bluuebunny/crossref_metadata_2025 huggingface dataset:
Tobacco use among urban Aboriginal Australian young people: a qualitative study of reasons for smoking, barriers to cessation and motivators for smoking cessation
Authors: Cosh Suzanne , Hawkins Kimberley , Skaczkowski Gemma , Copley David , Bowden Jacqueline
Published: July 2014

Smoking prevalence among Aboriginal Australian young people greatly exceeds the prevalence in the broader population of Australian young people, yet limited research has explored the social context in which young Aboriginal Australians smoke. Four focus groups were conducted in 2009 with South Australian Aboriginal smokers aged 15–29 years residing in urban areas (n = 32) to examine attitudes and experiences surrounding smoking and quitting. The primary reasons for smoking initiation and maintenance among Aboriginal Australian young people were identified as stress, social influence and boredom. Motivators for quitting were identified as pregnancy and/or children, sporting performance (males only), cost issues and, to a lesser extent, health reasons. The barriers to cessation were identified as social influence, the perception of quitting as a distant event and reluctance to access cessation support. However, it appears that social influences and stress were particularly salient contributors to smoking maintenance among Aboriginal Australian young people. Smoking cessation interventions targeted at young urban Aboriginal Australian smokers should aim to build motivation to quit by utilising the motivators of pregnancy and/or children, sporting performance (males only), cost issues and, to a lesser extent, health reasons, while acknowledging the pertinent role of social influence and stress in the lives of young urban Aboriginal Australian smokers.
Cluster-like coordinates in supersymmetric quantum field theory
Authors: Neitzke Andrew
Published: July 2014

Significance

The subject of cluster algebras was born out of the study of concrete mathematical questions such as “how can we detect when a matrix will have all eigenvalues positive?” Recently it has turned out that cluster algebras show up in all kinds of unexpected places, even in the physicists’ playground of quantum field theory. This paper is a review of one way in which quantum field theory and cluster algebras interact. In particular, the paper argues that geometric ideas coming from quantum field theory lead to a natural extension of the theory of cluster algebras.
Evolutionary trends inTriceratopsfrom the Hell Creek Formation, Montana
Authors: Scannella John B. , Fowler Denver W. , Goodwin Mark B. , Horner John R.
Published: July 2014

Significance

The deciphering of evolutionary trends in nonavian dinosaurs can be impeded by a combination of small sample sizes, low stratigraphic resolution, and lack of ontogenetic (developmental) details for many taxa. Analysis of a large sample (n> 50) of the famous horned dinosaurTriceratopsfrom the Hell Creek Formation of Montana incorporates new stratigraphic and ontogenetic findings to permit the investigation of evolution within this genus. Our research indicates that the two currently recognized species ofTriceratops(T. horridusandT. prorsus) are stratigraphically separated and that the evolution of this genus likely incorporated anagenetic (transformational) change. These findings impact interpretations of dinosaur diversity at the end of the Cretaceous and illuminate potential modes of evolution in the Dinosauria.
Cremmer–Gervais cluster structure on
SL

n
Authors: Gekhtman Michael , Shapiro Michael , Vainshtein Alek
Published: July 2014

Significance

Coexistence of diverse mathematical structures supported on the same variety leads to deeper understanding of its features. If the manifold is a Lie group, endowing it with a Poisson structure that respects group multiplication (Poisson–Lie structure) is instrumental in a study of classical and quantum-mechanical systems with symmetries. In turn, a Poisson structure on a variety can be compatible with a cluster structure—a useful combinatorial tool that organizes generators of the ring of regular functions into a collection of overlapping clusters connected via rational transformations. We conjectured that this is the case for an important class of Poisson–Lie groups. The paper verifies this conjecture for a group of invertible matrices equipped with a nonstandard Poisson–Lie structure.
Time-resolved resting-state brain networks
Authors: Zalesky Andrew , Fornito Alex , Cocchi Luca , Gollo Leonardo L. , Breakspear Michael
Published: July 2014

Significance

Large-scale organizational properties of brain networks mapped with functional magnetic resonance imaging have been studied in a time-averaged sense. This is an oversimplification. We demonstrate that brain activity between multiple pairs of spatially distributed regions spontaneously fluctuates in and out of correlation over time in a globally coordinated manner, giving rise to sporadic intervals during which information can be efficiently exchanged between neuronal populations. We argue that dynamic fluctuations in the brain’s organizational properties may minimize metabolic requirements while maintaining the brain in a responsive state.
Three-dimensionally printed biological machines powered by skeletal muscle
Authors: Cvetkovic Caroline , Raman Ritu , Chan Vincent , Williams Brian J. , Tolish Madeline , Bajaj Piyush , Sakar Mahmut Selman , Asada H. Harry , Saif M. Taher A. , Bashir Rashid
Published: July 2014

