bluuebunny/crossref_metadata_2025 huggingface dataset:
Liquid biofuels in Greece—Current status in production and research
Authors: Vouitsis Ilias , Geivanidis Savvas , Samaras Zissis
Published: April 2014

This paper reviews the state of liquid biofuels in Greece and presents the current situation in production and research. The first part presents the production potential in terms of cultivated crops along with the industrial activity on biofuels and their distribution in the country. In the second part, the research activities are discussed. It is shown that the Greek biofuel potential is significant, although some problems in the allocation of the fuel resulted in severe constraints to efficiency. Research on the optimization of biodiesel properties and on the development of 2nd generation biofuels as well on the assessment of their impacts on engine performance and emissions is remarkable and promising.
Giant room-temperature barocaloric effect and pressure-mediated electrocaloric effect in BaTiO3 single crystal
Authors: Liu Yang , Wei Jie , Janolin Pierre-Eymeric , Infante Ingrid C. , Lou Xiaojie , Dkhil Brahim
Published: April 2014

Barocaloric effect in BaTiO3 single crystal is studied by a thermodynamic phenomenological model. It is demonstrated that a giant barocaloric effect can be achieved near room temperature with an adiabatic temperature change of more than 3 K and a temperature span about 50 K. As expected, the electrocaloric peak can be shifted towards room temperature by pressure. However, a slight reduction of the electrocaloric peak is found in contrast to relaxor ferroelectrics and LiNbO3. We believe that our findings could open a potential route by combining the barocaloric effect and pressure-mediated electrocaloric effect in BaTiO3 single crystal for cooling devices.
Anisotropic emission and photon-recycling in strain-balanced quantum well solar cells
Authors: Cabrera C. I. , Rimada J. C. , Hernandez L. , Connolly J. P. , Enciso A. , Contreras-Solorio D. A.
Published: April 2014

Strain-balanced quantum well solar cells (SB-QWSCs) extend the photon absorption edge beyond that of bulk GaAs by incorporation of quantum wells in the i-region of a p–i–n device. Anisotropy arises from a splitting of the valence band due to compressive strain in the quantum wells, suppressing a transition which contributes to emission from the edge of the quantum wells. We have studied both the emission light polarized in the plane perpendicular (TM) to the quantum well which couples exclusively to the light hole transition and the emission polarized in the plane of the quantum wells (TE) which couples mainly to the heavy hole transition. It was found that the spontaneous emission rates TM and TE increase when the quantum wells are deeper. The addition of a distributed Bragg reflector can substantially increase the photocurrent while decreasing the radiative recombination current. We have examined the impact of the photon recycling effect on SB-QWSC performance. We have optimized SB-QWSC design to achieve single junction efficiencies above 30%.
On the notch sensitivity of CuZr nanoglass
Authors: Sha Z. D. , He L. C. , Pei Q. X. , Pan H. , Liu Z. S. , Zhang Y. W. , Wang T. J.
Published: April 2014

Recently, nanoglass (NG) was found to exhibit a surprising homogeneous superplastic deformation behavior. However, how the presence of notch affects its mechanical properties remains unexplored. Here, we perform molecular dynamics simulations on a superplastic Cu50Zr50 NG containing a pre-existing notch under tensile loading, with focus on the notch sensitivity. Our results show that when the notch size is smaller than or comparable to the average grain size (d), the NG still exhibits a superplastic deformation and shows notch-insensitivity. When the notch size is larger than d, however, the NG fails by localized shear banding emanating from the notch root and shows notch-sensitivity. The origin of this transition arises from the competition between the shear band nucleation induced by the stress concentration at the notch root and the growth of shear transformation zones distributed in the glass-glass interfaces. Our results provide useful guidelines for the design and engineering of NG with notch for structural applications.
Metastable magnetic state and magnetotransport in disordered manganite thin films
Authors: Kumar Manish , Choudhary R. J. , Shukla D. K. , Phase D. M.
Published: April 2014

We report on the magnetic, electrical, and magnetotransport properties of La0.7Ca0.3Mn1−XAlXO3 (X = 0, 0.05, 0.15) thin films grown on LaAlO3 (001) substrate. It is observed that the low temperature ferromagnetic phase of La0.7Ca0.3MnO3 transforms into metastable magnetic state in 15 at. % Al doped sample, which has been characterized using long-time relaxation measurement as well as different temperature sweep rates (during cooling and heating) of magnetization measurements. Our results clearly show that the magnetic transition in this film is connected with the kinetics of first order phase transition. The metastable magnetic phase also shows increased magnetoresistance.
Magnetoelectric transport and quantum interference effect in ultrathin manganite films
Authors: Wang Cong , Jin Kui-juan , Gu Lin , Lu Hui-bin , Li Shan-ming , Zhou Wen-jia , Zhao Rui-qiang , Guo Hai-zhong , He Meng , Yang Guo-zhen
Published: April 2014

The magnetoelectric transport behavior with respect to the thicknesses of ultrathin La0.9Sr0.1MnO3 films is investigated in detail. The metal-insulator phase transition, which has never been observed in bulk La0.9Sr0.1MnO3, is found in ultrathin films with thicknesses larger than 6 unit cells. Low-temperature resistivity minima appeared in films with thicknesses less than 10 unit cells. This is attributed to the presence of quantum interference effects. These data suggest that the influence of the weak localization becomes much pronounced as the film thickness decreases from 16 to 8 unit cells.
Landau damping and the onset of particle trapping in quantum plasmas
Authors: Daligault Jérôme
Published: April 2014

