bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capture of algae promotes growth and propagation in aquaticUtricularia
Authors: Koller-Peroutka Marianne , Lendl Thomas , Watzka Margarete , Adlassnig Wolfram 
Published: December 2014

AbstractBackground and Aims Some carnivorous plants trap not only small animals but also algae and pollen grains. However, it remains unclear if these trapped particles are useless bycatch or whether they provide nutrients for the plant. The present study examines this question in Utricularia, which forms the largest and most widely spread genus of carnivorous plants, and which captures prey by means of sophisticated suction traps.Methods Utricularia plants of three different species (U. australis, U. vulgaris and U. minor) were collected in eight different water bodies including peat bogs, lakes and artificial ponds in three regions of Austria. The prey spectrum of each population was analysed qualitatively and quantitatively, and correlated with data on growth and propagation, C/N ratio and δ15N.Key Results More than 50 % of the prey of the Utricularia populations investigated consisted of algae and pollen, and U. vulgaris in particular was found to capture large amounts of gymnosperm pollen. The capture of algae and pollen grains was strongly correlated with most growth parameters, including weight, length, budding and elongation of internodes. The C/N ratio, however, was less well correlated. Other prey, such as moss leaflets, fungal hyphae and mineral particles, were negatively correlated with most growth parameters. δ15N was positively correlated with prey capture, but in situations where algae were the main prey objects it was found that the standard formula for calculation of prey-derived N was no longer applicable.Conclusions The mass capture of immotile particles confirms the ecological importance of autonomous firing of the traps. Although the C/N ratio was little influenced by algae, they clearly provide other nutrients, possibly including phosphorus and trace elements. By contrast, mosses, fungi and mineral particles appear to be useless bycatch. Correlations with chemical parameters indicate that Utricularia benefits from nutrient-rich waters by uptake of inorganic nutrients from the water, by the production of more traps per unit of shoot length, and by the capture of more prey particles per trap, as nutrient-rich waters harbour more prey organisms.
MicroRNA modules prefer to bind weak and unconventional target sites
Authors: Ding Jun , Li Xiaoman , Hu Haiyan 
Published: December 2014

Abstract
Motivation: MicroRNAs (miRNAs) play critical roles in gene regulation. Although it is well known that multiple miRNAs may work as miRNA modules to synergistically regulate common target mRNAs, the understanding of miRNA modules is still in its infancy.
Results: We employed the recently generated high throughput experimental data to study miRNA modules. We predicted 181 miRNA modules and 306 potential miRNA modules. We observed that the target sites of these predicted modules were in general weaker compared with those not bound by miRNA modules. We also discovered that miRNAs in predicted modules preferred to bind unconventional target sites rather than canonical sites. Surprisingly, contrary to a previous study, we found that most adjacent miRNA target sites from the same miRNA modules were not within the range of 10–130 nucleotides. Interestingly, the distance of target sites bound by miRNAs in the same modules was shorter when miRNA modules bound unconventional instead of canonical sites. Our study shed new light on miRNA binding and miRNA target sites, which will likely advance our understanding of miRNA regulation.
Availability and implementation: The software miRModule can be freely downloaded at http://hulab.ucf.edu/research/projects/miRNA/miRModule.
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu.
Empowering biologists with multi-omics data: colorectal cancer as a paradigm
Authors: Zhu Jing , Shi Zhiao , Wang Jing , Zhang Bing 
Published: December 2014

