bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context dependency of rewards and services in an Indian ant–plant interaction: southern sites favour the mutualism between plants and ants
Authors: Chanam Joyshree , Kasinathan Srinivasan , Pramanik Gautam K. , Jagdeesh Amaraja , Joshi Kanchan A. , Borges Renee M. 
Published: April 2014

Abstract:Protection-based ant–plant mutualisms may vary in strength due to differences in ant rewards, abundance of protective ants and herbivory pressure. We investigated geographical and temporal variation in host plant traits and herbivory pressure at five sites spanning the distribution range of the myrmecophyteHumboldtia brunonis(Fabaceae) in the Indian Western Ghats. Southern sites had, on average, 2.4 times greater abundance of domatia-bearing individuals, 1.6 times greater extrafloral nectary numbers per leaf, 1.2 times larger extrafloral nectary sizes, 2.2 times greater extrafloral nectar (EFN) volumes and a two-fold increase in total amino acid and total sugar concentrations in EFN compared with northern sites. A strong protection-based mutualism with ants occurred at only one southern site where herbivory was highest, suggesting that investments in attracting ants correlate with anti-herbivore benefits gained from the presence of protective ants. Our results confirm a temporally stable north–south gradient in myrmecophytic traits in this ant-plant as several of these traits were re-sampled after a 5-y interval. However, the chemical composition of EFN varied at both spatial and short-term temporal scales suggesting that only repeated measurements of rewards such as EFN can reveal the real spectrum of trait variation in an ant–plant mutualistic system.
Local and regional determinants of galling-insect richness in Neotropical savanna
Authors: Araújo Walter Santos de , Cuevas-Reyes Pablo , Guilherme Frederico Augusto Guimarães 
Published: April 2014

Abstract:In this study, we determined the effects of plant richness, total plant abundance and abundance of plants with high galling diversity (super-hosts) on the local and regional galling richness in 15 areas of Neotropical savanna in different parts of Brazil. We established in each area 10 plots of 10 × 10 m, where we sampled a total of 131 plant species and 112 galling insect species. We considered all areas at the regional level and plots within each area at the local level. We found that at the regional level a combination of plant richness and plant abundance is the best model to explain the gall-inducing richness. We also found that at the local scale the most important factors are plant abundance and super-host abundance, but the plant richness is irrelevant. These findings confirm recent results that plant richness is an important predictor of galling species richness at the regional level, whereas the vegetation composition and structure act at the local level. Furthermore, this study contributes to the knowledge of the ecology of galling by showing how local factors influence the richness of this insect guild.
Differing influences of resource availability on the demographics and habitat selection of wildebeest compared with impala
Authors: O'Kane Christopher A.J. , Page Bruce R. , Macdonald David W. 
Published: April 2014

Abstract:Although what drives the abundance and habitat selection of ungulates is a long-standing question, coherent datasets investigating the influences of rainfall, competition and fire on ungulates are unusual. Over 4 y we carried out extensive monthly road transects in Ithala Game Reserve, South Africa, to determine the demographics and habitat occupancy of the region's prevalent grazer (wildebeest) and mixed-feeder (impala). Habitat occupancy was determined using a GIS-based approach. We obtained 8742 sighting records, encompassing 8400 wildebeest and 10071 impala. Annual rainfall did not significantly correlate with population sizes of either species. Fecundity of wildebeest, but not of impala, showed a significant positive relationship with rainfall specifically over the perinatal period (November–December), whilst no significant relationships were found for either species between fecundity and rainfall over the previous year, 2 y, rut (February–April) or height of the dry season (June–August). Impala unexpectedly favoured browse habitats to grassland year round, probably consequent on competition for grass with wildebeest. Dry-season grass flushes attracted both wildebeest and impala. The study emphasized how rainfall, competition and fire regimes may affect differently grazers compared with mixed-feeders.
Radiation therapist peer review: raising the bar on quality and safety in radiation oncology
Authors: Chamunyonga Crispen , Bridge Pete 
Published: April 2014