Significance

Cell-based soft robotic devices could have a transformative impact on our ability to design machines and systems that can dynamically sense and respond to a range of complex environmental signals. We demonstrate innovative advancements in biomaterials, tissue engineering, and 3D printing, as well as an integration of these technologies, to forward engineer a controllable centimeter-scale biological machine capable of locomotion on a surface in fluid. Due in part to their elastic nature and the living components that can permit a dynamic response to environmental and applied stimuli, these biological machines can have diverse applications and represent a significant advancement toward high-level functional control over soft biorobotic systems.
Cep164 triggers ciliogenesis by recruiting Tau tubulin kinase 2 to the mother centriole
Authors: Čajánek Lukáš , Nigg Erich A.
Published: July 2014

Significance

The primary cilium is an organelle typically found on postmitotic vertebrate cells. Cilia serve as antennae to receive signals from extracellular space and thus play important roles in both development and disease. Understanding the mechanisms controlling their formation (ciliogenesis) is of great importance. Ciliogenesis is known to depend on basal bodies, but although major steps have been described at a morphological level, the underlying mechanism and its regulation remain poorly understood. In our study, we characterized Cep164, a key component of basal bodies that is crucial for ciliogenesis. We show that one major function of Cep164 is to recruit a protein kinase, TTBK2, to basal bodies. Once localized correctly, TTBK2 then functions in distal appendage assembly and primary cilia formation.
Structural basis for the recruitment of glycogen synthase by glycogenin
Authors: Zeqiraj Elton , Tang Xiaojing , Hunter Roger W. , García-Rocha Mar , Judd Andrew , Deak Maria , von Wilamowitz-Moellendorff Alexander , Kurinov Igor , Guinovart Joan J. , Tyers Mike , Sakamoto Kei , Sicheri Frank
Published: July 2014

Significance

The body stores excess blood glucose as glycogen, a sugary substance that contains up to 55,000 glucose molecules joined together as a chain, mostly in liver and muscle cells. Conversion of glucose to glycogen and glycogen to glucose in these cells plays an important role in regulating blood glucose levels. Glycogen ensures that we don’t run out of fuel during prolonged exercise. To make glycogen from blood sugar, cells need two enzymes: glycogenin and glycogen synthase. Glycogenin kick starts the process by first linking to itself a string of glucose residues and then recruiting glycogen synthase to elaborate this “seed” glycogen particle. Here, we describe the molecular details of how these two enzymes come together and begin to make glycogen.
Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome
Authors: Burgie E. Sethe , Bussell Adam N. , Walker Joseph M. , Dubiel Katarzyna , Vierstra Richard D.
Published: July 2014

Significance

Much of plant growth and development is regulated by the phytochrome (Phy) family of photoreceptors. We present an atomic perspective of plant Phy signaling through a crystal structure of the photosensing module as Pr from
Arabidopsis
PhyB assembled with its native chromophore phytochromobilin. Although its overall architecture and chromophore/protein contacts are reminiscent of bacterial relatives, significant structural differences are seen within the prominent knot, hairpin and helical spine features. Subsequent mutational analyses lend support to a toggle model for how Phys reversibly switch between their Pr and Pfr end states. This 3D structure along with the identified suite of photochemical variants should accelerate the rational redesign of Phy signaling for improved crop performance and optogenetic application.
Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors
Authors: Kelly Linda W. , Williams Gareth J. , Barott Katie L. , Carlson Craig A. , Dinsdale Elizabeth A. , Edwards Robert A. , Haas Andreas F. , Haynes Matthew , Lim Yan Wei , McDole Tracey , Nelson Craig E. , Sala Enric , Sandin Stuart A. , Smith Jennifer E. , Vermeij Mark J. A. , Youle Merry , Rohwer Forest
Published: July 2014

Significance

Microbial communities associated with coral reefs influence the health and sustenance of keystone benthic organisms (e.g., coral holobionts). The present study investigated the community structure and metabolic potential of microbes inhabiting coral reefs located across an extensive area in the central Pacific. We found that the taxa present correlated strongly with the percent coverage of corals and algae, while community metabolic potential correlated best with geographic location. These findings are inconsistent with prevailing biogeographic models of microbial diversity (e.g., distance decay) and metabolic potential (i.e., similar functional profiles regardless of phylogenetic variability). Based on these findings, we propose that the primary carbon sources determine community structure and that local biogeochemistry determines finer-scale metabolic function.
Long and spatially variable Neolithic Demographic Transition in the North American Southwest
Authors: Kohler Timothy A. , Reese Kelsey M.
Published: July 2014

Significance

Population size greatly affects the human condition but is difficult for archaeologists to estimate. For the Neolithic North American Southwest, we use indirect methods to estimate birth rate and life expectancy, two major factors determining population size. The population boom usually accompanying the introduction of cultivated plants and animals, the “Neolithic Demographic Transition,” was slow to emerge here and was marked by considerable subregional variability in birth rate. This variability is likely related to differing morbidities and availability of agricultural lands in various subregions. In common with many Neolithic peoples, pre-Hispanic Puebloans experienced very high birth rates, especially between A.D. 500 and 1300 when they possibly exceeded the highest in the world today, and quite low life expectancy at birth.
Human endothelial colony-forming cells serve as trophic mediators for mesenchymal stem cell engraftment via paracrine signaling
Authors: Lin Ruei-Zeng , Moreno-Luna Rafael , Li Dan , Jaminet Shou-Ching , Greene Arin K. , Melero-Martin Juan M.
Published: July 2014

