bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sea level and climate forcing of the Sr isotope composition of lateMioceneMediterranean marine basins
Authors: Schildgen T. F. , Cosentino D. , Frijia G. , Castorina F. , Dudas F. Ö. , Iadanza A. , Sampalmieri G. , Cipollari P. , Caruso A. , Bowring S. A. , Strecker M. R. 
Published: July 2014

AbstractSr isotope records from marginal marine basins track the mixing between seawater and local continental runoff, potentially recording the effects of sea level, tectonic, and climate forcing in marine fossils and sediments. Our 110 new87Sr/86Sr analyses on oyster and foraminifera samples from six late Miocene stratigraphic sections in southern Turkey, Crete, and Sicily show that87Sr/86Sr fell below global seawater values in the basins several million years before the Messinian Salinity Crisis, coinciding with tectonic uplift and basin shallowing.87Sr/86Sr from more centrally located basins (away from the Mediterranean coast) drop below global seawater values only during the Messinian Salinity Crisis. In addition to this general trend, 55 new87Sr/86Sr analyses from the astronomically tuned Lower Evaporites in the central Apennines (Italy) allow us to explore the effect of glacio‐eustatic sea level and precipitation changes on87Sr/86Sr. Most variation in our data can be explained by changes in sea level, with greatest negative excursions from global seawater values occurring during relative sea level lowstands, which generally coincided with arid conditions in the Mediterranean realm. We suggest that this greater sensitivity to lowered sea level compared with higher runoff could relate to the inverse relationship between Sr concentration and river discharge. Variations in the residence time of groundwater within the karst terrain of the circum‐Mediterranean region during arid and wet phases may help to explain the single (robust) occurrence of a negative excursion during a sea level highstand, but this explanation remains speculative without more detailed paleoclimatic data for the region.
Highly Crystalline Lithium Titanium Oxide Sheets Coated with Nitrogen‐Doped Carbon enable High‐Rate Lithium‐Ion Batteries
Authors: Han Cuiping , He Yan‐Bing , Li Baohua , Li Hongfei , Ma Jun , Du Hongda , Qin Xianying , Yang Quan‐Hong , Kang Feiyu 
Published: July 2014

AbstractSheets of Li4Ti5O12 with high crystallinity are coated with nitrogen‐doped carbon (NC‐LTO) using a controlled process, comprising hydrothermal reaction followed by chemical vapor deposition (CVD). Acetonitrile (CH3CN) vapor is used as carbon and nitrogen source to obtain a thin coating layer of nitrogen‐doped carbon. The layer enables the NC‐LTO material to maintain its sheet structure during the high‐temperature CVD process and to achieve high crystallinity. Doping with nitrogen introduces defects into the carbon coating layer, and this increased degree of disorder allows fast transportation of lithium ions in the layer. An electrode of NC‐LTO synthesized at 700 °C exhibits greatly improved rate and cycling performance due to a markedly decreased total cell resistance and enhanced Li‐ion diffusion coefficient (DLi). Specific capacities of 159.2 and 145.8 mA h g−1 are obtained using the NC‐LTO sheets, at charge/discharge rates of 1 and 10 C, respectively. These values are much higher than values for LTO particles did not undergo the acetonitrile CVD treatment. A capacity retention value as high as 94.7 % is achieved for the NC‐LTO sheets after 400 cycles in a half‐cell at 5 C discharge rate.
Structure and function of pseudoknots involved in gene expression control
Authors: Peselis Alla , Serganov Alexander 
Published: July 2014

