bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of the axial magnetic field on coexisting stimulated Raman and Brillouin scattering of a circularly polarized beam
Authors: Vyas Ashish , Sharma Swati , Singh Ram Kishor , Sharma R.P.
Published: December 2016

This paper presents a model to study the two prominent coexisting instabilities, stimulated Raman (SRS), and stimulated Brillouin scattering (SBS) in the presence of background axial magnetic field. In the context of laser-produced plasmas, this model is very useful in the situations where a self-generated axial magnetic field is present as well as where an external axial magnetic field is applied. Due to the interplay between both the scattering processes, the behavior of one scattering process is greatly modified in the presence of another coexisting scattering process. The impact of this coexisting phenomenon and axial magnetic field on the back reflectivity of scattered beams has been explored. It has been demonstrated that the back reflectivity gets modified significantly due to the coexistence of both the scattering processes (SRS and SBS) as well as due to the axial magnetic field. Results are also compared with the three-wave interaction case (isolated SRS or SBS case).
Sketching in three dimensions: A beautification scheme
Authors: Shankar Sree , Rai Rahul
Published: December 2016

Primary among all the activities involved in conceptual design is freehand sketching. There have been significant efforts in recent years to enable digital design methods that leverage humans’ sketching skills. Conventional sketch-based digital interfaces are built on two-dimensional touch-based devices like sketchers and drawing pads. The transition from two-dimensional to three-dimensional (3-D) digital sketch interfaces represents the latest trend in developing new interfaces that embody intuitiveness and human–human interaction characteristics. In this paper, we outline a novel screenless 3-D sketching system. The system uses a noncontact depth-sensing RGB-D camera for user input. Only depth information (no RGB information) is used in the framework. The system tracks the user's palm during the sketching process and converts the data into a 3-D sketch. As the generated data is noisy, making sense of what is sketched is facilitated through a beautification process that is suited to 3-D sketches. To evaluate the performance of the system and the beautification scheme, user studies were performed on multiple participants for both single-stroke and multistroke sketching scenarios.
Pilot study to harmonize the reported influenza intensity levels within the Spanish Influenza Sentinel Surveillance System (SISSS) using the Moving Epidemic Method (MEM)
Authors: BANGERT M. , GIL H. , OLIVA J. , DELGADO C. , VEGA T. , DE MATEO S. , LARRAURI A. ,   the Epidemiology Working Group of the Spanish Influenza Sentinel Surveillance System
Published: December 2016

The intensity of annual Spanish influenza activity is currently estimated from historical data of the Spanish Influenza Sentinel Surveillance System (SISSS) using qualitative indicators from the European Influenza Surveillance Network. However, these indicators are subjective, based on qualitative comparison with historical data of influenza-like illness rates. This pilot study assesses the implementation of Moving Epidemic Method (MEM) intensity levels during the 2014–2015 influenza season within the 17 sentinel networks covered by SISSS, comparing them to historically reported indicators. Intensity levels reported and those obtained with MEM at the epidemic peak of the influenza wave, and at national and regional levels did not show statistical difference (P = 0·74, Wilcoxon signed-rank test), suggesting that the implementation of MEM would have limited disrupting effects on the dynamic of notification within the surveillance system. MEM allows objective influenza surveillance monitoring and standardization of criteria for comparing the intensity of influenza epidemics in regions in Spain. Following this pilot study, MEM has been adopted to harmonize the reporting of intensity levels of influenza activity in Spain, starting in the 2015–2016 season.
The future of social care funding: who pays?
Authors: Kenny T. , Barnfield J. , Daly L. , Dunn A. , Passey D. , Rickayzen B. , Teow A.
Published: December 2016

With the UK population ageing, deciding upon a satisfactory and sustainable system for the funding of people’s long-term care (LTC) needs has long been a topic of political debate. Phase 1 of the Care Act 2014 (“the Act”) brought in some of the reforms recommended by the Dilnot Commission in 2011. However, the Government announced during 2015 that Phase 2 of “the Act” such as the introduction of a £72,000 cap on Local Authority care costs and a change in the means testing thresholds1 would be deferred until 2020. In addition to this delay, the “freedom and choice” agenda for pensions has come into force. It is therefore timely that the potential market responses to help people pay for their care within the new pensions environment should be considered. In this paper, we analyse whether the proposed reforms meet the policy intention of protecting people from catastrophic care costs, whilst facilitating individual understanding of their potential care funding requirements. In particular, we review a number of financial products and ascertain the extent to which such products might help individuals to fund the LTC costs for which they would be responsible for meeting. We also produce case studies to demonstrate the complexities of the care funding system. Finally, we review the potential impact on incentives for individuals to save for care costs under the proposed new means testing thresholds and compare these with the current thresholds. We conclude that:

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Although it is still too early to understand exactly how individuals will respond to the pensions freedom and choice agenda, there are a number of financial products that might complement the new flexibilities and help people make provision for care costs.

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The new care funding system is complex making it difficult for people to understand their potential care costs.

