bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple dye-doped NIR-emitting silica nanoparticles for both flow cytometry and in vivo imaging
Authors: Biffi Stefania , Petrizza Luca , Rampazzo Enrico , Voltan Rebecca , Sgarzi Massimo , Garrovo Chiara , Prodi Luca , Andolfi Laura , Agnoletto Chiara , Zauli Giorgio , Secchiero Paola
Published: April 2014

Dye-doped near infrared-emitting silica nanoparticles (DD-NIRsiNPs) represent a valuable tool in bioimaging, because they provide sufficient brightness, resistance to photobleaching and consist of hydrophilic non-toxic materials.
Thermodynamic stability and impedance measurements of perovskite LuRhO3(s) in the Lu–Rh–O system
Authors: Banerjee Aparna , Sawant Pooja , Mishra R. , Bharadwaj S. R. , Joshi A. R.
Published: April 2014

The Gibbs energy of formation of LuRhO3(s) has been determined using a solid-state electrochemical technique employing an oxide ion conducting electrolyte.
Ammonia-assisted epitaxial assembly of Cu2O@Ag yolk–shell and Ag cage
Authors: Zhang Jiqiao , Zhang Cui , Liu Shuangxi
Published: April 2014

Pure Cu2O@Ag and Ag cages were synthesized by introducing a [Ag (NH3)2]+ complexant to a Cu2O suspension, in the absence of any other chemical.
Surface passivated carbon nanodots prepared by microwave assisted pyrolysis: effect of carboxyl group in precursors on fluorescence properties
Authors: Hu Xiufeng , Cheng Lu , Wang Ning , Sun Liang , Wang Wei , Liu Wenguang
Published: April 2014

Carbon sources with different numbers of carboxyl groups greatly affect the photoluminescence and quantum yield of carbon nanodots.
Chemical colorimetric square wave and its derived logic gates based on tunable growth of plasmonic gold nanoparticles
Authors: Zhou Yanjuan , He Kaiyu , Liu Shengquan , Li Yong , Nie Zhou , Huang Yan , Yao Shouzhuo
Published: April 2014

AuNP-based chemical colorimetric square wave (CCSW) and logic gates were constructed based on the colorimetric signal change via the controllable growth of AuNPs.
Mapping the multimodal action of melamine-poly(aluminium phosphate) in the flame retardancy of polyamide 66
Authors: Naik Anil D. , Fontaine Gaëlle , Samyn Fabienne , Delva Xavier , Louisy Jérémie , Bellayer Séverine , Bourgeois Yann , Bourbigot Serge
Published: April 2014

Multimodal action and synergism of melamine poly(aluminum phosphate) in the flame retardancy of polyamide 66.
Novel poly-pyridyl ruthenium complexes with bis- and tris-tetrazolate mono-dentate ligands for dye sensitized solar cells
Authors: Shoker Tharallah A. , Ghaddar Tarek H.
Published: April 2014

New RuII complexes bearing bis- and tris-tetrazolate ligands, and their application as efficient sensitizers in dye-sensitized solar cells are presented.
Novel C-rich carbon nitride for room temperature NO2 gas sensors
Authors: Wang Donghong , Gu Wen , Zhang Yuewei , Hu Ying , Zhang Ting , Tao Xiaoming , Chen Wei
Published: April 2014

A p-type gas sensor based on C-rich carbon nitride exhibits good sensitivity and high selectivity toward NO2 at room temperature.
Students' application of chemical concepts when solving chemistry problems in different contexts
Authors: Broman Karolina , Parchmann Ilka
Published: April 2014

Context-based learning approaches have been implemented in school science over the last 40 years as a way to enhance students' interest in, as well as learning outcomes from, science. Contexts are used to connect science with the students' lives and to provide a frame in which concepts can be learned and applied on a ‘need-to-know’-principle. While effects on interest are coherently reported as positive, they are more diverse regarding cognitive learning outcomes. Hence, the demand for further research on criteria of context-based problems and problem-solving processes has been stated. In this paper, a study is presented investigating students' application of chemical concepts when solving context-based chemistry problems. Tasks for context-based problem solving have been designed systematically, using different combinations of contexts, topics and chemistry concepts in relation to the syllabus. Empirical data were collected using think-aloud interviews where 20 upper secondary students used their chemical content knowledge to solve the problems. The 15 context-based problems raised challenges within organic chemistry where concepts like electronegativity, polarity and solubility had to be applied. The difficulty to differentiate between intra- and intermolecular bonding emphasised in earlier research has also been apparent in this study. Besides the structural formula, which was an important part for the students when solving the tasks, the contextualisation of the problems was often used in the responses; students related their answers to the personal, societal or professional context in different ways. The paper explores the results and gives implications for context-based teaching, learning and assessment.
5-(Methylthio)tetrazoles as versatile synthons in the stereoselective synthesis of polycyclic pyrazolines via photoinduced intramolecular nitrile imine–alkene 1,3-dipolar cycloaddition
Authors: Pla Daniel , Tan Derek S. , Gin David Y.
Published: April 2014

A versatile thioether substituent on tetrazoles enables facile photoinduced intramolecular nitrile imine cycloadditions to form polycyclic pyrazolines.
Turning on the biradical state of tetracyano-perylene and quaterrylenequinodimethanes by incorporation of additional thiophene rings
Authors: Zeng Zebing , Lee Sangsu , Zafra José L. , Ishida Masatoshi , Bao Nina , Webster Richard D. , López Navarrete Juan T. , Ding Jun , Casado Juan , Kim Dongho , Wu Jishan
Published: April 2014

