bluuebunny/crossref_metadata_2025 huggingface dataset:
Defect and field-enhancement characterization through electron-beam-induced current analysis
Authors: Umezawa Hitoshi , Gima Hiroki , Driche Khaled , Kato Yukako , Yoshitake Tsuyoshi , Mokuno Yoshiaki , Gheeraert Etienne
Published: May 2017

To investigate the effects of defects and field enhancement in diamond power devices, a biased Schottky barrier diode was characterized by electron-beam-induced current (EBIC) analysis. The nonuniform distribution of the electrical field was revealed by bright spots on the laterally expanded depletion layer of the EBIC intensity map when the applied electrical field exceeded 0.95 MV/cm. The nonuniformity is partly due to a structural effect: the roughness at the edge of the Schottky electrode, induced by lithography and lift-off processes. A second family of spots was shown to increase the leakage current of the device. The time constant associated with this second spot family was 0.98 ms, which is three orders of magnitude shorter than that for defects previously characterized by deep-level transient spectroscopy.
Intermediate state dependence of the photoelectron circular dichroism of fenchone observed via femtosecond resonance-enhanced multi-photon ionization
Authors: Kastner Alexander , Ring Tom , Krüger Bastian C. , Park G. Barratt , Schäfer Tim , Senftleben Arne , Baumert Thomas
Published: May 2017

The intermediate state dependence of photoelectron circular dichroism (PECD) in resonance-enhanced multi-photon ionization of fenchone in the gas phase is experimentally studied. By scanning the excitation wavelength from 359 to 431 nm, we simultaneously excite up to three electronically distinct resonances. In the PECD experiment performed with a broadband femtosecond laser, their respective contributions to the photoelectron spectrum can be resolved. High-resolution spectroscopy allows us to identify two of the resonances as belonging to the B- and C-bands, which involve excitation to states with 3s and 3p Rydberg character, respectively. We observe a sign change in the PECD signal, depending on which electronic state is used as an intermediate, and are able to identify two differently behaving contributions within the C-band. Scanning the laser wavelength reveals a decrease of PECD magnitude with increasing photoelectron energy for the 3s state. Combining the results of high-resolution spectroscopy and femtosecond experiment, the adiabatic ionization potential of fenchone is determined to be IPaFen=(8.49±0.06) eV.
An exergy approach to efficiency evaluation of desalination
Authors: Ng Kim Choon , Shahzad Muhammad Wakil , Son Hyuk Soo , Hamed Osman A.
Published: May 2017

This paper presents an evaluation process efficiency based on the consumption of primary energy for all types of practical desalination methods available hitherto. The conventional performance ratio has, thus far, been defined with respect to the consumption of derived energy, such as the electricity or steam, which are susceptible to the conversion losses of power plants and boilers that burned the input primary fuels. As derived energies are usually expressed by the units, either kWh or Joules, these units cannot differentiate the grade of energy supplied to the processes accurately. In this paper, the specific energy consumption is revisited for the efficacy of all large-scale desalination plants. In today's combined production of electricity and desalinated water, accomplished with advanced cogeneration concept, the input exergy of fuels is utilized optimally and efficiently in a temperature cascaded manner. By discerning the exergy destruction successively in the turbines and desalination processes, the relative contribution of primary energy to the processes can be accurately apportioned to the input primary energy. Although efficiency is not a law of thermodynamics, however, a common platform for expressing the figures of merit explicit to the efficacy of desalination processes can be developed meaningfully that has the thermodynamic rigor up to the ideal or thermodynamic limit of seawater desalination for all scientists and engineers to aspire to.
119Sn Mössbauer spectroscopy for assessing the local stress and defect state towards the tuning of Ni-Mn-Sn alloys
Authors: Unzueta I. , López-García J. , Sánchez-Alarcos V. , Recarte V. , Pérez-Landazábal J. I. , Rodríguez-Velamazán J. A. , Garitaonandia J. S. , García J. A. , Plazaola F.
Published: May 2017

The influence of defects and local stresses on the magnetic properties and martensitic transformation in Ni50Mn35Sn15 is studied at macroscopic and atomic scale levels. We show that both the structural and magnetic properties of the alloy are very sensitive to slight microstructural distortions. Even though no atomic disorder is induced by milling, the antiphase boundaries linked to dislocations promote the antiferromagnetic coupling of Mn, resulting in a significant decrease in the saturation magnetization. On the other hand, the temperature range of the transformation is considerably affected by the mechanically induced local stresses, which in turn does not affect the equilibrium temperature between the austenitic and martensitic phases. Finally, we demonstrate that the recovery of the martensitic transformation is directly related to the intensity of the non-magnetic component revealed by 119Sn Mössbauer spectroscopy. This result opens the possibility of quantifying the whole contribution of defects and the local stresses on the martensitic transformation in Ni-Mn-Sn alloys.
Probing carbon impurities in hexagonal boron nitride epilayers
Authors: Uddin M. R. , Li J. , Lin J. Y. , Jiang H. X.
Published: May 2017

