bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next Generation Device Grade Silicon-Germanium on Insulator
Authors: Littlejohns Callum G. , Nedeljkovic Milos , Mallinson Christopher F. , Watts John F. , Mashanovich Goran Z. , Reed Graham T. , Gardes Frederic Y. 
Published: February 2015

AbstractHigh quality single crystal silicon-germanium-on-insulator has the potential to facilitate the next generation of photonic and electronic devices. Using a rapid melt growth technique we engineer tailored single crystal silicon-germanium-on-insulator structures with near constant composition over large areas. The proposed structures avoid the problem of laterally graded SiGe compositions, caused by preferential Si rich solid formation, encountered in straight SiGe wires by providing radiating elements distributed along the structures. This method enables the fabrication of multiple single crystal silicon-germanium-on-insulator layers of different compositions, on the same Si wafer, using only a single deposition process and a single anneal process, simply by modifying the structural design and/or the anneal temperature. This facilitates a host of device designs, within a relatively simple growth environment, as compared to the complexities of other methods and also offers flexibility in device designs within that growth environment.
Ultrafast Multi-Level Logic Gates with Spin-Valley Coupled Polarization Anisotropy in Monolayer MoS2
Authors: Wang Yu-Ting , Luo Chih-Wei , Yabushita Atsushi , Wu Kaung-Hsiung , Kobayashi Takayoshi , Chen Chang-Hsiao , Li Lain-Jong 
Published: February 2015

AbstractThe inherent valley-contrasting optical selection rules for interband transitions at the K and K′ valleys in monolayer MoS2 have attracted extensive interest. Carriers in these two valleys can be selectively excited by circularly polarized optical fields. The comprehensive dynamics of spin valley coupled polarization and polarized exciton are completely resolved in this work. Here, we present a systematic study of the ultrafast dynamics of monolayer MoS2 including spin randomization, exciton dissociation, free carrier relaxation and electron-hole recombination by helicity- and photon energy-resolved transient spectroscopy. The time constants for these processes are 60 fs, 1 ps, 25 ps and ~300 ps, respectively. The ultrafast dynamics of spin polarization, valley population and exciton dissociation provides the desired information about the mechanism of radiationless transitions in various applications of 2D transition metal dichalcogenides. For example, spin valley coupled polarization provides a promising way to build optically selective-driven ultrafast valleytronics at room temperature. Therefore, a full understanding of the ultrafast dynamics in MoS2 is expected to provide important fundamental and technological perspectives.
Evidences of grain boundary capacitance effect on the colossal dielectric permittivity in (Nb + In) co-doped TiO2 ceramics
Authors: Li Jinglei , Li Fei , Li Chao , Yang Guang , Xu Zhuo , Zhang Shujun 
Published: February 2015

AbstractThe (Nb + In) co-doped TiO2 ceramics were synthesized by conventional solid-state sintering (CSSS) and spark plasma sintering (SPS) methods. The phases and microstructures were studied by X-ray diffraction, Raman spectra, field-emission scanning electron microscopy and transmission electron microscopy, indicating that both samples were in pure rutile phase while showing significant difference in grain size. The dielectric and I–V behaviors of SPS and CSSS samples were investigated. Though both possess colossal permittivity (CP), the SPS samples exhibited much higher dielectric permittivity/loss factor and lower breakdown electric field when compared to their CSSS counterparts. To further explore the origin of CP in co-doped TiO2 ceramics, the I–V behavior was studied on single grain and grain boundary in CSSS sample. The nearly ohmic I–V behavior was observed in single grain, while GBs showed nonlinear behavior and much higher resistance. The higher dielectric permittivity and lower breakdown electric field in SPS samples, thus, were thought to be associated with the feature of SPS, by which reduced space charges and/or impurity segregation can be achieved at grain boundaries. The present results support that the grain boundary capacitance effect plays an important role in the CP and nonlinear I–V behavior of (Nb + In) co-doped TiO2 ceramics.
Anatomical networks reveal the musculoskeletal modularity of the human head
Authors: Esteve-Altava Borja , Diogo Rui , Smith Christopher , Boughner Julia C. , Rasskin-Gutman Diego 
Published: February 2015