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The current means testing system causes a disincentive to save. The new means testing thresholds provide a greater level of reward for savers than the existing thresholds and therefore may increase the level of saving for care; however, the new thresholds could still act as a barrier since disincentives still exist.
Finding peace in clinical settings: A narrative review of concept and practice
Authors: Austin Philip , MacLeod Roderick
Published: December 2016

The purpose of this review was to investigate and review the concept of “peace” and the role it plays in the spiritual well-being and care of people with a chronic or terminal illness. Our objectives were, first, to examine the importance of peace in palliative care as a measure of acceptance and in chronic illness settings as a predictor of improved survival. Second, we explored the dimensions of peace and their relationships with spiritual well-being. We further examined how the constructs of peace are assessed both within valid spiritual well-being measures and as individual items related solely to peace. Finally, we examined therapies aimed at promoting peace and emotional well-being in palliative and chronic illness settings. Despite much being written about different constructs of peace and the positive effects of being at peace during times of illness, the effects of therapies on the feeling of peace are not well-studied.
The people have spoken: abide? A critical view of the EU’s dramatic referendum (in)experience
Authors: Auer Andreas
Published: December 2016

6 December 1992 – 9 February 2014 – 23 June 2016: three national referendums related to the European integration process, the first two in Switzerland, the third in the United Kingdom, with a hardly expected but unmistakably clear anti-European and anti-establishment outcome. The people have spoken, the matter is settled, governments have to abide. So goes the common understanding. In constitutional terms and in the theory of (direct) democracy, however, things may look different.
The relevance of uncertainty and goal conflict to mental disorders, their prevention and management: a unifying approach
Authors: Einstein Danielle A. , Mansell Warren
Published: December 2016

Intolerance of Uncertainty (IU) has been shown to underlie a range of disorders. Technological advances have produced a decline in our development of an ability to wait in the face of uncertainty. The paper provides an update on empirical, theoretical and neural research in IU. Einstein's extended trandiagnostic model of IU is described. This model is based on control theory. The research update and IU model propose specific tools which can be implemented within transdiagnostic treatment approaches.
Green tea extract intake during lactation modified cardiac macrophage infiltration and AMP-activated protein kinase phosphorylation in weanling rats from undernourished mother during gestation and lactation
Authors: Matsumoto E. , Kataoka S. , Mukai Y. , Sato M. , Sato S.
Published: December 2016

Maternal dietary restriction is often associated with cardiovascular disease in offspring. The aim of this study was to investigate the effect of green tea extract (GTE) intake during lactation on macrophage infiltration, and activation of adenosine monophosphate (AMP)-activated protein kinase (AMPK) and serine-threonine kinase Akt (Akt) in the hearts of weanlings exposed to maternal dietary protein restriction. Pregnant Wistar rats were fed control (C) or low-protein diets (LP) throughout gestation. Following delivery, the dams received a control or a GTE-containing control diet during lactation: control diet during gestation and lactation (CC), low-protein diet during gestation and lactation (LPC), low-protein diet during gestation and 0.12% GTE-containing low-protein diet during lactation (LPL), and low-protein diet during gestation and 0.24% GTE-containing low-protein diet during lactation (LPH). The female offspring were sacrificed at day 22. Biochemical parameters in the plasma, macrophage infiltration, degree of fibrosis and expression levels of AMPK and Akt were examined. The plasma insulin level increased in LPH compared with LPC. Percentage of the fibrotic areas and the number of macrophages in LPC were higher than those in CC. Conversely, the fibrotic areas and the macrophage number in LPH were smaller (21 and 56%, respectively) than those in LPC. The levels of phosphorylated AMPK in LPL and LPH, and Akt in LPH were greater than those in LPC. In conclusion, maternal protein restriction may induce macrophage infiltration and the decrease of insulin levels. However, GTE intake during lactation may suppress macrophage infiltration and restore insulin secretion function via upregulation of AMPK and insulin signaling in weanlings.
Education and Intelligence: Pity the Poor Teacher because Student Characteristics are more Significant than Teachers or Schools
Authors: Detterman Douglas K.
Published: December 2016

Education has not changed from the beginning of recorded history. The problem is that focus has been on schools and teachers and not students. Here is a simple thought experiment with two conditions: 1) 50 teachers are assigned by their teaching quality to randomly composed classes of 20 students, 2) 50 classes of 20 each are composed by selecting the most able students to fill each class in order and teachers are assigned randomly to classes. In condition 1, teaching ability of each teacher and in condition 2, mean ability level of students in each class is correlated with average gain over the course of instruction. Educational gain will be best predicted by student abilities (up tor= 0.95) and much less by teachers’ skill (up tor= 0.32). I argue that seemingly immutable education will not change until we fully understand students and particularly human intelligence. Over the last 50 years in developed countries, evidence has accumulated that only about 10% of school achievement can be attributed to schools and teachers while the remaining 90% is due to characteristics associated with students. Teachers account for from 1% to 7% of total variance at every level of education. For students, intelligence accounts for much of the 90% of variance associated with learning gains. This evidence is reviewed.
Advances in the Neuroscience of Intelligence: from Brain Connectivity to Brain Perturbation
Authors: Santarnecchi Emiliano , Rossi Simone
Published: December 2016