Carbon doped hexagonal boron nitride epilayers have been grown by metal organic chemical vapor deposition. Photocurrent excitation spectroscopy has been utilized to probe the energy levels associated with carbon impurities in hexagonal boron nitride (h-BN). The observed transition peaks in photocurrent excitation spectra correspond well to the energy positions of the bandgap, substitutional donors (CB, carbon impurities occupying boron sites), and substitutional acceptors (CN, carbon impurities occupying nitrogen sites). From the observed transition peak positions, the derived energy level of CB donors in h-BN is ED ∼ 0.45 eV, which agrees well with the value deduced from the temperature dependent electrical resistivity. The present study further confirms that the room temperature bandgap of h-BN is about 6.42–6.45 eV, and the CN deep acceptors have an energy level of about 2.2–2.3 eV. The results also infer that carbon doping introduces both shallow donors (CB) and deep acceptors (CN) via self-compensation, and the energy level of carbon donors appears to be too deep to enable carbon as a viable candidate as an n-type dopant in h-BN epilayers.
Study of multipactor suppression of microwave components using perforated waveguide technology for space applications
Authors: Ye Ming , Li Yun , He Yongning , Daneshmand Mojgan
Published: May 2017

With the development of space technology, microwave components with increased power handling capability and reduced weight have been urgently required. In this work, the perforated waveguide technology is proposed to suppress the multipactor effect of high power microwave components. Meanwhile, this novel method has the advantage of reducing components' weight, which makes it to have great potential in space applications. The perforated part of the waveguide components can be seen as an electron absorber (namely, its total electron emission yield is zero) since most of the electrons impacting on this part will go out of the components. Based on thoroughly benchmarked numerical simulation procedures, we simulated an S band and an X band waveguide transformer to conceptually verify this idea. Both electron dynamic simulations and electrical loss simulations demonstrate that the perforation technology can improve the multipactor threshold at least ∼8 dB while maintaining the acceptable insertion loss level compared with its un-perforated components. We also found that the component with larger minimum gap is easier to achieve multipactor suppression. This effect is interpreted by a parallel plate waveguide model. What's more, to improve the multipactor threshold of the X band waveguide transformer with a minimum gap of ∼0.1 mm, we proposed a perforation structure with the slope edge and explained its mechanism. Future study will focus on further optimization of the perforation structure, size, and distribution to maximize the comprehensive performances of microwave components.
Development of modified Pro-Energy algorithm for future solar irradiance estimation using level and trend factors in time series analysis
Authors: Sharma Amandeep , Kakkar Ajay
Published: May 2017

Modelling of solar irradiance is an imperative function for renewable energy based power systems. In the proposed work, a modified Pro-Energy algorithm is developed using level and trend factors in time series analysis for future solar irradiance. The performance of the proposed algorithm has been compared with exponentially weighted moving-average, weather conditioned moving average, and Pro-Energy on the basis of prediction error. The prediction error has been reduced up to 7.68%, 4.24%, 4.3%, and 5.84% in 30, 60, 90, and 120 min ahead of solar irradiance prediction, respectively, in comparison to the existing Pro-Energy algorithm.
Formation of gold grating structures on fused silica substrates by femtosecond laser irradiation
Authors: Takami Akihiro , Nakajima Yasutaka , Terakawa Mitsuhiro
Published: May 2017

Despite the attractive optical properties of gold nanostructures for emerging applications, the formation of sharp laser-induced periodic gold structures has not been reported. In this study, we experimentally demonstrate the formation of micro- and nanoscale periodic gold grating structures on fused silica substrates using a femtosecond laser. The experimental and calculated results show good agreement, indicating that the gold grating structures were formed by a beat formed in a gold thin film. We also propose that the beat was formed by interference of two surface plasmon polaritons with different periods excited in a gold thin film and calculated their periods.
Joining cross-stacked carbon nanotube architecture with covalent bonding
Authors: Li Ru , Gong Wenbin , He Qiang , Li Qingwen , Lu Weibang , Zhu Wenjun
Published: May 2017

Carbon nanotubes (CNTs) have superior mechanical properties that make them highly attractive for high performance bulk structures such as CNT fibers and films; however, the weak wan der Waals interaction between CNTs gives degraded strength and modulus, forming covalent bonding between CNTs which is considered to be highly promising but remains a considerable challenge due to the inert nature of the carbon surface. An appropriate electron-beam, as yet, has been used to introduce covalent bonding but limited to CNT bundles. Here, we used a spinnable CNT array to form a cross-stacked CNT architecture first, a bulk film, and proved that sp3 covalent bonding can be directly formed between cross-stacked CNTs under high pressure at appropriate temperatures via a laser heated diamond anvil cell method. The Raman spectrum and molecular dynamic simulations were used to probe and interpret the bonding formation process, respectively. It was found that under 30 GPa with the temperature of 765–1345 K, sp3 covalent bonding was mainly formed in the cross-stacked region. We anticipate that the formation of sp3 covalent bonding between CNTs under high pressure could offer a general pathway to enhance the performance of nano-carbon based materials.
Chemical bond imaging using higher eigenmodes of tuning fork sensors in atomic force microscopy
Authors: Ebeling Daniel , Zhong Qigang , Ahles Sebastian , Chi Lifeng , Wegner Hermann A. , Schirmeisen André
Published: May 2017

