved interaction between a C-terminal motif in Norovirus VPg and the HEAT-1 domain of eIF4G is essential for translation initiation
Authors: Leen Eoin N. , Sorgeloos Frédéric , Correia Samantha , Chaudhry Yasmin , Cannac Fabien , pastore Chiara , Xu Yingqi , Graham Stephen C. , Matthews Stephen J. , Goodfellow Ian G. , Curry Stephen 
Published: August 2015

AbstractTranslation initiation is a critical early step in the replication cycle of the positive-sense, single-stranded RNA genome of noroviruses, a major cause of gastroenteritis in humans. Norovirus RNA, which has neither a 5′ m7G cap nor an internal ribosome entry site (IRES), adopts an unusual mechanism to initiate protein synthesis that relies on interactions between the VPg protein covalently attached to the 5′-end of the viral RNA and eukaryotic initiation factors (eIFs) in the host cell.For murine norovirus (MNV) we previously showed that VPg binds to the middle fragment of eIF4G (4GM; residues 652-1132). Here we have used pull-down assays, fluorescence anisotropy, and isothermal titration calorimetry (ITC) to demonstrate that a stretch of ∼20 amino acids at the C terminus of MNV VPg mediates direct and specific binding to the HEAT-1 domain within the 4GM fragment of eIF4G. Our analysis further reveals that the MNV C-terminus binds to eIF4G HEAT-1 via a motif that is conserved in all known noroviruses. Fine mutagenic mapping suggests that the MNV VPg C terminus may interact with eIF4G in a helical conformation. NMR spectroscopy was used to define the VPg binding site on eIF4G HEAT-1, which was confirmed by mutagenesis and binding assays. We have found that this site is non-overlapping with the binding site for eIF4A on eIF4G HEAT-1 by demonstrating that norovirus VPg can form ternary VPg-eIF4G-eIF4A complexes. The functional significance of the VPg-eIF4G interaction was shown by the ability of fusion proteins containing the C-terminal peptide of MNV VPg to inhibit translation of norovirus RNA but not cap- or IRES-dependent translation. These observations define important structural details of a functional interaction between norovirus VPg and eIF4G and reveal a binding interface that might be exploited as a target for antiviral therapy.
Prediction of Primary Somatosensory Neuron Activity During Active Tactile Exploration
Authors: Campagner Dario , Evans Mathew , Bale Michael R. , Erskine Andrew , Petersen Rasmus S. 
Published: August 2015

ABSTRACTPrimary sensory neurons form the interface between world and brain. Their function is well-understood during passive stimulation but, under natural behaving conditions, sense organs are under active, motor control. In an attempt to predict primary neuron firing under natural conditions of sensorimotor integration, we recorded from primary mechanosensory neuronsof awake, head-fixed mice as they explored a pole with their whiskers, and simultaneously measured both whisker motion and forces with high-speed videography. Using Generalised Linear Models, we found that primary neuron responses were poorly predicted by kinematics but well-predicted by rotational forces acting on the whisker: both during touch and free-air whisker motion. These results are discrepant with previous studies of passive stimulation, but could be reconciled by differences in the kinematics-force relationship between active and passive conditions. Thus, simple statistical models can predict rich neural activity elicited by natural, exploratory behaviour involving active movement of the sense organs.
Borderline intellectual functioning and neurodevelopmental disorders: prevalence, comorbidities and treatment approaches
Authors: Hassiotis Angela 
Published: August 2015

Purpose– The purpose of this paper is to provide a synthesis of the literature on the topic of developmental framework and health comorbidities of children and adults with borderline intellectual functioning (BIF) and neurodevelopmental disorders.Design/methodology/approach– A rapid review of the literature and hand searching of relevant papers from 1999 to 2015 was carried out. Totally, 21 papers were identified covering a range of perspectives from neurodevelopmental trajectories to prevalence, treatment and service use.Findings– All papers were utilised and complemented a previous review which, however, had not covered the aspect of treatment approaches for this population. As a group they appear to have distinctly different profiles from people with mild intellectual disability and of peers with average intelligence.Practical implications– The evidence summary indicates an ongoing interest by the international scientific community in the topic of BIF. This group are often lost in the health system and may not receive appropriate care given their unique clinical profile. More should be done to increase clinicians’ awareness of their health needs.Originality/value– The paper adds substantially to a previous review of the topic. An international collaboration may help to increase the profile of this work and lead to further changes in the care these individuals receive across the diagnostic and treatment spectrum.
Diversity management through a neuro-scientific lens
Authors: Jeffrey Jackie 
Published: August 2015

Purpose
– Introduces the emerging evidence from the neurosciences and provides an account of how it is causing a learning and development practitioner to re-evaluate understanding of human diversity and therefore diversity management within organizations.