AbstractMosaic evolution is a key mechanism that promotes robustness and evolvability in living beings. For the human head, to have a modular organization would imply that each phenotypic module could grow and function semi-independently. Delimiting the boundaries of head modules and even assessing their existence, is essential to understand human evolution. Here we provide the first study of the human head using anatomical network analysis (AnNA), offering the most complete overview of the modularity of the head to date. Our analysis integrates the many biological dependences that tie hard and soft tissues together, arising as a consequence of development, growth, stresses and loads and motion. We created an anatomical network model of the human head, where nodes represent anatomical units and links represent their physical articulations. The analysis of the human head network uncovers the presence of 10 musculoskeletal modules, deep-rooted in these biological dependences, of developmental and evolutionary significance. In sum, this study uncovers new anatomical and functional modules of the human head using a novel quantitative method that enables a more comprehensive understanding of the evolutionary anatomy of our lineage, including the evolution of facial expression and facial asymmetry.
Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions
Authors: Aygun Nevim 
Published: February 2015

AbstractLong inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5′ and 3′ LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = −0.18, P < 0.05) and stem length (r = −0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3′ LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion.
Ranking the impact of human health disorders on gut metabolism: Systemic lupus erythematosus and obesity as study cases
Authors: Rojo David , Hevia Arancha , Bargiela Rafael , López Patricia , Cuervo Adriana , González Sonia , Suárez Ana , Sánchez Borja , Martínez-Martínez Mónica , Milani Christian , Ventura Marco , Barbas Coral , Moya Andrés , Suárez Antonio , Margolles Abelardo , Ferrer Manuel 
Published: February 2015

AbstractMultiple factors have been shown to alter intestinal microbial diversity. It remains to be seen, however, how multiple collective pressures impact the activity in the gut environment and which, if any, is positioned as a dominant driving factor determining the final metabolic outcomes. Here, we describe the results of a metabolome-wide scan of gut microbiota in 18 subjects with systemic lupus erythematosus (SLE) and 17 healthy control subjects and demonstrate a statistically significant difference (p < 0.05) between the two groups. Healthy controls could be categorized (p < 0.05) based on their body mass index (BMI), whereas individuals with SLE could not. We discuss the prevalence of SLE compared with BMI as the dominant factor that regulates gastrointestinal microbial metabolism and provide plausible explanatory causes. Our results uncover novel perspectives with clinical relevance for human biology. In particular, we rank the importance of various pathophysiologies for gut homeostasis.
Diversification of importin-α isoforms in cellular trafficking and disease states
Authors: Pumroy Ruth A. , Cingolani Gino 
Published: February 2015

The human genome encodes seven isoforms of importin α which are grouped into three subfamilies known as α1, α2 and α3. All isoforms share a fundamentally conserved architecture that consists of an N-terminal, autoinhibitory, importin-β-binding (IBB) domain and a C-terminal Arm (Armadillo)-core that associates with nuclear localization signal (NLS) cargoes. Despite striking similarity in amino acid sequence and 3D structure, importin-α isoforms display remarkable substrate specificity in vivo. In the present review, we look at key differences among importin-α isoforms and provide a comprehensive inventory of known viral and cellular cargoes that have been shown to associate preferentially with specific isoforms. We illustrate how the diversification of the adaptor importin α into seven isoforms expands the dynamic range and regulatory control of nucleocytoplasmic transport, offering unexpected opportunities for pharmacological intervention. The emerging view of importin α is that of a key signalling molecule, with isoforms that confer preferential nuclear entry and spatiotemporal specificity on viral and cellular cargoes directly linked to human diseases.
Modulation of spectral properties and pump activity of proteorhodopsins by retinal analogues
Authors: Ganapathy Srividya , Bécheau Odette , Venselaar Hanka , Frölich Siebren , van der Steen Jeroen B. , Chen Que , Radwan Sarah , Lugtenburg Johan , Hellingwerf Klaas J. , de Groot Huub J. M. , de Grip Willem J. 
Published: February 2015