We demonstrate the ability of resolving the chemical structure of single organic molecules using non-contact atomic force microscopy with higher normal eigenmodes of quartz tuning fork sensors. In order to achieve submolecular resolution, CO-functionalized tips at low temperatures are used. The tuning fork sensors are operated in ultrahigh vacuum in the frequency modulation mode by exciting either their first or second eigenmode. Despite the high effective spring constant of the second eigenmode (on the order of several tens of kN/m), the force sensitivity is sufficiently high to achieve atomic resolution above the organic molecules. This is observed for two different tuning fork sensors with different tip geometries (small tip vs. large tip). These results represent an important step towards resolving the chemical structure of single molecules with multifrequency atomic force microscopy techniques where two or more eigenmodes are driven simultaneously.
Type–I pseudo–first–order phase transition induced electrocaloric effect in lead–free Bi0.5Na0.5TiO3–0.06BaTiO3 ceramics
Authors: Li Feng , Chen Guorui , Liu Xing , Zhai Jiwei , Shen Bo , Li Shandong , Li Peng , Yang Ke , Zeng Huarong , Yan Haixue
Published: May 2017

In this study, the electrocaloric effect (ECE) of Bi0.5Na0.5TiO3–0.06BaTiO3 (BNT–0.06BT) ceramic has been directly measured using a home-made adiabatic calorimeter. The maximum adiabatic temperature change (ΔT) approaches 0.86 K under an electric field of 5 kV/mm at 110 °C, which provides experimental evidence for optimizing the ECE near the type–I pseudo–first–order phase transition (PFOPT). Most importantly, a considerable ΔT value can be maintained over a wide temperature range well above the temperature of the PFOPT under a high electric field. In addition, ΔT is closely related to the structural transition and electric field strength. This work provides a guideline to investigate the high ECE in BNT–based ferroelectric ceramics for applications in cooling technologies.
Residency and movement patterns of yellowfin bream (Acanthopagrus australis) released at natural and artificial reef sites
Authors: Lowry Michael , Becker Alistair , Folpp Heath , McLeod James , Taylor Matthew D.
Published: May 2017

The present study investigated the long-term (>2 years) site fidelity, residency and movement patterns of Acanthopagrus australis (Sparidae) at artificial (AR) and natural reef (NR) sites. Acoustic telemetry was used to assess movement patterns of 39 fish released at NR and AR locations and other habitat types within the study area. Detection periods ranged from 1 day to a maximum of 912 days, with 36% of fish detected by the array for >1 year and a further 7% detected for >2 years. Results indicate that tagged fish tended to remain associated with the release site; however, AR fish were detected for considerably longer periods with greater numbers of fish identified as resident within the AR system. AR-released fish were also identified more frequently across the entire array, with the majority (90%) of detections between receiver stations located within the AR system. Results were affected by short detection periods (<6 days) of a relatively high proportion of fish released at the NR, possibly indicating differential rates of fishing mortality between locations. Longer range movements of >200km were also detected, but there was no obvious trend with release location. The results of the present study indicate interactions between existing and introduced artificial habitat are more complex than a ‘draw-down’ effect and provide further evidence that AR systems provide suitable habitat for a variety of species, as well as further support for the use of AR systems in fisheries enhancement initiatives. The results also have important implications for understanding the effect of AR systems and indicate that the size of the reef system may be an important factor in controlling for levels of fishing-related mortality.
Compositional data supports decentralized model of production and circulation of artifacts in the pre-Columbian south-central Andes
Authors: Lazzari Marisa , Pereyra Domingorena Lucas , Stoner Wesley D. , Scattolin María Cristina , Korstanje María Alejandra , Glascock Michael D.
Published: May 2017

Significance

The exchange of goods is a key factor in the development of complex societies. The Andes have provided a fertile ground for investigating this process, yet the long-standing emphasis on qualitative assessments of artifact similarities has left important aspects of ancient exchange open to speculation. Through a multianalytical and multimaterial approach we examine regional connections in Formative Period northwest Argentina. The results unveil a far more multifaceted, decentralized network than previously thought, challenging standard approaches that have favored centralized patterns of regional interaction. The study opens avenues for investigating the dynamic interaction between local and regional networks in small-scale societies through actual material transfers, both in the Andes and beyond.
Effects of habitat disturbance on tropical forest biodiversity
Authors: Alroy John
Published: May 2017

Significance

Biologists believe that a major mass extinction is happening in the tropics. Destruction of forests is a key reason. However, there are no solid predictions of the percentage of species that will go extinct as more and more forests are disturbed. This paper provides estimates based on extrapolating the respective numbers of species in disturbed and undisturbed habitats. It uses a large global database of species inventories at particular sites. Trees and 10 groups of animals are analyzed. All the disturbed habitats put together include 41% fewer species than the undisturbed forests. This proportion varies among groups but is always substantial. Furthermore, disturbed local communities are dominated by widespread species such as rats and electric ants.
Evidence of strain structure in
Plasmodium falciparum var
gene repertoires in children from Gabon, West Africa
Authors: Day Karen P. , Artzy-Randrup Yael , Tiedje Kathryn E. , Rougeron Virginie , Chen Donald S. , Rask Thomas S. , Rorick Mary M. , Migot-Nabias Florence , Deloron Philippe , Luty Adrian J. F. , Pascual Mercedes
Published: May 2017