Design/methodology/approach
– Defines neuroplasticity and identifies four of the key findings before moving on to consider what this suggests about human diversity.

Findings
– Shows an application of this new knowledge to diversity management as a way of exploring how the concept of collective intelligence could lead to a transformation of this new knowledge into organizational development practices that meet the needs of all people.

Practical implications
– Advances the view that if organizations can find a way to connect people, places and ideas in a way that generates a deeper appreciation of the value proposition inherent in human diversity, the business case will make itself.

Social implications
– Recognizes the need for a collective intelligence that has the “potential to liberate us from the social and political hierarchies that have stood in the way of mankind’s advancement”.

Originality/value
– Claims that this new science of learning has the potential to create a revelation of personal constructs in a way that leads to a safe revolution in the way we view and appreciate each other.
On the damages detection in aluminium beam using Hilbert-Huang transformation
Authors: Nikolakopoulos Pantelis G. , Zavos Anastasios , Bompos Dimitrios A. 
Published: August 2015

Purpose– Continuous on-line monitoring of structural integrity are in priority in many engineering fields such as aerospace, automotive, civilian structures, and industrial applications. Of all these possible applications, the aerospace industry has one of the highest payoffs. Possible damage can lead to catastrophic failures and costly inspections. On the other hand, processing a signal consists of important feature from sensors measurements to reach the considered target. Typically, the sensors translate a physical phenomenon from one or many sources in temporal variations or in spatial variations. The purpose of this paper is to investigate damages, in terms of suddenly screw removal or in a small cut, detection in vibrating (clamped-free) aluminum beam structures using the empirical mode decomposition (EMD) method along with the Hilbert-Huang transformation (HHT). The perspective is to identify very small defects in real aircraft structures.Design/methodology/approach– The proposed method deals with a new time-frequency signal processing analysis tool, for damages detection in a vibrating plate. An experimental test ring is used in order to excite a clamped-free aluminum plate. Two types of excitations are used. The first one is a harmonic excitation and the second one is a random excitation provided by an impact hammer. A hole and its filled by a screw with mass of 0.2 g, and a small cut is created, simulating a cut creation, are produced afterword, and the HHT is used in order to arise the developed oscillations, and to reveal hidden reflections in the data and to provide a high-resolution energy-time frequency spectrum.Findings– The major finding was the clear amplitude increment either for screw removal or for cut creation, using the EMD process with the HHT, giving the possibility to detect them.Originality/value– The use of the HHT to detect, using an experimental procedure, two different defects: a suddenly screw removal and a cut creation, in a clamped-free beam, excited by non-stationary and non-linear signals.
Numerical simulation of tensile behavior of corroded aluminum alloy 2024 T3
Authors: Setsika Dorothea , Tserpes Konstantinos , Pantelakis Spiros 
Published: August 2015

Purpose
– The purpose of this paper is to develop a multi-scale modeling approach for simulating the tensile behavior of corroded aluminum alloy 2024 T3.

Design/methodology/approach
– The approach combines two FE models: a model of a three-dimensional representative unit cell representing a pit and a model of the tensile specimen. The models lie at the micro- and macro-scales, respectively. The local homogenized mechanical behavior of the corroded material is simulated for different pit configurations. Then, the behavior of the pits is introduced into different areas (elements) of the tensile specimen and final analyses are performed to simulate the mechanical behavior of the corroded material. The approach has been applied to six different exposure periods of the exfoliation corrosion test.

Findings
– The numerical results show that the presence of pits and exfoliated areas reduces the yield strength of the material. The comparison of predicted elongation to fracture with the experimental of each exposure period value allows for the indirect assessment of the effect of hydrogen embrittlement.

Originality/value
– Since the characteristics of corrosion damage evolution with exposure time are constant for the specific material, the model could be applied for the simulation of the mechanical behavior of any corroded structural part (e.g. a mechanically fastened panel) made from the aluminum 2024 T3 alloy.
Enterprise education with Chinese characteristics; policy, practices and uneven development in PRC
Authors: Anderson Alistair R. , Zhang Xiuxiang 
Published: August 2015

Purpose
– The paper aims to review the emergence and nature of entrepreneurship education in China. This paper considers the variability of developments in practices despite policy. In turn, this allows one to consider the implications of this uneven distribution of expertise and resources.

Design/methodology/approach
– The paper is primarily empirically descriptive, but it draws upon different literatures to examine entrepreneurship education in the uniqueness of its Chinese context. The authors offer two comparative cases to illustrate the arguments.

