bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effectiveness of plant conservation measures: the Dianthus morisianus reintroduction
Authors: Cogoni Donatella , Fenu Giuseppe , Concas Erica , Bacchetta Gianluigi 
Published: April 2013

AbstractThe plant Dianthus morisianus Vals. (Caryophyllaceae) is endemic to Sardinia. The Autonomous Region of Sardinia funded a conservation project for this species because it is one of the most threatened plant on the island. The project comprises in situ and ex situ research and experimental projects, such as the construction of protective fences and reintroduction. Juvenile plants, germinated from 200 seeds collected over 2 years and propagated without horticultural treatment, were reintroduced in November 2010. The surviving 113 plants were reintroduced 150 m from the natural population and were monitored monthly. Two years later the survival rate was > 95%, and the fruit yield per plant was higher than that recorded in the natural population. This research emphasizes the importance of identifying an appropriate microhabitat for plant reintroduction. The use of juvenile plants aided the success of the reintroduction and reduced the mortality rate; the knowledge of the species biology, in particular the critical stage of their life cycle, is a crucial factor in plant reintroduction.
Extant population of the Critically Endangered central rock-rat Zyzomys pedunculatus located in the Northern territory, Australia
Authors: McDonald Peter J. , Pavey Chris R. , Knights Kelly , Grantham Deon , Ward Simon J. , Nano Catherine E. M. 
Published: April 2013

AbstractThe central rock-rat Zyzomys pedunculatus is categorized as Critically Endangered on the IUCN Red List. Over the last 50 years the species had only been recorded from 14 sites within a 600 km2 area of the West MacDonnell National Park and immediate surroundings in the Northern Territory, Australia. The central rock-rat disappeared from monitoring sites in 2002, coincident with the onset of drought conditions and extensive wildfires. With concern growing for the survival of the species, we sought to locate an extant population. During 2009–2012 we surveyed sites throughout the western sector of the West MacDonnell National Park, including sites where rock-rats had previously been recorded. From a total of 55 sites and 5,000 trap nights we located eight central rock-rats from only five sites (overall detection rate = 0.16 rock-rats per 100 trap nights). All sites were on two mountain-top locations, both of which are over 1,250 m altitude. Evidence of reproductive activity was observed at both locations but the subpopulations were relatively localized and no individuals were captured at any of the sites from which the species was known previous to these surveys. Although the rugged mountains may provide the central rock-rat with some refuge from predation and wildfires, more research is needed to understand better the factors suppressing and constraining the species at the population and landscape scales. Immediate management priorities are prescribed burning to limit the extent and severity of wildfires and trialling a baiting programme with 1080 to target feral cats in the mountains.
X-ray powder diffraction data for inclusion complex of β-cyclodextrin with fraxinellone
Authors: Wang Qing , Zhang Li Li , Wu Xiao Qing , Pan Qing Qing , Su Yan Hong , Li Hui 
Published: April 2013

X-ray powder diffraction data, unit-cell parameters, and space group for inclusion complex of β-cyclodextrin with fraxinellone, C42H70O35·C14H16O3·3H2O, are reported [a = 19.294(2) Å, b = 26.639(1) Å, c = 16.467(3) Å, β = 110.451(9)°, cell volume V = 7930.34 Å3, Z = 4 and space group C2]. All measured lines were indexed and are consistent with the C2 space group. No detectable impurities were observed.
Reduction in cryptosporidiosis associated with introduction of enhanced filtration of drinking water at Loch Katrine, Scotland
Authors: POLLOCK K. G. J. , YOUNG D. , ROBERTSON C. , AHMED S. , RAMSAY C. N. 
Published: April 2013