Significance

Endothelial colony-forming cells (ECFCs) circulate in peripheral blood and contribute to the formation of new vasculature. Here, we demonstrate that ECFCs can also function as paracrine mediators prior to the establishment of blood perfusion, modulating the regenerative potential of human mesenchymal stem cells (MSCs). We show that MSCs are highly dependable on platelet-derived growth factor BB and that ECFCs provide critical angiocrine factors needed to preserve MSCs as viable. This early angiocrine support ultimately enables extensive engraftment and long-term differentiation of transplanted MSCs. This study provides new insights into the biological attributes of ECFCs that may expand their therapeutic potential. We foresee the use of ECFCs as a means to improve the outcome of MSC transplantation.
Distinct synthetic Aβ prion strains producing different amyloid deposits in bigenic mice
Authors: Stöhr Jan , Condello Carlo , Watts Joel C. , Bloch Lillian , Oehler Abby , Nick Mimi , DeArmond Stephen J. , Giles Kurt , DeGrado William F. , Prusiner Stanley B.
Published: July 2014

Significance

Alzheimer’s disease is the most common neurodegenerative disorder; it is a progressive dementia for which there is currently no effective therapeutic intervention. The brains of patients with Alzheimer’s disease exhibit numerous amyloid β (Aβ) amyloid plaques and tau-laden neurofibrillary tangles. Our studies show that synthetic Aβ peptides can form prions that infect mice and induce Aβ amyloid plaque pathology. Two different Aβ prion strains were produced from Aβ peptides. When injected into transgenic mice, one Aβ strain produced large plaques and the other strain induced small but more numerous plaques. Our findings may help to delineate the molecular pathogenesis of Alzheimer’s disease and the development of anti-Aβ prion therapeutics.
Arabidopsis
noncoding RNA mediates control of photomorphogenesis by red light
Authors: Wang Yuqiu , Fan Xiuduo , Lin Fang , He Guangming , Terzaghi William , Zhu Danmeng , Deng Xing Wang
Published: July 2014

Significance

The dynamic regulation of gene-expression programs is both critical to and regulated precisely in the light-mediated seedling photomorphogenesis of higher plants. Our work adds
HIDDEN TREASURE 1
(
HID1
), a noncoding RNA that acts as a positive regulator of photomorphogenesis, to the current group of pivotal genetic factors known to control photomorphogenesis. Specifically, our data obtained by numerous approaches reveal that
HID1
modulates red light-mediated photomorphogenesis by directly repressing
PHYTOCHROME-INTERACTING FACTOR 3
, which encodes a key transcription factor that inhibits red light responses.
HID1
appears to be highly conserved among higher plants.
Engineered red blood cells as carriers for systemic delivery of a wide array of functional probes
Authors: Shi Jiahai , Kundrat Lenka , Pishesha Novalia , Bilate Angelina , Theile Chris , Maruyama Takeshi , Dougan Stephanie K. , Ploegh Hidde L. , Lodish Harvey F.
Published: July 2014

Significance

Engineered human RBCs are attractive carriers for the introduction of novel therapeutics, immunomodulatory agents, and diagnostic imaging probes into the human body. Normal murine and human RBCs can be produced in tissue culture from progenitors; we have introduced genes into these cells encoding surface proteins that can be covalently and site-specifically modified on the cell surface. The engineering and labeling processes do not damage the cells or affect their survival in vivo. Most importantly, the engineered RBCs can be labeled with a wide array of functional probes, including small molecules, peptides, and proteins, and thus have the potential to be carriers of a variety of therapeutic substances into the bloodstream.
How big is the positive effect of assonance on the recall of L2 collocations?
Authors: Lindstromberg Seth , Eyckmans June
Published: July 2014

High proficiency in L2 partly depends on acquiring many formulaic sequences (FSs), yet post-childhood learners find this difficult. Ways of accelerating the acquisition of FSs would be welcome. Small-scale studies have indicated that assonance (e.g., strong bond) makes studied FSs especially retrievable if, during exposure, assonance is made the object of teacher-instigated awareness-raising and attention direction. However, questions remain about effect size and duration. In two new experiments a mnemonic effect of assonance was detected after 5–10 minutes. This was despite a sorting task thought likely to direct participants’ attention particularly to the control collocations. The effect appeared to fade over an hour and disappear after a day. A small-scale meta-analysis indicates the effect is initially of medium size. We discuss how short-term operation of such an effect could facilitate the fuller acquisition of partly learned assonant FSs. We propose avenues for research into means whereby the mnemonic effect of assonance might be exploited in learning materials. We touch on effects of item frequency, mutual information, and concreteness-imageability of meaning.
DNA breaks and chromosomal aberrations arise when replication meets base excision repair
Authors: Ensminger Michael , Iloff Lucie , Ebel Christian , Nikolova Teodora , Kaina Bernd , Lӧbrich Markus
Published: July 2014