AbstractPurposeAn emerging developmental tool to help radiation therapists achieve better outcomes is ‘peer review’. This review of the current literature summarises the challenges and benefits of peer review in both individual and departmental practice.DiscussionThere is compelling evidence supporting peer review implementation at both individual and department level in many professions. Implementing peer review requires that radiation therapists and other radiation oncology professionals embrace a culture that supports safety. Peer review can identify trends and barriers associated with quality radiotherapy and share best practice or recommend changes accordingly. Support for peer review must come from pre-registration educational systems as well as clinical managers. Continuing professional development in the workplace is nurtured by peer review of radiotherapy practice and an aptitude for this should be viewed as important to the profession as technical and clinical skills.ConclusionIt is clear that peer review has the potential to facilitate reflective practice, improve staff motivation and help foster a culture of quality and safety in radiation oncology. To drive the issues of quality and safety a step further radiation therapists need to accept the challenge of adopting peer review methods in day-to-day practice.
Marine ice regulates the future stability of a large Antarctic ice shelf
Authors: Kulessa Bernd , Jansen Daniela , Luckman Adrian J. , King Edward C. , Sammonds Peter R. 
Published: April 2014

AbstractThe collapses of the Larsen A and B ice shelves on the Antarctic Peninsula in 1995 and 2002 confirm the impact of southward-propagating climate warming in this region. Recent mass and dynamic changes of Larsen B’s southern neighbour Larsen C, the fourth largest ice shelf in Antarctica, may herald a similar instability. Here, using a validated ice-shelf model run in diagnostic mode, constrained by satellite and in situ geophysical data, we identify the nature of this potential instability. We demonstrate that the present-day spatial distribution and orientation of the principal stresses within Larsen C ice shelf are akin to those within pre-collapse Larsen B. When Larsen B’s stabilizing frontal portion was lost in 1995, the unstable remaining shelf accelerated, crumbled and ultimately collapsed. We hypothesize that Larsen C ice shelf may suffer a similar fate if it were not stabilized by warm and mechanically soft marine ice, entrained within narrow suture zones.
Anti-inflammatory effects of green soybean extract irradiated with visible light
Authors: Tanaka Keiko , Ohgo Yasushi , Katayanagi Yuki , Yasui Kensuke , Hiramoto Shigeru , Ikemoto Hiroyuki , Nakata Yumi , Miyoshi Noriyuki , Isemura Mamoru , Ohashi Norio , Imai Shinjiro 
Published: April 2014

AbstractWe conducted a preliminary investigation of the effects of visible light irradiation on plant extracts and we observed a strong suppressive effect on interleukin (IL) 2 expression with the inhibition of c-Jun amino-terminal kinase (JNK) phosphorylation in Jurkat cells by visible light irradiation to ethanol extract from green soybeans (LIEGS). This effect was produced only by extracts from green soybeans (Glycine max) and not other-color soybeans. LIEGS suppressed the lipopolysaccharide-induced IL-6, IL-12 and TNF-α expression levels in human monocyte THP-1 cells in a concentration-dependent manner. LIEGS was applied for 8 weeks to NC/Nga mice. LIEGS suppressed the development of atopic dermatitis (AD)-like skin lesions and reduced the dermatitis scores of the mice. The light irradiation changed the various types of small-molecule compounds in extracts. Visible light irradiation to daidzein with chlorophyll b induced a novel oxidative product of daidzein. This product suppressed IL-2 expression in Jurkat cells.
Mutated tumor alleles are expressed according to their DNA frequency
Authors: Castle John C. , Loewer Martin , Boegel Sebastian , Tadmor Arbel D. , Boisguerin Valesca , de Graaf Jos , Paret Claudia , Diken Mustafa , Kreiter Sebastian , Türeci Özlem , Sahin Ugur 
Published: April 2014

AbstractThe transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type and thus transcribed in proportion to their DNA allele frequency.
Multiple lines of evidence for the origin of domesticated chili pepper,Capsicum annuum, in Mexico
Authors: Kraft Kraig H. , Brown Cecil H. , Nabhan Gary P. , Luedeling Eike , Luna Ruiz José de Jesús , Coppens d’Eeckenbrugge Geo , Hijmans Robert J. , Gepts Paul 
Published: April 2014