Proteorhodopsins are heptahelical membrane proteins which function as light-driven proton pumps. They use all-trans-retinal A1 as a ligand and chromophore and absorb visible light (520–540 nm). In the present paper, we describe modulation of the absorbance band of the proteorhodopsin from Monterey Bay SAR 86 gammaproteobacteria (PR), its red-shifted double mutant PR-D212N/F234S (PR-DNFS) and Gloeobacter rhodopsin (GR). This was approached using three analogues of all-trans-retinal A1, which differ in their electronic and conformational properties: all-trans-6,7-s-trans-locked retinal A1, all-trans-phenyl-retinal A1 and all-trans-retinal A2. We further probed the effect of these retinal analogues on the proton pump activity of the proteorhodopsins. Our results indicate that, whereas the constraints of the retinal-binding pocket differ for the proteorhodopsins, at least two of the retinal analogues are capable of shifting the absorbance bands of the pigments either bathochromically or hypsochromically, while maintaining their proton pump activity. Furthermore, the shifts implemented by the analogues add up to the shift induced by the double mutation in PR-DNFS. This type of chromophore substitution may present attractive applications in the field of optogenetics, towards increasing the flexibility of optogenetic tools or for membrane potential probes.
Vinexin-β exacerbates cardiac dysfunction post-myocardial infarction via mediating apoptotic and inflammatory responses
Authors: Liu Xiaoxiong , Wan Nian , Zhang Xiao-Jing , Zhao Yichao , Zhang Yan , Hu Gangying , Wan Fengwei , Zhang Rui , Zhu Xueyong , Xia Hao , Li Hongliang 
Published: February 2015

Vinexin-β is one of the adaptor proteins that are primarily involved in signal transduction and cytoskeletal organization under various pathological conditions, including cardiac hypertrophy. However, the role of Vinexin-β in myocardial infarction (MI) remains unknown. In this study, dramatically up-regulated Vinexin-β expression was observed in both ischaemic human hearts and infarcted animal hearts. To explore the potential involvement of Vinexin-β in MI further, we induced MI injury in global Vinexin-β-knockout mice and wild-type (WT) controls as well as in mice with cardiac-specific over-expression of the human Vinexin-β gene-transgenic (TG) and -non-transgenic (NTG) littermates. Compared with that observed in WT controls, Vinexin-β deficiency significantly decreased MI-induced infarct size, concomitant with an improved cardiac function, leading to an increase in the survival rate. The myocardial apoptosis in the border zone was dramatically reduced by Vinexin-β deficiency, resulting from the altered expression of apoptotic factors. Furthermore, Vinexin-β depletion mitigated the inflammatory response, as evidenced by reduced inflammatory cell infiltration, decreased expression of cytokines and the inactivation of NF-κB (nuclear factor κB) signalling. In contrast, Vinexin-β-TG mice were much more susceptible to MI injury compared with NTG controls. Further mechanism analyses suggested that Vinexin-β exerted detrimental effects largely dependent on blocking AKT signalling. The effects and mechanisms of Vinexin-β on MI observed in vivo were further confirmed by our in vitro assays. When collected, these data demonstrate for the first time that Vinexin-β increases MI-induced mortality and worsens cardiac dysfunction through aggravation of myocardial apoptosis and inflammatory response.
Hypotensive and sympathoinhibitory responses to selective central AT2 receptor stimulation in spontaneously hypertensive rats
Authors: Brouwers Sofie , Smolders Ilse , Wainford Richard D. , Dupont Alain G. 
Published: February 2015