Exposures that methylate DNA potently induce DNA double-strand breaks (DSBs) and chromosomal aberrations, which are thought to arise when damaged bases block DNA replication. Here, we demonstrate that DNA methylation damage causes DSB formation when replication interferes with base excision repair (BER), the predominant pathway for repairing methylated bases. We show that cells defective in the N-methylpurine DNA glycosylase, which fail to remove N-methylpurines from DNA and do not initiate BER, display strongly reduced levels of methylation-induced DSBs and chromosomal aberrations compared with wild-type cells. Also, cells unable to generate single-strand breaks (SSBs) at apurinic/apyrimidinic sites do not form DSBs immediately after methylation damage. In contrast, cells deficient in x-ray cross-complementing protein 1, DNA polymerase β, or poly (ADP-ribose) polymerase 1 activity, all of which fail to seal SSBs induced at apurinic/apyrimidinic sites, exhibit strongly elevated levels of methylation-induced DSBs and chromosomal aberrations. We propose that DSBs and chromosomal aberrations after treatment with N-alkylators arise when replication forks collide with SSBs generated during BER.
Recovery in eastern Baltic cod: is increased recruitment caused by decreased predation on early life stages?
Authors: Neumann Viola , Köster Friedrich W. , Schaber Matthias , Eero Margit
Published: July 2014

Cod (Gadus morhua) recruitment in the eastern Baltic Sea is influenced by predation on early life stages by sprat (Sprattus sprattus) and herring (Clupea harengus), which is considered as one of the mechanisms preventing cod recovery in the 1990s. In the light of improved cod recruitment in the second half of the 2000s, new analyses of stomach content of sprat and herring were conducted, to elucidate the contribution of changes in predation pressure on cod recruitment. Comparison of stomach contents of sprat and herring in 2004–2008 with data from the 1990s showed a similar diet composition in the two periods; however, changes were found in the ichthyoplankton abundance and composition in the diet, indicating reduced predation pressure on cod eggs in the most recent period. The abundance of cod eggs in the field, availability of other prey, and horizontal and vertical overlap between predator and prey were investigated as potential factors influencing cod egg predation.
Multiscale modelling and simulation: a position paper
Authors: Hoekstra Alfons , Chopard Bastien , Coveney Peter
Published: July 2014

We argue that, despite the fact that the field of multiscale modelling and simulation has enjoyed significant success within the past decade, it still holds many open questions that are deemed important but so far have barely been explored. We believe that this is at least in part due to the fact that the field has been mainly developed within disciplinary silos. The principal topics that in our view would benefit from a targetedmultidisciplinaryresearch effort are related to reaching consensus as to what exactly one means by ‘multiscale modelling’, formulating a generic theory or calculus of multiscale modelling, applying such concepts to the urgent question of validation and verification of multiscale models, and the issue of numerical error propagation in multiscale models. Moreover, we believe that this would, in principle, also lay the foundation for more efficient, well-defined and usable multiscale computing environments. We believe that multidisciplinary research to fill in the gaps is timely, highly relevant, and with substantial potential impact on many scientific disciplines.
Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model
Authors: Li Xuejin , Peng Zhangli , Lei Huan , Dao Ming , Karniadakis George Em
Published: July 2014

This study is partially motivated by the validation of a new two-component multi-scale cell model we developed recently that treats the lipid bilayer and the cytoskeleton as two distinct components. Here, the whole cell model is validated and compared against several available experiments that examine red blood cell (RBC) mechanics, rheology and dynamics. First, we investigated RBC deformability in a microfluidic channel with a very small cross-sectional area and quantified the mechanical properties of the RBC membrane. Second, we simulated twisting torque cytometry and compared predicted rheological properties of the RBC membrane with experimental measurements. Finally, we modelled the tank-treading (TT) motion of a RBC in a shear flow and explored the effect of channel width variation on the TT frequency. We also investigated the effects of bilayer–cytoskeletal interactions on these experiments and our simulations clearly indicated that they play key roles in the determination of cell membrane mechanical, rheological and dynamical properties. These simulations serve as validation tests and moreover reveal the capabilities and limitations of the new whole cell model.
Performance of distributed multiscale simulations
Authors: Borgdorff J. , Ben Belgacem M. , Bona-Casas C. , Fazendeiro L. , Groen D. , Hoenen O. , Mizeranschi A. , Suter J. L. , Coster D. , Coveney P. V. , Dubitzky W. , Hoekstra A. G. , Strand P. , Chopard B.
Published: July 2014

Multiscale simulations model phenomena across natural scales using monolithic or component-based code, running on local or distributed resources. In this work, we investigate the performance of distributed multiscale computing of component-based models, guided by six multiscale applications with different characteristics and from several disciplines. Three modes of distributed multiscale computing are identified: supplementing local dependencies with large-scale resources, load distribution over multiple resources, and load balancing of small- and large-scale resources. We find that the first mode has the apparent benefit of increasing simulation speed, and the second mode can increase simulation speed if local resources are limited. Depending on resource reservation and model coupling topology, the third mode may result in a reduction of resource consumption.
Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum
Authors: Takeuchi Mio , Kamagata Yoichi , Oshima Kenshiro , Hanada Satoshi , Tamaki Hideyuki , Marumo Katsumi , Maeda Hiroto , Nedachi Munetomo , Hattori Masahira , Iwasaki Wataru , Sakata Susumu
Published: July 2014