Abstract
Motivation: Recent completion of the global proteomic characterization of The Cancer Genome Atlas (TCGA) colorectal cancer (CRC) cohort resulted in the first tumor dataset with complete molecular measurements at DNA, RNA and protein levels. Using CRC as a paradigm, we describe the application of the NetGestalt framework to provide easy access and interpretation of multi-omics data.
Results: The NetGestalt CRC portal includes genomic, epigenomic, transcriptomic, proteomic and clinical data for the TCGA CRC cohort, data from other CRC tumor cohorts and cell lines, and existing knowledge on pathways and networks, giving a total of more than 17 million data points. The portal provides features for data query, upload, visualization and integration. These features can be flexibly combined to serve various needs of the users, maximizing the synergy among omics data, human visualization and quantitative analysis. Using three case studies, we demonstrate that the portal not only provides user-friendly data query and visualization but also enables efficient data integration within a single omics data type, across multiple omics data types, and over biological networks.
Availability and implementation: The NetGestalt CRC portal can be freely accessed at http://www.netgestalt.org.
Contact: bing.zhang@vanderbilt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Genomic insights into the rapid emergence and evolution of MDR inStaphylococcus pseudintermedius
Authors: McCarthy Alex J. , Harrison Ewan M. , Stanczak-Mrozek Kinga , Leggett Bernadette , Waller Andrew , Holmes Mark A. , Lloyd David H. , Lindsay Jodi A. , Loeffler Anette 
Published: December 2014

AbstractObjectivesMDR methicillin-resistant Staphylococcus pseudintermedius (MRSP) strains have emerged rapidly as major canine pathogens and present serious treatment issues and concerns to public health due to their, albeit low, zoonotic potential. A further understanding of the genetics of resistance arising from a broadly susceptible background of S. pseudintermedius is needed.MethodsWe sequenced the genomes of 12 S. pseudintermedius isolates of varied STs and resistance phenotypes.ResultsNine distinct clonal lineages had acquired either staphylococcal cassette chromosome (SCC) mec elements and/or Tn5405-like elements carrying up to five resistance genes [aphA3, sat, aadE, erm(B), dfrG] to generate MRSP, MDR methicillin-susceptible S. pseudintermedius and MDR MRSP populations. The most successful and clinically problematic MDR MRSP clones, ST68 SCCmecV(T) and ST71 SCCmecII-III, have further accumulated mutations in gyrA and grlA conferring resistance to fluoroquinolones. The carriage of additional mobile genetic elements (MGEs) was highly variable, suggesting that horizontal gene transfer is frequent in S. pseudintermedius populations.ConclusionsImportantly, the data suggest that MDR MRSP evolved rapidly by the acquisition of a very limited number of MGEs and mutations, and that the use of many classes of antimicrobials may co-select for the spread and emergence of MDR and XDR strains. Antimicrobial stewardship will need to be comprehensive, encompassing human medicine and veterinary disciplines to successfully preserve antimicrobial efficacy.
VLBI astrometry of AGB variables with VERA: A Mira-type variable T Lepus
Authors: Nakagawa Akiharu , Omodaka Toshihiro , Handa Toshihiro , Honma Mareki , Kawaguchi Noriyuki , Kobayashi Hideyuki , Oyama Tomoaki , Sato Katsuhisa , Shibata Katsunori M. , Shizugami Makoto , Tamura Yoshiaki , Ueno Yuji 
Published: December 2014

Abstract
We conducted phase referencing VLBI observations of the Mira variable T Lepus (T Lep) using VERA, from 2003 to 2006. The distance to the source was determined from its annual parallax which was measured to be 3.06 ± 0.04 mas, corresponding to a distance of 327 ± 4 pc. Our observations revealed the distribution and internal kinematics of H2O masers in T Lep, and we derived source systemic motions of 14.60 ± 0.50 mas yr−1 and −35.43 ± 0.79 mas yr−1 in right ascension and declination, respectively. We also determined an LSR velocity of $V_\mathrm{LSR}^{\ast } = -$27.63 km s−1. Comparison of our result with an image recently obtained from the VLTI infrared interferometer reveals a linear scale picture of the circumstellar structure of T Lep. Analysis of the source systemic motion in the Galactocentric coordinate frame indicates a large peculiar motion, which is consistent with the general characteristics of AGB stars. This source makes a contribution to the calibration of the period–luminosity relation of Galactic Mira variables. From the compilation of data for nearby Mira variables found in the literature, whose distances were derived from astrometric VLBI observations, we have calibrated the Galactic Mira period–luminosity relation to a high degree of accuracy.
OT J075418.7+381225 and OT J230425.8+062546: Promising candidates for the period bouncer
Authors: Nakata Chikako , Kato Taichi , Nogami Daisaku , Pavlenko Elena P. , Ohshima Tomohito , de Miguel Enrique , Stein William , Siokawa Kazuhiko , Morelle Etienne , Itoh Hiroshi , Dubovsky Pavol A. , Kudzej Igor , Maehara Hiroyuki , Henden Arne , Goff William N. , Dvorak Shawn , Antonyuk Oksana I. , Muyllaert Eddy 
Published: December 2014