Using analytical theory and simulations, we assess the impact of quantum effects on non-linear wave-particle interactions in quantum plasmas. We more specifically focus on the resonant interaction between Langmuir waves and electrons, which, in classical plasmas, lead to particle trapping. Two regimes are identified depending on the difference between the time scale of oscillation tB(k)=m/eEk of a trapped electron and the quantum time scale tq(k)=2m/ℏk2 related to recoil effect, where E and k are the wave amplitude and wave vector. In the classical-like regime, tB(k) < tq(k), resonant electrons are trapped in the wave troughs and greatly affect the evolution of the system long before the wave has had time to Landau damp by a large amount according to linear theory. In the quantum regime, tB(k) > tq(k), particle trapping is hampered by the finite recoil imparted to resonant electrons in their interactions with plasmons.
Zonal flows in tokamaks with anisotropic pressure
Authors: Ren Haijun
Published: April 2014

Zonal flows (ZFs) in a tokamak plasma with anisotropic pressure are investigated. The dynamics of perpendicular and parallel pressures are determined by the Chew-Goldberger-Low double equations and low-β condition is adopted, where β is the ratio of plasma pressure to the magnetic field pressure. The dispersion relation is analytically derived and illustrates two branches of ZFs. The low frequency zonal flow (LFZF) branch becomes unstable when χ, the ratio of the perpendicular pressure to the parallel one, is greater than a threshold value χc, which is about 3.8. In the stable region, its frequency increases first and then decreases with increasing χ. For χ = 1, the frequency of LFZF agrees well with the experimental observation. For the instability, the growth rate of LFZF increases with χ. The geodesic acoustic mode branch is shown to be always stable with a frequency increasing with χ. The safety factor is shown to diminish the frequencies of both branches or the growth rate of LFZF.
Natural discharge after pulse and cooperative electrodes to enhance droplet velocity in digital microfluidics
Authors: Chen Tianlan , Dong Cheng , Gao Jie , Jia Yanwei , Mak Pui-In , Vai Mang-I , Martins Rui P.
Published: April 2014

Digital Microfluidics (DMF) is a promising technology for biological/chemical micro-reactions due to its distinct droplet manageability via electronic automation, but the limited velocity of droplet transportation has hindered DMF from utilization in high throughput applications. In this paper, by adaptively fitting the actuation voltages to the dynamic motions of droplet movement under real-time feedback monitoring, two control-engaged electrode-driving techniques: Natural Discharge after Pulse (NDAP) and Cooperative Electrodes (CE) are proposed. They together lead to, for the first time, enhanced droplet velocity with lower root mean square voltage value.
E3 ubiquitin ligase Cullin-5 modulates multiple molecular and cellular responses to heat shock protein 90 inhibition in human cancer cells
Authors: Samant Rahul S. , Clarke Paul A. , Workman Paul
Published: April 2014

Significance

The protective molecular chaperone protein heat shock protein 90 (HSP90) is required for the activity and stability of its client proteins, which play diverse roles in both normal cell homeostasis and diseases such as cancer. Pharmacologic inhibition of HSP90 leads to the deactivation and degradation of these clients. Here we report that depleting levels of the degradative enzyme Cullin-5 (CUL5) reduces both client breakdown and loss of signaling output normally observed upon HSP90 inhibitor treatment for five important oncogenic protein kinase clients in four different cancer types. Depleting CUL5 also reduces the sensitivity of a variety of human cancers to HSP90 inhibitors. Our results provide important translational as well as mechanistic insights into the molecular pharmacology of HSP90 inhibitors that are currently undergoing clinical trials.
Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates
Authors: Ghodke Harshad , Wang Hong , Hsieh Ching L. , Woldemeskel Selamawit , Watkins Simon C. , Rapić-Otrin Vesna , Van Houten Bennett
Published: April 2014

Significance

UV damage in genomic DNA is identified by the human UV-damaged DNA-binding protein (UV-DDB). Recognition of DNA damage by UV-DDB serves to initiate global genomic nucleotide excision repair (NER) in humans. Recent work has revealed that UV-DDB dimerizes at sites of damage. This study demonstrates that prior to stable damage recognition, UV-DDB interrogates DNA for damage via a 3D diffusion mechanism coupled to the formation of multiple transient intermediates. Stable binding at sites of damage is achieved by dimerization of UV-DDB. This study also analyzed a disease-causing mutant of UV-DDB, which was found to slide on DNA, while retaining the ability to dimerize on DNA. These results enhance our understanding of damage recognition in NER in humans.
Homeland tour guide narratives and the discursive construction of the diasporic
Authors: Avni Sharon
Published: April 2014

By analyzing the constitutive role of tour guides narratives, this article addresses the recruitment of tourism as a means of forging transnational ties between diasporans and their ethnic homeland. Combining theoretical frameworks from linguistic anthropology and the sociology of tourism, it examines the narratives told to American Jewish youth at three graves at a military cemetery in Israel and analyzes the discursive, linguistic, and rhetorical strategies in the narratives, including stancetaking, reported speech, and pronominal usage. Attending to the growing phenomenon of diaspora homeland tourism, it analyzes how tour guide narratives about the past work as a form of social action in constituting present day transnational identifications.
“That really was a good method for beginners”
Authors: Launspach Sonja
Published: April 2014