Natural RNA molecules can have a high degree of structural complexity but even the most complexly folded RNAs are assembled from simple structural building blocks. Among the simplest RNA elements are double‐stranded helices that participate in the formation of different folding topologies and constitute the major fraction of RNA structures. One common folding motif of RNA is a pseudoknot, defined as a bipartite helical structure formed by base‐pairing of the apical loop in the stem‐loop structure with an outside sequence. Pseudoknots constitute integral parts of the RNA structures essential for various cellular activities. Among many functions of pseudoknotted RNAs is feedback regulation of gene expression, carried out through specific recognition of various molecules. Pseudoknotted RNAs autoregulate ribosomal and phage protein genes in response to downstream encoded proteins, while many metabolic and transport genes are controlled by cellular metabolites interacting with pseudoknotted RNA elements from the riboswitch family. Modulation of some genes also depends on metabolite‐induced messenger RNA (mRNA) cleavage performed by pseudoknotted ribozymes. Several regulatory pseudoknots have been characterized biochemically and structurally in great detail. These studies have demonstrated a plethora of pseudoknot‐based folds and have begun uncovering diverse molecular principles of the ligand‐dependent gene expression control. The pseudoknot‐mediated mechanisms of gene control and many unexpected and interesting features of the regulatory pseudoknots have significantly advanced our understanding of the genetic circuits and laid the foundation for modulation of their outcomes. WIREs RNA 2014, 5:803–822. doi: 10.1002/wrna.1247This article is categorized under:

RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition
RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
In Operando GIXRD and XRR on Polycrystalline In52Pd48
Authors: Ivarsson Dennis C. A. , Neumann Matthias , Levin Alexander A. , Keilhauer Toni , Wochner Peter , Armbrüster Marc 
Published: July 2014

AbstractA combined approach of grazing incidence X‐ray diffraction (GIXRD) and X‐ray reflectivity (XRR) under in operando conditions on polycrystalline materials is presented. This approach allows tracking of material changes of amorphous or crystalline nature in the near‐surface region. Crystalline phases formed in operando can be identified by X‐ray diffraction, while by XRR measurements information about the thickness and the density of overlayers is obtained. The setup also allows collection of data generated with higher incident angles which permit a direct comparison of the changes close to the surface and in the bulk of the materials. Results for the composition In52Pd48 – a mixture of the intermetallic compounds InPd and In3Pd2 catalyzing the steam reforming of methanol – in reducing atmosphere and under methanol steam reforming (MSR) conditions are presented. InPd exhibits a dynamic behavior, reacting to changes in atmosphere and temperature. The combination of GIXRD and XRR proves to be a powerful tool to examine model catalysts under catalytically relevant conditions providing complementary information to other methods.
DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA
Authors: Jarmoskaite Inga , Bhaskaran Hari , Seifert Soenke , Russell Rick 
Published: July 2014

Significance
DEAD-box proteins are ubiquitous in RNA metabolism and can act as RNA chaperones by promoting folding and rearrangements of structured RNAs. However, the mechanistic basis for these chaperone activities is not well understood. Here we show that the DEAD-box protein CYT-19 unfolds a large, structured RNA molecule in a stability-dependent fashion and is more active toward less compact conformations of the RNA. Our results indicate that CYT-19 functions predominantly by disrupting accessible RNA secondary structure and depends on spontaneous openings in tightly packed RNAs to gain access to RNA helices. Unwinding of exposed secondary structure promotes global RNA unfolding and facilitates formation of new structures. Analogous mechanisms are observed in other molecular chaperones and are likely widespread among DEAD-box helicases.
Molecular mechanisms for the regulation of histone mRNA stem-loop–binding protein by phosphorylation
Authors: Zhang Jun , Tan Dazhi , DeRose Eugene F. , Perera Lalith , Dominski Zbigniew , Marzluff William F. , Tong Liang , Hall Traci M. Tanaka 
Published: July 2014

SignificanceAs DNA is replicated during cell division, it must be packaged by histones. To match the level of available histones to DNA replication, histone mRNA expression is controlled by a 3′-end stem-loop structure unique to replication-dependent histone mRNAs. InDrosophila, this regulation is mediated by histone mRNA stem-loop–binding protein (dSLBP), which has minimal tertiary structure when not bound to RNA. We show here that phosphorylation of dSLBP dramatically increases binding affinity for stem-loop RNA. The phosphorylated C-terminal tail of dSLBP does not contact RNA. Instead, increased negative charge on the C-terminal tail and stabilization of structural elements by a phosphorylation site within the RNA-binding domain promote more compact conformations that should reduce the entropic barrier to binding histone mRNA.
Crystal structure and encapsulation dynamics of ice II-structured neon hydrate
Authors: Yu Xiaohui , Zhu Jinlong , Du Shiyu , Xu Hongwu , Vogel Sven C. , Han Jiantao , Germann Timothy C. , Zhang Jianzhong , Jin Changqing , Francisco Joseph S. , Zhao Yusheng 
Published: July 2014