Existing theory on competition for hosts between pathogen strains has proposed that immune selection can lead to the maintenance of strain structure consisting of discrete, weakly overlapping antigenic repertoires. This prediction of strain theory has conceptual overlap with fundamental ideas in ecology on niche partitioning and limiting similarity between coexisting species in an ecosystem, which oppose the hypothesis of neutral coexistence. For
Plasmodium falciparum
, strain theory has been specifically proposed in relation to the major surface antigen of the blood stage, known as
Pf
EMP1 and encoded by the multicopy multigene family known as the
var
genes. Deep sampling of the DBLα domain of
var
genes in the local population of Bakoumba, West Africa, was completed to define whether patterns of repertoire overlap support a role of immune selection under the opposing force of high outcrossing, a characteristic of areas of intense malaria transmission. Using a 454 high-throughput sequencing protocol, we report extremely high diversity of the DBLα domain and a large parasite population with DBLα repertoires structured into nonrandom patterns of overlap. Such population structure, significant for the high diversity of
var
genes that compose it at a local level, supports the existence of “strains” characterized by distinct
var
gene repertoires. Nonneutral, frequency-dependent competition would be at play and could underlie these patterns. With a computational experiment that simulates an intervention similar to mass drug administration, we argue that the observed repertoire structure matters for the antigenic
var
diversity of the parasite population remaining after intervention.
Molecular mechanism of multispecific recognition of Calmodulin through conformational changes
Authors: Liu Fei , Chu Xiakun , Lu H. Peter , Wang Jin
Published: May 2017

Significance

Understanding how Calmodulin (CaM) is able to recruit more than 300 binding targets is crucial for solving the multispecificity in molecular recognition. To address the molecular mechanism for CaM recognition, we studied the association process that simultaneously involves both the local conformational change of CaM and the global conformational changes of CaM-binding peptide skMLCK with molecular simulations. An energy landscape with a mixture of the atypical “induced fit,” the atypical “conformational selection,” and “simultaneously binding–folding” is uncovered for the CaM–peptide recognition process. The underlying interactions, which lead to this complicated association process, are found to fine-tune the multiple conformational changes during the recognition process, leading to high affinity and specificity. The association characteristic proposed for CaM and skMLCK can provide insights toward multispecific binding of CaM with its target.
Inducible
Fgf13
ablation enhances caveolae-mediated cardioprotection during cardiac pressure overload
Authors: Wei Eric Q. , Sinden Daniel S. , Mao Lan , Zhang Hailin , Wang Chuan , Pitt Geoffrey S.
Published: May 2017

Significance

In response to chronic pressure overload, the heart undergoes pathological hypertrophy associated with adverse remodeling, fibrosis, and cardiac dysfunction. Caveolae, membrane invaginations that organize protective signaling pathways and provide a reservoir to buffer membrane tension, can ameliorate maladaptive hypertrophy. However, the factors that govern caveolae assembly in the heart are not fully understood. Here, we report that the fibroblast growth factor (FGF) homologous factor FGF13 is a negative regulator of caveolae density in cardiomyocytes. Adult mice lacking FGF13 in the heart have increased caveolae abundance in cardiomyocytes and are thereby protected from the pathological effects of chronic pressure overload. Our findings, identifying an unexpected role for FGF13, provide insight into the mechanisms underlying caveolae-mediated adaptation to cardiac stress.
Visual working memory buffers information retrieved from visual long-term memory
Authors: Fukuda Keisuke , Woodman Geoffrey F.
Published: May 2017

Significance

How do we retrieve long-term memory? Here, we show that by measuring subjects’ electroencephalogram (EEG), we can directly observe the dynamic process of long-term memory retrieval. Our findings suggest that retrieved information becomes consciously available by being represented in a working-memory format that is similar to that used to represent new perceptual inputs. Furthermore, we show that our EEG measures can track the process of retrieving and combining two long-term memories acquired separately (e.g., image of a horse and a pair of wings) into one working-memory representation (e.g., a Pegasus). Thus, our results not only provide direct neural support for a long-assumed theory of memory retrieval but also demonstrate how flexible retrieval allows for creative thought.
Optimal incentives for collective intelligence
Authors: Mann Richard P. , Helbing Dirk
Published: May 2017

Significance

Diversity of information and expertise among group members has been identified as a crucial ingredient of collective intelligence. However, many factors tend to reduce the diversity of groups, such as herding, groupthink, and conformity. We show why the individual incentives in financial and prediction markets and the scientific community reduce diversity of information and how these incentives can be changed to improve the accuracy of collective forecasting. Our results, therefore, suggest ways to improve the poor performance of collective forecasting seen in recent political events and how to change career rewards to make scientific research more successful.
A normalization model suggests that attention changes the weighting of inputs between visual areas
Authors: Ruff Douglas A. , Cohen Marlene R.
Published: May 2017