Abstract
We report on photometric observations of two dwarf novae, OT J075418.7+381225 and OT J230425.8+062546, which showed superoutbursts in 2013 (OT J075418) and in 2011 (OT J230425). Their mean periods of the superhump were 0.0722403(26) d (OT J075418) and 0.067317(35) d (OT J230425). These objects showed a very long growth stage of the superhump (stage A) and a large period decrease in the stage A–B transition. The long stage A suggests slow evolution of the superhump due to the very small mass ratio of these objects. The declining rates during the plateau phase in the superoutburst of these objects were lower than those of SU UMa-type dwarf novae (DNe) with a similar superhump period. These properties were similar to those of SSS J122221.7−311523, the most likely candidate for the period bouncer. Therefore, these two DNe are regarded as likely candidates for the period bouncer. We estimated the number density of period bouncers roughly from our observations for the last five years. There is a possibility that these WZ Sge-type DNe with unusual outburst properties might account for the missing population of the period bouncer suggested by the evolutionary scenario.
Treatments of Negative Symptoms in Schizophrenia: Meta-Analysis of 168 Randomized Placebo-Controlled Trials
Authors: Fusar-Poli Paolo , Papanastasiou Evangelos , Stahl Daniel , Rocchetti Matteo , Carpenter William , Shergill Sukhwinder , McGuire Philip 
Published: December 2014

Abstract

Objectives
Existing treatments for schizophrenia can improve positive symptoms, but it is unclear if they have any impact on negative symptoms. This meta-analysis was conducted to assess the efficacy of available treatments for negative symptoms in schizophrenia.

Methods
All randomized-controlled trials of interventions for negative symptoms in schizophrenia until December 2013 were retrieved; 168 unique and independent placebo-controlled trials were used. Negative symptom scores at baseline and follow-up, duration of illness, doses of medication, type of interventions, and sample demographics were extracted. Heterogeneity was addressed with the I2 and Q statistic. Standardized mean difference in values of the Negative Symptom Rating Scale used in each study was calculated as the main outcome measure.

Results
6503 patients in the treatment arm and 5815 patients in the placebo arm were included. No evidence of publication biases found. Most treatments reduced negative symptoms at follow-up relative to placebo: second-generation antipsychotics: −0.579 (−0.755 to −0.404); antidepressants: −0.349 (−0.551 to −0.146); combinations of pharmacological agents: −0.518 (−0.757 to −0.279); glutamatergic medications: −0.289 (−0.478 to −0.1); psychological interventions: −0.396 (−0.563 to −0.229). No significant effect was found for first-generation antipsychotics: −0.531 (−1.104 to 0.041) and brain stimulation: −0.228 (−0.775 to 0.319). Effects of most treatments were not clinically meaningful as measured on Clinical Global Impression Severity Scale.

Conclusions and Relevance
Although some statistically significant effects on negative symptoms were evident, none reached the threshold for clinically significant improvement.
Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multi-drug resistance
Authors: Moreno-Gamez Stefany , Hill Alison L. , Rosenbloom Daniel I. S. , Petrov Dmitri A. , Nowak Martin A. , Pennings Pleuni 
Published: December 2014