Significance
Clathrate hydrates have ice-like crystalline structures typically stabled under low-temperature and high-pressure conditions. They are of great importance as potential materials for energy storage and production and carbon dioxide sequestration. Here the first structural refinement data of neon hydrate, to our knowledge, are presented. Both the experimental observations by in situ neutron diffraction and molecular dynamics simulations demonstrate that neon atoms can be enclathrated to form ice II-structured hydrates. The guest Ne atoms occupy the center of ice channels and have substantial freedom of movement owing to the lack of strong bonding between guest molecules and host lattices. The framework of Ne hydrate can be self-stabilized without the encapsulation of guest atoms, which is very special in the hydrate family.
Transformation of the Agrifood Industry in Developing Countries
Authors: Reardon Thomas , Timmer C. Peter 
Published: July 2014

AbstractOver the past 30 years, the agrifood industry in developing countries has been undergoing rapid transformation in structure and behavior. These changes have been driven by both market forces and government policy, particularly foreign direct investment, and have the potential to affect farmers and consumers; the former via increased incomes and modernized technologies, and the latter via cheaper and safer food. This article examines the transformation of the agrifood industry in developing countries, focusing on the sector’s three segments: retail, wholesale, and processing. It first looks at the factors that drive the transformation of the industry and its procurement systems/supply chains that are shared across the segments. It then considers the “symbioses” among the three segments, highlighting how they reinforce each other and enter preferred supplier relations with one another. It also discusses emerging impacts of the above transformations on farmers as well as small and medium enterprises. Finally, it describes programs that promote linkages for a faster, more integrated, and more inclusive growth path for these transformations over the next decade.
Developmental Dyscalculia as a Heterogeneous Disability
Authors: Henik Avishai , Rubinsten Orly , Ashkenazi Sarit 
Published: July 2014

Abstract
This chapter discusses heterogeneous aspects of developmental dyscalculia (DD) in terms of behaviour, cognitive operations, and neural structures. It has been suggested that DD is an isolated learning deficiency, involves a domain-specific deficit (in the capacity to enumerate), and a specific neural deficiency (in the intraparietal sulcus). We present findings that (1) DD involves both domain-specific and domain-general abilities; (2) in many cases behaviours, as well as cognition in those with DD are characterized by deficits in other areas, such as attention or memory and not only as a number sense deficiency; and (3) studies of the neural structures involved in DD reveal areas and mechanisms that hint toward heterogeneous damage. We suggest that similar to other learning disabilities, heterogeneity is the rule, rather than an exception. Accordingly, in order to reach a comprehensive understanding of DD, studies should aim at unravelling the basis for this heterogeneity.
Cognitive Predictors of Mathematical Abilities and Disabilities
Authors: Desoete Annemie 
Published: July 2014

AbstractThe cognitive predictors of mathematical abilities and disabilities/disorders (MD) were investigated. An overview is given of the prediction by early numeracy skills such as Piagetian logical thinking, counting, and number comparison skills. In addition, studies of relationships between language and numeracy in kindergarten and grade 1 are discussed. Moreover, the chapter sought out to extend our knowledge regarding the relationship between motor, visual and visuomotor skills and mathematical abilities and disabilities. Furthermore, the chapter discusses studies of working memory, inhibition, naming speed and inference control as cognitive predictors for mathematical abilities and MD. Finally findings about the sensitivity of number sense for MD are provided.
Number Processing and Arithmetic in Children and Adults with Reading Difficulties
Authors: Göbel Silke M. 
Published: July 2014