Our view is that intelligence, as expression of the complexity of the human brain and of its evolutionary path, represents an intriguing example of “system level brain plasticity”: tangible proofs of this assertion lie in the strong links intelligence has with vital brain capacities as information processing (i.e., pure, rough capacity to transfer information in an efficient way), resilience (i.e., the ability to cope with loss of efficiency and/or loss of physical elements in a network) and adaptability (i.e., being able to efficiently rearrange its dynamics in response to environmental demands). Current evidence supporting this view move from theoretical models correlating intelligence and individual response to systematic “lesions” of brain connectivity, as well as from the field of Noninvasive Brain Stimulation (NiBS). Perturbation-based approaches based on techniques as transcranial magnetic stimulation (TMS) and transcranial alternating current stimulation (tACS), are opening newin vivoscenarios which could allow to disclose more causal relationship between intelligence and brain plasticity, overcoming the limitations of brain-behavior correlational evidence
Emotional Responses to Disturbing Political News: The Role of Personality
Authors: Ryan Timothy J. , Wells Matthew S. , Acree Brice D. L.
Published: December 2016

Recent scholarship in political science identifies emotions as an important antecedent to political behavior. Existing work, however, has focused much more on the political effects of emotions than on their causes. Here, we begin to examine how personality moderates emotional responses to political events. We hypothesized that the personality trait need for affect (NFA) would moderate the emotions evoked by disturbing political news. Drawing data from a survey experiment conducted on a national sample, we find that individuals high in NFA have an especially vivid emotional response to disturbing news—a moderating relationship that has the potential to surpass those associated with symbolic attachments.
HnRNPA2 is a novel histone acetyltransferase that mediates mitochondrial stress-induced nuclear gene expression
Authors: Guha Manti , Srinivasan Satish , Guja Kip , Mejia Edison , Garcia-Diaz Miguel , Johnson F Brad , Ruthel Gordon , Kaufman Brett A , Rappaport Eric F , Glineburg M Rebecca , Fang Ji-Kang , Szanto Andres Klein , Nakagawa Hiroshi , Basha Jeelan , Kundu Tapas , Avadhani Narayan G
Published: December 2016

Reduced mitochondrial DNA copy number, mitochondrial DNA mutations or disruption of electron transfer chain complexes induce mitochondria-to-nucleus retrograde signaling, which induces global change in nuclear gene expression ultimately contributing to various human pathologies including cancer. Recent studies suggest that these mitochondrial changes cause transcriptional reprogramming of nuclear genes although the mechanism of this cross talk remains unclear. Here, we provide evidence that mitochondria-to-nucleus retrograde signaling regulates chromatin acetylation and alters nuclear gene expression through the heterogeneous ribonucleoprotein A2 (hnRNAP2). These processes are reversed when mitochondrial DNA content is restored to near normal cell levels. We show that the mitochondrial stress-induced transcription coactivator hnRNAP2 acetylates Lys 8 of H4 through an intrinsic histone lysine acetyltransferase (KAT) activity with Arg 48 and Arg 50 of hnRNAP2 being essential for acetyl-CoA binding and acetyltransferase activity. H4K8 acetylation at the mitochondrial stress-responsive promoters by hnRNAP2 is essential for transcriptional activation. We found that the previously described mitochondria-to-nucleus retrograde signaling-mediated transformation of C2C12 cells caused an increased expression of genes involved in various oncogenic processes, which is retarded in hnRNAP2 silenced or hnRNAP2 KAT mutant cells. Taken together, these data show that altered gene expression by mitochondria-to-nucleus retrograde signaling involves a novel hnRNAP2-dependent epigenetic mechanism that may have a role in cancer and other pathologies.
Defining functional interactions during biogenesis of epithelial junctions
Authors: Erasmus J. C. , Bruche S. , Pizarro L. , Maimari N. , Poggioli T. , Tomlinson C. , Lees J. , Zalivina I. , Wheeler A. , Alberts A. , Russo A. , Braga V. M. M.
Published: December 2016

In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases.
Blood flow controls bone vascular function and osteogenesis
Authors: Ramasamy Saravana K. , Kusumbe Anjali P. , Schiller Maria , Zeuschner Dagmar , Bixel M. Gabriele , Milia Carlo , Gamrekelashvili Jaba , Limbourg Anne , Medvinsky Alexander , Santoro Massimo M. , Limbourg Florian P. , Adams Ralf H.
Published: December 2016