Incorporation of additional thiophene rings to the quinoidal rylenes results in dramatic changes of their ground states and physical properties.
Droplet topology control of Janus emulsion prepared in one-step high energy mixing
Authors: Ge Lingling , Shao Wanqing , Lu Shuhui , Guo Rong
Published: April 2014

Projection of rotationally and translational free droplets of Janus emulsions between slides with spacers and the topology elements of Janus droplets.
High-temperature failure behaviour and mechanism of K-based additives in Li–Mg–N–H hydrogen storage systems
Authors: Li Chao , Liu Yongfeng , Yang Yanjing , Gao Mingxia , Pan Hongge
Published: April 2014

The high-temperature failure mechanism of K-based additives in a Mg(NH2)2–2LiH system was clarified for the first time.
Coal based activated carbon nanofibers prepared by electrospinning
Authors: Zhao Hongyang , Wang Luxiang , Jia Dianzeng , Xia Wei , Li Jun , Guo Zaiping
Published: April 2014

Porous carbon nanofibers were prepared by electrospinning using coal as the raw material. The activated carbon fiber mat is a promising candidate for the electrode of supercapacitors.
A lithium iron phosphate/nitrogen-doped reduced graphene oxide nanocomposite as a cathode material for high-power lithium ion batteries
Authors: Jegal Jong-Pil , Kim Kwang-Chun , Kim Myeong Seong , Kim Kwang-Bum
Published: April 2014

Lithium iron phosphate/nitrogen-doped reduced graphene oxide is synthesized with the aid of urea, which exhibits low polarization and excellent rate performance.
Flexible, sandwich-like Ag-nanowire/PEDOT:PSS-nanopillar/MnO2high performance supercapacitors
Authors: Yu Zenan , Li Chao , Abbitt Danielle , Thomas Jayan
Published: April 2014

We demonstrate the design and fabrication of a Ag/PEDOT:PSS/MnO2layer by layer structure for high performance flexible supercapacitors.
Tuning oxygen content and distribution by substitution at Co site in 112 YBaCo2O5+δ: impact on transport and thermal expansion properties
Authors: Urusova A. S. , Cherepanov V. A. , Lebedev O. I. , Aksenova T. V. , Gavrilova L. Ya. , Caignaert V. , Raveau B.
Published: April 2014

Polycrystalline “112” ordered oxygen deficient double perovskites YBaCo2−xMexO5+δ (Me = Fe, Cu, Ni) were synthesized by a glycerol-nitrate route with 0.0 ≤ x ≤ 0.7 for Me = Fe, 0.0 ≤ x ≤ 0.6 for Me = Cu and x = 0.1 for Me = Ni.
Reduction breakable cholesteryl pullulan nanoparticles for targeted hepatocellular carcinoma chemotherapy
Authors: Li Huanan , Cui Yani , Liu Jun , Bian Shaoquan , Liang Jie , Fan Yujiang , Zhang Xingdong
Published: April 2014

Reduction breakable nanoparticles derived from pullulan enhanced the tumor accumulation and intracellular release of DOX in hepatocellular carcinoma.
White light and multicolor emission tuning in triply doped Yb3+/Tm3+/Er3+ novel fluoro-phosphate transparent glass-ceramics
Authors: Ledemi Yannick , Trudel Andrée-Anne , Rivera Victor A. G. , Chenu Sébastien , Véron Emmanuel , Nunes Luiz Antonio , Allix Mathieu , Messaddeq Younès
Published: April 2014

Wide emission tunability was obtained in rare-earth ions doped NaPO3–YF3–BaF2–CaF2 glassy material by controlling the laser excitation and its crystallization rate.
The cystathionine γ-lyase/hydrogen sulfide system maintains cellular glutathione status
Authors: Lee Zheng-Wei , Low Yi-Lian , Huang Shufen , Wang Tianxiao , Deng Lih-Wen
Published: April 2014

Hydrogen sulfide (H2S) has been implicated to exhibit antioxidative properties in many models. CSE (cystathionine γ-lyase) is an important enzyme responsible for endogenous H2S production in mammalian systems, but little is known about the modulation of endogenous H2S production and its antioxidative activity. We found that inhibiting CSE activity with PAG (propargylglycine) or silencing CSE expression using an siRNA approach resulted in a greater reduction in cell viability under exposure to the oxidizing agent hydrogen peroxide (H2O2). Cellular oxidative stress also increased significantly upon PAG inhibition or CSE knockdown. Further experiments using an activity-null Y60A mutant, a hyperactive E339A mutant and a control E349A mutant demonstrated that modulation of CSE catalytic activity altered its antioxidative activity. The increased sensitivity towards H2O2-induced cytotoxicity in CSE-siRNA-transfected cells was associated with a decreased glutathione concentration (GSH) and glutathione ratio (GSH/GSSG). Incubation of cells with exogenous H2S increased the GSH concentration and GSH/GSSG ratio. Moreover, exogenous H2S preserved the cellular glutathione status under BSO (buthionine sulfoximine)-induced glutathione depletion. Taken together, the results of the present study provide molecular insights into the antioxidative activity of CSE and highlights the importance of the CSE/H2S system in maintaining cellular glutathione status.
Epoxyeicosatrienoic acid analogue lowers blood pressure through vasodilation and sodium channel inhibition
Authors: Khan Md. Abdul Hye , Pavlov Tengis S. , Christain Sarah V. , Neckář Jan , Staruschenko Alexander , Gauthier Kathryn M. , Capdevila Jorge H. , Falck John R. , Campbell William B. , Imig John D.
Published: April 2014