Significance

Visual attention dramatically improves the perception of attended stimuli, but the mechanism by which this improvement occurs is unknown. Here we combine simultaneous recordings in multiple visual cortical areas, electrical microstimulation paired with multineuron recordings, and a descriptive normalization model to probe the mechanisms underlying attention. We found that the relationship between the activity in different visual areas is well described by normalization and that a mechanism that changes the weights of connections between areas can best describe our physiological observations. This study shows that normalization can explain interactions between neurons in different areas and provides a framework for using multiarea recordings and stimulation techniques to probe the neural mechanisms underlying neuronal computations.
Nasal-associated lymphoid tissues (NALTs) support the recall but not priming of influenza virus-specific cytotoxic T cells
Authors: Pizzolla Angela , Wang Zhongfang , Groom Joanna R. , Kedzierska Katherine , Brooks Andrew G. , Reading Patrick C. , Wakim Linda M.
Published: May 2017

Significance

The upper respiratory tract (URT) is the first contact site for inhaled pathogens and intranasal vaccines, and is serviced by a network of lymphoid-tissues, including draining lymph nodes and nasal-associated lymphoid tissues (NALTs). Whether these lymphoid structures have distinct roles in facilitating T-cell immunity to inhaled antigens is unclear. We show, following antigen delivery into the URT, NALTs failed to support naïve T-cell priming; however, they supported the recall expansion of memory T cells. Although antigen delivery to the URT may not induce effective T-cell priming, it would be an effective means of boosting responses in the context of preexisting T-cell immunity. These results have significant implications for intranasal vaccines that deliver antigen to NALTs and aim to elicit protective T-cell immunity.
Brd4 modulates the innate immune response through Mnk2–eIF4E pathway-dependent translational control of IκBα
Authors: Bao Yan , Wu Xuewei , Chen Jinjing , Hu Xiangming , Zeng Fuxing , Cheng Jianjun , Jin Hong , Lin Xin , Chen Lin-Feng
Published: May 2017

Significance

We generated myeloid lineage-specificBrd4conditional-knockout mice and demonstrated the critical role ofBrd4in the innate immune response in vivo.Brd4CKO mice were resistant to LPS-induced sepsis but were more susceptible to bacterial infection. Deletion ofBrd4in macrophages decreased the TLR-mediated inflammatory cytokine expression. We also uncovered a mechanism by which Brd4 regulates the NF-κB signaling via initiation of translation. In response to LPS stimulation, deletion ofBrd4in macrophages led to the sustained expression ofMknk2and the enhanced activation of eIF4E, which stimulates the translation of IκBα mRNA, resulting in decreased NF-κB–dependent inflammatory gene expression and compromised innate immune response.
Variation in the β-endorphin, oxytocin, and dopamine receptor genes is associated with different dimensions of human sociality
Authors: Pearce Eiluned , Wlodarski Rafael , Machin Anna , Dunbar Robin I. M.
Published: May 2017

Significance

Social behavior in mammals is underpinned by a number of social neuropeptides. Most studies, however, focus on a single neuropeptide (often oxytocin), and invariably only in the context of reproductive relationships. Here, we examine the associations between the six main social neuropeptides (endorphins, oxytocin, vasopressin, dopamine, serotonin, and testosterone) and social indices in three separate social domains (disposition, dyadic/romantic relationships, and social network). We show that each neuropeptide is quite specific in its domain of influence, although endorphins and dopamine influence all three social domains. The results suggest that the social importance of endorphins may have been underestimated.
Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization
Authors: Sergeyev Ivan V. , Itin Boris , Rogawski Rivkah , Day Loren A. , McDermott Ann E.
Published: May 2017

Significance

This work presents a technique for dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) solid-state NMR studies of complex proteins and biological assemblies. The sequential side-chain correlation approach streamlines the site-specific assignment of NMR peaks in multidimensional spectra, a critical step in determining structural information such as distances. When combined with DNP enhancement, fast MAS, and nonuniform sampling, this technique allows for faster data acquisition than previously possible. Applied to the intact Pf1 bacteriophage, sequential side-chain correlation spectra have enabled a virtually complete assignment using DNP data alone. These assignments shed insight into the chemical shift and linewidth changes associated with cryogenic temperatures. Our data point to hydration as a key variable influencing these parameters.
Novel quantum phase transition from bounded to extensive entanglement
Authors: Zhang Zhao , Ahmadain Amr , Klich Israel
Published: May 2017

Significance

One of the main quests of many-body physics and quantum information is to understand various quantum phases and in particular the entanglement present in them. In this work we have uncovered a unique, physically transparent quantum phase transition in a spin chain where entanglement entropy itself jumps from low scaling, most typical for gapped models and short-range correlations, to a critical phase where the scaling exhibits an extraordinary amount of entanglement. This discovery pushes the boundaries of a possible range of nonlocal quantum correlations displayed by local Hamiltonians and opens a door to fundamental and practical questions about the interplay of entanglement and locality in many-body systems.
Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement
Authors: Dai Yu-Jun , Wang Yue-Ying , Huang Jin-Yan , Xia Li , Shi Xiao-Dong , Xu Jie , Lu Jing , Su Xian-Bin , Yang Ying , Zhang Wei-Na , Wang Pan-Pan , Wu Song-Fang , Huang Ting , Mi Jian-Qing , Han Ze-Guang , Chen Zhu , Chen Sai-Juan
Published: May 2017