SUMMARYPrevious evidence has suggested an association between cryptosporidiosis and consumption of unfiltered drinking water from Loch Katrine in Scotland. Before September 2007, the water was only micro-strained and chlorinated; however, since that time, coagulation and rapid gravity filtration have been installed. In order to determine risk factors associated with cryptosporidiosis, including drinking water, we analysed data on microbiologically confirmed cases of cryptosporidiosis from 2004 to 2010. We identified an association between the incidence of cryptosporidiosis and unfiltered Loch Katrine drinking water supplied to the home (odds ratio 1·86, 95% confidence interval 1·11–3·11, P = 0·019). However, while filtration appears to be associated with initially reduced rates of cryptosporidiosis, evidence suggests it may paradoxically make those consumers more susceptible to other transmission routes in the long-term. These findings support implementation of similar treatment for other unfiltered drinking-water supplies, as a means of reducing cryptosporidiosis associated with drinking water.
Population decline of the Elfin-woods WarblerSetophaga angelaein eastern Puerto Rico
Authors: ARENDT WAYNE J. , QIAN SONG S. , MINEARD KELLI A. 
Published: April 2013

SummaryWe estimated the population density of the globally threatened Elfin-woods WarblerSetophaga angelaewithin two forest types at different elevations in the Luquillo Experimental Forest in north-eastern Puerto Rico. Population densities ranged from 0.01 to 0.02 individuals/ha in elfin woodland and 0.06–0.26 individuals/ha inpalo coloradoforest in 2006, with average rates of decline since 1989 of 0.002–0.01 and 0.003–0.06 individuals/ha respectively. These estimates show a significant general declining trend from c.0.2 individuals/ha in 1989 in elfin woodland to c.0.02/ha in 2006, and from 1 to 0.2 inpalo coloradoforest. Although variation in estimated population density depended on the statistical method used, we document and discuss possible causes of an overall population decline from 1989 to 2006, lending support to previous initiatives to reclassify the species from the IUCN Red List category of “Vulnerable” to “Endangered”.
Corticotropin-releasing factor (CRF) and α2 adrenergic receptors mediate heroin withdrawal-potentiated startle in rats
Authors: Park Paula E. , Vendruscolo Leandro F. , Schlosburg Joel E. , Edwards Scott , Schulteis Gery , Koob George F. 
Published: April 2013

Abstract
Anxiety is one of the early symptoms of opioid withdrawal and contributes to continued drug use and relapse. The acoustic startle response (ASR) is a component of anxiety that has been shown to increase during opioid withdrawal in both humans and animals. We investigated the role of corticotropin-releasing factor (CRF) and norepinephrine (NE), two key mediators of the brain stress system, on acute heroin withdrawal-potentiated ASR. Rats injected with heroin (2 mg/kg s.c.) displayed an increased ASR when tested 4 h after heroin treatment. A similar increase in ASR was found in rats 10–20 h into withdrawal from extended access (12 h) to i.v. heroin self-administration, a model that captures several aspects of heroin addiction in humans. Both the α2 adrenergic receptor agonist clonidine (10 µg/kg s.c.) and CRF1 receptor antagonist N,N-bis(2-methoxyethyl)-3-(4-methoxy-2-methylphenyl)-2,5-dimethyl-pyrazolo[1,5-a] pyrimidin-7-amine (MPZP; 20 mg/kg s.c.) blocked heroin withdrawal-potentiated startle. To investigate the relationship between CRF1 and α2 adrenergic receptors in the potentiation of the ASR, we tested the effect of MPZP on yohimbine (1.25 mg/kg s.c.)-potentiated startle and clonidine on CRF (2 µg i.c.v.)-potentiated startle. Clonidine blocked CRF-potentiated startle, whereas MPZP partially attenuated but did not reverse yohimbine-potentiated startle, suggesting that CRF may drive NE release to potentiate startle. These results suggest that CRF1 and α2 receptors play an important role in the heightened anxiety-like behaviour observed during acute withdrawal from heroin, possibly via CRF inducing the release of NE in stress-related brain regions.
Peroxisome membrane proteins: multiple trafficking routes and multiple functions?
Authors: Theodoulou Frederica L. , Bernhardt Kristin , Linka Nicole , Baker Alison 
Published: April 2013