Epoxyeicosatrienoic acids (EETs) contribute to haemodynamics, electrolyte homoeostasis and blood pressure regulation, leading to the concept that EETs can be therapeutically targeted for hypertension. In the present study, multiple structural EET analogues were synthesized based on the EET pharmacophore and vasodilator structure-activity studies. Four EET analogues with 91–119% vasodilatory activity in the isolated bovine coronary artery (EC50: 0.18–1.6 μM) were identified and studied for blood-pressure-lowering in hypertension. Two EET analogues in which the COOH group at carbon 1 of the EET pharmacophore was replaced with either an aspartic acid (EET-A) or a heterocyclic surrogate (EET-X) were administered for 14 days [10 mg/kg per day intraperitoneally (i.p.)]. Both EET-A and EET-X lowered blood pressure in spontaneously hypertensive rats (SHRs) and in angiotensin II (AngII) hypertension. On day 14, the mean arterial pressures in EET analogue-treated AngII-hypertensive and SHRs were 30–50 mmHg (EET-A) and 15–20 mmHg (EET-X) lower than those in vehicle-treated controls. These EET analogues (10 mg/kg per day) were further tested in AngII hypertension by administering orally in drinking water for 14 days and EET-A lowered blood pressure. Additional experiments demonstrated that EET-A inhibits epithelial sodium channel (ENaC) activity in cultured cortical collecting duct cells and reduced renal expression of ENaC subunits in AngII hypertension. In conclusion, we have characterized EET-A as an orally active antihypertensive EET analogue that protects vascular endothelial function and has ENaC inhibitory activity in AngII hypertension.
The Causes of Natural Durability in Timber I. The Role of Toxic Extractives in the Resistance of Tallowwood (Eucalyptus Microcorys F. Muell.) to Decay
Authors: Da Costa EWB , Rudman P
Published: April 2014

The hypothesis that the natural resistance of certain timbers to decay is due to the deposition in the heartwood of materials toxic to fungi is discussed, and criteria for assessing the role of these materials are outlined. These criteria have been applied in a study of the decay resistance of the highly durable Australian timber tallowwood (Eucalyptu8 microcory8 F. Muell.).
Bayesian inference for an emerging arboreal epidemic in the presence of control
Authors: Parry Matthew , Gibson Gavin J. , Parnell Stephen , Gottwald Tim R. , Irey Michael S. , Gast Timothy C. , Gilligan Christopher A.
Published: April 2014

Significance

Fast-moving and destructive emerging epidemics are seldom left to run their course because of the imperative to control further spread. Contemporaneous control measures, however, greatly complicate the characterization of the disease transmission process and the extraction of the epidemiological parameters of interest. The spread of Huanglongbing on orchard scales is used as a case study for modeling an emerging epidemic in the presence of control. We show that even with missing and censored data, and with seasonal and host age dependencies, it is possible to infer the parameters of a fully spatiotemporal stochastic model of disease spread. The value of the fitted model is to provide an engine for simulation studies of the costs and benefits of proposed disease control strategies.
Erbin is a negative modulator of cardiac hypertrophy
Authors: Rachmin Inbal , Tshori Sagi , Smith Yoav , Oppenheim Amit , Marchetto Sylvie , Kay Gillian , Foo Roger S.-Y. , Dagan Noa , Golomb Eliahu , Gilon Dan , Borg Jean-Paul , Razin Ehud
Published: April 2014

Significance

The cellular mechanisms underlying the transition from compensatory to deleterious cardiac hypertrophy remain to be elucidated. In the current work, we demonstrate decreased ErbB2 interacting protein (Erbin) expression in human failing hearts and, using mice models, we show that Erbin expression is important for compensated hypertrophy. Our findings reveal a previously unidentified link between Erbin and ERK signaling in the heart and implicate Erbin in the development of cardiac hypertrophy and heart failure. Erbin is particularly interesting due to its well-established interaction with the ErBb2/Her2 receptor. Clinical studies have observed cardiotoxicity associated with Herceptin therapy, reflecting the crucial role of Her2-mediated signaling in cardiac homeostasis. In this study, we describe a cardioprotective role for Erbin, which suggests it is a potential target for cardiac gene therapy.
Quinacrine promotes replication and conformational mutation of chronic wasting disease prions
Authors: Bian Jifeng , Kang Hae-Eun , Telling Glenn C.
Published: April 2014

Significance

Searching for drugs to prevent conversion of host-encoded prion protein (PrP
C
) to its infectious conformation (PrP
Sc
) is a key strategy in the pursuit of therapies for prion disorders: fatal, transmissible epidemic diseases of unpredictable occurrence and uncertain zoonotic potential. Despite quinacrine’s ability to reduce mouse PrP
Sc
in cell models, its use to treat patients has been unsuccessful. Here, we show that quinacrine augments PrP
Sc
and intensifies replication of prions, causing chronic wasting disease of deer, elk, and moose, and that the resulting prions have altered conformational and transmission properties. Our finding, that a drug capable of restraining PrP
Sc
in one species acts to improve replicative ability and induce mutation in another, forces reexamination of current strategies to combat these diseases.
Evolutionary diversity and taxon-specific modifications of the RNA polymerase II C-terminal domain
Authors: Yang Chunlin , Stiller John W.
Published: April 2014