SignificanceThe novelty of the information of this manuscript resides in the addition of species distribution modeling and paleobiolinguistics data, combined with genetic and existing archaeobotanical data, to trace back the geographic origin of a crop, namely domesticated pepper,Capsicum annuum. Furthermore, the utilization of a geographic framework of reference for the four types of data has allowed us to combine these independent data types into a single hypothesis about the origin of this crop. Our results suggest that food crops in Mexico had a multiregional origin with chili pepper originating in central-east Mexico, maize in the Balsas River Basin and common bean in the Lerma–Santiago River Basin, resembling similar finds for the Fertile Crescent and China.
Millisecond dynamics of RNA polymerase II translocation at atomic resolution
Authors: Silva Daniel-Adriano , Weiss Dahlia R. , Pardo Avila Fátima , Da Lin-Tai , Levitt Michael , Wang Dong , Huang Xuhui 
Published: April 2014

Significance
In this study, by using molecular dynamics simulations and Markov state models, we reveal that RNA polymerase II translocation is driven purely by thermal energy and does not require the input of any additional chemical energy. Our simulations show an important role for the bridge helix: Large thermal oscillations of this structural element facilitate the translocation by specific interactions that lower the free-energy barriers between four metastable states. Among these states, we identify two previously unidentified intermediates that have not been previously captured by crystallography. The dynamic view of translocation presented in our study represents a substantial advance over the current understanding based on the static snapshots provided by X-ray structures of transcribing complexes.
Mechanisms of noise robust representation of speech in primary auditory cortex
Authors: Mesgarani Nima , David Stephen V. , Fritz Jonathan B. , Shamma Shihab A. 
Published: April 2014

Significance
We show that the auditory system maintains a robust representation of speech in noisy and reverberant conditions by preserving the same statistical distribution of responses in all conditions. Reconstructed stimulus from population of cortical neurons resembles more the original clean than the distorted signal. We show that a linear spectrotemporal receptive field model of neurons with a static nonlinearity fails to account for the neural noise reduction. Although replacing static nonlinearity with a dynamic model of synaptic depression can account for the reduction of additive noise, only the combined model with feedback gain normalization is able to predict the effects across both additive and reverberant conditions.
Accumulation and enhanced cycling of polyphosphate by Sargasso Sea plankton in response to low phosphorus
Authors: Martin Patrick , Dyhrman Sonya T. , Lomas Michael W. , Poulton Nicole J. , Van Mooy Benjamin A. S. 
Published: April 2014

Significance
Phosphorus is scarce in many subtropical ocean regions, and phytoplankton in these regions adjust their biochemical composition such that they require less of it. We show here that phytoplankton in the ultra–low-phosphorus Sargasso Sea are enriched in polyphosphate (polyP), a phosphorus molecule hitherto thought of primarily as a luxury storage product in marine phytoplankton. We further show that polyP appears to be more readily recycled in the surface ocean than other phosphorus-containing biochemicals. Thus, the high relative levels, and fast cycling, of polyP in low-phosphorus environments may form a feedback loop that contributes bioavailable phosphorus for primary production, potentially reducing the likelihood of growth limitation by phosphorus.
Neural sensitivity to eudaimonic and hedonic rewards differentially predict adolescent depressive symptoms over time
Authors: Telzer Eva H. , Fuligni Andrew J. , Lieberman Matthew D. , Galván Adriana 
Published: April 2014

Significance
Although optimal well-being may be achieved through eudaimonic activities (meaning and purpose), individuals tend to orient toward hedonic activities (pleasure seeking), potentially placing them at risk for ill-being. We find that reward-related neural activation during eudaimonic decisions predicts longitudinal declines in depressive symptoms, whereas reward-related neural activation to hedonic decisions predicts longitudinal increases in depressive symptoms. We identified a potential neural mechanism by which adolescents may develop or be protected from developing ill-being. These findings underscore how the motivational context underlying neural sensitivity to rewards can differentially predict changes in well-being over time. To our knowledge, this is the first study to show that reward-related neural activation within an individual can be both a source of risk and protection.
A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1
Authors: Barraud Pierre , Banerjee Silpi , Mohamed Weaam I. , Jantsch Michael F. , Allain Frédéric H.-T. 
Published: April 2014