AbstractInfections with rapidly evolving pathogens are often treated using combinations of drugs with different mechanisms of action. One of the major goals of combination therapy is to reduce the risk of drug resistance emerging during a patient’s treatment. While this strategy generally has significant benefits over monotherapy, it may also select for multi-drug resistant strains, which present an important clinical and public health problem. For many antimicrobial treatment regimes, individual drugs have imperfect penetration throughout the body, so there may be regions where only one drug reaches an effective concentration. Here we propose that mismatched drug coverage can greatly speed up the evolution of multi-drug resistance by allowing mutations to accumulate in a stepwise fashion. We develop a mathematical model of within-host pathogen evolution under spatially heterogeneous drug coverage and demonstrate that even very small single-drug compartments lead to dramatically higher resistance risk. We find that it is often better to use drug combinations with matched penetration profiles, although there may be a trade-off between preventing eventual treatment failure due to resistance in this way, and temporarily reducing pathogen levels systemically. Our results show that drugs with the most extensive distribution are likely to be the most vulnerable to resistance. We conclude that optimal combination treatments should be designed to prevent thisspatial effective monotherapy. These results are widely applicable to diverse microbial infections including viruses, bacteria and parasites.
E. coliOxyS non-coding RNA does not trigger RNAi inC. elegans
Authors: Akay Alper , Sarkies Peter , Miska Eric A. 
Published: December 2014

AbstractThe discovery of RNA interference (RNAi) inC. eleganshas had a major impact on scientific research, led to the rapid development of RNAi tools and has inspired RNA-based therapeutics. Astonishingly, nematodes, planaria and many insects take up double-stranded RNA (dsRNA) from their environment to elicit RNAi; the biological function of this mechanism is unclear. Recently, theE. coliOxyS non-coding RNA was shown to regulate gene expression inC. eleganswhenE. coliis offered as food. This was surprising given thatC. elegansis unlikely to encounterE. coliin nature. To directly test the hypothesis that theE. coliOxyS non-coding RNA triggers theC. elegansRNAi pathway, we sequenced small RNAs fromC. elegansafter feeding with bacteria. We clearly demonstrate that the OxyS non-coding RNA does not trigger an RNAi response inC. elegans. We conclude that the biology of environmental RNAi remains to be discovered.
Quality attracts parasites: host condition‐dependent chemo‐orientation of trematode larvae
Authors: Seppälä Otto , Leicht Katja 
Published: December 2014

Summary

Environmental factors impairing physiological condition of organisms are assumed to predispose them to parasite infections. This is because host immune function is typically condition‐dependent. However, poor physiological condition has been reported to reduce host susceptibility to parasites in various systems.

We examined whether such an effect can be due to altered exposure of hosts to active parasite transmission stages by investigating chemo‐orientation of free‐swimming cercariae larvae of a parasite Echinoparyphium aconiatum towards its snail host Lymnaea stagnalis.

We used both long‐term and short‐term feeding treatments to manipulate the body condition and physiological traits related to food processing in experimental (i.e. target) snails and measured the preference of cercariae towards snail‐conditioned water (SCW) over clean water.

We found that chemo‐orientation of cercariae depended on the nutritional status of target snails. High physiological condition (long‐term feeding) attracted parasites, but cercariae did not show preference towards SCW from individuals in poor physiological condition (long‐term starvation). Food processing (short‐term feeding treatments) did not affect chemo‐orientation.

Our results suggest that host condition‐dependent chemo‐orientation of parasite larvae is a likely mechanism explaining the reduced susceptibility of snails to infection due to food limitation in our study system. In general, the use of condition‐dependent host cues can be highly beneficial for parasites as it increases their transmission to high‐quality hosts. Furthermore, evolving counter adaptations to such a transmission strategy can be very difficult for hosts.
Edaphic rather than climatic controls over 13C enrichment between soil and vegetation in alpine grasslands on the Tibetan Plateau
Authors: Yang Yuanhe , Ji Chengjun , Chen Leiyi , Ding Jinzhi , Cheng Xiaoli , Robinson David 
Published: December 2014

Summary

Soil organic carbon (SOC) dynamics is crucial for evaluating ecosystem carbon balance and its feedback to climate warming. However, it is difficult to detect statistically significant changes in SOC stock over short‐time period due to its large pool size, slow turnover time and huge spatial heterogeneity. Stable isotopic measurements, such as Δ δ13C (i.e. the difference of natural abundance of 13C and 12C (δ13C) between surface soils and source plants) and its variations along environmental gradients provide an alternative approach inferring soil carbon dynamics over broad geographical scale. However, current isotopic evidence is primarily derived from temperate and tropical regions, with very limited measurements available in alpine regions.