Significance

The C-terminal domain (CTD) of the largest subunit of RNA polymerase II is responsible for coordinating a wide range of cotranscriptional functions. Although tandem repeats of a 7-aa motif comprise the CTD in model organisms, the domain is highly unordered in many other species. To our knowledge, this study represents the most comprehensive investigation of CTD diversity and evolution to date, and finds that the CTD’s tandem structure likely existed in the last eukaryotic common ancestor; that unordered CTDs have resulted from extensive, lineage-specific sequence modifications; and that tandem heptads have been lost and reinvented many times. We also highlight interesting parallels in CTD evolution that appear to be associated with the requirements of developmental complexity and adaptations to parasitism.
Characterizing asthma from a drop of blood using neutrophil chemotaxis
Authors: Sackmann Eric Karl-Heinz , Berthier Erwin , Schwantes Elizabeth A. , Fichtinger Paul S. , Evans Michael D. , Dziadzio Laura L. , Huttenlocher Anna , Mathur Sameer K. , Beebe David J.
Published: April 2014

Significance

Asthma is a chronic inflammatory disorder that is notoriously difficult to diagnose, characterize, and properly treat with tests that are available to clinicians today. Therefore, clinicians would benefit from additional tools that objectively characterize asthma in patients. In this work, we describe a handheld microfluidic device that discriminates asthma from allergic rhinitis patients based on neutrophil function—an inflammatory cell that has been implicated in the pathogenesis of asthma. The device can sort neutrophils from a drop of whole blood within minutes, and was used in a clinical setting to characterize asthmatic and nonasthmatic patients. This technology provides a new tool for clinicians to characterize asthma based on cellular function.
Degenerate target sites mediate rapid primed CRISPR adaptation
Authors: Fineran Peter C. , Gerritzen Matthias J. H. , Suárez-Diez María , Künne Tim , Boekhorst Jos , van Hijum Sacha A. F. T. , Staals Raymond H. J. , Brouns Stan J. J.
Published: April 2014

Significance

Bacteria are constantly exposed to foreign elements, such as bacteriophages and plasmids. The CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR associated) adaptive immune systems provide heritable sequence-specific protection against these invaders. To develop immunity, bacteria add segments of foreign nucleic acid to their CRISPR memory. However, phage and plasmid mutants can evade CRISPR-Cas recognition by altering their targeted sequence. CRISPR-Cas responds to evasion by quickly generating immunity by acquiring new pieces of invader genome. We determined that this rapid generation of resistance is promiscuous, with recognition of highly diverged or related elements eliciting new immunity. Our results demonstrate that CRISPR-Cas systems are more robust than previously thought and, not only have a highly specific resistance memory, but also have a broad ability to identify divergent genetic elements.
Differentiation of CD11c
+
CX
3
CR1
+
cells in the small intestine requires Notch signaling
Authors: Ishifune Chieko , Maruyama Satoshi , Sasaki Yuki , Yagita Hideo , Hozumi Katsuto , Tomita Taisuke , Kishihara Kenji , Yasutomo Koji
Published: April 2014

Significance

The gastrointestinal tract directly faces an array of environmental agents, including bacteria and food. Intestine-specific subsets of immune cells maintain gut homeostasis by continuously sampling luminal antigens and maintaining immune tolerance. We here demonstrated that Rbpj, an essential molecule for Notch signaling, is essential for the development of CD11c
+
CX
3
CR1
+
cells that are crucial for sampling luminal antigens with dendrites projecting through the epithelial cell layer. These findings indicate that Notch signaling is required for maintaining the repertoires of intestinal antigen-presenting cells and suggest new ways to keep immune tolerance by modulating Notch-mediated CD11c
+
CX
3
CR1
+
cells.
Synthetic control of mammalian-cell motility by engineering chemotaxis to an orthogonal bioinert chemical signal
Authors: Park Jason S. , Rhau Benjamin , Hermann Aynur , McNally Krista A. , Zhou Carmen , Gong Delquin , Weiner Orion D. , Conklin Bruce R. , Onuffer James , Lim Wendell A.
Published: April 2014

Significance

Directed migration of diverse cell types is critical in biological processes ranging from development and morphogenesis to immune response, wound healing, and regeneration. However, techniques to specifically and easily direct, manipulate, and study cell migration in vitro and in vivo are currently limited. We conceived of a strategy to directly control cell migration to arbitrary user-defined locations, independent of native chemotaxis receptors. In this work, we demonstrate that genetic modification of cells with an engineered G protein-coupled receptor allows us to redirect their migration to a bioinert drug-like small molecule, clozapine-
N
-oxide. This technology provides a generalizable tool to systematically control cell migration in vitro and in vivo and could be a valuable module for engineering future therapeutic cellular devices.
An engineered muscle flap for reconstruction of large soft tissue defects
Authors: Shandalov Yulia , Egozi Dana , Koffler Jacob , Dado-Rosenfeld Dekel , Ben-Shimol David , Freiman Alina , Shor Erez , Kabala Aviva , Levenberg Shulamit
Published: April 2014