While blood vessels play important roles in bone homeostasis and repair, fundamental aspects of vascular function in the skeletal system remain poorly understood. Here we show that the long bone vasculature generates a peculiar flow pattern, which is important for proper angiogenesis. Intravital imaging reveals that vessel growth in murine long bone involves the extension and anastomotic fusion of endothelial buds. Impaired blood flow leads to defective angiogenesis and osteogenesis, and downregulation of Notch signalling in endothelial cells. In aged mice, skeletal blood flow and endothelial Notch activity are also reduced leading to decreased angiogenesis and osteogenesis, which is reverted by genetic reactivation of Notch. Blood flow and angiogenesis in aged mice are also enhanced on administration of bisphosphonate, a class of drugs frequently used for the treatment of osteoporosis. We propose that blood flow and endothelial Notch signalling are key factors controlling ageing processes in the skeletal system.
Generation of internal solitary waves by frontally forced intrusions in geophysical flows
Authors: Bourgault Daniel , Galbraith Peter S. , Chavanne Cédric
Published: December 2016

Internal solitary waves are hump-shaped, large-amplitude waves that are physically analogous to surface waves except that they propagate within the fluid, along density steps that typically characterize the layered vertical structure of lakes, oceans and the atmosphere. As do surface waves, internal solitary waves may overturn and break, and the process is thought to provide a globally significant source of turbulent mixing and energy dissipation. Although commonly observed in geophysical fluids, the origins of internal solitary waves remain unclear. Here we report a rarely observed natural case of the birth of internal solitary waves from a frontally forced interfacial gravity current intruding into a two-layer and vertically sheared background environment. The results of the analysis carried out suggest that fronts may represent additional and unexpected sources of internal solitary waves in regions of lakes, oceans and atmospheres that are dynamically similar to the situation examined here in the Saguenay Fjord, Canada.
Targeting the Notch-regulated non-coding RNA TUG1 for glioma treatment
Authors: Katsushima Keisuke , Natsume Atsushi , Ohka Fumiharu , Shinjo Keiko , Hatanaka Akira , Ichimura Norihisa , Sato Shinya , Takahashi Satoru , Kimura Hiroshi , Totoki Yasushi , Shibata Tatsuhiro , Naito Mitsuru , Kim Hyun Jin , Miyata Kanjiro , Kataoka Kazunori , Kondo Yutaka
Published: December 2016

Targeting self-renewal is an important goal in cancer therapy and recent studies have focused on Notch signalling in the maintenance of stemness of glioma stem cells (GSCs). Understanding cancer-specific Notch regulation would improve specificity of targeting this pathway. In this study, we find that Notch1 activation in GSCs specifically induces expression of the lncRNA, TUG1. TUG1 coordinately promotes self-renewal by sponging miR-145 in the cytoplasm and recruiting polycomb to repress differentiation genes by locus-specific methylation of histone H3K27 via YY1-binding activity in the nucleus. Furthermore, intravenous treatment with antisense oligonucleotides targeting TUG1 coupled with a drug delivery system induces GSC differentiation and efficiently represses GSC growth in vivo. Our results highlight the importance of the Notch-lncRNA axis in regulating self-renewal of glioma cells and provide a strong rationale for targeting TUG1 as a specific and potent therapeutic approach to eliminate the GSC population.
Re-assessment of net energy production and greenhouse gas emissions avoidance after 40 years of photovoltaics development
Authors: Louwen Atse , van Sark Wilfried G. J. H. M. , Faaij André P. C. , Schropp Ruud E. I.
Published: December 2016

Since the 1970s, installed solar photovoltaic capacity has grown tremendously to 230 gigawatt worldwide in 2015, with a growth rate between 1975 and 2015 of 45%. This rapid growth has led to concerns regarding the energy consumption and greenhouse gas emissions of photovoltaics production. We present a review of 40 years of photovoltaics development, analysing the development of energy demand and greenhouse gas emissions associated with photovoltaics production. Here we show strong downward trends of environmental impact of photovoltaics production, following the experience curve law. For every doubling of installed photovoltaic capacity, energy use decreases by 13 and 12% and greenhouse gas footprints by 17 and 24%, for poly- and monocrystalline based photovoltaic systems, respectively. As a result, we show a break-even between the cumulative disadvantages and benefits of photovoltaics, for both energy use and greenhouse gas emissions, occurs between 1997 and 2018, depending on photovoltaic performance and model uncertainties.
Variability of space-use patterns in a free living eusocial rodent, Ansell’s mole-rat indicates age-based rather than caste polyethism
Authors: Šklíba Jan , Lövy Matěj , Burda Hynek , Šumbera Radim
Published: December 2016

Eusocial species of African mole-rats live in groups cooperating on multiple tasks and employing division of labour. In captivity, individuals of the same group differ in cooperative contribution as well as in preference for a particular task. Both can be viewed as polyethism. However, little information is available from free-ranging mole-rats, which live in large burrow systems. We made an attempt to detect polyethism in the free-living Ansell’s mole-rat (Fukomys anselli) as differences in individuals’ space-use patterns. We radio-tracked 17 adults from five groups. Large individuals, including breeding males, spent more time inside the nest than smaller individuals. Breeding females were more often located <10 m from the nest in comparison to non-breeding females, who were relatively more often located 30–90 m and exclusively >90 m from the nest. One non-breeding female even conducted a brief intrusion into a neighbouring group’s territory via an open tunnel connection. A significant part of the variability in mole-rat space-use patterns was explained by body mass which is probably related to age in this species. This result can therefore be attributed to age polyethism. There was no apparent discontinuity in the space-use patterns of non-breeders that would indicate existence of castes.
Fast and behavior-selective exploitation of a marine fish targeted by anglers
Authors: Alós Josep , Palmer Miquel , Rosselló Rosario , Arlinghaus Robert
Published: December 2016