Significance
The double-stranded RNA-binding domain (dsRBD) is an abundant, conserved RNA-binding motif. Besides RNA binding, dsRBDs can serve as protein-interaction domains. In the human RNA-editing enzyme adenosine deaminase acting on RNA (ADAR1), one of its three dsRBDs mediates nuclear import by interacting with the import receptor transportin 1 (Trn1). RNA binding interferes with Trn1 binding, thereby preventing nuclear import. Using NMR spectroscopy and cell biological analysis, we show that the regions flanking this dsRBD form a bimodular Trn1-dependent nuclear localization signal. The dsRBD itself is not involved in Trn1 interaction but properly positions the Trn1 interacting regions. Using molecular modeling, we provide a structural explanation on how dsRNA binding prevents the dsRBD from accessing the interacting cavity of Trn1, thereby preventing nuclear import of RNA-bound ADAR1.
Hypermutable DNA chronicles the evolution of human colon cancer
Authors: Naxerova Kamila , Brachtel Elena , Salk Jesse J. , Seese Aaron M. , Power Karen , Abbasi Bardia , Snuderl Matija , Chiang Sarah , Kasif Simon , Jain Rakesh K. 
Published: April 2014

Significance
Genetic heterogeneity in systemic cancer is of great clinical interest because it impacts therapeutic response and reflects how tumor cells grow and spread. We present a methodology that enables efficient evaluation of intratumor heterogeneity in patients through analysis of neutral somatic variation hotspots. Using only 20 genomic markers, we demonstrate a unique pattern of clonal diversity in each patient. Some tumors are significantly more diversified than others. Our data suggest that distinct clones can give rise to lymphatic and distant metastases. Our methodology is applicable to other human cancer types and facilitates high-throughput investigation of tumor evolution.
Symbol addition by monkeys provides evidence for normalized quantity coding
Authors: Livingstone Margaret S. , Pettine Warren W. , Srihasam Krishna , Moore Brandon , Morocz Istvan A. , Lee Daeyeol 
Published: April 2014

Significance
Symbol-literate monkeys can be trained to combine, or add, pairs of large numbers. They transfer to a novel symbol set, ruling out memorization of each symbol pair. Their addition behavior indicates an underlying relative scaling of magnitude.
Patterns of coding variation in the complete exomes of three Neandertals
Authors: Castellano Sergi , Parra Genís , Sánchez-Quinto Federico A. , Racimo Fernando , Kuhlwilm Martin , Kircher Martin , Sawyer Susanna , Fu Qiaomei , Heinze Anja , Nickel Birgit , Dabney Jesse , Siebauer Michael , White Louise , Burbano Hernán A. , Renaud Gabriel , Stenzel Udo , Lalueza-Fox Carles , de la Rasilla Marco , Rosas Antonio , Rudan Pavao , Brajković Dejana , Kucan Željko , Gušic Ivan , Shunkov Michael V. , Derevianko Anatoli P. , Viola Bence , Meyer Matthias , Kelso Janet , Andrés Aida M. , Pääbo Svante 
Published: April 2014

Significance
We use a hybridization approach to enrich the DNA from the protein-coding fraction of the genomes of two Neandertal individuals from Spain and Croatia. By analyzing these two exomes together with the genome sequence of a Neandertal from Siberia we show that the genetic diversity of Neandertals was lower than that of present-day humans and that the pattern of coding variation suggests that Neandertal populations were small and isolated from one another. We also show that genes involved in skeletal morphology have changed more than expected on the Neandertal evolutionary lineage whereas genes involved in pigmentation and behavior have changed more on the modern human lineage.
The ‘Yidishe Paganini’: Sholem Aleichem's Stempenyu, the Music of Yiddish Theatre and the Character of the Shtetl Fiddler
Authors: Walden Joshua S. 
Published: April 2014

