bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crete (Iron Age to Hellenistic)
Authors: Haysom Matthew 
Published: November 2013

This year, the newly-published material bookends nearly a decade of archaeological work on the island with ADelt covering work on Crete from 2001 to 2004 and the second volume of Archaiologiko Ergo Kritis showcasing work in the years immediately before 2010. Several of the more impressive discoveries from the beginning of the decade have been known to the wider archaeological community for some time, but their publication in ADelt allows us to discuss them in greater detail and in their broader context. Overall, this is an opportune time to look at how some of the fieldwork done between 2001 and 2010 might contribute to our view of post-Bronze Age Crete.The largest single contribution of the 2012–2013 reports to the Iron Age came in the form of the publication of the 2001–2004 seasons at the settlement site on Prophitis Elias hill near Smari (ID3655): an account that rounds out earlier notices for the 1999 and 2000 seasons (AR 53 [2006–2007] 107–08; ID1814). The site of Smari has entered the literature principally thanks to the megara with stone-lined hearths at their centre. The buildings have been interpreted as a ruler's dwelling, with some relationship to Cretan hearth temples, and as a locale for communal dining (Mazarakis-Ainian [1997] 220–21, 296; Prent [2007] 143; Sjogren [2007] 153; Wallace [2010] 112, 119). After a Middle Minoan occupation, the site's main period of use covers the whole of the Iron Age from Late Minoan IIIC through to the Orientalizing period, after which a small cult place remained in use through to the Classical period (fifth-to third-century BC figurines: Hatzi-Vallianou [2000]).
The fungus-growing termite Macrotermes natalensis harbors bacillaene-producing Bacillus sp. that inhibit potentially antagonistic fungi
Authors: Um Soohyun , Fraimout Antoine , Sapountzis Panagiotis , Oh Dong-Chan , Poulsen Michael 
Published: November 2013

AbstractThe ancient fungus-growing termite (Mactrotermitinae) symbiosis involves the obligate association between a lineage of higher termites and basidiomyceteTermitomycescultivar fungi. Our investigation of the fungus-growing termiteMacrotermes natalensisshows thatBacillusstrains fromM. natalensiscolonies produce a single major antibiotic, bacillaene A (1), which selectively inhibits known and putatively antagonistic fungi ofTermitomyces. Comparative analyses of the genomes of symbioticBacillusstrains revealed that they are phylogenetically closely related toBacillus subtilis, their genomes have high homology with more than 90% of ORFs being 100% identical and the sequence identities across the biosynthetic gene cluster for bacillaene are higher between termite-associated strains than to the cluster previously reported inB. subtilis. Our findings suggest that this lineage of antibiotic-producingBacillusmay be a defensive symbiont involved in the protection of the fungus-growing termite cultivar.
Influence of spatial configurations on electromagnetic interference shielding of ordered mesoporous carbon/ordered mesoporous silica/silica composites
Authors: Wang Jiacheng , Zhou Hu , Zhuang Jiandong , Liu Qian 
Published: November 2013

AbstractOrdered mesoporous carbons (OMCs), obtained by nanocasting using ordered mesoporous silicas (OMSs) as hard templates, exhibit unique arrangements of ordered regular nanopore/nanowire mesostructures. Here, we used nanocasting combined with hot-pressing to prepare 10 wt% OMC/OMS/SiO2 ternary composites possessing various carbon mesostructure configurations of different dimensionalities (1D isolated CS41 carbon nanowires, 2D hexagonal CMK-3 carbon and 3D cubic CMK-1 carbon). The electric/dielectric properties and electromagnetic interference (EMI) shielding efficiency (SE) of the composites were influenced by spatial configurations of carbon networks. The complex permittivity and the EMI SE of the composites in the X-band frequency range decreased for the carbon mesostructures in the following order: CMK-3-filled > CMK-1-filled > CS41-filled. Our study provides technical directions for designing and preparing high-performance EMI shielding materials. Our OMC-based silica composites can be used for EMI shielding, especially in high-temperature or corrosive environments, owing to the high stability of the OMC/OMS fillers and the SiO2 matrix. Related shielding mechanisms are also discussed.
RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomain
Authors: Picaud Sarah , Wells Christopher , Felletar Ildiko , Brotherton Deborah , Martin Sarah , Savitsky Pavel , Diez-Dacal Beatriz , Philpott Martin , Bountra Chas , Lingard Hannah , Fedorov Oleg , Müller Susanne , Brennan Paul E. , Knapp Stefan , Filippakopoulos Panagis 
Published: November 2013