Using conversational data from an ethnographic study of a quilting guild, this article examines the way narratives are used to situate quilted objects and techniques by indexing particular alignment frames for the viewer recipient. As a community of practice, the quilting guild provides an excellent interactional context to explore how narratives are used to construct and reinforce community practices. Working within the framework of conversation analysis, the study found that quilters utilized narratives argumentatively to support specific characterizations of quilted objects and quilting techniques. In the data, situating narratives initiate an interactional sequence consisting of two parts: the narrative and an expansion and integration sequence. Quilters make use of different syntactic and story elements in order to signal the appropriate alignment frames. Further, the expansion and integration segments provide space for the women to negotiate and integrate individual and group meanings for the quilting practices presented in the narrative.
Young children on the stages
Authors: Puroila Anna-Maija
Published: April 2014

In this article, I approach day care centers as stages upon which various small stories are constructed and performed by young children and other interlocutors. The aim of the article is two-fold. Methodologically, the paper is a tentative application of Erving Goffman’s dramaturgical perspective onto narrative research with children. Empirically, the aim is to explore day care centers as narrative environments that constitute children’s lives and identities. I anchor my analysis and interpretation of research material, collected in two groups of children, in three perspectives. Firstly, I focus on the spatial practices of the day care centers, framing the construction of small stories. Secondly, I deal with the production of small stories between cultural routines and active reconstruction. Finally, I draw attention to children’s identity construction as a continuous process influenced by a variety of individual, material, contextual, cultural, and interactional factors.
The successes and failure of narratology
Authors: Stock Richard
Published: April 2014

Twentieth-century study of narrative featured many successes and one grave failure. Narratology taught us the basics of how to study the structure of narrative, but proves to be a dead end in the study of texts. This was clear soon after Gérard Genette’s groundbreaking studies, but later works such as Paul Ricoeur’s fail to get beyond narratology. This paper therefore claims that narrative theory has not changed since its inception several decades ago, even though the need for such a change is broadly supported. Attention has been paid to expanding narrative methods to other fields like medicine and education rather than further developing the theory. I advocate a more serious consideration of contemporary literature to renew narrative theory.
Reported speech and the development of authorial voice in middle childhood
Authors: Walton Marsha D. , Walton-Wetzel Jenny
Published: April 2014

The presentation of speech-in-text is an inherently meta-linguistic practice. When children bring speech into their writing, they are necessarily attending to speech as such. Constructing reported speech requires them to use language reflexively and may be a critical component of the development of an authorial voice. We examined 3495 occasions of reported speech or talk about speech in 689 personal narratives by 4th, 5th, and 6th graders in two inner-city schools. We found grade-related increases in the use of reported speech, in the variety of forms of reported speech used, and in the strategic alignment of reported speech form with plot. We also found a relationship between the use of reported speech and explicitly meta-narrative comments. We argue that as children begin to perform Bahktin’s ‘layering of voices’ in their stories, they are developing a meta-awareness of stories-as-stories. This meta-awareness, we propose, co-evolves with children’s use of reported speech forms, reveals itself in their strategic use of these forms, and gives us a glimpse of an emerging self-conscious narrator. As they become more conscious of themselves as authors in middle childhood, their stories begin to demonstrate qualities of literariness–the qualities of an authorial voice.
The Status of Environmentally Enhanced Hydropower Turbines
Authors: Hogan Timothy W , Cada Glenn F , Amaral Stephen V
Published: April 2014

Environmentally enhanced hydroelectric turbines have been developed to reduce injury and mortality of downstream-migrating fishes and to improve downstream water quality. Significant progress has been made in the past decade in the development of such turbines and in the methods to evaluate their biological and power generating performance. Full-scale demonstrations have verified the performance of Voith Hydro's minimum gap runner turbine, which maintains high survival rates for fish while producing more power than conventional designs. Despite a promising pilot study and subsequent design enhancements, similar full-scale demonstrations of the fish-friendly Alden turbine have yet to be conducted. Furthermore, the tools with which to predict and evaluate the performance of new turbine designs are available and are continually being improved. This article provides a status update of advances in this field over the past decade.

RESUMEN

las turbinas hidroeléctricas ambientalmente mejoradas se desarrollaron para reducir los daños y mortalidad en los peces migratorios en los ríos y para mejorar la calidad del agua en éstos. Se ha logrado un progreso significativo en la última década en el desarrollo de las turbinas y de los métodos de evaluación de su desempeño en cuanto a generación de poder e impacto biológico. Demostraciones a escala real han servido para verificar el desempeño de una hidroturbina Voith de mínimo distanciamiento, la cual mantiene altas tasas de supervivencia en los peces al mismo tiempo que produce mayor cantidad de poder en comparación a los diseños tradicionales. Pese al prometedor estudio piloto y a las subsecuentes mejorías en el diseño, aún están por realizarse demostraciones similares en escala real de la turbina Alden “ictiológicamenteamigable”. De hecho, las herramientas con las que se predice y evalúa el desempeño de nuevos diseños de turbinas, ya están disponibles y se encuentran en un continuo proceso de mejoramiento. Este artículo muestra una actualización del estado y avances en este campo durante la última década.
Erythropoietin Upregulation in Pulmonary Arterial Hypertension
Authors: Karamanian Vanesa A. , Harhay Michael , Grant Gregory R. , Palevsky Harold I. , Grizzle William E. , Zamanian Roham T. , Ihida‐Stansbury Kaori , Taichman Darren B. , Kawut Steven M. , Jones Peter L.
Published: April 2014