PMPs (peroxisome membrane proteins) play essential roles in organelle biogenesis and in co-ordinating peroxisomal metabolism with pathways in other subcellular compartments through transport of metabolites and the operation of redox shuttles. Although the import of soluble proteins into the peroxisome matrix has been well studied, much less is known about the trafficking of PMPs. Pex3 and Pex19 (and Pex16 in mammals) were identified over a decade ago as critical components of PMP import; however, it has proved surprisingly difficult to produce a unified model for their function in PMP import and peroxisome biogenesis. It has become apparent that each of these peroxins has multiple functions and in the present review we focus on both the classical and the more recently identified roles of Pex19 and Pex3 as informed by structural, biochemical and live cell imaging studies. We consider the different models proposed for peroxisome biogenesis and the role of PMP import within them, and propose that the differences may be more perceived than real and may reflect the highly dynamic nature of peroxisomes.
Measurement of the elastic modulus of spider mite silk fibers using atomic force microscopy
Authors: Hudson Stephen D. , Zhurov Vladimir , Grbić Vojislava , Grbić Miodrag , Hutter Jeffrey L. 
Published: April 2013

Bio-nanomaterials are one of the fastest developing sectors of industry and technology. Spider silk, a highly attractive light-weight biomaterial, has high tensile strength and elasticity and is compatible with human tissues, allowing for many areas of application. In comparison to spider silk fibers with diameters of several micrometers, spider mite silk fibers have much smaller diameters of tens of nanometers, making conventional tensile testing methods impractical. To determine the mechanical properties of adult and larval Tetranychus urticae silk fibers, we have performed three-point bending tests with an atomic force microscope. We found that because of the small diameters of these fibers, axial tension—due to both the applied force and a pre-existing strain—has a significant effect on the fiber response, even in the small-deformation limit. As a result, the typical Euler-Bernoulli-Timoshenko theory cannot be applied. We therefore follow the approach of Heidelberg et al. to develop a mechanical model of the fiber response that accounts for bending, an initial tension in the fibers, and a tension due to elongation during testing. This model provides self-consistent results, allowing us to determine that adult and larval fibers have Young's moduli of 24±3 GPa and 15±3 GPa, respectively. Both adult and larval fibers have an estimated ultimate strength of 200–300 MPa and a toughness of order 9 MJ/m3. We note that with increasing interest in the mechanical properties of very high aspect ratio nanomaterials, the influence of pre-existing tension must be considered in any measurements involving a bending test.
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Authors: Yu Danni , Huber Wolfgang , Vitek Olga 
Published: April 2013

AbstractMotivation: RNA-seq experiments produce digital counts of reads that are affected by both biological and technical variation. To distinguish the systematic changes in expression between conditions from noise, the counts are frequently modeled by the Negative Binomial distribution. However, in experiments with small sample size, the per-gene estimates of the dispersion parameter are unreliable.Method: We propose a simple and effective approach for estimating the dispersions. First, we obtain the initial estimates for each gene using the method of moments. Second, the estimates are regularized, i.e. shrunk towards a common value that minimizes the average squared difference between the initial estimates and the shrinkage estimates. The approach does not require extra modeling assumptions, is easy to compute and is compatible with the exact test of differential expression.Results: We evaluated the proposed approach using 10 simulated and experimental datasets and compared its performance with that of currently popular packages edgeR, DESeq, baySeq, BBSeq and SAMseq. For these datasets, sSeq performed favorably for experiments with small sample size in sensitivity, specificity and computational time.Availability: http://www.stat.purdue.edu/∼ovitek/Software.html and Bioconductor.Contact: ovitek@purdue.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences
Authors: Kalkatawi Manal , Rangkuti Farania , Schramm Michael , Jankovic Boris R. , Kamau Allan , Chowdhary Rajesh , Archer John A. C. , Bajic Vladimir B. 
Published: April 2013

Abstract
Contact: vladimir.bajic@kaust.edu.sa
Supplementary information: Supplementary data are available at Bioinformatics online.
Exome-based analysis for RNA epigenome sequencing data
Authors: Meng Jia , Cui Xiaodong , Rao Manjeet K. , Chen Yidong , Huang Yufei 
Published: April 2013

Abstract
Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques.
Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach ‘exomePeak’ for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome.
Availability: The MATLAB package ‘exomePeak’ and additional details are available at http://compgenomics.utsa.edu/exomePeak/.
Contact: yufei.huang@utsa.edu or jmeng@mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
SOLID-APPEARING RETINAL CYSTS IN DIABETIC MACULAR EDEMA
Authors: Liang Michelle C. , Vora Robin A. , Duker Jay S. , Reichel Elias 
Published: April 2013

Purpose:
To describe a novel finding of solid-appearing retinal cysts in patients with diabetic macular edema.