Significance

Effective restoration of large soft tissue defects requires the use of tissue flaps, with viability that is largely determined by degree of vascularization. In view of the tedious transfer procedures and donor site morbidity associated with autologous flaps, this work set out to design and evaluate an engineered muscle flap featuring a robust vascular port formed from preseeded endothelial cells and host vasculature. The implanted flap was highly vascularized, well-perfused, and anastomosed with host vessels. Engineered flaps of this nature promise to circumvent the need to harvest and transfer massive tissue volumes, while avoiding the consequential complications.
Concurrence of monoenergetic electron beams and bright X-rays from an evolving laser-plasma bubble
Authors: Yan Wenchao , Chen Liming , Li Dazhang , Zhang Lu , Hafz Nasr A. M. , Dunn James , Ma Yong , Huang Kai , Su Luning , Chen Min , Sheng Zhengming , Zhang Jie
Published: April 2014

Significance

Desktop laser plasma acceleration is able to generate monoenergetic electron beams, and such electron beams can oscillate in the plasma bubble, which results in the collimated X-rays with ability of femtosecond temporal resolution. However, high-flux X-ray emission and high-quality electron beams have not been obtained simultaneously because high-yield X-ray emission is usually produced at the cost of electron beam qualities. By stimulating double injections into a plasma bubble, we report our experimental observation in which both a monoenergetic electron beam at the gigaelectronvolt level and ultraintense hard X-rays with peak brightness higher than the third generation of synchrotrons. Due to the inherent temporal synchronization, this unique electron–photon source can be ideal for “single-shot” pump–probe applications at femtosecond and nanometer scales.
p53 constrains progression to anaplastic thyroid carcinoma in a
Braf
-mutant mouse model of papillary thyroid cancer
Authors: McFadden David G. , Vernon Amanda , Santiago Philip M. , Martinez-McFaline Raul , Bhutkar Arjun , Crowley Denise M. , McMahon Martin , Sadow Peter M. , Jacks Tyler
Published: April 2014

Significance

We generated a thyroid-specific CreER transgenic mouse and used this strain to model progression of
v-raf murine sarcoma viral oncogene homolog B
(
BRAF
)-mutant papillary thyroid cancer to anaplastic thyroid cancer (ATC). These murine tumors recapitulated the temporal progression and molecular hallmarks of human ATC. We demonstrated that combined mapk/Erk kinase (MEK) and BRAF inhibition resulted in enhanced antitumor activity vs. single-agent BRAF inhibitors in this preclinical model. This model represents a previously lacking mouse model of
BRAF
-mutant ATC and adds to the experimental armamentarium of a highly lethal disease in need of scientific advances. These data also suggest that potent inhibition of the MAPK pathway may improve outcomes in advanced thyroid cancers.
Substrate-induced changes in the structural properties of LacY
Authors: Serdiuk Tetiana , Madej M. Gregor , Sugihara Junichi , Kawamura Shiho , Mari Stefania A. , Kaback H. Ronald , Müller Daniel J.
Published: April 2014

Significance

Lactose permease of
Escherichia coli
(LacY), a model for the major facilitator superfamily, catalyzes galactopyranoside/H
+
symport across the membrane by a mechanism in which large conformational changes expose the sugar-binding site in the middle of the molecule alternatively to either side of the membrane (an alternating access mechanism). Despite substantial progress with respect to static X-ray crystal structures of LacY, the dynamics of the transport mechanism are not fully understood. Here we use dynamic single-molecule force spectroscopy to quantify the structural properties that change upon substrate binding. The results reveal very significant changes in conformational, kinetic, energetic, and mechanical properties primarily in the N-terminal 6-helix bundle, while the C-terminal 6-helix bundle remains largely unaffected.
Architecture and assembly of the archaeal Cdc48⋅20S proteasome
Authors: Barthelme Dominik , Chen James Z. , Grabenstatter Jonathan , Baker Tania A. , Sauer Robert T.
Published: April 2014

Significance

From microbes to humans, proteolytic machines called proteasomes cleave proteins that are damaged or unnecessary into peptide fragments. Proteasomes minimally consist of the barrel-like 20S peptidase and an AAA+ ring, which harnesses chemical energy to unfold and translocate proteins into the 20S chamber for degradation. Here, we determine the architecture of a recently discovered proteasome, Cdc48⋅20S, by electron microscopy. A continuous axial channel allows translocation through the double AAA+ rings of Cdc48 into the 20S chamber. A model in which dynamic “wobbling” of the AAA+ unfoldase relative to 20S is necessary for function is ruled out for Cdc48⋅20S by electron-microscopy results showing coaxial alignment of Cdc48 and 20S and by the proteolytic activity of cross-linked complexes.
Legal linguistics as a mutual arena for cooperation
Authors: Engberg Jan
Published: April 2014

This article reports on some of the recent projects and individual works in the field of Legal Linguistics as examples of cooperation between Applied Linguistics and law. The article starts by discussing relevant prototypical concepts of Legal Linguistics. Legal Linguistics scrutinizes interactions between human beings in the framework of legal institutions involving language as a means of communication. Focus is upon creating a mutual arena for cooperation between disciplines, including Applied Linguistics. Legal Linguistics is thus seen as an interdisciplinary approach treating problems of relevance to the law from the point of view of non-legal disciplines. Subsequently, the paper presents four domains of study in Legal Linguistics all characterised by offering opportunities for interdisciplinary cooperation: Forensic linguistic evidence analysis, Drafting and intelligibility, Legal interpretation and meaning, and Discourse studies of law.
Diaspora
Authors: Li Wei  , Hua Zhu
Published: April 2014