The pathophysiologic alterations of patients with pulmonary arterial hypertension (PAH) are diverse. We aimed to determine novel pathogenic pathways from circulating proteins in patients with PAH. Multianalyte profiling (MAP) was used to measure 90 specifically selected antigens in the plasma of 113 PAH patients and 51 control patients. Erythropoietin (EPO) functional activity was assessed via in vitro pulmonary artery endothelial cell networking and smooth muscle cell proliferation assays. Fifty‐eight patients had idiopathic PAH, whereas 55 had other forms of PAH; 5 had heritable PAH, 18 had connective tissue disease (15 with scleroderma and 3 with lupus erythematosis), 13 had portopulmonary hypertension, 6 had PAH associated with drugs or toxins, and 5 had congenital heart disease. The plasma‐antigen profile of PAH revealed increased levels of several novel biomarkers, including EPO. Immune quantitative and histochemical studies revealed that EPO not only was significantly elevated in the plasma of PAH patients but also promoted pulmonary artery endothelial cell network formation and smooth muscle cell proliferation. MAP is a hypothesis‐generating approach to identifying novel pathophysiologic pathways in PAH. EPO is upregulated in the circulation and lungs of patients with PAH and may affect endothelial and smooth muscle cell proliferation.
On packing measures and a theorem of Besicovitch
Authors: Garcia Ignacio , Shmerkin Pablo
Published: April 2014

Let

H

h

\mathcal {H}^h

be the

h
h

-dimensional Hausdorff measure on

R

d

\mathbb {R}^d

. Besicovitch showed that if a set

E
E

is null for

H

h

\mathcal {H}^h

, then it is null for

H

g

\mathcal {H}^g

, for some dimension

g
g

smaller than

h
h

. We prove that this is not true for packing measures. Moreover, we consider the corresponding questions for sets of non-

σ
\sigma

-finite packing measure and for pre-packing measure instead of packing measure.
Actomyosin sliding is attenuated in contractile biomimetic cortices
Authors: Murrell Michael , Gardel Margaret L.
Published: April 2014

Myosin II motors embedded within the actin cortex generate contractile forces to modulate cell shape in essential behaviors, including polarization, migration, and division. In sarcomeres, myosin II–mediated sliding of antiparallel F-actin is tightly coupled to myofibril contraction. By contrast, cortical F-actin is highly disordered in polarity, orientation, and length. How the disordered nature of the actin cortex affects actin and myosin movements and resultant contraction is unknown. Here we reconstitute a model cortex in vitro to monitor the relative movements of actin and myosin under conditions that promote or abrogate network contraction. In weakly contractile networks, myosin can translocate large distances across stationary F-actin. By contrast, the extent of relative actomyosin sliding is attenuated during contraction. Thus actomyosin sliding efficiently drives contraction in actomyosin networks despite the high degree of disorder. These results are consistent with the nominal degree of relative actomyosin movement observed in actomyosin assemblies in nonmuscle cells.
Loss of Ubp3 increases silencing, decreases unequal recombination in rDNA, and shortens the replicative life span inSaccharomyces cerevisiae
Authors: Öling David , Masoom Rehan , Kvint Kristian
Published: April 2014

Ubp3 is a conserved ubiquitin protease that acts as an antisilencing factor in MAT and telomeric regions. Here we show that ubp3∆ mutants also display increased silencing in ribosomal DNA (rDNA). Consistent with this, RNA polymerase II occupancy is lower in cells lacking Ubp3 than in wild-type cells in all heterochromatic regions. Moreover, in a ubp3∆ mutant, unequal recombination in rDNA is highly suppressed. We present genetic evidence that this effect on rDNA recombination, but not silencing, is entirely dependent on the silencing factor Sir2. Further, ubp3∆ sir2∆ mutants age prematurely at the same rate as sir2∆ mutants. Thus our data suggest that recombination negatively influences replicative life span more so than silencing. However, in ubp3∆ mutants, recombination is not a prerequisite for aging, since cells lacking Ubp3 have a shorter life span than isogenic wild-type cells. We discuss the data in view of different models on how silencing and unequal recombination affect replicative life span and the role of Ubp3 in these processes.
Role of Pediatric Endoscopic Retrograde Cholangiopancreatography in an Era Stressing Less‐Invasive Imaging Modalities
Authors: Saito Takeshi , Terui Keita , Mitsunaga Tetsuya , Nakata Mitsuyuki , Kuriyama Yutaka , Higashimoto Yasuyuki , Kouchi Katsunori , Onuma Naomi , Takahashi Hideo , Yoshida Hideo
Published: April 2014

Background:

The significance of pediatric endoscopic retrograde cholangiopancreatography (ERCP) according to age or disease variation is inconclusive. This study aimed to evaluate the usefulness of pediatric ERCP in diagnosing or treating small children with pancreaticobiliary disorders, including choledochal cyst (CC) and biliary atresia (BA).