The type 2 angiotensin receptor (AT2R) has been suggested to counterbalance the type 1 angiotensin receptor (AT1R) in the central regulation of blood pressure and sympathetic tone. In the present study we investigated the blood pressure responses to stimulation of central AT2Rs by the selective agonist Compound 21 in conscious spontaneously hypertensive rats (SHRs) and normotensive Wistar Kyoto rats (WKY rats). We also assessed the impact on noradrenaline [norepinephrine (NE)] plasma levels, autonomic function, spontaneous baroreflex sensitivity, and the possible involvement of the nitric oxide (NO) pathway and the AT1Rs. Chronic intracerebroventricular Compound 21 infusion lowered blood pressure and NE plasma levels in both rat strains. The night-time hypotensive effect was greater in SHRs compared with WKY rats. Compound 21 improved spontaneous baroreflex sensitivity more in SHRs than in WKY rats. These effects were abolished by co-administration of the AT2R antagonist PD123319 or the NO synthase inhibitor Nω-nitro-L-arginine methyl ester hydrochloride (L-NAME). Central AT1R blockade did not enhance the hypotensive response to Compound 21. Chronic selective stimulation of central AT2Rs lowers blood pressure through sympathoinhibition, and improves spontaneous baroreflex sensitivity more in SHRs than in WKY rats. These responses appear to require a functioning central NO pathway, but are not modified by central AT1R blockade. Collectively, the data demonstrate specific beneficial effects of stimulation of central AT2Rs in hypertension associated with increased sympathetic tone, and suggest that central AT2Rs may represent a potential new therapeutic target for the treatment of neurogenic hypertension.
Gramaticalización y tradiciones discursivas
Authors: Garcés Gómez María Pilar 
Published: February 2015

This article examines the evolution of the adverbial phraseen efecto(in truth) and of the adverbefectivamente(truly), which while originating from a common semantic base, have followed different evolutionary processes. Eventually, they have come to share a common function as discursive markers to indicate a confirmation of the discursive message or a reinforcement of an assertion.Our goal is to describe the evolution of the acquisition process for the discursive value of these forms. We also analyze whether these changes are the results of a grammaticalization process and we describe the impact of discursive traditions in the incorporation of certain values. Finally, we show how this evolution is influenced by the paradigm changes caused by the incorporation, elimination or modification of the various lexical units in these forms through out the different stages in their development.
Application of clinical text data for phenome-wide association studies (PheWASs)
Authors: Hebbring Scott J. , Rastegar-Mojarad Majid , Ye Zhan , Mayer John , Jacobson Crystal , Lin Simon 
Published: February 2015

Abstract
Motivation: Genome-wide association studies (GWASs) are effective for describing genetic complexities of common diseases. Phenome-wide association studies (PheWASs) offer an alternative and complementary approach to GWAS using data embedded in the electronic health record (EHR) to define the phenome. International Classification of Disease version 9 (ICD9) codes are used frequently to define the phenome, but using ICD9 codes alone misses other clinically relevant information from the EHR that can be used for PheWAS analyses and discovery.
Results: As an alternative to ICD9 coding, a text-based phenome was defined by 23 384 clinically relevant terms extracted from Marshfield Clinic’s EHR. Five single nucleotide polymorphisms (SNPs) with known phenotypic associations were genotyped in 4235 individuals and associated across the text-based phenome. All five SNPs genotyped were associated with expected terms (P &lt; 0.02), most at or near the top of their respective PheWAS ranking. Raw association results indicate that text data performed equivalently to ICD9 coding and demonstrate the utility of information beyond ICD9 coding for application in PheWAS.
Contact: hebbring.scott@mcrf.mfldclin.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Evolutionary profiles improve protein–protein interaction prediction from sequence
Authors: Hamp Tobias , Rost Burkhard 
Published: February 2015