SignificanceBromo and extraterminal (BET) proteins have diverse roles in regulating tissue-specific transcriptional programs, raising safety concerns for their inhibition and suggesting that targeting of specific isoforms or even specific domains within this subfamily is important. We report the discovery and characterization of RVX-208 as a domain-selective inhibitor of BETs and provide a potential mechanism of action of a clinical compound that was identified based on phenotypic screens.
Gas production in the Barnett Shale obeys a simple scaling theory
Authors: Patzek Tad W. , Male Frank , Marder Michael 
Published: November 2013

Significance
Ten years ago, US natural gas cost 50% more than that from Russia. Now, it is threefold less. US gas prices plummeted because of the shale gas revolution. However, a key question remains: At what rate will the new hydrofractured horizontal wells in shales continue to produce gas? We analyze the simplest model of gas production consistent with basic physics of the extraction process. Its exact solution produces a nearly universal scaling law for gas wells in each shale play, where production first declines as 1 over the square root of time and then exponentially. The result is a surprisingly accurate description of gas extraction from thousands of wells in the United States’ oldest shale play, the Barnett Shale.
Arctic sea-ice decline archived by multicentury annual-resolution record from crustose coralline algal proxy
Authors: Halfar Jochen , Adey Walter H. , Kronz Andreas , Hetzinger Steffen , Edinger Evan , Fitzhugh William W. 
Published: November 2013

Significance
The most concerning example of ongoing climate change is the rapid Arctic sea-ice retreat. While just a few years ago ice-free Arctic summers were expected by the end of this century, current models predict this to happen by 2030. This shows that our understanding of rapid changes in the cryosphere is limited, which is largely due to a lack of long-term observations. Newly discovered long-lived algae growing on the Arctic seafloor and forming tree-ring–like growth bands in a hard, calcified crust have recorded centuries of sea-ice history. The algae show that, while fast short-term changes have occurred in the past, the 20th century exhibited the lowest sea-ice cover in the past 646 years.
Diffusion modifies the connectivity of kinetic schemes for multisite binding and catalysis
Authors: Gopich Irina V. , Szabo Attila 
Published: November 2013

Significance
Repeated modification of a multisite protein plays a key role in cell signaling. After an enzyme catalyzes a reaction at one site, it can modify another site before diffusing away. This physical process, which is amplified in the crowded environment of the cell, has been recently shown by stochastic simulations of hundreds of particles to dramatically change the response of a biochemical network. Here we show that the influence of diffusion on multisite protein modification can be described in a much simpler way, by introducing new connections into the kinetic scheme with rates depending on the probability that an enzyme–substrate pair diffuses apart rather than reacts. Our approach is applicable to complex reaction networks.
Metastatic castration-resistant prostate cancer reveals intrapatient similarity and interpatient heterogeneity of therapeutic kinase targets
Authors: Drake Justin M. , Graham Nicholas A. , Lee John K. , Stoyanova Tanya , Faltermeier Claire M. , Sud Sudha , Titz Björn , Huang Jiaoti , Pienta Kenneth J. , Graeber Thomas G. , Witte Owen N. 
Published: November 2013

Significance
Metastatic castration-resistant prostate cancer (CRPC) remains incurable due to the lack of effective therapies. The need to identify new actionable targets in CRPC is crucial as we begin to examine the resistance mechanisms related to androgen withdrawal. Here, we report an unbiased quantitative phosphoproteomic approach to identify druggable kinases in metastatic CRPC. These kinase activation patterns revealed intrapatient similarity and interpatient heterogeneity across a large panel of targets. Interestingly, these kinase activities are not a result of mutation but rather pathway activation within the tumors themselves. The observation that similar kinase activities are present in most if not all anatomically disparate metastatic lesions from the same patient suggests that CRPC patients may benefit from individualized, targeted combination therapies.
NFATc1 and NFATc2 repress spontaneous osteoarthritis
Authors: Greenblatt Matthew B. , Ritter Susan Y. , Wright John , Tsang Kelly , Hu Dorothy , Glimcher Laurie H. , Aliprantis Antonios O. 
Published: November 2013

