bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overexpression of RelA/SpoT homologs, PpRSH2a and PpRSH2b, induces the growth suppression of the moss Physcomitrella patens
Authors: Sato Michio , Takahashi Tomohiro , Ochi Kozo , Matsuura Hideyuki , Nabeta Kensuke , Takahashi Kosaku 
Published: September 2014

Abstract
Two genes encoding RelA/SpoT homologs, PpRSH2a and PpRSH2b, which are involved in the synthesis of bacterial alarmone guanosine 5′-diphosphate 3′-diphosphate (ppGpp) for the stringent response, were isolated from the moss, Physcomitrella patens. A complementary analysis of PpRSH2a and PpRSH2b in Escherichia coli showed that these genes had ppGpp biosynthetic activity. The recombinant PpRSH2a and PpRSH2b were also shown to synthesize ppGpp in vitro. Both proteins were localized to the chloroplasts of P. patens. Expression of the PpRSH genes was induced upon treatment with abscisic acid or abiotic stresses, such as dehydration and UV irradiation. Overexpression of PpRSH2a and PpRSH2b caused suppression of the growth in response to 1% (w/v) of glucose. The present study suggests the existence of a mechanism to regulate the growth of P. patens, which is governed by plant RSH in chloroplasts
Mergers drive spin swings along the cosmic web
Authors: Welker C. , Devriendt J. , Dubois Y. , Pichon C. , Peirani S. 
Published: September 2014

Abstract
The close relationship between mergers and the reorientation of the spin for galaxies and their host dark haloes is investigated using a cosmological hydrodynamical simulation (Horizon-AGN). Through a statistical analysis of merger trees, we show that spin swings are mainly driven by mergers along the filamentary structure of the cosmic web, and that these events account for the preferred perpendicular orientation of massive galaxies with respect to their nearest filament. By contrast, low-mass galaxies (Ms &lt; 1010 M⊙ at redshift 1.5) having undergone very few mergers, if at all, tend to possess a spin well aligned with their filament. Haloes follow the same trend as galaxies but display a greater sensitivity to smooth anisotropic accretion. The relative effect of mergers on magnitude is qualitatively different for minor and major mergers: mergers (and diffuse accretion) generally increase the magnitude of the specific angular momentum, but major mergers also give rise to a population of objects with less specific angular momentum left. Without mergers, secular accretion builds up the specific angular momentum of galaxies but not that of haloes. It also (re)aligns galaxies with their filament.
The dust masses of powerful radio galaxies: clues to the triggering of their activity
Authors: Tadhunter C. , Dicken D. , Morganti R. , Konyves V. , Ysard N. , Nesvadba N. , Almeida C. Ramos 
Published: September 2014

Abstract
We use deep Herschel Space Observatory observations of a 90 per cent complete sample of 32 intermediate-redshift 2Jy radio galaxies (0.05 &lt; z &lt; 0.7) with strong emission lines to estimate the dust masses of their host galaxies and thereby investigate the triggering mechanisms for their quasar-like AGN. The dust masses derived for the radio galaxies (7.2 × 105 &lt; Md &lt; 2.6 × 108 M⊙) are intermediate between those of quiescent elliptical galaxies on the one hand, and ultraluminous infrared galaxies (ULIRGs) on the other. Consistent with simple models for the co-evolution of supermassive black holes and their host galaxies, these results suggest that most radio galaxies represent the late time re-triggering of AGN activity via mergers between the host giant elliptical galaxies and companion galaxies with relatively low gas masses. However, a minority of the radio galaxies in our sample (∼20 per cent) have high, ULIRG-like dust masses, along with evidence for prodigious star formation activity. The latter objects are more likely to have been triggered in major, gas-rich mergers that represent a rapid growth phase for both their host galaxies and their supermassive black holes.
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression
Authors: Libbrecht Maxwell W. , Ay Ferhat , Hoffman Michael M. , Gilbert David M. , Bilmes Jeffrey A. , Noble William Stafford 
Published: September 2014