An aerobic, methane-oxidizing bacterium (strain S8T) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain is closely related to members of the genus

Methylocaldum

(97.6–97.9 % similarity) within the class

Gammaproteobacteria

. Strain S8T was a Gram-staining-negative, non-motile, coccoid or short rod-shaped organism. The temperature range for growth of strain S8T was 20–47 °C (optimum growth at 36 °C). It required NaCl (>0.5 %), tolerated up to 5 % NaCl and utilized methane and methanol. The major cellular fatty acid and major respiratory quinone were C16 : 0 and 18-methylene ubiquinone 8, respectively. The DNA G+C content was 59.7 mol%. Strain S8T possessed mmoX, which encodes soluble methane monooxygenase, as well as pmoA, which encodes the particulate methane monooxygenase. On the basis of this morphological, physiological, biochemical and genetic information, the first marine species in the genus

Methylocaldum

is proposed, with the name Methylocaldum marinum sp. nov. The type strain is S8T ( = NBRC 109686T = DSM 27392T). An emended description of the genus

Methylocaldum

is also provided.
Burkholderia
jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil
Authors: Liu Xu-Yun , Li Chun-Xiu , Luo Xiao-Jing , Lai Qi-Liang , Xu Jian-He
Published: July 2014

A methyl parathion (MP) degrading bacterial strain, designated MP-1T, was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1T is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0–1 % (w/v) and temperatures of 15–40 °C. Strain MP-1T could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1T belongs to the genus

Burkholderia

, showing highest sequence similarity to

Burkholderia grimmiae

DSM 25160T (98.5 %), and similar strains including

Burkholderia zhejiangensis

OP-1T (98.2 %),

Burkholderia choica

LMG 22940T (97.5 %),

Burkholderia glathei

DSM 50014T (97.4 %),

Burkholderia terrestris

LMG 22937T (97.2 %) and

Burkholderia telluris

LMG 22936T (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1T exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1T was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1T were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA–DNA relatedness values between strain MP-1T and the three type strains (

B. grimmiae

DSM 25160T,

B. zhejiangensis

OP-1T and

B. glathei

DSM 50014T) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1T represents a novel species of the genus

Burkholderia

, for which the name Burkholderia jiangsuensis sp. nov. is proposed, the type strain is MP-1T (LMG 27927T = MCCC 1K00250T).
Structure of the Zymomonas mobilis respiratory chain: oxygen affinity of electron transport and the role of cytochrome c peroxidase
Authors: Balodite Elina , Strazdina Inese , Galinina Nina , McLean Samantha , Rutkis Reinis , Poole Robert K. , Kalnenieks Uldis
Published: July 2014

The genome of the ethanol-producing bacterium Zymomonas mobilis encodes a bd-type terminal oxidase, cytochrome bc
1 complex and several c-type cytochromes, yet lacks sequences homologous to any of the known bacterial cytochrome c oxidase genes. Recently, it was suggested that a putative respiratory cytochrome c peroxidase, receiving electrons from the cytochrome bc
1 complex via cytochrome c
552, might function as a peroxidase and/or an alternative oxidase. The present study was designed to test this hypothesis, by construction of a cytochrome c peroxidase mutant (Zm6-perC), and comparison of its properties with those of a mutant defective in the cytochrome b subunit of the bc
1 complex (Zm6-cytB). Disruption of the cytochrome c peroxidase gene (ZZ60192) caused a decrease of the membrane NADH peroxidase activity, impaired the resistance of growing culture to exogenous hydrogen peroxide and hampered aerobic growth. However, this mutation did not affect the activity or oxygen affinity of the respiratory chain, or the kinetics of cytochrome d reduction. Furthermore, the peroxide resistance and membrane NADH peroxidase activity of strain Zm6-cytB had not decreased, but both the oxygen affinity of electron transport and the kinetics of cytochrome d reduction were affected. It is therefore concluded that the cytochrome c peroxidase does not terminate the cytochrome bc
1 branch of Z. mobilis, and that it is functioning as a quinol peroxidase.
Comparative validation of the D. melanogaster modENCODE transcriptome annotation
Authors: Chen Zhen-Xia , Sturgill David , Qu Jiaxin , Jiang Huaiyang , Park Soo , Boley Nathan , Suzuki Ana Maria , Fletcher Anthony R. , Plachetzki David C. , FitzGerald Peter C. , Artieri Carlo G. , Atallah Joel , Barmina Olga , Brown James B. , Blankenburg Kerstin P. , Clough Emily , Dasgupta Abhijit , Gubbala Sai , Han Yi , Jayaseelan Joy C. , Kalra Divya , Kim Yoo-Ah , Kovar Christie L. , Lee Sandra L. , Li Mingmei , Malley James D. , Malone John H. , Mathew Tittu , Mattiuzzo Nicolas R. , Munidasa Mala , Muzny Donna M. , Ongeri Fiona , Perales Lora , Przytycka Teresa M. , Pu Ling-Ling , Robinson Garrett , Thornton Rebecca L. , Saada Nehad , Scherer Steven E. , Smith Harold E. , Vinson Charles , Warner Crystal B. , Worley Kim C. , Wu Yuan-Qing , Zou Xiaoyan , Cherbas Peter , Kellis Manolis , Eisen Michael B. , Piano Fabio , Kionte Karin , Fitch David H. , Sternberg Paul W. , Cutter Asher D. , Duff Michael O. , Hoskins Roger A. , Graveley Brenton R. , Gibbs Richard A. , Bickel Peter J. , Kopp Artyom , Carninci Piero , Celniker Susan E. , Oliver Brian , Richards Stephen
Published: July 2014