Significance
Currently, little is understood about how the transcriptional regulation of cartilage breakdown contributes to pathogenesis of osteoarthritis (OA). Here, we report that, within cartilage, the transcription factor Nuclear factor of activated T cells c1 (NFATc1) displays selective expression in superficial articular chondrocytes. Accordingly, mice lacking both NFATc1 and NFATc2 in cartilage were generated and found to develop a severe, spontaneous and early-onset OA. These findings establish NFATc1 as a key transcriptional repressor of cartilage breakdown and OA. Additionally, these findings provide a unique model of OA that is an attractive platform for the preclinical development of treatments to alter the course of OA.
Circular dichroism and site-directed spin labeling reveal structural and dynamical features of high-pressure states of myoglobin
Authors: Lerch Michael T. , Horwitz Joseph , McCoy John , Hubbell Wayne L. 
Published: November 2013

Significance
High hydrostatic pressure facilitates the characterization of functionally relevant, but sparsely populated, excited conformational states of proteins by reversibly increasing their equilibrium population. Here, high-pressure instrumentation for circular dichroism and developments in high-pressure site-directed spin-labeling EPR are reported, and a combination of EPR and circular dichroism is used to map pressure-populated structural changes in various states of myoglobin. The data reveal that the high-pressure molten globule (MG) of apomyoglobin at neutral pH retains native-like helical content despite a fluctuating tertiary fold, an MG state of holomyoglobin populated at low pH and high-pressure retains ligand-binding capacity, and a transient folding intermediate of apomyoglobin is populated under similar conditions at equilibrium.
Spatial variation in the relationship between performance and metabolic rate in wild juvenile Atlantic salmon
Authors: Robertsen Grethe , Armstrong John D. , Nislow Keith H. , Herfindal Ivar , McKelvey Simon , Einum Sigurd 
Published: November 2013

Summary

Maintenance of metabolic rate (MR, the energy cost of self‐maintenance) is linked to behavioural traits and fitness and varies substantially within populations. Despite having received much attention, the causes and consequences of this variation remain obscure.

Theoretically, such within‐population variation in fitness‐related traits can be maintained by environmental heterogeneity in selection patterns, but for MR, this has rarely been tested in nature.

Here, we experimentally test whether the relationship between MR and performance can vary spatially by assessing survival, growth rate and movement of Atlantic salmon (Salmo salar L.) juveniles from 10 family groups differing in MR (measured as egg metabolism) that were stocked in parallel across 10 tributaries of a single watershed.

The relationship between MR and relative survival and growth rate varied significantly among tributaries. Specifically, the effect of MR ranged from negative to positive for relative survival, whereas it was negative for growth rate. The association between MR and movement was positive and did not vary significantly among tributaries.

These results are consistent with a fitness cost of traits associated with behavioural dominance that varies across relatively small spatial scales (within a single watershed). More generally, our results support the hypothesis that spatial heterogeneity in environmental conditions contributes to maintain within‐population variation in fitness‐related traits, such as MR.
Foliar nutrient concentrations and resorption efficiency in plants of contrasting nutrient‐acquisition strategies along a 2‐million‐year dune chronosequence
Authors: Hayes Patrick , Turner Benjamin L. , Lambers Hans , Laliberté Etienne 
Published: November 2013

Summary

Long‐term pedogenesis leads to important changes in the availability of soil nutrients, especially nitrogen (N) and phosphorus (P). Changes in the availability of micronutrients can also occur, but are less well understood. We explored whether changes in leaf nutrient concentrations and resorption were consistent with a shift from N to P limitation of plant productivity with soil age along a > 2‐million‐year dune chronosequence in south‐western Australia. We also compared these traits among plants of contrasting nutrient‐acquisition strategies, focusing on N, P and micronutrients.

The range in leaf [P] for individual species along the chronosequence was exceptionally large for both green (103–3000 μg P g−1) and senesced (19–5600 μg P g−1) leaves, almost equalling that found globally. From the youngest to the oldest soil, cover‐weighted mean leaf [P] declined from 1840 to 228 μg P g−1, while P‐resorption efficiency increased from 0% to 79%. All species converged towards a highly conservative P‐use strategy on the oldest soils.