AbstractThe genomic neighborhood of a gene influences its activity, a behavior that is attributable in part to domain-scale regulation, in which regions of hundreds or thousands of kilobases known as domains are regulated as a unit. Previous studies using genomics assays such as chromatin immunoprecipitation (ChIP)-seq and chromatin conformation capture (3C)-based assays have identified many types of regulatory domains. However, due to the difficulty of integrating genomics data sets, the relationships among these domain types are poorly understood. Semi-automated genome annotation (SAGA) algorithms facilitate human interpretation of heterogeneous collections of genomics data by simultaneously partitioning the human genome and assigning labels to the resulting genomic segments. However, existing SAGA methods can incorporate only data sets that can be expressed as a one-dimensional vector over the genome and therefore cannot integrate inherently pairwise chromatin conformation data. We developed a new computational method, called graph-based regularization (GBR), for expressing apairwise priorthat encourages certain pairs of genomic loci to receive the same label in a genome annotation. We used GBR to exploit chromatin conformation information during genome annotation by encouraging positions that are close in 3D to occupy the same type of domain. Using this approach, we produced a comprehensive model of chromatin domains in eight human cell types, thereby revealing the relationships among known domain types. Through this model, we identified clusters of tightly-regulated genes expressed in only a small number of cell types, which we term “specific expression domains.” We additionally found that a subset of domain boundaries marked by promoters and CTCF motifs are consistent between cell types even when domain activity changes. Finally, we showed that GBR can be used for the seemingly unrelated task of transferring information from well-studied cell types to less well characterized cell types during genome annotation, making it possible to produce high-quality annotations of the hundreds of cell types with limited available data.
An introduction to LifeLines DEEP: study design and baseline characteristics
Authors: Tigchelaar Ettje F. , Zhernakova Alexandra , Dekens Jackie A.M. , Hermes Gerben , Baranska Agnieszka , Mujagic Zlatan , Swertz Morris A. , Muñoz Angélica M. , Deelen Patrick , Cénit Maria C. , Franke Lude , Scholtens Salome , Stolk Ronald P. , Wijmenga Cisca , Feskens Edith J.M. 
Published: September 2014

ABSTRACTThere is a critical need for population-based prospective cohort studies because they follow individuals before the onset of disease, allowing for studies that can identify biomarkers and disease-modifying effects and thereby contributing to systems epidemiology. This paper describes the design and baseline characteristics of an intensively examined subpopulation of the LifeLines cohort in the Netherlands. For this unique sub-cohort, LifeLines DEEP, additional blood (n=1387), exhaled air (n=1425), fecal samples (n=1248) and gastrointestinal health questionnaires (n=1176) were collected for analysis of the genome, epigenome, transcriptome, microbiome, metabolome and other biological levels. Here, we provide an overview of the different data layers in LifeLines DEEP and present baseline characteristics of the study population including food intake and quality of life. We also describe how the LifeLines DEEP cohort allows for the detailed investigation of genetic, genomic and metabolic variation on a wealth of phenotypic outcomes. Finally, we examine the determinants of gastrointestinal health, an area of particular interest to us that can be addressed by LifeLines DEEP.
Structural Basis for the Oligomerization of the MADS Domain Transcription Factor SEPALLATA3 in Arabidopsis
Authors: Puranik Sriharsha , Acajjaoui Samira , Conn Simon , Costa Luca , Conn Vanessa , Vial Anthony , Marcellin Romain , Melzer Rainer , Brown Elizabeth , Hart Darren , Theißen Günter , Silva Catarina S. , Parcy François , Dumas Renaud , Nanao Max , Zubieta Chloe 
Published: September 2014

Abstract
In plants, MADS domain transcription factors act as central regulators of diverse developmental pathways. In Arabidopsis thaliana, one of the most central members of this family is SEPALLATA3 (SEP3), which is involved in many aspects of plant reproduction, including floral meristem and floral organ development. SEP3 has been shown to form homo and heterooligomeric complexes with other MADS domain transcription factors through its intervening (I) and keratin-like (K) domains. SEP3 function depends on its ability to form specific protein-protein complexes; however, the atomic level determinants of oligomerization are poorly understood. Here, we report the 2.5-Å crystal structure of a small portion of the intervening and the complete keratin-like domain of SEP3. The domains form two amphipathic alpha helices separated by a rigid kink, which prevents intramolecular association and presents separate dimerization and tetramerization interfaces comprising predominantly hydrophobic patches. Mutations to the tetramerization interface demonstrate the importance of highly conserved hydrophobic residues for tetramer stability. Atomic force microscopy was used to show SEP3-DNA interactions and the role of oligomerization in DNA binding and conformation. Based on these data, the oligomerization patterns of the larger family of MADS domain transcription factors can be predicted and manipulated based on the primary sequence.
Influence of thermal deformation of drilling machine on hole registration accuracy
Authors: Zou Haitian , Wang Baolin 
Published: September 2014

Purpose
– The purpose of this study was to investigate the thermal deformation effect of a machine tool frame on hole registration accuracy. Hole registration accuracy represents the drilling performance of a machine tool, and it greatly depends on the thermal deformation of the machine frame structures in practical engineering. Reducing thermally induced errors is crucial to improve the hole quality.