Harvesting of wild-living animals is often intensive and may selectively target heritable behavioral traits. We studied the exploitation dynamics and the vulnerability consequences of individual heterogeneity in movement-related behaviors in free-ranging pearly razorfish (Xyrichthys novacula). Using underwater-video recording, we firstly document a fast and high exploitation rate of about 60% of the adult population removed in just few days after the opening of the season. Subsequently, we tagged a sample of individuals with acoustic transmitters and studied whether behavioral traits were significant predictors of the vulnerability to angling. Tagged individuals revealed repeatable behaviors in several home range-related traits, suggesting the presence of spatial behavioral types. The individuals surviving the experimental fishery showed only localized and low-intensity movement patterns. Our study provides new insights for understanding the harvesting pressures and selective properties acting on behavioral traits of recreational fishing. Many fish stocks around the globe are today predominantly exploited by recreational fisheries. The fisheries-induced change in fish behavior described here may be therefore widespread, and has the potential to alter food-webs, profitability of the fisheries and to affect stock assessment by eroding catchability in the long-term.
Systematic site-directed mutagenesis of the Helicobacter pylori CagL protein of the Cag type IV secretion system identifies novel functional domains
Authors: Bönig Tobias , Olbermann Patrick , Bats Simon H. , Fischer Wolfgang , Josenhans Christine
Published: December 2016

The Cag Type IV secretion system, which contributes to inflammation and cancerogenesis during chronic infection, is one of the major virulence factors of the bacterial gastric pathogen Helicobacter pylori. We have generated and characterized a series of non-marked site-directed chromosomal mutants in H. pylori to define domains of unknown function of the essential tip protein CagL of the Cag secretion system. Characterizing the CagL mutants, we determined that their function to activate cells and transport the effector CagA was reduced to different extents. We identified three novel regions of the CagL protein, involved in its structural integrity, its possible interaction with the CagPAI T4SS pilus protein CagI, and in its binding to integrins and other host cell ligands. In particular two novel variable CagL motifs were involved in integrin binding, TSPSA, and TASLI, which is located opposite of its integrin binding motif RGD. We thereby defined
functionally important subdomains within the CagL structure, which can be used to clarify CagL contributions in the context of other CagPAI proteins or for inhibition of the CagT4SS. This structure-function correlation of CagL domains can also be instructive for the functional characterization of other potential VirB5 orthologs whose structure is not yet known.
New arylated benzo[h]quinolines induce anti-cancer activity by oxidative stress-mediated DNA damage
Authors: Yadav Dharmendra K. , Rai Reeta , Kumar Naresh , Singh Surjeet , Misra Sanjeev , Sharma Praveen , Shaw Priyanka , Pérez-Sánchez Horacio , Mancera Ricardo L. , Choi Eun Ha , Kim Mi-hyun , Pratap Ramendra
Published: December 2016

The anti-cancer activity of the benzo[h]quinolines was evaluated on cultured human skin cancer (G361), lung cancer (H460), breast cancer (MCF7) and colon cancer (HCT116) cell lines. The inhibitory effect of these compounds on the cell growth was determined by the MTT assay. The compounds 3e, 3f, 3h and 3j showed potential cytotoxicity against these human cancer cell lines. Effect of active compounds on DNA oxidation and expression of apoptosis related gene was studied. We also developed a quantitative method to measure the activity of cyclin-dependent kinases-2 (CDK2) by western blotting in the presence of active compound. In addition, molecular docking revealed that benzo[h]quinolines can correctly dock into the hydrophobic pocket of the targets receptor protein aromatase and CDK2, while their bioavailability/drug-likeness was predicted to be acceptable but requires future optimization. These findings reveal that benzo[h]quinolines act as anti-cancer agents by inducing oxidative stress-mediated DNA damage.
Mining, visualizing and comparing multidimensional biomolecular data using the Genomics Data Miner (GMine) Web-Server
Authors: Proietti Carla , Zakrzewski Martha , Watkins Thomas S. , Berger Bernard , Hasan Shihab , Ratnatunga Champa N. , Brion Marie-Jo , Crompton Peter D. , Miles John J. , Doolan Denise L. , Krause Lutz
Published: December 2016

Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression. The software has a focus on multivariate techniques, which can attribute variance in the measurements to multiple explanatory variables and confounders. Various normalization methods are provided. Extensive help pages and a tutorial are available via a wiki server. Using GMine we reanalyzed proteome microarray data of host antibody response against Plasmodium falciparum. Our results support the hypothesis that immunity to malaria is a higher-order phenomenon related to a pattern of responses and not attributable to any single antigen. We also analyzed gene expression across resting and activated T cells, identifying many immune-related genes with differential expression. This highlights both the plasticity of T cells and the operation of a hardwired activation program. These application examples demonstrate that GMine facilitates an accurate and in-depth analysis of complex molecular datasets, including genomics, transcriptomics and proteomics data.
De Novo transcriptome characterization of Dracaena cambodiana and analysis of genes involved in flavonoid accumulation during formation of dragon’s blood
Authors: Zhu Jia-Hong , Cao Tian-Jun , Dai Hao-Fu , Li Hui-Liang , Guo Dong , Mei Wen-Li , Peng Shi-Qing
Published: December 2016