Methods:

From 1980 to 2011, 235 ERCPs were performed in 220 pediatric patients (median age, 2 years) at our institution. Underlying pathology was CC in 92 patients (3 years), BA in 62 patients (55 days), and others in 66 patients. Success and complication rates, and ERCP findings were retrospectively analyzed.

Results:

The overall success rate was 96%. Rates for individual pathologies were 99% for CC, 92% for BA, and 96% for others. The success rate was 100% among children >3 years, but 92% when limited to infants. Post‐ERCP hyperamylasemia and duodenal perforation occurred in 9% and 0.4% of cases, respectively. Regarding preoperative evaluation of the pancreaticobiliary system in CC, ERCP clearly delineated pancreaticobiliary maljunction (79%) and the pancreatic duct (94%), whereas it visualized the common bile duct and intrahepatic bile duct at relatively low rates (77% and 33%, respectively). ERCP successfully identified 16 cases (18%) with non‐BA of 90 patients with suspected BA. Moreover, ERCP demonstrated only pancreatic duct in 70% of all BA.

Conclusions:

ERCP among children including infants with CC and BA can be performed with fairly satisfactory results. Although pediatric ERCP can also help describe the pancreaticobiliary system in detail, its indication should be deliberately considered when anatomical information from less‐invasive imaging modalities is insufficient.
Do Pediatricians Apply the 2009 NASPGHAN–ESPGHAN Guidelines for the Diagnosis and Management of Gastroesophageal Reflux After Being Trained?
Authors: Quitadamo Paolo , Urbonas Vaidotas , Papadopoulou Alexandra , Roman Enriqueta , Pavkov Danijela J. , Orel Rok , Dias Jorge A. , Kostovski Aco , Miele Erasmo , Villani Alberto , Staiano Annamaria
Published: April 2014

Background:

According to a recent survey, the 2009 North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition–European Society for Pediatric Gastroenterology, Hepatology, and Nutrition gastroesophageal reflux guidelines are poorly adhered to by European primary care pediatricians. The main issue raised from the survey was the prescription of unnecessary acid suppressive medications, especially in infants. No inquiry into the reasons was made. The primary objective of the present study was to assess the applicability of the guidelines in European primary care pediatricians undergoing specific trainings.

Methods:

One hundred pediatricians involved in the previous survey agreed to participate and were randomly divided into 2 groups: one group was trained in the guidelines through an online podcast and the other group was trained through a synopsis. During the following 3 months, each involved pediatrician was asked to enroll every consecutive infant, child, or adolescent with suggestive reflux symptoms. For every enrolled patient, pediatricians filled in a report concerning their diagnostic and therapeutic choices.

Results:

A total of 382 patients (boys/girls 186/196, infants/children/adolescents 194/123/65) were enrolled by pediatricians. Infants with unexplained crying and/or distressed behavior who were prescribed proton‐pump inhibitors were 3.7% compared with 45.2% of the survey data obtained before the training (P < 0.05). Infants with uncomplicated recurrent regurgitation and vomiting who were prescribed proton‐pump inhibitors were 4.5% against 37.1% of the baseline survey data (P < 0.05). The overall rate of children managed in full compliance with the guidelines was 46.1% after the training compared with 1.8% before the training (P < 0.05). No significant differences were seen between pediatricians from podcast and synopsis group.

Conclusions:

The North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition–European Society for Pediatric Gastroenterology, Hepatology, and Nutrition gastroesophageal reflux guidelines have good applicability, despite that they are presently poorly adhered to by European primary care pediatricians. Simple, inexpensive trainings were proven to be effective in increasing adherence by pediatricians. The increase in compliance clearly favors the role of continuous medical education through simple educational tools and subsequent assessment of practice.
Incomplete pneumolysin oligomers form membrane pores
Authors: Sonnen Andreas F.-P. , Plitzko Jürgen M. , Gilbert Robert J. C.
Published: April 2014

Pneumolysin is a member of the cholesterol-dependent cytolysin (CDC) family of pore-forming proteins that are produced as water-soluble monomers or dimers, bind to target membranes and oligomerize into large ring-shaped assemblies comprising approximately 40 subunits and approximately 30 nm across. This pre-pore assembly then refolds to punch a large hole in the lipid bilayer. However, in addition to forming large pores, pneumolysin and other CDCs form smaller lesions characterized by low electrical conductance. Owing to the observation of arc-like (rather than full-ring) oligomers by electron microscopy, it has been hypothesized that smaller oligomers explain smaller functional pores. To investigate whether this is the case, we performed cryo-electron tomography of pneumolysin oligomers on model lipid membranes. We then used sub-tomogram classification and averaging to determine representative membrane-bound low-resolution structures and identified pre-pores versus pores by the presence of membrane within the oligomeric curve. We found pre-pore and pore forms of both complete (ring) and incomplete (arc) oligomers and conclude that arc-shaped oligomeric assemblies of pneumolysin can form pores. As the CDCs are evolutionarily related to the membrane attack complex/perforin family of proteins, which also form variably sized pores, our findings are of relevance to that class of proteins as well.
Oryzihumus terrae sp. nov., isolated from soil and emended description of the genus Oryzihumus
Authors: Lim Jun-Muk , Kim Soo-Jin , Hamada Moriyuki , Ahn Jae-Hyung , Weon Hang-Yeon , Suzuki Ken-ichiro , Ahn Tae-Young , Kwon Soon-Wo
Published: April 2014