Design/methodology/approach
– First, the thermal design of the machine frame was performed via an optimization procedure to reduce the thermal deformation at an early stage. Then, a thermal–mechanical coupling finite element method model was established to quantify the thermal deformation of the machine tool under environmental temperature fluctuations, and the validity of the presented model was confirmed experimentally using laser interferometry. Finally, a series of drilling tests, including micro-holes and medium holes, was carried out to practically investigate the hole drilling registration accuracy of the machine with a mineral casting frame under different thermal conditions.

Findings
– Hole registration accuracy showed positional dependency and distinctly non-linear behaviour at different drilling axes which was closely related with the thermal conditions. The positional deviations of medium holes and micro-holes all showed an increasing trend in different degrees under the same temperature fluctuations, and the former were more sensitive to the latter. Therefore, keeping the drilling workshop under thermally stable conditions is crucial for improving the drilling performance of the machine.

Originality/value
– The goal of this paper is to reveal the mechanism of hole registration accuracy variations with thermal fluctuations and to provide a strategy for the machine tool industry to further improve the drilling performance during the machining process.
Product weakness finder: an opinion-aware system through sentiment analysis
Authors: Wang Hongwei , Wang Wei 
Published: September 2014

Purpose
– Extant methods of product weakness detection usually depend on time-consuming questionnaire with high artificial involvement, so the efficiency and accuracy are not satisfied. The purpose of this paper is to propose an opinion-aware analytical framework – PRODWeakFinder – to expect to detect product weaknesses through sentiment analysis in an effective way.

Design/methodology/approach
– PRODWeakFinder detects product weakness by considering both comparative and non-comparative evaluations in online reviews. For comparative evaluation, an aspect-oriented comparison network is built, and the authority is assessed for each node by network analysis. For non-comparative evaluation, sentiment score is calculated through sentiment analysis. The composite score of aspects is calculated by combing the two types of evaluations.

Findings
– The experiments show that the comparative authority score and the non-comparative sentiment score are not highly correlated. It also shows that PRODWeakFinder outperforms the baseline methods in terms of accuracy.

Research limitations/implications
– Semantic-based method such as ontology are expected to be applied to identify the implicit features. Furthermore, besides PageRank, other sophisticated network algorithms such as HITS will be further employed to improve the framework.

Practical implications
– The link-based network is more suitable for weakness detection than the weight-based network. PRODWeakFinder shows the potential on reducing overall costs of detecting product weaknesses for companies.

Social implications
– A quicker and more effective way would be possible for weakness detection, enabling to reduce product defects and improve product quality, and thus raising the overall social welfare.

Originality/value
– An opinion-aware analytical framework is proposed to sentiment mining of online product reviews, which offer important implications regarding how to detect product weaknesses.
Evaluating the role of a humanoid robot to support learning in children with profound and multiple disabilities
Authors: Hedgecock Joseph , Standen P.J. , Beer Charlotte , Brown David , S. Stewart David 
Published: September 2014

Purpose
– The purpose of this paper is to identify ways teachers might employ a robot to achieve learning objectives with pupils with intellectual disabilities and potential outcome measures.

Design/methodology/approach
– A series of five case studies where teacher-pupil dyads were observed during five planned video-recorded sessions with a humanoid robot. Engagement was rated in a classroom setting and during the last session with the robot. Video recordings were analysed for duration of engagement, teacher assistance and number of goals achieved.

Findings
– Teachers identified a wide range of learning objectives ranging from an appreciation of cause and effect to improving the pupil's sense of direction. The robot's role could be to reward behaviour, provide cues or provide an active element to learning. Rated engagement was significantly higher with the robot than in the classroom.

Research limitations/implications
– A robot with a range of functions that allowed it to be engaging and motivating for the wide range of pupils in special education would be expensive and require teachers to learn how to use it. The findings identify ways to provide evidence that this expenditure of time and money is worthwhile.

Originality/value
– There is almost no research teachers can refer to on using robots to support learning in children with intellectual disabilities. This paper is therefore of value for researchers who wish to investigate using robots to educate children with intellectual disabilities, as it can provide vital information to aid study design.
Close range depth sensing cameras for virtual reality based hand rehabilitation
Authors: Charles Darryl , Pedlow Katy , McDonough Suzanne , Shek Ka , Charles Therese 
Published: September 2014

Purpose
– The Leap Motion represents a new generation of depth sensing cameras designed for close range tracking of hands and fingers, operating with minimal latency and high spatial precision (0.01 mm). The purpose of this paper is to develop virtual reality (VR) simulations of three well-known hand-based rehabilitation tasks using a commercial game engine and utilising a Leap camera as the primary mode of interaction. The authors present results from an initial evaluation by professional clinicians of these VR simulations for use in their hand and finger physical therapy practice.