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.
Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
Authors: Slattery Matthew , Ma Lijia , Spokony Rebecca F. , Arthur Robert K. , Kheradpour Pouya , Kundaje Anshul , Nègre Nicolas , Crofts Alex , Ptashkin Ryan , Zieba Jennifer , Ostapenko Alexander , Suchy Sarah , Victorsen Alec , Jameel Nader , Grundstad A. Jason , Gao Wenxuan , Moran Jennifer R. , Rehm E. Jay , Grossman Robert L. , Kellis Manolis , White Kevin P.
Published: July 2014

Annotation of regulatory elements and identification of the transcription-related factors (TRFs) targeting these elements are key steps in understanding how cells interpret their genetic blueprint and their environment during development, and how that process goes awry in the case of disease. One goal of the modENCODE (model organism ENCyclopedia of DNA Elements) Project is to survey a diverse sampling of TRFs, both DNA-binding and non-DNA-binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TRFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also highlight the stringency of the Polycomb regulatory network, and show association of the Trithorax-like (Trl) protein with hotspots of DNA binding throughout development. Furthermore, the data identify more than 5800 instances in which TRFs target DNA regions with demonstrated enhancer activity. Regions of high TRF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TRF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. Together these data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development.
Measuring the Steady-State Properties of Ca2+ Indicators with a Set of Calibrated [Ca2+] Solutions
Authors: Faas Guido C. , Mody Istvan
Published: July 2014

Fluorescent Ca2+ indicators are widely used to measure the concentration of free Ca2+ ([Ca2+]free) in biological processes. By calibrating the dye under the same experimental conditions as employed during its planned use, the actual [Ca2+] can be calculated from the measured fluorescence. When using non ratiometric dyes, such as the Oregon Green BAPTA (OGB) family of dyes or the Fluo dyes, the steady-state affinity (Kd) and the ratio between the maximal and minimal fluorescence (Fratio = Fmax/Fmin) of the particular dye are needed for this conversion. Although these values are usually given by the manufacturer, we consistently find that the actual values can differ between various batches delivered by the companies that make the dyes. In this protocol, we provide the recipe for a series of solutions with a known and tightly buffered [Ca2+]free and describe how to use these mixtures to determine the exact Kd and Fratio of a fluorescent Ca2+ dye.
Measuring the Rate Constants of Ca2+ Indicators
Authors: Faas Guido C. , Mody Istvan
Published: July 2014

Fluorescent Ca2+ indicators are widely used to measure the concentration of free Ca2+ ([Ca2+]free) in biological processes. To determine the exact kinetics of changes in [Ca2+]free and the processes underlying these changes (e.g., Ca2+ binding to Ca2+-binding proteins), it is necessary to know the exact binding properties of the indicator used. Here, we describe how to determine the binding rate constants (kon and koff) of Ca2+ indicators.
4-{Phenyl[4-(6-phenyl-2,2′-bipyridin-4-yl)phenyl]amino}benzaldehyde
Authors: Zhang Yu-yang , Pan Jian-Ting , Huang Jian-Yan
Published: July 2014

The title molecule, C35H25N3O, is a triphenylamine derivative with the 4-position substituted by an aldehyde group, and the 4′-position substituted by a 6-phenyl-2,2′-bipyridine group. The whole molecule is non-planar and the dihedral angle between the core benzene and pyridine rings is 36.96 (5)°. The dihedral angle between the phenyl and benzaldehyde groups bonded to the amine N atom is 70.86 (5)°.
1-[3-(Morpholin-4-yl)propyl]-3-[(naphthalen-2-yl)oxy]-4-(3-nitrophenyl)azetidin-2-one
Authors: Atioğlu Zeliha , Akkurt Mehmet , Jarrahpour Aliasghar , Heiran Roghayeh , Özdemir Namık
Published: July 2014

In the title compound, C26H27N3O5, the β-lactam (azetidin-2-one) ring is nearly planar [maximum deviation = 0.011 (3) Å]. The mean plane formed by the four C atoms of the morpholine ring, which adopts a chair conformation, the benzene ring and the naphthalene ring system form dihedral angles of 72.85 (17), 87.46 (15) and 65.96 (11)°, respectively, with the β-lactam ring. In the crystal, molecules are linkedviaC—H...O hydrogen bonds, forming inversion dimers withR22(8).
(5R*)-5-[(2S*,5S*)-1-Methoxy-5-phenylpyrrolidin-2-yl]-3-methylfuran-2(5H)-one
Authors: Oishi Takeshi , Yoritate Makoto , Sato Takaaki , Chida Noritaka
Published: July 2014