A Gram-stain-positive, aerobic, non-flagellated bacterium, designated KIS22-12T, was isolated from a soil sample of Baengnyeong Island in Onjin county, Republic of Korea. Cells were non-spore-forming cocci showing catalase-positive and oxidase-negative reactions. Growth of strain KIS22-12T was observed between 10 and 35 °C (optimum, 28–30 °C), between pH 5.0 and 9.0 (optimum, pH 7.0) and with 0–3 % (w/v) NaCl. Strain KIS22-12T contained MK-8(H4) as the predominant menaquinone, and C17 : 1ω8c, iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Strain KIS22-12T contained diphosphatidylglycerol, phosphatidylinositol, one unknown aminophospholipid, one unknown aminolipid, two unknown phospholipids and one unknown lipid. The peptidoglycan type was A1γ. The G+C content of the genomic DNA was 75.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS22-12T formed a phyletic lineage with

Oryzihumus leptocrescens

KV-628T. 16S rRNA gene sequence similarity between the two strains was 96.5 %. On the basis of phenotypic, chemotaxonomic and molecular properties, strain KIS22-12T represents a novel species within the genus

Oryzihumus

, for which the name Oryzihumus terrae sp. nov. is proposed. The type strain is KIS22-12T ( = KACC 16543T = DSM 27161T = NBRC 109596T). An emended description of the genus

Oryzihumus

is also provided.
Comprehensive overexpression analysis of cyclic-di-GMP signalling proteins in the phytopathogen Pectobacterium atrosepticum reveals diverse effects on motility and virulence phenotypes
Authors: Tan H. , West J. A. , Ramsay J. P. , Monson R. E. , Griffin J. L. , Toth I. K. , Salmond G. P. C.
Published: April 2014

Bis-(3′-5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial signalling molecule produced by diguanylate cyclases of the GGDEF-domain family. Elevated c-di-GMP levels or increased GGDEF protein expression is frequently associated with the onset of sessility and biofilm formation in numerous bacterial species. Conversely, phosphodiesterase-dependent diminution of c-di-GMP levels by EAL- and HD-GYP-domain proteins is often accompanied by increased motility and virulence. In this study, we individually overexpressed 23 predicted GGDEF, EAL or HD-GYP-domain proteins encoded by the phytopathogenPectobacterium atrosepticumstrain SCRI1043. MS-based detection of c-di-GMP and 5′-phosphoguanylyl-(3′-5′)-guanosine in these strains revealed that overexpression of most genes promoted modest 1–10-fold changes in cellular levels of c-di-GMP, with the exception of the GGDEF-domain proteins ECA0659 and ECA3374, which induced 1290- and 7660-fold increases, respectively. Overexpression of most EAL domain proteins increased motility, while overexpression of most GGDEF domain proteins reduced motility and increased poly-β-1,6-N-acetyl-glucosamine-dependent flocculation. In contrast to domain-based predictions, overexpression of the EAL protein ECA3549 or the HD-GYP protein ECA3548 increased c-di-GMP concentrations and reduced motility. Most overexpression constructs altered the levels of secreted cellulases, pectinases and proteases, confirming c-di-GMP regulation of virulence inPe.atrosepticum. However, there was no apparent correlation between virulence-factor induction and the domain class expressed or cellular c-di-GMP levels, suggesting that regulation was in response to specific effectors within the network, rather than total c-di-GMP concentration. Finally, we demonstrated that the cellular localization patterns vary considerably for GGDEF/EAL/HD-GYP proteins, indicating it is a likely factor restricting specific interactions within the c-di-GMP network.
The Evolution of Power and the Divergence of Cooperative Norms
Authors: Makowsky Michael D , Smaldino Paul E
Published: April 2014

We consider a model of multilevel selection and the evolution of institutions that distribute power in the form of influence in a group's collective interactions with other groups. In the absence of direct group-level interactions, groups with the most cooperative members will outcompete less cooperative groups, while within any group the least cooperative members will be the most successful. Introducing group-level interactions, however, such as raiding or warfare, changes the selective landscape for groups. Our model suggests that as the global population becomes more integrated and the rate of intergroup conflict increases, selection increasingly favors unequally distributed power structures, where individual influence is weighted by acquired resources. The advantage to less democratic groups rests in their ability to facilitate selection for cooperative strategies – involving cooperation both among themselves and with outsiders – in order to produce the resources necessary to fuel their success in inter-group conflicts, while simultaneously selecting for leaders (and corresponding collective behavior) who are unburdened with those same prosocial norms. The coevolution of cooperative social norms and institutions of power facilitates the emergence of a leadership class of the selfish and has implications for theories of inequality, structures of governance, non-cooperative personality traits, and hierarchy. Our findings suggest an amendment to the well-known doctrine of multilevel selection that "Selfishness beats altruism within groups. Altruistic groups beat selfish groups." In an interconnected world, altruistic groups led by selfish individuals can beat them both.
Soft selective sweeps in complex demographic scenarios
Authors: Wilson Benjamin A , Petrov Dmitri , Messer Philipp W
Published: April 2014