Methods:
Case series of four patients with diabetic retinopathy discovered to have solid-appearing retinal cysts on spectral-domain optical coherence tomography.

Results:
These cases demonstrate the presence of inner retinal hyporeflective cysts filled with an isoreflective substance on spectral-domain optical coherence tomography. These solid-appearing cysts arise from previously fluid-filled cysts and are not found in relation to intraretinal hemorrhage. Treatment with intravitreal anti–vascular endothelial growth factor agents did not seem to directly alter their natural course.

Conclusion:
The authors report solid-appearing retinal cysts as a new optical coherence tomography finding in four patients with diabetic macular edema. The exact composition of this isoreflective material is unknown. The authors hypothesize that fibrin or other inflammatory by-products fill these spaces.
Gastrointestinal Mucosal Involvement Without Amyloidosis in Children With Familial Mediterranean Fever
Authors: Gurkan Odul Egritas , Dalgic Buket 
Published: April 2013

ABSTRACTBackground and Objectives:Familial Mediterranean fever (FMF) and inflammatory bowel disease togetherness is well described in the literature. Abdominal pain and various gastrointestinal manifestations may arise directly from FMF or secondary to FMF‐associated diseases such as inflammatory bowel disease, vasculitidies, or amyloidosis. The aim of the study was to document gastrointestinal involvement in familial Mediterranean fever.Methods:The medical files of the patients who were diagnosed as having FMF at the Department of Pediatric Gastroenterology, Gazi University School of Medicine between 2007 and 2012 were examined retrospectively. FMF diagnosis was made through performing clinical, laboratory, colonoscopy, endoscopy, and genetic analysis.Results:Thirty‐six patients were diagnosed as having FMF during this period. Among them, 11 patients were admitted with vomiting or diarrhea. Colonoscopy and upper gastrointestinal endoscopy were performed. Colonic inflammation and multiple gastric aphthous ulcerations were observed.Conclusions:In this report, we described 11 patients who presented with gastrointestinal symptoms and eventually diagnosed as having FMF. Gastrointestinal mucosal involvement without amyloidosis is documented by endoscopic and histopathologic investigations in these patients. We concluded that mucosal involvement of the gastrointestinal tract may be attack‐related manifestations in these patients.
Polyethylene Glycol
Authors: Alper Arik , Pashankar Dinesh S. 
Published: April 2013

ABSTRACTConstipation is a common problem in children worldwide. It can also be a chronic problem persisting for many months to years. Successful treatment of constipation requires long‐term use of laxatives. Commonly used laxatives in children include milk of magnesia, lactulose, mineral oil, and polyethylene glycol. Compared with other laxatives, polyethylene glycol (with and without electrolytes) is a relatively new laxative used during the last decade. Recent studies report excellent efficacy and safety of polyethylene glycol for the long‐term treatment of constipation in children. Because of excellent patient acceptance, polyethylene glycol has become a preferred choice of laxative for many practitioners. This article reviews the recently published pediatric literature on biochemistry, efficacy, safety, patient acceptance, and pharmacoeconomics of polyethylene glycol.
Lactobacillus plantarum CS24.2 prevents Escherichia coli adhesion to HT‐29 cells and also down‐regulates enteropathogen‐induced tumor necrosis factor‐α and interleukin‐8 expression
Authors: Dhanani Akhilesh S. , Bagchi Tamishraha 
Published: April 2013