Here, we examined spatial variations of Δ δ13C in alpine grasslands on the Tibetan Plateau, using large‐scale isotopic measurements obtained from consecutive field samplings. We aimed to test whether previously observed isotopic patterns in temperate and tropical regions still hold true in alpine regions and whether climatic or edaphic variables regulated large‐scale patterns of 13C enrichment between soil and vegetation in alpine ecosystems.

Our results showed that topsoil stable carbon isotope composition in alpine steppe and meadow ranged from −26·1‰ to −19·7‰ and from −25·7‰ to −22·2‰, with an average of −23·7‰ and −24·1‰, respectively. As previously observed in temperate forests, soil δ13C exhibited linear increases with plant δ13C in alpine grasslands.

In contrast to earlier findings, our results revealed that edaphic rather than climatic factors regulated spatial variability of the Δ δ13C in high‐altitude regions. Moreover, edaphic controls over Δ δ13C exhibited meaningful differences between alpine steppe and meadow. The Δ δ13C exhibited an initial increase and a subsequent decrease with soil carbon content in alpine steppe, but was negatively associated with silt content and carbon: nitrogen ratio in alpine meadow.

Our results confirmed the association between the δ13C of surface soils and vegetation across contrasting ecosystems, but revealed that edaphic rather than climatic variables were better explanations of 13C enrichment between soil and vegetation at high altitudes. Changes in soil texture and substrate quality could therefore induce soil carbon dynamics in alpine ecosystems.
Potential challenges facing distributed leadership in health care: evidence from the UK National Health Service
Authors: Martin Graeme , Beech Nic , MacIntosh Robert , Bushfield Stacey 
Published: December 2014

AbstractThe discourse of leaderism in health care has been a subject of much academic and practical debate. Recently, distributed leadership (DL) has been adopted as a key strand of policy in the UK National Health Service (NHS). However, there is some confusion over the meaning of DL and uncertainty over its application to clinical and non‐clinical staff. This article examines the potential for DL in the NHS by drawing on qualitative data from three co‐located health‐care organisations that embraced DL as part of their organisational strategy. Recent theorising positions DL as a hybrid model combining focused and dispersed leadership; however, our data raise important challenges for policymakers and senior managers who are implementing such a leadership policy. We show that there are three distinct forms of disconnect and that these pose a significant problem for DL. However, we argue that instead of these disconnects posing a significant problem for the discourse of leaderism, they enable a fantasy of leadership that draws on and supports the discourse.
Symbolic boundaries, subcultural capital and prescription drug misuse across youth cultures
Authors: Kelly Brian C. , Trimarco James , LeClair Amy , Pawson Mark , Parsons Jeffrey T. , Golub Sarit A. 
Published: December 2014

AbstractPrescription drug misuse among young adults has surged over the past decade. Yet the contexts surrounding this misuse remain unclear, particularly the subcultural contexts. Many young urban adults participate in youth cultures. This article describes the subcultural contexts of prescription drug misuse in youth subcultures. Drawing on ethnographic data collected over 12 months from different youth cultural scenes, the authors describe the subcultural bases of prescription drug misuse. The symbolic boundaries and subcultural capital inherent in these scenes shape the ways youth think about drugs and behave accordingly. While young adults are often lumped together by theorists, ethnographic data show considerable variation across these subcultures with regard to what may enable or inhibit prescription drug misuse. The broader subcultural ethos in each scene, as well as attitudes towards other types of drugs, frame the ways that prescription drugs are perceived and used in each of these settings. The findings highlight the role of symbolic boundaries and subcultural capital in shaping routine practices of drug use among young adults. These data show that education campaigns about prescription drug misuse should take into account the variability in youth cultural scenes to maximise the efficacy of these messages aimed at young adults.