bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size
Authors: Kelly Laura J. , Renny‐Byfield Simon , Pellicer Jaume , Macas Jiří , Novák Petr , Neumann Pavel , Lysak Martin A. , Day Peter D. , Berger Madeleine , Fay Michael F. , Nichols Richard A. , Leitch Andrew R. , Leitch Ilia J. 
Published: June 2015

Summary

Plants exhibit an extraordinary range of genome sizes, varying by > 2000‐fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size.

Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria.

We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low‐abundance repeat‐derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal.

Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high‐abundance repeat families.
Application of an ELISA Milk Pregnancy Test in Beef Cows
Authors: Roberts JN , Byrem TM , Grooms DL 
Published: June 2015

ContentsPregnancy‐associated glycoproteins (PAG) are secreted by the binucleate giant cells of the ruminant placenta and enter maternal circulation at the time of placental attachment. The IDEXX Milk Pregnancy Test (IDEXX, Westbrook, ME) detects a subset of PAG in milk. Although designed as a management tool for dairy cows, there is potential for using the milk PAG test in beef cows. Our objective was to compare the performance of the milk PAG ELISA with a gold standard method for pregnancy diagnosis and determine the agreement between milk and serum PAG analysis in lactating beef cows. Angus and Angus‐crossed cows (n = 332) from two Michigan beef herds were enrolled in this study. Cows were subjected either to timed artificial insemination followed by exposure to a bull or exclusively exposed to a bull. The bulls and cows were separated 30 days prior to examination. Serum and milk samples were collected and submitted within 24 h of collection to a commercial laboratory for PAG analysis using the IDEXX Milk Pregnancy Assay (milk) and the IDEXX Bovine Pregnancy Assay (serum). Concurrently with milk and serum collection, each cow was examined transrectally by palpation or ultrasonography. When compared to transrectal examination, the performance (and 95% confidence intervals) of the milk PAG ELISA was sensitivity of 99.7% (99.0–100.0%) and specificity of 80.8% (65.6–95.9%). The lower specificity is likely due to the low prevalence (9.9%) of open cows (n = 30) in the herds examined. Of the 332 cows examined, 1.8% (n = 6) were classified as rechecks using the milk PAG ELISA. Results of the milk and serum PAG ELISA were in high agreement (kappa coefficient = 0.91). The milk PAG ELISA was accurate in predicting pregnancy status using milk collected from beef cattle between days 37 and 125 post‐insemination and may be useful for aiding management decisions in beef herds.
MDT lung cancer care: Input from the Surgical Oncologist
Authors: Kidane Biniam , Toyooka Shinichi , Yasufuku Kazuhiro 
Published: June 2015

AbstractAlthough there have been many advancements in the multidisciplinary management of non‐small cell lung cancer (NSCLC), surgery remains the primary modality of choice for resectable lung cancer when the patient is able to tolerate lung resection physiologically. There have been recent advances in surgical diagnosis and treatment of lung cancer. Increasing use of low‐dose computed tomography (CT) screening for lung cancer has resulted in increased detection of small peripheral nodules or semi‐solid ground glass opacities. Here, we review different modalities of localization techniques that have been used to aid surgical excisional biopsy when needle biopsy has failed to provide tissue diagnosis. We also report on the current debates regarding the use of sublobar resections for Stage I NSCLC as well as the surgical management of locally advanced NSCLC. Finally, we discuss the complex surgical management of T4 NSCLC lung cancers.
Functional assessment of the elderly with the use of EASY‐Care Standard 2010 and Comprehensive Geriatric Assessment
Authors: Talarska Dorota , Pacholska Renata , Strugała Magdalena , Wieczorowska‐Tobis Katarzyna 
Published: June 2015

BackgroundThe wide variation in performance among the elderly leads to the search for a suitable instrument to identify the necessary support.The aim of this study was to examine the scope of independent functioning of the elderly and to indicate the necessary support using basic instruments, Comprehensive Geriatric Assessment (CGA) and EASY‐Care Standard 2010.MethodsFor statistical analysis were qualified 101 questionnaires of patients from oncological surgery clinic.ResultsThe study group was dominated by women (79.2%). The average age for the entire group was 74.7 ± 7.5 years. In terms of basic life activities (Barthel Index), 75.2% of the elderly performed most of their activities independently. The Lawton IADL (Instrumental Activity of Daily Living Scale) median was 25 points. Moderate depression (Geriatric Depression Scale) reported 37.6% of the group. The influence of age, education, mode of movement and efficiency in basic and instrumental life activities and depression (Geriatric Depression Scale) was demonstrated in the results in three scales of the EASY‐Care Standard 2010 questionnaire: Independence score, Risk of break down in care and Risk of falls. There was no difference in terms of gender and the nature of the residence.ConclusionThe study group of the elderly was characterised by a good level of efficiency in basic and instrumental activities of daily living. Questionnaire EASY‐Care Standard 2010 enables to identify functional limitations of the elderly that may form the basis for planning individual support.
A Difficult Encounter – National Health Care Models and the EU
Authors: Martinsen Dorte Sindbjerg , Vasev Nikolay 
Published: June 2015