Declines in cover‐weighted mean leaf [N] with soil age were less strong than for leaf [P], ranging from 13.4 mg N g−1 on the youngest soil to 9.5 mg N g−1 on the oldest soil. However, mean leaf N‐resorption efficiency was greatest (45%) on the youngest, N‐poor soils. Leaf N:P ratio increased from 8 on the youngest soil to 42 on the oldest soil.

Leaf zinc (Zn) concentrations were low across all chronosequence stages, but mean Zn‐resorption efficiency was greatest (55–74%) on the youngest calcareous dunes, reflecting low Zn availability at high pH.

N2‐fixing species had high leaf [N] compared with other species. Non‐mycorrhizal species had very low leaf [P] and accumulated Mn across all soils. We surmise that this reflects Mn solubilization by organic acids released for P acquisition.

Synthesis. Our results show community‐wide variation in leaf nutrient concentrations and resorption that is consistent with a shift from N to P limitation during long‐term ecosystem development. High Zn resorption on young calcareous dunes supports the possibility of micronutrient co‐limitation. High leaf [Mn] on older dunes suggests the importance of carboxylate release for P acquisition. Our results show a strong effect of soil nutrient availability on nutrient‐use efficiency and reveal considerable differences among plants of contrasting nutrient‐acquisition strategies.
Suitability of Bifidobacterium spp. and Lactobacillus plantarum as Probiotics Intended for Fruit Juices Containing Citrus Extracts
Authors: Bevilacqua Antonio , Campaniello Daniela , Corbo Maria Rosaria , Maddalena Lucia , Sinigaglia Milena 
Published: November 2013

AbstractA strain of Lactobacillus plantarum and 4 strains of bifidobacteria were inoculated in apple juice and in a commercial beverage labeled as “red‐fruit juice,” containing citrus extracts as natural preservatives; the suitability of the probiotics was evaluated in relation to their resistance to 2 kinds of citrus extracts (biocitro and lemon extract), survival in juices at 4 and 37 °C, and inhibition of Zygosaccharomyces bailii. Cell count of L. plantarum and bifidobacteria over time was fitted through the Weibull equation, for the evaluation of the first reduction time (δ), death time, and microbiological shelf life (the break‐point was set to 7 log cfu/mL). Bifidobacterium animalis subsp. lactis experienced the highest δ‐value (23.21 d) and death time (96.59 d) in the red‐fruit juice at 4 °C, whereas L. plantarum was the most promising strain in apple juice at 37 °C. Biocitro and lemon extract did not exert a biocidal effect toward probiotics; moreover, the probiotics controlled the growth of Z. bailii and the combination of L. plantarum with 40 ppm of biocitro reduced the level of the yeast after 18 d by 2 log cfu/mL.
Aflatoxin (B1, B2, G1, and G2) Contamination in Rice of Mexico and Spain, from Local Sources or Imported
Authors: Suárez‐Bonnet Elena , Carvajal Magda , Méndez‐Ramírez Ignacio , Castillo‐Urueta Pável , Cortés‐Eslava Josefina , Gómez‐Arroyo Sandra , Melero‐Vara José María 
Published: November 2013

AbstractRice is an important cereal but it is often contaminated with aflatoxins (AFs). The purpose of this study was to identify and quantify AF (B1, B2, G1, and G2) in 67 rice samples cultivated in Mexico and Spain, and from imported crops collected in 2008 and 2009. The methodology was validated, the rice samples were concentrated and purified with immunoaffinity columns and were quantified by high‐pressure liquid chromatography (HPLC). The average total AF (AFt) in the Spanish rice was 37.3 μg/kg, the range was from 1.6 to 1383 μg/kg, the most contaminated samples being from San Juan de Aznalfarache, Sevilla (AFt = 138.6 μg/kg), from Tortosa, Tarragona (AFt = 104.6 μg/kg), and Calasparra, Murcia (AFt = 103.9 μg/kg). The rice imported from France to Spain had AFt of 26.6 μg/kg and from Pakistan AFt of 18.4 μg/kg, showing less AF contamination than the local one. The rice which originated from Mexico contained (AFt = 16.9 μg/kg), and those imported from the United States (AFt = 14.4 μg/kg) and Uruguay (AFt = 15.6 μg/kg). The imported rice had better quality in terms of the presence of AFs.
A resource of single‐nucleotide polymorphisms for rainbow trout generated by restriction‐site associated DNA sequencing of doubled haploids
Authors: Palti Yniv , Gao Guangtu , Miller Michael R. , Vallejo Roger L. , Wheeler Paul A. , Quillet Edwige , Yao Jianbo , Thorgaard Gary H. , Salem Mohamed , Rexroad Caird E. 
Published: November 2013