Dragon’s blood is a red resin mainly extracted from Dracaena plants, and has been widely used as a traditional medicine in East and Southeast Asia. The major components of dragon’s blood are flavonoids. Owing to a lack of Dracaena plants genomic information, the flavonoids biosynthesis and regulation in Dracaena plants remain unknown. In this study, three cDNA libraries were constructed from the stems of D. cambodiana after injecting the inducer. Approximately 266.57 million raw sequencing reads were de novo assembled into 198,204 unigenes, of which 34,873 unique sequences were annotated in public protein databases. Many candidate genes involved in flavonoid accumulation were identified. Differential expression analysis identified 20 genes involved in flavonoid biosynthesis, 27 unigenes involved in flavonoid modification and 68 genes involved in flavonoid transport that were up-regulated in the stems of D. cambodiana after injecting the inducer, consistent with the accumulation of flavonoids. Furthermore, we have revealed the differential expression of transcripts encoding for transcription factors (MYB, bHLH and WD40) involved in flavonoid metabolism. These de novo transcriptome data sets provide insights on pathways and molecular regulation of flavonoid biosynthesis and transport, and improve our understanding of molecular mechanisms of dragon’s blood formation in D. cambodiana.
The NMDA receptor GluN2C subunit controls cortical excitatory-inhibitory balance, neuronal oscillations and cognitive function
Authors: Gupta Subhash C. , Ravikrishnan Aparna , Liu Jinxu , Mao Zhihao , Pavuluri Ratnamala , Hillman Brandon G. , Gandhi Pauravi J. , Stairs Dustin J. , Li Ming , Ugale Rajesh R. , Monaghan Daniel T. , Dravid Shashank M.
Published: December 2016

Despite strong evidence for NMDA receptor (NMDAR) hypofunction as an underlying factor for cognitive disorders, the precise roles of various NMDAR subtypes remains unknown. The GluN2C-containing NMDARs exhibit unique biophysical properties and expression pattern, and lower expression of GluN2C subunit has been reported in postmortem brains from schizophrenia patients. We found that loss of GluN2C subunit leads to a shift in cortical excitatory-inhibitory balance towards greater inhibition. Specifically, pyramidal neurons in the medial prefrontal cortex (mPFC) of GluN2C knockout mice have reduced mEPSC frequency and dendritic spine density and a contrasting higher frequency of mIPSCs. In addition a greater number of perisomatic GAD67 puncta was observed suggesting a potential increase in parvalbumin interneuron inputs. At a network level the GluN2C knockout mice were found to have a more robust increase in power of oscillations in response to NMDAR blocker MK-801. Furthermore, GluN2C heterozygous and knockout mice exhibited abnormalities in cognition and sensorimotor gating. Our results demonstrate that loss of GluN2C subunit leads to cortical excitatory-inhibitory imbalance and abnormal neuronal oscillations associated with neurodevelopmental disorders.
Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development
Authors: Li Jingyu , Gao Zhengling , Wang Xingyu , Liu Hongbo , Zhang Yan , Liu Zhonghua
Published: December 2016

Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species. By weighted co-expression network analysis, we identified 5 developmental stages specific co-expression modules. Gene ontology enrichment analysis of these specific co-expression modules suggested that many lincRNAs are associated with cell cycle regulation, transcription and metabolism to regulate the process of zygotic genome activation. Futhermore, we identified hub lincRNAs in each co-expression modules, and found two lincRNAs TCONS_00166370 and TCONS_00020255 may play a vital role in porcine PED. This study systematically analyze lincRNAs in pig and provides the first catalog of lincRNAs that might function as gene regulatory factors of porcine PED.
miR-146a-mediated suppression of the inflammatory response in human adipocytes
Authors: Roos Julian , Enlund Eveliina , Funcke Jan-Bernd , Tews Daniel , Holzmann Karlheinz , Debatin Klaus-Michael , Wabitsch Martin , Fischer-Posovszky Pamela
Published: December 2016