AbstractBasic number processing skills in individuals with reading difficulties (RD) are intact. However, children and adults with RD show clear difficulties in arithmetic, in particular in retrieving known answers from long-term memory (fact retrieval). Fact retrieval deficits are associated with weaknesses in phonological awareness, the ability to segment and manipulate speech sounds. The left angular gyrus has been suggested as a site of neurological overlap between RD and fact retrieval deficits. While there is evidence for an involvement of the angular gyrus in fact retrieval in adults, the evidence for children is less clear. The same genetic risk factors may underlie difficulties in reading and mathematics and cause the high co-morbidity between RD and mathematical difficulties. Implications for interventions are discussed.
Phage–bacteria network analysis and its implication for the understanding of coral disease
Authors: Soffer Nitzan , Zaneveld Jesse , Vega Thurber Rebecca 
Published: July 2014

SummaryMultiple studies have explored microbial shifts in diseased or stressed corals; however, little is known about bacteriophage interactions with microbes in this context. This study characterized microbial 16S rRNA amplicons and phage metagenomes associated with Montastraea annularis corals during a concurrent white plague disease outbreak and bleaching event. Phage consortia differed between bleached and diseased tissues. Phages in the family Inoviridae were elevated in diseased or healthy tissues compared with bleached portions of diseased tissues. Microbial communities also differed between diseased and bleached corals. Bacteria in the orders Rhodobacterales and Campylobacterales were increased while Kiloniellales was decreased in diseased compared with other tissues. A network of phage–bacteria interactions was constructed of all phage strains and 11 bacterial genera that differed across health states. Phage–bacteria interactions varied in specificity: phages interacted with one to eight bacterial hosts while bacteria interacted with up to 59 phages. Six phages were identified that interacted exclusively with Rhodobacterales and Campylobacterales. These results suggest that phages have a role in controlling stress‐associated bacteria, and that networks can be utilized to select potential phages for mitigating detrimental bacterial growth in phage therapy applications.
The Effect of Electrode Placement and Interphase Interval on Force Production During Stimulation of the Dorsiflexor Muscles
Authors: Springer Shmuel , Braun‐Benyamin Orit , Abraham‐Shitreet Chen , Becher Meni , Laufer Yocheved 
Published: July 2014

AbstractThe aims of this study were to investigate whether introducing an interphase interval (IPI) to biphasic pulses during stimulation of the dorsiflexor muscles would affect force production and to determine whether the IPI effect is dependent on electrode position. Twelve healthy volunteers participated in the study. Each subject participated in one session during which electrically induced contraction (EIC) forces of the ankle dorsiflexors were measured with five different IPI settings ranging from 0 to 400 μs. Forces of EICs were assessed with the electrodes placed either with the proximal electrode positioned over the common peroneal nerve and the second electrode over the dorsiflexor muscles or with both electrodes located over the dorsiflexor muscles. The order of electrode placements and of the different IPI settings was randomized across subjects. The results indicated that the introduction of a 100‐μs‐long IPI may enhance force production when one electrode is located over the common peroneal nerve. However, increasing the duration of the IPI beyond 100 μs did not result in further increase in force production. In contrast, the introduction of an IPI did not increase force production when both electrodes were located over the dorsiflexor muscles. These findings may help to optimize stimulation settings during functional electrical stimulation to prevent foot‐drop.
Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.)
Authors: Dierking Jan , Phelps Luke , Præbel Kim , Ramm Gesine , Prigge Enno , Borcherding Jost , Brunke Matthias , Eizaguirre Christophe 
Published: July 2014

AbstractNatural hybridization plays a key role in the process of speciation. However, anthropogenic (human induced) hybridization of historically isolated taxa raises conservation issues. Due to weak barriers to gene flow and the presence of endangered taxa, the whitefish species complex is an excellent study system to investigate the consequences of hybridization in conservation. We focused on three naturally reproductively isolated whitefish taxa in Germany: the endangered, anadromous North Sea houting (NSH) and Baltic houting (BH), which were reintroduced after local extinction, and the commercially stocked European whitefish (EW). To evaluate the genetic integrity of each taxon, source and reintroduced populations of NSH and BH, and EW populations were characterized based on two mitochondrial and 17 microsatellite loci. Additionally, we investigated gill raker counts as an adaptive phenotypic trait. Even though clear genetic and phenotypic differentiation confirmed the houtings as separate evolutionarily significant units, admixture analyses revealed an extensive hybrid zone. Hybridizations were introgressive, positively correlated with genetic diversity, and were reflected in the gill raker counts. The BH distribution range showed higher heterogeneity and stronger admixture than the NSH range. Erroneous stocking with non‐native genotypes best explained these patterns, which pose challenges for the conservation of the endangered NSH and BH.
Hindering and buffering factors for parental sleep in neonatal care. A phenomenographic study
Authors: Edéll‐Gustafsson Ulla , Angelhoff Charlotte , Johnsson Ewa , Karlsson Jenny , Mörelius Evalotte 
Published: July 2014