ABSTRACTThe aim of the present study was to evaluate the potential of Lactobacillus plantarum CS24.2 to antagonize Escherichia coli adhesion and modulate expression of the responses by HT‐29 cells of inflammatory molecules to E. coli adhesion. Experiments were performed under different adhesion conditions and findings compared with the responses of Lactobacillus rhamnosus GG. Tests of competitive adhesion, adhesion inhibition and displacement assays were performed for lactobacilli (L. rhamnosus GG and L. plantarum CS24.2) and E. coli O26:H11 to HT‐29 cells. Both the lactobacilli significantly reduced E. coli adhesion to HT‐29 cells (P < 0.05). The ability of lactobacilli to modulate tumor necrosis factor‐α and interleukin‐8 expression was analyzed in HT‐29 cells stimulated with E. coli using qRT‐PCR. L. plantarum CS24.2 significantly down regulated expression of both the genes induced by E. coli in HT‐29 cells at 6 hr as well as 24 hr, which was more significant than the corresponding findings for L. rhamnosus GG. The present findings suggest that L. plantarum CS24.2 inhibits pathogen adhesion to a similar extent as does the established probiotic strain L. rhamnosus GG. It may also attenuate tumor necrosis factor‐α and interleukin‐8 expression in HT‐29 cells stimulated with E. coli.
Strains in the genus Thauera exhibit remarkably different denitrification regulatory phenotypes
Authors: Liu Binbin , Mao Yuejian , Bergaust Linda , Bakken Lars R. , Frostegård Åsa 
Published: April 2013

SummaryDenitrifiers differ in how they handle the transition from oxic to anoxic respiration, with consequences for NO and N2O emissions. To enable stringent comparisons we defined parameters to describe denitrification regulatory phenotype (DRP) based on accumulation of NO2−, NO and N2O, oxic/anoxic growth and transcription of functional genes. Eight Thauera strains were divided into two distinct DRP types. Four strains were characterized by a rapid, complete onset (RCO) of all denitrification genes and no detectable nitrite accumulation. The others showed progressive onset (PO) of the different denitrification genes. The PO group accumulated nitrite, and no transcription of nirS (encoding nitrite reductase) was detected until all available nitrate (2 mM) was consumed. Addition of a new portion of nitrate to an actively denitrifying culture of a PO strain (T. terpenica) resulted in a transient halt in nitrite reduction, indicating that the electron flow was redirected to nitrate reductase. All eight strains controlled NO at nano‐molar concentrations, possibly reflecting the importance of strict control for survival. Transient N2O accumulation differed by two orders of magnitude between strains, indicating that control of N2O is less essential. No correlation was seen between phylogeny (based on 16S rRNA and functional genes) and DRP.
Globalisation and the Resilience of Social Democracy: Reassessing New Labour's Political Economy
Authors: Smith Martin 
Published: April 2013

Research Highlights and Abstract This article: Places New Labour's political economy in historical context using macro-economic data; Demonstrates that the arguments on policy convergence have led to a simplification of the nuances of Labour's political economy and underestimated its partisan nature; Highlights how globalisation rather than restraining Labour allowed an unprecedented increase in borrowing and spending making Labour very different to Conservative administrations and more ‘old’ Labour than previous Labour administrations. There has been considerable debate about the way in which globalisation and neo-liberalism have produced convergence in macro-economic policy. In the British case this convergence is seen in the adoption by the Labour Government (1997–2010) of the core elements of Thatcherite economic policy. However, this article argues that that an examination of macro-economic data demonstrates that is difficult to characterise New Labour as neo-liberal and indeed there is some evidence that it shared a number of commonalities with ‘Old’ Labour. Indeed, in many ways the changing structure of the financial markets removed, to some degree, the shackles from Labour and allowed greater borrowing and spending than previous left of centre administrations. Consequently, as Geoffrey Garrett suggests, partisanship remains an important determinant of economic policy in the UK case.
Grammatical Profiles and Aspect in Old Church Slavonic
Authors: Eckhoff Hanne M. , Janda Laura A. 
Published: April 2013

AbstractWe employ a new empirical approach to an enduring controversy concerning the development of a system of imperfective vs. perfective verbs in Slavic. While scholars once claimed that this is an ancient inherited system, dating from the prehistoric era, most now believe that the Slavic aspect‐pair system is an innovation. Different opinions concerning the date of this innovation range from the time of the earliest Slavic texts to the late middle ages. We use two different statistical models to sort Old Church Slavonic data from the PROIEL corpus and compare the results to distributions of verb forms in modern Russian. This comparison shows that there are indeed differences among verbs in Old Church Slavonic that suggest a division into imperfective vs. perfective verbs, although this division is clearly not identical to the division found in modern Russian.