Significance

DNMT3A is a critical epigenetic modifier and tumor suppressor in the hematopoietic system. This gene is frequently mutated in hematopoietic malignancies, including acute myeloid leukemia (AML), with Dnmt3a R878H being the most common mutant. By using a conditional knockin approach, this study shows that Dnmt3a R878H is sufficient to initiate AML and recapitulate human leukemic features in mice. The leukemia-initiating cells are enriched in hematopoietic stem/progenitor cells. Through gene expression profiling, DNA methylation and histone modification analysis, and functional tests on important regulators for cell proliferation and differentiation in an animal model, this study has not only discovered mTOR pathway activation as a key player in the disease mechanism but also revealed the potential therapeutic effects of mTOR inhibition on
DNMT3A
mutation-related leukemia.
Metaphors of womanhood in the literary works of contemporary Indian writers
Authors: Ahuja Atula , Techacharoenrungrueang Suparak , Luksaneeyanawin Sudaporn
Published: May 2017

This study examines the notion of womanhood in the literary works of contemporary Indian authors by analyzing conceptual metaphors of womanhood. More specifically, the data collected in this study are metaphorical expressions (MEs) from nine fictional works set in India’s three main ethnically and linguistically diverse regions occupied by three linguistic groups, namely, the Indo-Aryan, the Dravidian, and the Tibeto-Burmese. The identification of MEs follows the Metaphor Identification Procedure VU University Amsterdam (MIPVU; Steen et al. 2010a). The analysis focuses on cross-cultural variation in conceptual metaphor, applying Conceptual Metaphor Theory (CMT; Lakoff & Johnson 1980) and the cognitive dimension of socio-cultural diversity proposed by Kövecses (2008). Through the analysis of conceptual metaphor, the paper provides insights into the current social context regarding the status and roles of women in India.
Salmon nasal cartilage proteoglycan enhances growth of normal human dermal fibroblast through Erk1/2 phosphorylation
Authors: Sano Masahiro , Shang Yi , Nakane Akio , Saito Tomoaki
Published: May 2017

Proteoglycan (PG) is a heavily glycosylated protein, localized to cell surface and extracellular matrix, and has various functions. Recently, it has been gradually revealed that PG interacts with various growth factors and morphogens and regulates cellular functions. Although salmon nasal cartilage PG (Salmon-PG) increases proliferation of immortalized cells, its mechanism remains unclear. In this study, we confirmed the effect of Salmon-PG on normal human dermal fibroblast (NHDF) and investigated the mechanism of PG action on NHDF. Salmon-PG dose- and time-dependently increased NHDF proliferation. Receptor tyrosine kinase array revealed that Salmon-PG increased only Erk1/2 signaling. Erk1/2 phosphorylation was significantly increased by Salmon-PG in a time-(10 min) and dose-(400 or 800 μg/mL) dependent manner. MEK inhibitor suppressed the enhancement of NHDF proliferation by Salmon-PG. The overall findings indicate that Salmon-PG plays a role as a growth factor in NHDF via Erk1/2 activation, suggesting that Salmon-PG contributes to the maintenance of skin homeostasis.
Characterization and comparison of recombinant honeybee chymotrypsin-like protease (HCLPase) expressed in Escherichia coli and insect cells
Authors: Matsuoka Takuma , Kawashima Takuji , Nakamura Tadashi , Yabe Tomio
Published: May 2017

We previously found a novel chymotrypsin-like protease in honeybee, designated as HCLPase. The recombinant enzyme expressed in insect cells was produced and compared to that in Escherichia coli. Both enzymes showed equivalent molecular size and specificity. However, HCLPase produced in insect cells showed higher specific activity. The C-terminal cleavage sites of HCLPase were phenylalanine, leucine, and tyrosine residues.
Enrolment, content and assessment: a review of examinable senior secondary (16–19 year olds) physical education courses: an international perspective
Authors: Whittle Rachael Jayne , Benson Amanda Clare , Telford Amanda
Published: May 2017

Senior secondary physical education courses for certification continue to attract increasing student enrolments amidst international concerns for the state and status of physical education in schools. Curricula analysis of senior secondary physical education has typically focussed on courses in local contexts. This review aims to contribute to the current discussion around physical education curricula through a document analysis of 15 senior secondary physical education courses for certification. Results from the analysis of curricula documents reveal similarities in subject aims, objectives and rationales, subject specific content and assessment. Senior secondary physical education is firmly based in both the biophysical and sociocultural fields of study and draws on a broad range of disciplines from which to study human movement. The stated rationales of the courses reviewed suggested that an understanding of the complex interrelationships between content areas underpins senior secondary physical education; however content was mostly prescribed in stand‐alone units. This review identified more similarities than differences in content and assessment practices in senior secondary physical education, a point of distinction between the courses reviewed was those that assess physical performance and those that do not. Internal assessment provided for a variety of tasks to determine student learning, however, external assessment was dominated by a written examination.
Development of two short measures for recovery and stress in sport
Authors: Nässi Anu , Ferrauti Alexander , Meyer Tim , Pfeiffer Mark , Kellmann Michael
Published: May 2017