AbstractSalmonid genomes are considered to be in a pseudo‐tetraploid state as a result of a genome duplication event that occurred between 25 and 100 Ma. This situation complicates single‐nucleotide polymorphism (SNP) discovery in rainbow trout as many putative SNPs are actually paralogous sequence variants (PSVs) and not simple allelic variants. To differentiate PSVs from simple allelic variants, we used 19 homozygous doubled haploid (DH) lines that represent a wide geographical range of rainbow trout populations. In the first phase of the study, we analysed SbfI restriction‐site associated DNA (RAD) sequence data from all the 19 lines and selected 11 lines for an extended SNP discovery. In the second phase, we conducted the extended SNP discovery using PstI RAD sequence data from the selected 11 lines. The complete data set is composed of 145 168 high‐quality putative SNPs that were genotyped in at least nine of the 11 lines, of which 71 446 (49%) had minor allele frequencies (MAF) of at least 18% (i.e. at least two of the 11 lines). Approximately 14% of the RAD SNPs in this data set are from expressed or coding rainbow trout sequences. Our comparison of the current data set with previous SNP discovery data sets revealed that 99% of our SNPs are novel. In the support files for this resource, we provide annotation to the positions of the SNPs in the working draft of the rainbow trout reference genome, provide the genotypes of each sample in the discovery panel and identify SNPs that are likely to be in coding sequences.
Are sputum eosinophil cationic protein and eosinophils differently associated with clinical and functional findings of asthma?
Authors: Cianchetti S. , Bacci E. , Ruocco L. , Pavia T. , Bartoli M. L. , Cardini C. , Costa F. , Di Franco A. , Malagrinò L. , Novelli F. , Vagaggini B. , Celi A. , Dente F. , Paggiaro P. 
Published: November 2013

SummaryBackgroundSputum eosinophil counts and eosinophil cationic protein (ECP) levels are usually increased in asthmatic patients. The correlation between sputum eosinophils or ECP and clinical findings of asthma has been previously investigated but many of these studies have been performed on small samples of asthmatic patients, considering only few clinical indices and often including patients on oral or inhaled corticosteroids, which might be confounding when interpreting the relationship between disease activity and airway inflammation.ObjectiveTo assess whether sputum eosinophils and ECP were differently related to functional and clinical parameters of asthma in a large number of steroid‐naïve asthmatic patients, taking into account several potential determinants of activity and chronicity of asthma.MethodsOne hundred and twenty‐nine patients with mild–moderate asthma were studied. Sputum was induced by hypertonic saline inhalation and processed using the whole sample method.ResultsSputum eosinophils and ECP significantly correlated with each other (r = 0.41, P < 0.001). When patients were grouped on the basis of high/low sputum eosinophils and high/low sputum ECP levels, significant differences were observed among groups, with patients with high sputum eosinophils and ECP showing the greatest asthma severity. In the overall sample, disease duration inversely correlated with sputum eosinophils, whereas FEV1 and peak expiratory flow (PEF) inversely correlated with sputum ECP. Rescue β2‐agonist use and total symptom score positively correlated with both eosinophil counts and sputum ECP. Stepwise regression analysis showed that symptom score and disease duration accounted for 17.6% of sputum eosinophil variance, whereas symptom score and FEV1 accounted for 14.7% of sputum ECP variance.Conclusions and Clinical RelevanceBoth sputum eosinophils and ECP are weakly related to clinical markers of asthma severity. However, ECP was more closely related to lung function parameters than eosinophil counts.