The nature of diaspora is changing in the 21st century. Yet many of the communication issues remain the same. At the heart of it is
multilingual and intercultural communication across time and space. There is much that applied linguists can contribute to the
understanding of diaspora in the era of globalization. This article discusses some of the core issues of communication between the
diaspora and the homeland, the past and the present, the individual and the community, and the sense of belonging and the ascribed
category with a detailed analysis of empirical data collected through linguistic ethnography in the Chinese diaspora in Britain
and elsewhere. It also highlights the significance of dynamic multilingualism in everyday communication.
Investigating language and the media
Authors: Perrin Daniel
Published: April 2014

Drawing on a case study of newswriting, this article presents media linguistics as a subdiscipline of applied linguistics (AL),
dealing with a distinctive field of language use. Language in the media is characterized by specific environments, functions, and
structures. Medialinguistic research, however, tends to overcome disciplinary boundaries. In multidisciplinary collaboration, it
accesses a wide range of knowledge generation and transformation methods. In interdisciplinary collaboration, it contributes
precise analyses of situated linguistic activity to the development of empirically-grounded communication studies. In
transdisciplinary collaboration, it tests these theories against reality and solves practical problems. The article first outlines
such a practical problem (Section 1). After explaining key concepts of media lingustics (2), it focuses on the linguistics of
newswriting (3) and four related research methods (4). Finally, it discusses how the value media linguistics can add to both
theory and practice of language use and the media (5).
Linguistics in the service of communication disorders
Authors: Ravid Dorit , Bar-On Amalia , Dattner Elitzur
Published: April 2014

Linguistics and Communication Disorders are considered two different disciplines by most students and scholars in both fields as well as by researchers working in other relevant fields such as psychology and education. However, most core disorders, disabilities and delays in communicative ability directly concern language, especially in conjunction with human development from infancy to adulthood, but also as related to the loss of communicative skills in the aging brain. Linguistics thus emerges as a major source of scientific insights and practical applications for the field of communication disorders. While it is obviously impossible to account for the diverse and sometimes contradictory views of linguistics in a single paper, we nonetheless focus on the contribution of novel linguistic and psycholinguistic approaches to the current conceptualization of communication disorders from different perspectives. We first discuss the nature of evidence and research methods in the two disciplines, with the current usage-based and typological approaches to corpus linguistics as a case in point. Consequently, we discuss the interface of linguistics and communication disorders through four contexts which are considered infelicitous to language acquisition and processing. These are, as follows: (i) hearing loss, (ii) language impairment and dyslexia, (iii) growing up in a low socio-economic environment, and (iv) situations of bilingualism.
Tackler characteristics associated with tackle performance in rugby union
Authors: Hendricks Sharief , Matthews Bevan , Roode Brad , Lambert Mike
Published: April 2014

Tackling is an important skill for performance in rugby, yet little has been reported on tackler characteristics and its relationship to performance in competition. The aim of this study was to identify tackler characteristics and its association with tackle performance in matches. Eighteen matches of the 2010 Super 14 were analysed, which amounted to 2092 coded tackles. Tackler characteristics such as head position – in motion, up and forward, type of tackle – shoulder tackler, arm tackle or ball‐carrier fend – absent, moderate, strong and leg drive–absent, moderate, strong or shoulder usage were coded and associated with tackle outcomes. Relative risk ratio (RRR), the ratio of the probability of an outcome occurring when a characteristic was observed (versus the non‐observed characteristic) was determined using multinomial logistic regression. Having the head in motion decreased the tackler's chances of a successful tackle (RRR 2.24, 95% CI 1.72–2.92, p < 0.001) relative to an up and forward head position. Ball‐carriers using a fend significantly decreased the tackler's probability of success (moderate fend RRR 2.97, 95% CI 2.04–4.31, p < 0.001). Moderate leg drive (RRR 0.36, 95% CI 0.26–0.50, p < 0.001) by the tackler increased the likelihood of tackle success. Head up and forward, counter‐acting the ball‐carrier fend, shoulder tackles targeted at the ball‐carrier mid‐torso, using the arms to wrap or pull, and leg driving were key tackler characteristics associated with positive tackle outcome in matches. Based on these findings, it is recommended that these technical characteristics are emphasised and incorporated into training to effectively prepare tacklers for competition.
The intentionality bias and schizotypy
Authors: Moore J. W. , Pope A.
Published: April 2014

The “intentionality bias” refers to our automatic tendency to judge other people's actions to be intentional. In this experiment we extended research on this effect in two key ways. First, we developed a novel nonlinguistic task for assessing the intentionality bias. This task used video stimuli of ambiguous movements. Second, we investigated the relationship between the strength of this bias and schizotypy (schizophrenia-like symptoms in healthy individuals). Our results showed that the intentionality bias was replicated for the video stimuli and also that this bias is stronger in those individuals scoring higher on the schizotypy rating scales. Overall these findings lend further support for the existence of the intentionality bias. We also discuss the possible relevance of these findings for our understanding of certain symptoms of schizophrenic illness.
Wnt7a stimulates myogenic stem cell motility and engraftment resulting in improved muscle strength
Authors: Bentzinger C. Florian , von Maltzahn Julia , Dumont Nicolas A. , Stark Danny A. , Wang Yu Xin , Nhan Kevin , Frenette Jérôme , Cornelison DDW , Rudnicki Michael A.
Published: April 2014