Design/methodology/approach
– A cross-disciplinary team of researchers collaborated with a local software company to create three dimension interactive simulations of three hand focused rehabilitation tasks: Cotton Balls, Stacking Blocks, and the Nine Hole Peg Test. These simulations were presented to a group of eight physiotherapists and occupational therapists (n=8) based in the Regional Acquired Brain Injury Unit, Belfast Health, and Social Care Trust for evaluation. After induction, the clinicians attempted the tasks presented and provided feedback by filling out a questionnaire.

Findings
– Results from questionnaires (using a Likert scale 1-7, where 1 was the most favourable response) revealed a positive response to the simulations with an overall mean score across all questions equal to 2.59. Clinicians indicated that the system contained tasks that were easy to understand (mean score 1.88), and though it took several attempts to become competent, they predicted that they would improve with practice (mean score 2.25). In general, clinicians thought the prototypes provided a good illustration of the tasks required in their practice (mean score 2.38) and that patients would likely be motivated to use the system (mean score 2.38), especially young patients (mean score 1.63), and in the home environment (mean score 2.5).

Originality/value
– Cameras offer an unobtrusive and low maintenance approach to tracking user motion in VR therapy in comparison to methods based on wearable technologies. This paper presents positive results from an evaluation of the new Leap Motion camera for input control of VR simulations or games. This mode of interaction provides a low cost, easy to use, high-resolution system for tracking fingers and hands, and has great potential for home-based physical therapies, particularly for young people.
Using Wii technology to explore real spaces via virtual environments for people who are blind
Authors: Lahav O. , Gedalevitz H. , Battersby S. , Brown D. , Evett L. , Merritt P. 
Published: September 2014

Purpose– Virtual environments (VEs) that represent real spaces (RSs) give people who are blind the opportunity to build a cognitive map in advance that they will be able to use when arriving at the RS. The paper aims to discuss this issue.Design/methodology/approach– In this research study Nintendo Wii-based technology was used for exploring VEs via the Wiici application. The Wiimote allows the user to interact with VEs by simulating walking and scanning the space.Findings– By getting haptic and auditory feedback the user learned to explore new spaces. The authors examined the participants’ abilities to explore new simple and complex places, construct a cognitive map, and perform orientation tasks in the RS.Originality/value– To the authors’ knowledge, this finding presents the first VE for people who are blind that allow the participants to scan the environment and by this to construct map model spatial representations.
A contextualistic approach to antisocial personality
Authors: Carmelo Visdómine-Lozano J. 
Published: September 2014

Purpose
– The purpose of this paper is to introduce a contextualistic account of antisocial responding, with the addition of recent developments on the study of personality.

Design/methodology/approach
– A behavioural and contextualistic view point is developed to account for antisocial personality and related topics, inasmuch as traditional definitions of antisocial personality disorder as provided on formal diagnostic manuals derive on several and not always coherent classifications of antisocial behaviours. Some of these classifications centre on issues like guilt, impulsivity or aggressiveness for establishing different types of offending and antisocial patterns. This paper focuses on functional personal backgrounds.

Findings
– A total of five types of “potentiated contingencies” are described as being the main underpinnings involved in antisocial patterns. An analysis of the transformation of aversive functions of antisocial behaviours, leads to specify a distinctive rule-following behaviour that is concerned with that responding. Finally, the exposition of the four verbal clinical contexts that behaviour analysis highlights as taking place at therapeutic settings, serves to propose a fitter contextualistic intervention for antisocial personality patterns.

Research limitations/implications
– Novel investigations should contrast the functional classification of antisocial responding. Those studies should experimentally demonstrate the way in which the different instances of transformation of antisocial functions the author has described are prompted.

Practical implications
– The analysis also allows for the anticipation of the behaviour of individuals fitting to every category of antisocial avoidance. And as the functional analysis of “antisocial avoidance” uncovers specific relations between environmental stimuli as they are produced and established in the history of interactions of individuals, a more fitting intervention based upon those relations is feasible.

Originality/value
– An exhaustive functional taxonomy of antisocial personalities and delinquent behaviours has never been presented before elsewhere. Besides the author reinterprets from a contextualist position traditional empirical studies.