AbstractThis article examines the institutional output and preliminary outcome of the EU Patients' Rights Directive in two health care models: the Beveridge and Bismarck models in Denmark and Bulgaria, respectively. The study applies a most dissimilar system design to explain a similar transposition output through three explanatory variables, namely, institutional misfit, salience and administrative resources. We find that Denmark and Bulgaria have transposed the Directive in protectionist and minimalistic ways, thus far leading to a low outcome, i.e. low patient outflow. The encounter between the EU and the national health care models has not been enthusiastic but has instead been another example of reluctant and restrictive Europeanisation.
Europeanization, Welfare and Variegated Austerity Capitalisms – Hungary and Croatia
Authors: Lendvai Noémi , Stubbs Paul 
Published: June 2015

AbstractThis article focuses on the implications of understanding ‘Europeanization’ as a complex, dynamic and troubled translation process. It discusses post‐communist welfare in the context of variegated forms of austerity capitalism in the EU. In particular, the complex relationships between modalities of welfare, the uneven development of neo‐liberalisms and the multi‐scalar restructuring of welfare assemblages, are discussed in the context of the reframing of relationships between the economic, the political and the social in a period of deep crisis and austerity. Post‐communist Europe cannot be conceived as a flattened map or a singular regime type. Rather, diverse and often contradictory restructurings operate in different places at different times, and political agency continues to matter. Comparing and contrasting the changing relationships between neo‐liberalism, authoritarian populism and ethnicized nationalism in Hungary and Croatia provides a more nuanced understanding of the variable geometries of transnational translations.
Depression and Political Participation*
Authors: Ojeda Christopher 
Published: June 2015

ObjectiveI hypothesize that individuals with depression lack the motivation and physical capacity required to participate in politics due to somatic problems and feelings of hopelessness and apathy. Furthermore, I hypothesize that depression in adolescence can have negative downstream consequences for participation in young adulthood.MethodUsing the 1998 General Social Survey and the National Longitudinal Study of Adolescent Health, I employ logistic regression and mediation analysis to test the relationship between depression and voting as well as adolescent depression and political participation.ResultsThe results show that both depression and adolescent depression reduce the probability of political participation. The effect of adolescent depression on political participation is mediated by educational attainment and partisan affiliation.ConclusionDepression reduces participation and merits further attention as a political phenomenon. The possibility of depression as a disability is discussed, including potential efforts to boost participation among this group.
A Non‐linear Manifold Strategy for SHM Approaches
Authors: Dervilis N. , Antoniadou I. , Cross E. J. , Worden K. 
Published: June 2015

AbstractIn the data‐based approach to structural health monitoring (SHM) when novelty detection is utilised as a means of diagnosis, benign operational and environmental variations of the structure can lead to false alarms and mask the presence of damage. The key element of this paper is to demonstrate a series of pattern recognition approaches which investigate complex correlations between the variables and thus potentially shed light on the variations within the data that are of interest for SHM.The non‐linear manifold learning techniques discussed here, like locally linear embedding combined with robust discordance measures like the minimum covariance determinant and regression techniques like Gaussian processes offer a strategy that includes reliable novelty detection analysis but also a method of investigating the space where structural data clusters are lying.
Comparison of breathing gated CT images generated using a 5DCT technique and a commercial clinical protocol in a porcine model
Authors: O'Connell Dylan P. , Thomas David H. , Dou Tai H. , Lamb James M. , Feingold Franklin , Low Daniel A. , Fuld Matthew K. , Sieren Jered P. , Sloan Chelsea M. , Shirk Melissa A. , Hoffman Eric A. , Hofmann Christian 
Published: June 2015