Wnt7a/Fzd7 signaling stimulates skeletal muscle growth and repair by inducing the symmetric expansion of satellite stem cells through the planar cell polarity pathway and by activating the Akt/mTOR growth pathway in muscle fibers. Here we describe a third level of activity where Wnt7a/Fzd7 increases the polarity and directional migration of mouse satellite cells and human myogenic progenitors through activation of Dvl2 and the small GTPase Rac1. Importantly, these effects can be exploited to potentiate the outcome of myogenic cell transplantation into dystrophic muscles. We observed that a short Wnt7a treatment markedly stimulated tissue dispersal and engraftment, leading to significantly improved muscle function. Moreover, myofibers at distal sites that fused with Wnt7a-treated cells were hypertrophic, suggesting that the transplanted cells deliver activated Wnt7a/Fzd7 signaling complexes to recipient myofibers. Taken together, we describe a viable and effective ex vivo cell modulation process that profoundly enhances the efficacy of stem cell therapy for skeletal muscle.
Coordinated binding of Vps4 to ESCRT-III drives membrane neck constriction during MVB vesicle formation
Authors: Adell Manuel Alonso Y , Vogel Georg F. , Pakdel Mehrshad , Müller Martin , Lindner Herbert , Hess Michael W. , Teis David
Published: April 2014

Five endosomal sorting complexes required for transport (ESCRTs) mediate the degradation of ubiquitinated membrane proteins via multivesicular bodies (MVBs) in lysosomes. ESCRT-0, -I, and –II interact with cargo on endosomes. ESCRT-II also initiates the assembly of a ringlike ESCRT-III filament consisting of Vps20, Snf7, Vps24, and Vps2. The AAA–adenosine triphosphatase Vps4 disassembles and recycles the ESCRT-III complex, thereby terminating the ESCRT pathway. A mechanistic role for Vps4 in intraluminal vesicle (ILV) formation has been unclear. By combining yeast genetics, biochemistry, and electron tomography, we find that ESCRT-III assembly on endosomes is required to induce or stabilize the necks of growing MVB ILVs. Yet, ESCRT-III alone is not sufficient to complete ILV biogenesis. Rather, binding of Vps4 to ESCRT-III, coordinated by interactions with Vps2 and Snf7, is coupled to membrane neck constriction during ILV formation. Thus, Vps4 not only recycles ESCRT-III subunits but also cooperates with ESCRT-III to drive distinct membrane-remodeling steps, which lead to efficient membrane scission at the end of ILV biogenesis in vivo.
A contractile and counterbalancing adhesion system controls the 3D shape of crawling cells
Authors: Burnette Dylan T. , Shao Lin , Ott Carolyn , Pasapera Ana M. , Fischer Robert S. , Baird Michelle A. , Der Loughian Christelle , Delanoe-Ayari Helene , Paszek Matthew J. , Davidson Michael W. , Betzig Eric , Lippincott-Schwartz Jennifer
Published: April 2014

How adherent and contractile systems coordinate to promote cell shape changes is unclear. Here, we define a counterbalanced adhesion/contraction model for cell shape control. Live-cell microscopy data showed a crucial role for a contractile meshwork at the top of the cell, which is composed of actin arcs and myosin IIA filaments. The contractile actin meshwork is organized like muscle sarcomeres, with repeating myosin II filaments separated by the actin bundling protein α-actinin, and is mechanically coupled to noncontractile dorsal actin fibers that run from top to bottom in the cell. When the meshwork contracts, it pulls the dorsal fibers away from the substrate. This pulling force is counterbalanced by the dorsal fibers’ attachment to focal adhesions, causing the fibers to bend downward and flattening the cell. This model is likely to be relevant for understanding how cells configure themselves to complex surfaces, protrude into tight spaces, and generate three-dimensional forces on the growth substrate under both healthy and diseased conditions.
First remodel, then recycle
Authors: Short Ben
Published: April 2014

Study reveals how the AAA-ATPase Vps4 helps the ESCRT-III complex form multivesicular bodies.
Type I interferons directly inhibit regulatory T cells to allow optimal antiviral T cell responses during acute LCMV infection
Authors: Srivastava Shivani , Koch Meghan A. , Pepper Marion , Campbell Daniel J.
Published: April 2014

Regulatory T (T reg) cells play an essential role in preventing autoimmunity but can also impair clearance of foreign pathogens. Paradoxically, signals known to promote T reg cell function are abundant during infection and could inappropriately enhance T reg cell activity. How T reg cell function is restrained during infection to allow the generation of effective antiviral responses remains largely unclear. We demonstrate that the potent antiviral type I interferons (IFNs) directly inhibit co-stimulation–dependent T reg cell activation and proliferation, both in vitro and in vivo during acute infection with lymphocytic choriomeningitis virus (LCMV). Loss of the type I IFN receptor specifically in T reg cells results in functional impairment of virus-specific CD8+ and CD4+ T cells and inefficient viral clearance. Together, these data demonstrate that inhibition of T reg cells by IFNs is necessary for the generation of optimal antiviral T cell responses during acute LCMV infection.
The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity
Authors: Chevrier Stéphane , Emslie Dianne , Shi Wei , Kratina Tobias , Wellard Cameron , Karnowski Alexander , Erikci Erdem , Smyth Gordon K. , Chowdhury Kamal , Tarlinton David , Corcoran Lynn M.
Published: April 2014