In the title compound, C16H19NO3, the pyrrolidine ring is in a twist conformation. The dihedral angle between the dihydrofuran ring [maximum deviation = 0.0016 (11) Å] and the phenyl ring is 47.22 (8)°. In the crystal, molecules are linked by weak C—H...O hydrogen bonds, forming helical chains along theb-axis direction. The chains are further linked by C—H...π interactions to constitute a three-dimensional architecture.
3-Methylbenzo[1,2-c:5,4-c′]dichromen-6(8H)-one
Authors: Kayalvizhi M. , Vasuki G. , Khatri Adil I. , Samant Shriniwas D.
Published: July 2014

The title compound, C21H14O3, crystallizes with eight independent molecules (A–H) in the asymmetric unit which are arranged in four groups of two molecules each (AB,CD,EFandGH). In each molecule, the pyran-2-one ring is planar (r.m.s. deviations vary from 0.001 to 0.017 Å), while the pyran ring has a screw-boat conformation. In the crystal, molecules stack in two columns, along the [10-1] direction, composed of moleculesC,B,EandG, andD,A,FandH. MoleculesAandFare linkedviaC—H...O hydrogen bonds. In addition, there are a number of C—H...π contacts present involving all of the molecules. These interactions result in the formation of a three-dimensional network.
Bis{2-methoxy-6-[(E)-(4-methylbenzyl)iminomethyl]phenolato}palladium(II) chloroform monosolvate
Authors: Bahron Hadariah , Tajuddin Amalina Mohd , Ibrahim Wan Nazihah Wan , Chantrapromma Suchada , Fun Hoong-Kun
Published: July 2014

In the title complex, [Pd(C16H16NO2)2]·CHCl3, the PdIIcation lies on an inversion center. One Cl atom of the CHCl3solvent molecule lies on a twofold axis and the C—H group is disordered with equal occupancies about this axis with the other Cl atom in a general position with full occupancy. The PdIIcation is four-coordinate and adopts a square-planar geometryviacoordination of the imine N and phenolic O atoms of the two bidentate Schiff base anions. The N and O atoms of these ligands are mutuallytrans. The plane of the benzene ring makes a dihedral angle of 73.52 (10)° with that of the methoxyphenolate ring. In the crystal, molecules of the PdIIcomplex are arranged into sheets parallel to theacplane, and the chloroform solvent molecules are located in the interstitial areas between the complex molecules. Weak intermolecular C—H...O and C—H...π interactions stabilize the packing.
5-Hydroxy-2-nitrobenzaldehyde thiosemicarbazone (HNBATSC)
Authors: Reddy M. Sivasankar , Sarala Y. , Jagadeesh M. , Das Samar K. , Ammireddy Varada Reddy
Published: July 2014

The asymmetric unit of the title compound, C8H8N4O3S, consists of two independent molecules. Each molecule is approximately planar with dihedral angles of 8.71 (3) and 1.50 (2)° between the aromatic ring and the thiosemicarbazide moiety while the NO2group makes dihedral angles of 29.27 (3) and 17.78 (3)° with the benzene ring. In the crystal, the molecules are linked by N—H...S, O—H...O and N—H...O hydrogen bonds, forming two-dimensional networks parallel to (100).
Reordering Our Priorities by Putting Phenomena before Design: Escaping the Straitjacket of Null Hypothesis Significance Testing
Authors: Lockett Andy , McWilliams Abagail , Van Fleet David D.
Published: July 2014

In this paper we reflect on two related questions. First, how have we arrived at a position where null hypothesis significance testing is the dominant criterion employed by quantitative researchers when deciding on whether or not a result is ‘significant'? Second, how might we change the practice of quantitative management research by promoting a greater plurality of methods, and in doing so better enable scholars to put phenomena before design? We conclude by arguing that quantitative management researchers need to focus on the epistemological issues surrounding the role of scholarly reasoning in justifying knowledge claims. By embracing a plurality of approaches to reasoning quantitative researchers will be better able to escape the straitjacket of null hypothesis significance testing and, in doing so, reorder their priorities by putting phenomena before design.
Extension of Nakagawa & Schielzeth's R2GLMM to random slopes models
Authors: Johnson Paul C.D.
Published: July 2014

Nakagawa & Schielzeth extended the widely used goodness‐of‐fit statistic R2 to apply to generalized linear mixed models (GLMMs). However, their R2GLMM method is restricted to models with the simplest random effects structure, known as random intercepts models. It is not applicable to another common random effects structure, random slopes models.