Findings
– Substantial differences were found by region and by the status of the institution. The region aspect is paradoxical because the largest number of new businesses exists in those regions with the best provision of enterprise education. The channelling of resources to elite resources compounds the problem. Less prestigious universities make do with what they have, and this may be detrimental for the quality and effectiveness of enterprise education.

Research limitations/implications
– There may be some regional differences that have been overlooked, but the thrust is clear. Different resource allocations have shaped entrepreneurship education in the regions.

Practical implications
– Applied policy may have detrimental effects on less well-endowed universities and thus neglect less entrepreneurial places.

Social implications
– If entrepreneurship is to deliver its promise of opportunity, innovation and job creation, it needs to be taught by experienced and informed faculty. The uneven distribution of entrepreneurship pedagogy and expertise indicates that this may be more difficult to deliver in some places.

Originality/value
– Although entrepreneurship education in China is now pervasive, little work has been done in comparing policies with practices.
EDITOR'S CHOICE: Enhancing gardens as habitats for flower‐visiting aerial insects (pollinators): should we plant native or exotic species?
Authors: Salisbury Andrew , Armitage James , Bostock Helen , Perry Joe , Tatchell Mark , Thompson Ken 
Published: August 2015

Summary

Domestic gardens typically consist of a mixture of native and non‐native plants which support biodiversity and provide valuable ecosystem services, particularly in urban environments. Many gardeners wish to encourage biodiversity by choosing appropriate plant taxa. The value of native and non‐native plants in supporting animal biodiversity is, however, largely unknown.

The relative value of native and non‐native garden plants to invertebrates was investigated in a replicated field experiment. Plots (deliberately akin to garden borders) were planted with one of three treatments, representing assemblages of plants based on origin (native, near‐native and exotic). Invertebrates and resource measurements were recorded over four years. This paper reports the abundance of flower‐visiting aerial insects (‘pollinators’) associated with the three plant assemblages.

For all pollinator groups on all treatments, greater floral resource resulted in an increase in visits. There was, however, a greater abundance of total pollinators recorded on native and near‐native treatments compared with the exotic plots. Short‐tongued bumblebees followed the same pattern whilst more hoverflies were recorded on the native treatment than the other treatments, and more honeybees on the near‐native treatment. There was no difference between treatments in abundance of long‐tongued bumblebees or solitary bees. The lack of difference in solitary bee abundance between treatments was probably due to a third of individuals from this group being recorded on one exotic plant species.

The number of flower visitors corresponded to the peak flowering period of the treatments, that is there were fewer flower visitors to the exotic treatment compared with the other treatments in early summer but relatively more later in the season.

Synthesis and applications. This experiment has demonstrated that utilizing plants from only a single region of origin (i.e. nativeness) may not be an optimal strategy for resource provision for pollinating insects in gardens. Gardens can be enhanced as a habitat by planting a variety of flowering plants, biased towards native and near‐native species but with a selection of exotics to extend the flowering season and potentially provide resources for specialist groups.
Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type‐specific adaptation
Authors: Bruchmann Sebastian , Muthukumarasamy Uthayakumar , Pohl Sarah , Preusse Matthias , Bielecka Agata , Nicolai Tanja , Hamann Isabell , Hillert Roger , Kola Axel , Gastmeier Petra , Eckweiler Denitsa , Häussler Susanne 
Published: August 2015

SummaryHealth‐care‐associated infections by multi‐drug‐resistant bacteria constitute one of the greatest challenges to modern medicine. Bacterial pathogens devise various mechanisms to withstand the activity of a wide range of antimicrobial compounds, among which the acquisition of carbapenemases is one of the most concerning. In Klebsiella pneumoniae, the dissemination of the K. pneumoniae carbapenemase is tightly connected to the global spread of certain clonal lineages. Although antibiotic resistance is a key driver for the global distribution of epidemic high‐risk clones, there seem to be other adaptive traits that may explain their success. Here, we exploited the power of deep transcriptome profiling (RNA‐seq) to shed light on the transcriptomic landscape of 37 clinical K. pneumoniae isolates of diverse phylogenetic origins. We identified a large set of 3346 genes which was expressed in all isolates. While the core‐transcriptome profiles varied substantially between groups of different sequence types, they were more homogenous among isolates of the same sequence type. We furthermore linked the detailed information on differentially expressed genes with the clinically relevant phenotypes of biofilm formation and bacterial virulence. This allowed for the identification of a diminished expression of biofilm‐specific genes within the low biofilm producing ST258 isolates as a sequence type‐specific trait.