Recent studies have shown that adaptation from de novo mutation often produces so-called soft selective sweeps, where adaptive mutations of independent mutational origin sweep through the population at the same time. Population genetic theory predicts that soft sweeps should be likely if the product of the population size and the mutation rate towards the adaptive allele is sufficiently large, such that multiple adaptive mutations can establish before one has reached fixation; however, it remains unclear how demographic processes affect the probability of observing soft sweeps. Here we extend the theory of soft selective sweeps to realistic demographic scenarios that allow for changes in population size over time. We first show that population bottlenecks can lead to the removal of all but one adaptive lineage from an initially soft selective sweep. The parameter regime under which such 'hardening' of soft selective sweeps is likely is determined by a simple heuristic condition. We further develop a generalized analytical framework, based on an extension of the coalescent process, for calculating the probability of soft sweeps under arbitrary demographic scenarios. Two important limits emerge within this analytical framework: In the limit where population size fluctuations are fast compared to the duration of the sweep, the likelihood of soft sweeps is determined by the harmonic mean of the variance effective population size estimated over the duration of the sweep; in the opposing slow fluctuation limit, the likelihood of soft sweeps is determined by the instantaneous variance effective population size at the onset of the sweep. We show that as a consequence of this finding the probability of observing soft sweeps becomes a function of the strength of selection. Specifically, in species with sharply fluctuating population size, strong selection is more likely to produce soft sweeps than weak selection. Our results highlight the importance of accurate demographic estimates over short evolutionary timescales for understanding the population genetics of adaptation from de novo mutation.
An integrated RNA and CRISPR/Cas toolkit for multiplexed synthetic circuits and endogenous gene regulation in human cells
Authors: Nissim Lior , Perli Samuel D , Fridkin Alexandra , Perez-Pinera Pablo , Lu Timothy
Published: April 2014

RNA-based regulation, such as RNA interference, and CRISPR/Cas transcription factors (CRISPR-TFs), can enable scalable synthetic gene circuits and the modulation of endogenous networks but have yet to be integrated together. Here, we combined multiple mammalian RNA regulatory strategies, including RNA triple helix structures, introns, microRNAs, and ribozymes, with Cas9-based CRISPR-TFs and Cas6/Csy4-based RNA processing in human cells. We describe three complementary strategies for expressing functional gRNAs from transcripts generated by RNA polymerase II (RNAP II) promoters while allowing the harboring gene to be translated. These architectures enable the multiplexed expression of proteins and multiple gRNAs from a single compact transcript for efficient modulation of synthetic constructs and endogenous human promoters. We used these regulatory tools to implement tunable synthetic gene circuits, including multi-stage transcriptional cascades. Finally, we show that Csy4 can rewire regulatory connections in RNA-dependent gene circuits with multiple outputs and feedback loops to achieve complex functional behaviors. This multiplexable toolkit will be valuable for the construction of scalable gene circuits and the perturbation of natural regulatory networks in human cells for basic biology, therapeutic, and synthetic-biology applications.
The evolution of genetic diversity in changing environments
Authors: Carja Oana , Liberman Uri , Feldman Marcus W.
Published: April 2014

The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental and selective volatility in the patterns of genetic and phenotypic variation have been important areas of focus in population genetics. On one hand, stretches of constant selection pull the genetic makeup of populations towards local fitness optima. On the other, in order to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced, such as the rates of recombination, mutation or migration, populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that knowing the shape, size, variance and asymmetry of environmental runs is essential for accurate prediction of genetic evolutionary dynamics.
Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis
Authors: Holstege Henne , Pfeiffer Wayne , Sie Daoud , Hulsman Marc , Nicholas Thomas J. , Lee Clarence C. , Ross Tristen , Lin Jue , Miller Mark A. , Ylstra Bauke , Meijers-Heijboer Hanne , Brugman Martijn H. , Staal Frank J.T. , Holstege Gert , Reinders Marcel J.T. , Harkins Timothy T. , Levy Samuel , Sistermans Erik A.
Published: April 2014

The somatic mutation burden in healthy white blood cells (WBCs) is not well known. Based on deep whole-genome sequencing, we estimate that approximately 450 somatic mutations accumulated in the nonrepetitive genome within the healthy blood compartment of a 115-yr-old woman. The detected mutations appear to have been harmless passenger mutations: They were enriched in noncoding, AT-rich regions that are not evolutionarily conserved, and they were depleted for genomic elements where mutations might have favorable or adverse effects on cellular fitness, such as regions with actively transcribed genes. The distribution of variant allele frequencies of these mutations suggests that the majority of the peripheral white blood cells were offspring of two related hematopoietic stem cell (HSC) clones. Moreover, telomere lengths of the WBCs were significantly shorter than telomere lengths from other tissues. Together, this suggests that the finite lifespan of HSCs, rather than somatic mutation effects, may lead to hematopoietic clonal evolution at extreme ages.
Purification, crystallization and preliminary X-ray characterization of the third ScaB cohesin in complex with an ScaA X-dockerin fromAcetivibrio cellulolyticus
Authors: Cameron Kate , Alves Victor D. , Bule Pedro , Ferreira Luís M. A. , Fontes Carlos M. G. A. , Najmudin Shabir
Published: April 2014