ABSTRACTThis article explores the music of Yiddish theatre in early twentieth-century New York by considering multiple adaptations of Russian Jewish author Sholem Aleichem's 1888 novel Stempenyu, about a klezmer violinist, which was transformed into two theatrical productions in 1907 and 1929, and finally inspired a three-movement recital work for accompanied violin by Joseph Achron. The multiple versions of Stempenyu present the eponymous musician as an allegory for the ambivalent role of the shtetl – the predominantly Jewish small town of Eastern Europe – in defining diasporic Jewish life in Europe and America, and as a medium for the sonic representation of shtetl culture as it was reformulated in the memories of the first generations of Jewish immigrants. The variations in the evocations of Eastern European klezmer in these renderings of Stempenyu indicate complex changes in the ways Jewish immigrants and their children conceived of their connection to Eastern Europe over four decades. The paper concludes by viewing changes in the symbolic character type of the shtetl fiddler in its most famous and recent manifestation, in the stage and screen musical Fiddler on the Roof.
Pentraxin‐3 and the Right Ventricle: The Multi‐Ethnic Study of Atherosclerosis–Right Ventricle Study
Authors: Leary Peter J. , Jenny Nancy S. , Barr R. Graham , Bluemke David A. , Harhay Michael O. , Heckbert Susan R. , Kronmal Richard A. , Lima João A. , Mikacenic Carmen , Tracy Russell P. , Kawut Steven M. 
Published: April 2014

Pentraxin‐3 (PTX3) is a protein mediator of innate immunity that is elevated in the setting of left heart disease and pulmonary arterial hypertension. The relationship between PTX3 and right ventricular (RV) structure and function is not known. We included men and women with magnetic resonance imaging assessment of RV structure and function and measurement of PTX3 from the Multi‐Ethnic Study of Atherosclerosis, a study of individuals free of clinical cardiovascular disease. Multivariable linear regression estimated associations between PTX3 protein levels and RV measures after adjusting for demographic characteristics, anthropometrics, smoking status, diabetes mellitus, hypertension, and corresponding left ventricular (LV) parameters. Instrumental variable analysis exploiting Mendelian randomization was attempted using two‐stage least squares regression. The study sample included 1,779 participants with available PTX3 levels, RV measures, and all covariables. Mean PTX3 level was 2.1 ng/mL. Higher PTX3 was independently associated with greater RV mass and larger RV end‐diastolic volume with and without adjustment for the corresponding LV parameters or C‐reactive protein (all P <. 05). There was no association between PTX3 and RV ejection fraction or stroke volume. Single‐nucleotide polymorphisms were not associated with PTX3 protein levels or RV measures after accounting for race. Instrumental variable analysis could not be reliably performed. Higher PTX3 protein levels were associated with greater RV mass and larger RV end‐diastolic volume. These associations were independent of common cardiovascular risk factors and LV morphologic changes. Inflammation is associated with differences in the pulmonary circulation‐RV axis in adults without clinical cardiovascular disease.
Improving B-cell epitope prediction and its application to global antibody-antigen docking
Authors: Krawczyk Konrad , Liu Xiaofeng , Baker Terry , Shi Jiye , Deane Charlotte M. 
Published: April 2014

Motivation: Antibodies are currently the most important class of biopharmaceuticals. Development of such antibody-based drugs depends on costly and time-consuming screening campaigns. Computational techniques such as antibody–antigen docking hold the potential to facilitate the screening process by rapidly providing a list of initial poses that approximate the native complex.
Results: We have developed a new method to identify the epitope region on the antigen, given the structures of the antibody and the antigen—EpiPred. The method combines conformational matching of the antibody–antigen structures and a specific antibody–antigen score. We have tested the method on both a large non-redundant set of antibody–antigen complexes and on homology models of the antibodies and/or the unbound antigen structure. On a non-redundant test set, our epitope prediction method achieves 44% recall at 14% precision against 23% recall at 14% precision for a background random distribution. We use our epitope predictions to rescore the global docking results of two rigid-body docking algorithms: ZDOCK and ClusPro. In both cases including our epitope, prediction increases the number of near-native poses found among the top decoys.
Availability and implementation: Our software is available from http://www.stats.ox.ac.uk/research/proteins/resources.
Contact: deane@stats.ox.ac.uk
Supplementary information: Supplementary Data are available at Bioinformatics online.