The obesity-associated inflammation of white adipose tissue (WAT) is one of the factors leading to the development of related diseases such as insulin resistance and liver steatosis. Recently, microRNAs (miRNAs) were identified as important regulators of WAT functions. Herein, we cultured human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes with macrophage-conditioned medium (MacCM) and performed an Affimetrix miRNA array to identify miRNAs differentially expressed under inflammatory conditions. We identified 24 miRNAs differentially expressed upon inflammation in human adipocytes and miR-146a was the most up-regulated miRNA species. In subcutaneous WAT, miR-146a was elevated in both human and murine obesity. Transfection of miR-146a mimics prevented the MacCM-induced inflammatory response in SGBS adipocytes as seen by reduced levels of IL-8 and MCP-1 mRNA and protein. We identified IRAK1 and TRAF6 as targets of miR-146a in human adipocytes and detected a reduced inflammation-induced activation of JNK and p38 upon miR-146a transfection. Taken together, we could show that miR-146a reduces the inflammatory response in human adipocytes. In a negative feedback loop miR-146a might contribute to the regulation of inflammatory processes in WAT and possibly prevent an overwhelming inflammatory response.
Mast cell phenotype, TNFα expression and degranulation status in non-small cell lung cancer
Authors: Shikotra A. , Ohri C. M. , Green R. H. , Waller D. A. , Bradding P.
Published: December 2016

Mast cell infiltration of tumour islets represents a survival advantage in non-small cell lung cancer (NSCLC). The phenotype and activation status of these mast cells is unknown. We investigated the mast cell phenotype in terms of protease content (tryptase-only [MCT], tryptase + chymase [MCTC]) and tumour necrosis factor-alpha (TNFα) expression, and extent of degranulation, in NSCLC tumour stroma and islets. Surgically resected tumours from 24 patients with extended survival (ES; mean survival 86.5 months) were compared with 25 patients with poor survival (PS; mean survival 8.0 months) by immunohistochemistry. Both MCT and MCTC in tumour islets were higher in ES (20.0 and 5.6 cells/mm2 respectively) compared to PS patients (0.0 cells/mm2) (p < 0.0001). Both phenotypes expressed TNFα in the islets and stroma. In ES 44% of MCT and 37% of MCTC expressed TNFα in the tumour islets. MCT in the ES stroma were more degranulated than in those with PS (median degranulation index = 2.24 versus 1.73 respectively) (p = 0.0022), and ES islet mast cells (2.24 compared to 1.71, p < 0.0001). Since both MCT and MCTC infiltrating tumour islets in ES NSCLC patients express TNFα, the cytotoxic activity of this cytokine may confer improved survival in these patients. Manipulating mast cell microlocalisation and functional responses in NSCLC may offer a novel approach to the treatment of this disease.
Quantum State Transmission in a Superconducting Charge Qubit-Atom Hybrid
Authors: Yu Deshui , Valado María Martínez , Hufnagel Christoph , Kwek Leong Chuan , Amico Luigi , Dumke Rainer
Published: December 2016

Hybrids consisting of macroscopic superconducting circuits and microscopic components, such as atoms and spins, have the potential of transmitting an arbitrary state between different quantum species, leading to the prospective of high-speed operation and long-time storage of quantum information. Here we propose a novel hybrid structure, where a neutral-atom qubit directly interfaces with a superconducting charge qubit, to implement the qubit-state transmission. The highly-excited Rydberg atom located inside the gate capacitor strongly affects the behavior of Cooper pairs in the box while the atom in the ground state hardly interferes with the superconducting device. In addition, the DC Stark shift of the atomic states significantly depends on the charge-qubit states. By means of the standard spectroscopic techniques and sweeping the gate voltage bias, we show how to transfer an arbitrary quantum state from the superconducting device to the atom and vice versa.
A single-step method for RNA isolation from tropical crops in the field
Authors: Breitler J.-C. , Campa C. , Georget F. , Bertrand B. , Etienne H.
Published: December 2016

The RNAzol RT reagent was used to provide pure RNA from human cells. We develop a protocol using RNAzol RT reagent to extract pure RNA from plants tissues and demonstrate that this RNA extraction method works not only at room temperature but also at elevated temperatures and provides the simplest and most effective single-step method to extract pure and undegraded RNA directly from tropical plants in the field. RNA extraction directly in a complex field environment opens up the way for studying gene-environment interactions at transcriptome level to decipher the complex regulatory network involved in multiple-stress responses.
The impact of cold spells on mortality and effect modification by cold spell characteristics
Authors: Wang Lijun , Liu Tao , Hu Mengjue , Zeng Weilin , Zhang Yonghui , Rutherford Shannon , Lin Hualiang , Xiao Jianpeng , Yin Peng , Liu Jiangmei , Chu Cordia , Tong Shilu , Ma Wenjun , Zhou Maigeng
Published: December 2016

In China, the health impact of cold weather has received little attention, which limits our understanding of the health impacts of climate change. We collected daily mortality and meteorological data in 66 communities across China from 2006 to 2011. Within each community, we estimated the effect of cold spell exposure on mortality using a Distributed Lag Nonlinear Model (DLNM). We also examined the modification effect of cold spell characteristics (intensity, duration, and timing) and individual-specific factors (causes of death, age, gender and education). Meta-analysis method was finally used to estimate the overall effects. The overall cumulative excess risk (CER) of non-accidental mortality during cold spell days was 28.2% (95% CI: 21.4%, 35.3%) compared with non-cold spell days. There was a significant increase in mortality when the cold spell duration and intensity increased or occurred earlier in the season. Cold spell effects and effect modification by cold spell characteristics were more pronounced in south China. The elderly, people with low education level and those with respiratory diseases were generally more vulnerable to cold spells. Cold spells statistically significantly increase mortality risk in China, with greater effects in southern China. This effect is modified by cold spell characteristics and individual-level factors.
In-situ particles reorientation during magnetic hyperthermia application: Shape matters twice
Authors: Simeonidis Konstantinos , Morales M. Puerto , Marciello Marzia , Angelakeris Makis , de la Presa Patricia , Lazaro-Carrillo Ana , Tabero Andrea , Villanueva Angeles , Chubykalo-Fesenko Oksana , Serantes David
Published: December 2016