Interactions between cohesin and dockerin modules are critical for the formation of the cellulosome, which is responsible for the efficient degradation of plant cell-wall carbohydrates by anaerobes. Type I dockerin modules found in modular enzymatic components interact with type I cohesins in primary scaffoldins, enabling the assembly of the multi-enzyme complex. In contrast, type II dockerins located in primary scaffoldins bind to type II cohesins in adaptor scaffoldins or anchoring scaffoldins located at the bacterial envelope, contributing to the cell-surface attachment of the entire complex.Acetivibrio cellulolyticuspossesses an extremely complex cellulosome arrangement which is organized by a primary enzyme-binding scaffoldin (ScaA), two anchoring scaffoldins (ScaC and ScaD) and an unusual adaptor scaffoldin (ScaB). An ScaA X-dockerin mutated to inactivate one of the two putative cohesin-binding interfaces complexed with the third ScaB cohesin fromA. cellulolyticushas been purified and crystallized and data were collected to a resolution of 2.41 Å.
Expression, purification and crystallization of MnSOD fromArabidopsis thaliana
Authors: Marques Alexandra T. , Santos Sandra P. , Rosa Margarida G. , Rodrigues Mafalda A. A. , Abreu Isabel A. , Frazão Carlos , Romão Célia V.
Published: April 2014

Manganese superoxide dismutase (MnSOD) is an essential primary antioxidant enzyme. MnSOD plays an important role in plant tolerance to abiotic stress and is a target candidate for increasing stress tolerance in crop plants. Although the structure and kinetic parameters of MnSODs from several organisms have been determined, this information is still lacking for plant MnSODs. Here, recombinant MnSOD fromArabidopsis thaliana(AtMnSOD) was expressed, purified and crystallized. A nearly complete data set could only be obtained when a total rotation range of 180° was imposed during data collection, despite the seemingly tetragonal metric of the AtMnSOD crystal diffraction. The data set extended to 1.95 Å resolution and the crystal belonged to space groupP1. Molecular-replacement calculations using an ensemble of homologous SOD structures as a search model gave a unique and unambiguous solution corresponding to eight molecules in the asymmetric unit. Structural and kinetic analysis of AtMnSOD is currently being undertaken.
Crystallization and preliminary X-ray analysis of the ergothioneine-biosynthetic methyltransferase EgtD
Authors: Vit Allegra , Misson Laëtitia , Blankenfeldt Wulf , Seebeck Florian Peter
Published: April 2014

Ergothioneine is an amino-acid betaine derivative of histidine that was discovered more than one century ago. Despite significant research pointing to a function in oxidative stress defence, the exact mechanisms of action of ergothioneine remain elusive. Although both humans and bacterial pathogens such asMycobacterium tuberculosisseem to depend on ergothioneine, humans are devoid of the corresponding biosynthetic enzymes. Therefore, its biosynthesis may emerge as potential drug target in the development of novel therapeutics against tuberculosis. The recent identification of ergothioneine-biosynthetic genes inM. smegmatisenables a more systematic study of its biology. The pathway is initiated by EgtD, a SAM-dependent methyltransferase that catalyzes a trimethylation reaction of histidine to giveN(α),N(α),N(α)-trimethylhistidine. Here, the recombinant production, purification and crystallization of EgtD are reported. Crystals of native EgtD diffracted to 2.35 Å resolution at a synchrotron beamline, whereas crystals of seleno-L-methionine-labelled protein diffracted to 1.75 Å resolution and produced a significant anomalous signal to 2.77 Å resolution at theKedge. All of the crystals belonged to space groupP212121, with two EgtD monomers in the asymmetric unit.
The ethics of nobody I know: gender and the politics of description
Authors: Laurie Timothy
Published: April 2014

Purpose

– This paper aims to bring together feminist philosophy, phenomenology, and masculinity studies to consider the gendered formation of ethical practices, focusing on the construction of “male” and “female” identities in quotidian social encounters. While scholarship on masculinity has frequently focused on hegemonic modes of behaviour or normative gender relations, less attention has been paid to the “ethics of people I know” as informal political resources, ones that shapes not only conversations about how one should act (“people I know don’t do that”), but also about the diversity of situations that friends, acquaintances or strangers could plausibly have encountered (“that hasn’t happened to anyone I know”).

Design/methodology/approach

– The paper rethinks mundane social securities drawing on Martin Heidegger, Simone de Beauvoir, and Sara Ahmed to consider anecdotal case studies around gender recognition and political practice, and in doing so also develops the notion of interpellation in relation to everyday ethical problems.

Findings

– The paper suggests that inquiry into diverse modes of quotidian complicities – or what de Beauvoir calls the “snares” of a deeply human liberty – can be useful for describing the mixtures of sympathy, empathy, and disavowal in the performance of pro-feminist and queer-friendly masculinities or masculinist identities. It also suggests that the adoption of an “anti-normative” politics is insufficient for negotiating the problems of description and recognition involved in the articulation of gendered social experiences.

Originality/value

– This paper approaches questions around political identification commonly considered in queer theory from the viewpoint of descriptive practices themselves, and thus reorients problems of recognition and interpellation towards the expression of ethical statements, rather than focusing solely on the objects of such statements.