Aims and objectivesTo explore and describe how parents of preterm and/or sick infants in neonatal care perceive their sleep.BackgroundParents experience many stressful situations when their newborn infant is preterm and/or sick. This affects bonding. By developing more family‐centred care units with single‐family rooms, parents are given the opportunity to stay and care for their newborn infant(s) 24 hours a day. Lack of sleep may affect new parents' ability to cope with the many challenges they face on a daily basis.DesignA phenomenographic study with an inductive and exploratory design.MethodsSemi‐structured interviews were conducted with twelve parents of infants in neonatal care between January–March 2012. To describe variations in perception of the phenomenon, data were analysed using phenomenography.FindingsFour descriptive categories were identified within the phenomenon sleep in parents of preterm and/or sick infants in neonatal care: impact of stress on sleep; how the environment affects sleep; keeping the family together improves sleep; and, how parents manage and prevent tiredness.ConclusionAnxiety, uncertainty and powerlessness have a negative influence on sleep. This can be decreased by continuous information, guidance and practical support. Skin‐to‐skin care was perceived as a stress‐reducing factor that improved relaxation and sleep and should be encouraged by the nurse. The parents also mentioned the importance of being together. Having a private place where they could relax and take care of themselves and their newborn infant improved sleep. It was also desirable to involve older siblings in order to decrease feelings of loneliness, sadness and isolation.Relevance for clinical practiceImproved parental sleep in neonatal care may help the families cope with the situation and facilitate problem‐solving, emotional regulation and the transition to parenthood.
Cyclic lipopeptides from Bacillus subtilis activate distinct patterns of defence responses in grapevine
Authors: Farace Giovanni , Fernandez Olivier , Jacquens Lucile , Coutte François , Krier François , Jacques Philippe , Clément Christophe , Barka Essaid Ait , Jacquard Cédric , Dorey Stéphan 
Published: July 2014

SummaryNon‐self‐recognition of microorganisms partly relies on the perception of microbe‐associated molecular patterns (MAMPs) and leads to the activation of an innate immune response. Bacillus subtilis produces three main families of cyclic lipopeptides (LPs), namely surfactins, iturins and fengycins. Although LPs are involved in induced systemic resistance (ISR) activation, little is known about defence responses induced by these molecules and their involvement in local resistance to fungi. Here, we showed that purified surfactin, mycosubtilin (iturin family) and plipastatin (fengycin family) are perceived by grapevine plant cells. Although surfactin and mycosubtilin stimulated grapevine innate immune responses, they differentially activated early signalling pathways and defence gene expression. By contrast, plipastatin perception by grapevine cells only resulted in early signalling activation. Gene expression analysis suggested that mycosubtilin activated salicylic acid (SA) and jasmonic acid (JA) signalling pathways, whereas surfactin mainly induced an SA‐regulated response. Although mycosubtilin and plipastatin displayed direct antifungal activity, only surfactin and mycosubtilin treatments resulted in a local long‐lasting enhanced tolerance to the necrotrophic fungus Botrytis cinerea in grapevine leaves. Moreover, challenge with specific strains overproducing surfactin and mycosubtilin led to a slightly enhanced stimulation of the defence response compared with the LP‐non‐producing strain of B. subtilis. Altogether, our results provide the first comprehensive view of the involvement of LPs from B. subtilis in grapevine plant defence and local resistance against the necrotrophic pathogen Bo. cinerea. Moreover, this work is the first to highlight the ability of mycosubtilin to trigger an immune response in plants.