I show that R2GLMM can be extended to random slopes models using a simple formula that is straightforward to implement in statistical software. This extension substantially widens the potential application of R2GLMM.
Suicide in Happy Places Revisited: The Geographical Unit of Analysis Matters
Authors: Park Nansook , Peterson Christopher
Published: July 2014

Background: A recent study reported that the highest suicide rates in the US occurred in the happiest states. This is a counter‐intuitive finding. The present research investigated whether the same result occurred when the unit of analysis was city. The association between happiness (of most) and suicide (by some) might differ in cities versus states because those in a city provide a more immediate influence. Methods: Suicide rates were examined in 44 large US cities as a function of the average happiness reported by residents. Results: According to our results, happier cities had lower suicide rates (Spearman's rho = −.37, p < .014), implying that cities may be a more meaningful unit of analysis than states for studies of suicide risk. Conclusions: The appropriate geographical unit of analysis needs to be considered seriously in psychological studies.
High flow cytometric scores identify adverse prognostic subgroups within the revised international prognostic scoring system for myelodysplastic syndromes
Authors: Alhan Canan , Westers Theresia M. , Cremers Eline M. P. , Cali Claudia , Witte Birgit I. , Ossenkoppele Gert J. , van de Loosdrecht Arjan A.
Published: July 2014

The estimation of survival of myelodysplastic syndromes (MDS) and risk of progression into acute myeloid leukaemia is challenging due to the heterogeneous clinical course. The most widely used prognostic scoring system (International Prognostic Scoring System [IPSS]) was recently revised (IPSS‐R). The aim of this study was to investigate the prognostic relevance of flow cytometry (FC) in the context of theIPSS‐R. Bone marrow aspirates were analysed byFCin 159 patients withMDS. A flow score was calculated by applying the flow cytometric scoring system (FCSS). Patients were assigned toIPSSandIPSS‐R risk groups. TheFCSScorrelated with the World Health Organization classification,IPSSandIPSS‐R risk groups. Mild flow cytometric abnormalities were associated with significantly better overall survival (OS) and lower risk of disease evolution. The presence of aberrant myeloid progenitors was associated with transfusion dependency and disease progression. Most importantly, theFCSSidentified prognostic subgroups within theIPSS‐R cytogenetic good risk and low risk group. Flow cytometric analysis in patients withMDSprovides additional prognostic information and is complementary to theIPSS‐R. The addition of a flow cytometric score next to the clinical parameters within theIPSS‐R is a further refinement of prognostication of patients withMDS.
PIM and AKT kinase inhibitors show synergistic cytotoxicity in acute myeloid leukaemia that is associated with convergence on mTOR and MCL1 pathways
Authors: Meja Koremu , Stengel Chloe , Sellar Rob , Huszar Dennis , Davies Barry R. , Gale Rosemary E. , Linch David C. , Khwaja Asim
Published: July 2014

PIM kinases (PIM1, 2 and 3) are involved in cell proliferation and survival signalling and are emerging targets for the therapy of various malignancies. We found that a significant proportion of primary acute myeloid leukaemia (AML) samples showed PIM1 and PIM2 expression by quantitative reverse transcription polymerase chain reaction. Therefore, we investigated the effects of a novel ATP‐competitive pan‐PIM inhibitor, AZD1897, on AML cell growth and survival. PIM inhibition showed limited single agent activity in AML cell lines and primary AML cells, including those with or without FLT3‐internal tandem duplication (ITD) mutation. However, significant synergy was seen when AZD1897 was combined with the Akt inhibitor AZD5363, a compound that is in early‐phase clinical trials. AML cells from putative leukaemia stem cell subsets, including CD34+38− and CD34+38+ fractions, were equivalently affected by dual PIM/Akt inhibition when compared with bulk tumour cells. Analysis of downstream signalling pathways showed that combined PIM/Akt inhibition downregulated mTOR outputs (phosphorylation of 4EBP1 and S6) and markedly reduced levels of the anti‐apoptotic protein MCL1. The combination of PIM and Akt inhibition holds promise for the treatment of AML.
The Rautuvaara section, western Finnish Lapland, revisited – new age constraints indicate a complex Scandinavian Ice Sheet history in northern Fennoscandia during the Weichselian Stage
Authors: Lunkka Juha Pekka , Sarala Pertti , Gibbard Philip L.
Published: July 2014

The Rautuvaara section in northern Finnish Lapland has been widely considered as the stratotype for the northern Fennoscandian late Middle and Late Pleistocene. It exposes four till units interbedded with sorted sediments resting on Precambrian bedrock. In order to shed light on the Scandinavian Ice Sheet (SIS) history and palaeoenvironmental evolution in northern Fennoscandia through time, a chronostratigraphical study was carried out at the Rautuvaara site. The succession was studied using sedimentological methods and different sand‐rich units between till units were dated using the Optical Stimulated Luminescence (OSL) method. The results obtained indicate that the whole sediment succession at Rautuvaara was deposited during the Weichselian Stage and there is no indication of older deposits. The SIS advanced across Finnish Lapland to adjacent areas to the east at least once during the Early Weichselian, twice during the Middle Weichselian (∼MIS 4 and MIS 3) and once during the Late Weichselian substages. Glaciolacustrine sediments interbedded between the till units indicate that a glacial lake repeatedly existed after each deglacial phase. The results also suggest that there were two ice‐free intervals in northern Fennoscandia during the Middle Weichselian close to the SIS glaciation centre.