Promising advances in nanomedicine such as magnetic hyperthermia rely on a precise control of the nanoparticle performance in the cellular environment. This constitutes a huge research challenge due to difficulties for achieving a remote control within the human body. Here we report on the significant double role of the shape of ellipsoidal magnetic nanoparticles (nanorods) subjected to an external AC magnetic field: first, the heat release is increased due to the additional shape anisotropy; second, the rods dynamically reorientate in the orthogonal direction to the AC field direction. Importantly, the heating performance and the directional orientation occur in synergy and can be easily controlled by changing the AC field treatment duration, thus opening the pathway to combined hyperthermic/mechanical nanoactuators for biomedicine. Preliminary studies demonstrate the high accumulation of nanorods into HeLa cells whereas viability analysis supports their low toxicity and the absence of apoptotic or necrotic cell death after 24 or 48 h of incubation.
AlGaAs 55Fe X-ray radioisotope microbattery
Authors: Butera S. , Whitaker M. D. C. , Lioliou G. , Barnett A. M.
Published: December 2016

This paper describes the performance of a fabricated prototype Al0.2Ga0.8As 55Fe radioisotope microbattery photovoltaic cells over the temperature range −20 °C to 50 °C. Two 400 μm diameter p+-i-n+ (3 μm i-layer) Al0.2Ga0.8As mesa photodiodes were used as conversion devices in a novel X-ray microbattery prototype. The changes of the key microbattery parameters were analysed in response to temperature: the open circuit voltage, the maximum output power and the internal conversion efficiency decreased when the temperature was increased. At −20 °C, an open circuit voltage and a maximum output power of 0.2 V and 0.04 pW, respectively, were measured per photodiode. The best internal conversion efficiency achieved for the fabricated prototype was only 0.95% at −20 °C.
Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq
Authors: Wang Hui , Cheng Hongtao , Wang Wenxiang , Liu Jia , Hao Mengyu , Mei Desheng , Zhou Rijin , Fu Li , Hu Qiong
Published: December 2016

Oilseed rape (Brassica napus L.) is one of the most important oil crops in China as well as worldwide. Branch angle as a plant architecture component trait plays an important role for high density planting and yield performance. In this study, bulked segregant analysis (BSA) combined with next generation sequencing technology was used to fine map QTL for branch angle. A major QTL, designated as branch angle 1 (ba1) was identified on A06 and further validated by Indel marker-based classical QTL mapping in an F2 population. Eighty-two genes were identified in the ba1 region. Among these genes, BnaA0639380D is a homolog of AtYUCCA6. Sequence comparison of BnaA0639380D from small- and big-branch angle oilseed rape lines identified six SNPs and four amino acid variation in the promoter and coding region, respectively. The expression level of BnaA0639380D is significantly higher in the small branch angle line Purler than in the big branch angle line Huyou19, suggesting that the genomic mutations may result in reduced activity of BnaA0639380D in Huyou19. Phytohormone determination showed that the IAA content in Purler was also obviously increased. Taken together, our results suggested BnaA0639380D is a possible candidate gene for branch angle in oilseed rape.
An increased duplication of ZRS region that caused more than one supernumerary digits preaxial polydactyly in a large Chinese family
Authors: Wang Bin , Diao Yutao , Liu Qiji , An Hongqiang , Ma Ruiping , Jiang Guosheng , Lai Nannan , Li Ziwei , Zhu Xiaoxiao , Zhao Lin , Guo Qiang , Zhang Zhen , Sun Rong , Li Xia
Published: December 2016

Preaxial polydactyly (PPD) is inherited in an autosomal dominant fashion and characterized by the presence of one or more supernumerary digits on the thumb side. It had been identified that point mutation or genomic duplications of the long-range limb-specific cis-regulator - zone of polarizing activity regulatory sequence (ZRS) cause PPD or other limb deformities such as syndactyly type IV (SD4) and Triphalangeal thumb-polysyndactyly syndrome (TPTPS). Most previously reported cases involved with no more than one extra finger; however, the role of the point mutation or genomic duplications of ZRS in the case of more than one redundant finger polydactyly remains unclear. In this article, we reported a family case of more than one redundant finger polydactyly on the thumb side for bilateral hands with a pedigree chart of the family. Results of quantitative PCR (qPCR) and sequence analysis suggested that the relative copy number (RCN) of ZRS but not point mutation (including insertion and deletion) was involved in all affected individuals.