Abstract
Motivation: Many methods predict the physical interaction between two proteins (protein-protein interactions; PPIs) from sequence alone. Their performance drops substantially for proteins not used for training.
Results: Here, we introduce a new approach to predict PPIs from sequence alone which is based on evolutionary profiles and profile-kernel support vector machines. It improved over the state-of-the-art, in particular for proteins that are sequence-dissimilar to proteins with known interaction partners. Filtering by gene expression data increased accuracy further for the few, most reliably predicted interactions (low recall). The overall improvement was so substantial that we compiled a list of the most reliably predicted PPIs in human. Our method makes a significant difference for biology because it improves most for the majority of proteins without experimental annotations.
Availability and implementation: Implementation and most reliably predicted human PPIs available at https://rostlab.org/owiki/index.php/Profppikernel.
Contact: rost@in.tum.de
Supplementary information: Supplementary data are available at Bioinformatics online.
‘Ce qui est coupé repousse’: Jean Genet, Héléne Cixous, the Wound, and the Poetics of Omission
Authors: Fleishman Ian Thomas 
Published: February 2015

Abstract

This article explores the thematic and structural significance of the figure of the wound to Jean Genet's
Pompes funèbres
(1947) and Hélène Cixous's
Souffles
(1975). With reference to the differences between editions of
Pompes funèbres
and through a detailed genetic study of the hitherto unexamined manuscripts of
Souffles
(Cixous's direct response to Genet's novel), the article demonstrates how (self-)censorship becomes constitutive of narrative as such — of its deconstruction and its reconfiguration. By revealing how the later drafts of Cixous's book operate to conceal its poignant autobiographical origin, and playing with the author's ambiguous assertion that ‘Ce qui est coupé repousse’, the article exposes omission as a productive textual strategy.
Derrida, Proust, and the Promise of Writing
Authors: Rushworth Jennifer 
Published: February 2015

Abstract

This article explores the language of the promise in Derrida's ‘Avances’ and
Mémoires pour Paul de Man
and in Proust's
À la recherche du temps perdu
. Derrida considers the promise to be impossible and necessary, tenable and untenable, finite and infinite. These Derridean stipulations are used to read the imagery and structure of promises in Proust's novel. While the promise in
À la recherche
punctuates the lives of couples unreliably, it is also shown to be connected to epiphanic moments intermittently granted by nature and art, and often signalled by the figure of the rainbow. Special attention is paid to Vinteuil's septet as a promise, and to connected semantic fields within this episode. Finally, the Derridean promise of writing is proposed as a means of rereading
Le Temps retrouvé
, and the promise as compromise is suggested to be a useful intermediary between the two opposing critical views (circular versus open-ended) surrounding the close of
À la recherche
and the complex question of the relationship between the book we have just read and the book the protagonist plans to write.
Anti-CD81 but not anti-SR-BI blocks Plasmodium falciparum liver infection in a humanized mouse model
Authors: Foquet Lander , Hermsen Cornelus C. , Verhoye Lieven , van Gemert Geert-Jan , Cortese Riccardo , Nicosia Alfredo , Sauerwein Robert W. , Leroux-Roels Geert , Meuleman Philip 
Published: February 2015

Abstract

Objectives
Plasmodium falciparum sporozoites, deposited in the skin by infected Anopheles mosquitoes taking a blood meal, cross the endothelium of skin capillaries and travel to the liver where they traverse Kupffer cells and hepatocytes to finally invade a small number of the latter. In hepatocytes, sporozoites replicate, differentiate and give rise to large numbers of merozoites that are released into the bloodstream where they invade red blood cells, thus initiating the symptomatic blood stage. Using in vitro systems and rodent models, it has been shown that the hepatocyte receptors CD81 and scavenger receptor type B class I (SR-BI) play a pivotal role during sporozoite invasion. We wanted to evaluate whether these two entry factors are genuine drug targets for the prevention of P. falciparum infection in humans.

Methods
Immunodeficient mice of which the liver is largely repopulated by human hepatocytes were treated with monoclonal antibodies blocking either CD81 or SR-BI 1 day prior to challenge with infected mosquitoes. P. falciparum infection of the liver was demonstrated using a qPCR assay.

Results
In human liver chimeric mice, an antibody directed against CD81 completely blocked P. falciparum sporozoite invasion while SR-BI-specific monoclonal antibodies did not influence in vivo infection.

Conclusions
These observations confirm the role of CD81 in liver-stage malaria and question that of SR-BI. CD81 might be a valuable drug target for the prevention of malaria.