The Acute Recovery and Stress Scale (ARSS) and the Short Recovery and Stress Scale were first established in German for the purposes of monitoring athletes’ current recovery‐stress states in an economical and multidimensional manner. The aim of this paper is to document the development and initial validation of the English versions of these two psychometric monitoring tools. A total of 267 English‐speaking athletes from a variety of team and individual sports participated in the study. The English versions demonstrated satisfactory internal consistency for both instruments (Cronbach α of. 74–.89). Furthermore, good model fit was found for the eight scales of the ARSS, matching the structure and results of the German counterparts. Correlations among and between the scales reciprocate the theoretical constructs of stress and recovery, supporting the construct validity of the scales. Correlation coefficients within stress and recovery ranged between rs = .29 and. 68. The correlations between stress and recovery varied between rs = −.29 and −.64. These constructs were further supported by correlations with the scores of the Recovery‐Stress Questionnaire for Athletes, thereby showing convergent validity. The findings demonstrate initial validity and reliability of the two measures and reflect the results of the German versions. However, further research is needed before applying these scales in practical settings.
Compactification and trees of spheres covers
Authors: Arfeux Matthieu
Published: May 2017

The space of dynamically marked rational maps can be identified with a subspace of the space of covers between trees of spheres on which there is a notion of convergence that makes it sequentially compact. In this paper we describe a topology on the quotient of this space under the natural action of its group of isomorphisms. This topology is proved to be consistent with this notion of convergence.
Hollywood Aesthetic
Authors: Berliner Todd
Published: May 2017

Hollywood makes the most widely successful pleasure-giving artworks the world has ever known. The American film industry operates under the assumption that pleasurable aesthetic experiences, among large populations, translate into box office success. More than any other historical mode of art, Hollywood has systematized the delivery of aesthetic pleasure, packaging and selling it on a mass scale. If the Hollywood film industry succeeds in delivering aesthetic pleasure both routinely and, at times, in an outstanding way, then we should ultimately regard Hollywood cinema as an artistic achievement, not merely a commercial success. Hollywood Aesthetic accounts for the chief attraction of Hollywood cinema worldwide: its entertainment value. The book addresses four fundamental components of Hollywood’s aesthetic design: narrative, style, ideology, and genre. Grounded in film history and in the psychological and philosophical literature in aesthetics, the book explains: (1) the intrinsic properties characteristic of Hollywood cinema that induce aesthetic pleasure; (2) the cognitive and affective processes, sparked by Hollywood movies, that become engaged during aesthetic pleasure; and (3) the exhilarated aesthetic experiences afforded by an array of persistently entertaining Hollywood movies. Offering a comprehensive appraisal of the capacity of Hollywood cinema to provide aesthetic pleasure, the book sets out to explain how Hollywood creates, for masses of people, some of their most exhilarating experiences of art.
Sublexical modality in defeasible causative verbs
Authors: Martin Fabienne , Schäfer Florian
Published: May 2017

This chapter is dedicated to an ambiguity characteristic of what we call defeasible causative verbs (of which ‘teach’ is an example). With agentive subjects, the change of state (CoS) encoded by these verbs (e.g. a learning process) can be entirely denied, giving rise to what we call the “zero-CoS” non-culminating reading of these verbs. With causer subjects, however, the same verbs seem to entail the occurrence of (a part of) the CoS (including in imperfective sentences). We argue that this ambiguity cannot be handled by positing different event structures under the agentive and non-agentive uses. Under the analysis proposed, the semantics of these verbs involve a sublexical modal component à la Koenig and Davis (2001), both with agent and causer subjects. In favor of positing a sublexical modality with all types of subject, we investigate the conditions under which the zero-CoS reading is available even with a subset of inanimate subjects and “non-intentional” agents.
Straddling the line between attitude verbs and necessity modals
Authors: Rubinstein Aynat
Published: May 2017

This chapter explores the semantic properties of verbs and adjectives with closely related meanings having to do with desires and goals. I evaluate recent work on verbs of desire (e.g. ‘want’) which has suggested that these attitude predicates require access to multiple alternatives for their interpretation (Villalta 2006, 2008). I argue that this heavy machinery is in fact not required, integrating important insights proposed in this recent work into a quantificational modal analysis of comparison-based attitudes. The proposed analysis highlights the similarities and differences between ‘want’ and ‘necessary’, an adjective that is shown (including naturalistic corpus data) to be primarily goal-oriented and to be semantically dependent to a certain degree on the syntactic configuration it appears in. Whether or not the modality is lexically relativized to an individual is also suggested to play a role in defining the semantic properties of desire- and goal-oriented modal expressions.
In an imperfect world: Deriving the typology of counterfactual marking
Authors: Bjorkman Bronwyn M. , Halpert Claire
Published: May 2017