The transcriptional network regulating antibody-secreting cell (ASC) differentiation has been extensively studied, but our current understanding is limited. The mechanisms of action of known “master” regulators are still unclear, while the participation of new factors is being revealed. Here, we identify Zbtb20, a Bcl6 homologue, as a novel regulator of late B cell development. Within the B cell lineage, Zbtb20 is specifically expressed in B1 and germinal center B cells and peaks in long-lived bone marrow (BM) ASCs. Unlike Bcl6, an inhibitor of ASC differentiation, ectopic Zbtb20 expression in primary B cells facilitates terminal B cell differentiation to ASCs. In plasma cell lines, Zbtb20 induces cell survival and blocks cell cycle progression. Immunized Zbtb20-deficient mice exhibit curtailed humoral responses and accelerated loss of antigen-specific plasma cells, specifically from the BM pool. Strikingly, Zbtb20 induction does not require Blimp1 but depends directly on Irf4, acting at a newly identified Zbtb20 promoter in ASCs. These results identify Zbtb20 as an important player in late B cell differentiation and provide new insights into this complex process.
Large even order character sums
Authors: Goldmakher Leo , Lamzouri Youness
Published: April 2014

A classical theorem of Paley asserts the existence of an infinite family of quadratic characters whose character sums become exceptionally large. In this paper, we establish an analogous result for characters of any fixed even order. Previously our bounds were only known under the assumption of the Generalized Riemann Hypothesis.
Covariate-modulated local false discovery rate for genome-wide association studies
Authors: Zablocki Rong W. , Schork Andrew J. , Levine Richard A. , Andreassen Ole A. , Dale Anders M. , Thompson Wesley K.
Published: April 2014

Motivation: Genome-wide association studies (GWAS) have largely failed to identify most of the genetic basis of highly heritable diseases and complex traits. Recent work has suggested this could be because many genetic variants, each with individually small effects, compose their genetic architecture, limiting the power of GWAS, given currently obtainable sample sizes. In this scenario, Bonferroni-derived thresholds are severely underpowered to detect the vast majority of associations. Local false discovery rate (fdr) methods provide more power to detect non-null associations, but implicit assumptions about the exchangeability of single nucleotide polymorphisms (SNPs) limit their ability to discover non-null loci.

Methods: We propose a novel covariate-modulated local false discovery rate (cmfdr) that incorporates prior information about gene element–based functional annotations of SNPs, so that SNPs from categories enriched for non-null associations have a lower fdr for a given value of a test statistic than SNPs in unenriched categories. This readjustment of fdr based on functional annotations is achieved empirically by fitting a covariate-modulated parametric two-group mixture model. The proposed cmfdr methodology is applied to a large Crohn’s disease GWAS.

Results: Use of cmfdr dramatically improves power, e.g. increasing the number of loci declared significant at the 0.05 fdr level by a factor of 5.4. We also demonstrate that SNPs were declared significant using cmfdr compared with usual fdr replicate in much higher numbers, while maintaining similar replication rates for a given fdr cutoff in de novo samples, using the eight Crohn’s disease substudies as independent training and test datasets.

Availability an implementation:  https://sites.google.com/site/covmodfdr/

Contact : wes.stat@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Filling annotation gaps in yeast genomes using genome-wide contact maps
Authors: Marie-Nelly Hervé , Marbouty Martial , Cournac Axel , Liti Gianni , Fischer Gilles , Zimmer Christophe , Koszul Romain
Published: April 2014

Motivations:  De novo sequencing of genomes is followed by annotation analyses aiming at identifying functional genomic features such as genes, non-coding RNAs or regulatory sequences, taking advantage of diverse datasets. These steps sometimes fail at detecting non-coding functional sequences: for example, origins of replication, centromeres and rDNA positions have proven difficult to annotate with high confidence. Here, we demonstrate an unconventional application of Chromosome Conformation Capture (3C) technique, which typically aims at deciphering the average 3D organization of genomes, by showing how functional information about the sequence can be extracted solely from the chromosome contact map.

Results: Specifically, we describe a combined experimental and bioinformatic procedure that determines the genomic positions of centromeres and ribosomal DNA clusters in yeasts, including species where classical computational approaches fail. For instance, we determined the centromere positions in Naumovozyma castellii , where these coordinates could not be obtained previously. Although computed centromere positions were characterized by conserved synteny with neighboring species, no consensus sequences could be found, suggesting that centromeric binding proteins or mechanisms have significantly diverged. We also used our approach to refine centromere positions in Kuraishia capsulata and to identify rDNA positions in Debaryomyces hansenii . Our study demonstrates how 3C data can be used to complete the functional annotation of eukaryotic genomes.

Availability and implementation: The source code is provided in the Supplementary Material. This includes a zipped file with the Python code and a contact matrix of Saccharomyces cerevisiae .

Contact:  romain.koszul@pasteur.fr

Supplementary information:  Supplementary data are available at Bioinformatics online
Dynamic Panel Analysis under Cross-Sectional Dependence
Authors: Gaibulloev Khusrav , Sandler Todd , Sul Donggyu
Published: April 2014

This article investigates inconsistency and invalid statistical inference that often characterize dynamic panel analysis in international political economy. These econometric concerns are tied to Nickell bias and cross-sectional dependence. First, we discuss how to avoid Nickell bias in dynamic panels. Second, we put forward factor-augmented dynamic panel regression as a means for addressing cross-sectional dependence. As a specific application, we use our methods for an analysis of the impact of terrorism on economic growth. Different terrorism variables are shown to have no influence on economic growth for five regional samples when Nickell bias and cross-dependence are taken into account. Our finding about terrorism and growth is contrary to the extant literature.