Much work has focused on the use of “fake”’ past in marking counterfactual clauses. This chapter focuses instead on the contribution of aspect, evaluating claims that some languages require both fake past and fake (imperfective) aspect in counterfactual clauses. We argue that this appearance is an illusion, resulting from the fact that past tense forms are aspectually underspecified in many languages: this underspecification gives rise to an apparent requirement for imperfective marking in some languages (e.g. French, Zulu), but an apparent requirement for perfective marking in others (e.g. Palestinian Arabic). Finally, we suggest that in languages that truly require imperfective marking in counterfactuals, the requirement is for imperfective simpliciter, independent of tense (Hindi, Persian). The resulting typological picture has implications for how fake temporal marking is structurally represented in counterfactual clauses.
The Linguistic Structure of Berkeley’s World
Authors: Pearce Kenneth L.
Published: May 2017

Berkeley holds that the perceived world is “a most coherent, entertaining and instructive discourse” which is ‘spoken’ by God. Berkeley intends this claim literally and holds that this discourse exhibits linguistic structure: it has a lexicography, a syntax, and a semantics. Interpreting Berkeley’s claims about the world as a divine discourse in light of Berkeley’s own philosophy of language produces compelling solutions to a number of difficulties in Berkeley’s metaphysics and epistemology. Most notably, this chapter argues that our body talk, in both plain language and physics, aims to capture the grammatical structure of the divine discourse. This grammar aims to assist us in interpretation and the interpretation of the discourse brings us into appropriate relationship with God and other minds. Understanding our role as interpreters and grammarians and God’s role as ‘speaker’ also provides a solution to pressing problems about divine and human roles in object construction.
EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons
Authors: Hui Xinjie , Hu Yueming , Sun Ming-An , Shu Xingsheng , Han Rongfei , Ge Qinggang , Wang Yejun
Published: May 2017

Motivation

In genome-wide rate comparison studies, there is a big challenge for effective identification of an appropriate number of significant features objectively, since traditional statistical comparisons without multi-testing correction can generate a large number of false positives while multi-testing correction tremendously decreases the statistic power.

Results

In this study, we proposed a new exact test based on the translation of rate comparison to two binomial distributions. With modeling and real datasets, the exact binomial test (EBT) showed an advantage in balancing the statistical precision and power, by providing an appropriate size of significant features for further studies. Both correlation analysis and bootstrapping tests demonstrated that EBT is as robust as the typical rate-comparison methods, e.g. χ2 test, Fisher’s exact test and Binomial test. Performance comparison among machine learning models with features identified by different statistical tests further demonstrated the advantage of EBT. The new test was also applied to analyze the genome-wide somatic gene mutation rate difference between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), two main lung cancer subtypes and a list of new markers were identified that could be lineage-specifically associated with carcinogenesis of LUAD and LUSC, respectively. Interestingly, three cilia genes were found selectively with high mutation rates in LUSC, possibly implying the importance of cilia dysfunction in the carcinogenesis.

Availability and implementation

An R package implementing EBT could be downloaded from the website freely: http://www.szu-bioinf.org/EBT.

Supplementary information

Supplementary data are available at Bioinformatics online.
Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests
Authors: Le Trang T , Simmons W Kyle , Misaki Masaya , Bodurka Jerzy , White Bill C , Savitz Jonathan , McKinney Brett A
Published: May 2017

Motivation

Classification of individuals into disease or clinical categories from high-dimensional biological data with low prediction error is an important challenge of statistical learning in bioinformatics. Feature selection can improve classification accuracy but must be incorporated carefully into cross-validation to avoid overfitting. Recently, feature selection methods based on differential privacy, such as differentially private random forests and reusable holdout sets, have been proposed. However, for domains such as bioinformatics, where the number of features is much larger than the number of observations p≫n, these differential privacy methods are susceptible to overfitting.

Methods

We introduce private Evaporative Cooling, a stochastic privacy-preserving machine learning algorithm that uses Relief-F for feature selection and random forest for privacy preserving classification that also prevents overfitting. We relate the privacy-preserving threshold mechanism to a thermodynamic Maxwell-Boltzmann distribution, where the temperature represents the privacy threshold. We use the thermal statistical physics concept of Evaporative Cooling of atomic gases to perform backward stepwise privacy-preserving feature selection.

Results

On simulated data with main effects and statistical interactions, we compare accuracies on holdout and validation sets for three privacy-preserving methods: the reusable holdout, reusable holdout with random forest, and private Evaporative Cooling, which uses Relief-F feature selection and random forest classification. In simulations where interactions exist between attributes, private Evaporative Cooling provides higher classification accuracy without overfitting based on an independent validation set. In simulations without interactions, thresholdout with random forest and private Evaporative Cooling give comparable accuracies. We also apply these privacy methods to human brain resting-state fMRI data from a study of major depressive disorder.

Availability and implementation

Code available at http://insilico.utulsa.edu/software/privateEC.

Supplementary information

Supplementary data are available at Bioinformatics online.