Purpose:To demonstrate that a “5DCT” technique which utilizes fast helical acquisition yields the same respiratory‐gated images as a commercial technique for regular, mechanically produced breathing cycles.Methods:Respiratory‐gated images of an anesthetized, mechanically ventilated pig were generated using a Siemens low‐pitch helical protocol and 5DCT for a range of breathing rates and amplitudes and with standard and low dose imaging protocols. 5DCT reconstructions were independently evaluated by measuring the distances between tissue positions predicted by a 5D motion model and those measured using deformable registration, as well by reconstructing the originally acquired scans. Discrepancies between the 5DCT and commercial reconstructions were measured using landmark correspondences.Results:The mean distance between model predicted tissue positions and deformably registered tissue positions over the nine datasets was 0.65 ± 0.28 mm. Reconstructions of the original scans were on average accurate to 0.78 ± 0.57 mm. Mean landmark displacement between the commercial and 5DCT images was 1.76 ± 1.25 mm while the maximum lung tissue motion over the breathing cycle had a mean value of 27.2 ± 4.6 mm. An image composed of the average of 30 deformably registered images acquired with a low dose protocol had 6 HU image noise (single standard deviation) in the heart versus 31 HU for the commercial images.Conclusions:An end to end evaluation of the 5DCT technique was conducted through landmark based comparison to breathing gated images acquired with a commercial protocol under highly regular ventilation. The techniques were found to agree to within 2 mm for most respiratory phases and most points in the lung.
Correlated gene expression supports synchronous activity in brain networks
Authors: Richiardi Jonas , Altmann Andre , Milazzo Anna-Clare , Chang Catie , Chakravarty M. Mallar , Banaschewski Tobias , Barker Gareth J. , Bokde Arun L.W. , Bromberg Uli , Büchel Christian , Conrod Patricia , Fauth-Bühler Mira , Flor Herta , Frouin Vincent , Gallinat Jürgen , Garavan Hugh , Gowland Penny , Heinz Andreas , Lemaître Hervé , Mann Karl F. , Martinot Jean-Luc , Nees Frauke , Paus Tomáš , Pausova Zdenka , Rietschel Marcella , Robbins Trevor W. , Smolka Michael N. , Spanagel Rainer , Ströhle Andreas , Schumann Gunter , Hawrylycz Mike , Poline Jean-Baptiste , Greicius Michael D. ,   IMAGEN consortium, Albrecht Lisa , Andrew Chris , Arroyo Mercedes , Artiges Eric , Aydin Semiha , Bach Christine , Banaschewski Tobias , Barbot Alexis , Barker Gareth , Boddaert Nathalie , Bokde Arun , Bricaud Zuleima , Bromberg Uli , Bruehl Ruediger , Büchel Christian , Cachia Arnaud , Cattrell Anna , Conrod Patricia , Constant Patrick , Dalley Jeffrey , Decideur Benjamin , Desrivieres Sylvane , Fadai Tahmine , Flor Herta , Frouin Vincent , Gallinat Jürgen , Garavan Hugh , Briand Fanny Gollier , Gowland Penny , Heinrichs Bert , Heinz Andreas , Heym Nadja , Hübner Thomas , Ireland James , Ittermann Bernd , Jia Tianye , Lathrop Mark , Lanzerath Dirk , Lawrence Claire , Lemaitre Hervé , Lüdemann Katharina , Macare Christine , Mallik Catherine , Mangin Jean-François , Mann Karl , Martinot Jean- Luc , Mennigen Eva , Mesquita de Carvahlo Fabiana , Mignon Xavier , Miranda Ruben , Müller Kathrin , Nees Frauke , Nymberg Charlotte , Paillere Marie-Laure , Paus Tomas , Pausova Zdenka , Poline Jean-Baptiste , Poustka Luise , Rapp Michael , Robert Gabriel , Reuter Jan , Rietschel Marcella , Ripke Stephan , Robbins Trevor , Rodehacke Sarah , Rogers John , Romanowski Alexander , Ruggeri Barbara , Schmäl Christine , Schmidt Dirk , Schneider Sophia , Schumann MarkGunter , Schubert Florian , Schwartz Yannick , Smolka Michael , Sommer Wolfgang , Spanagel Rainer , Speiser Claudia , Spranger Tade , Stedman Alicia , Steiner Sabina , Stephens Dai , Strache Nicole , Ströhle Andreas , Struve Maren , Subramaniam Naresh , Topper Lauren , Whelan Robert , Williams Steve , Yacubian Juliana , Zilbovicius Monica , Wong C Peng , Lubbe Steven , Martinez-Medina Lourdes , Fernandes Alinda , Tahmasebi Amir 
Published: June 2015

Cooperating brain regions express similar genesWhen the brain is at rest, a number of distinct areas are functionally connected. They tend to be organized in networks. Richiardiet al.compared brain imaging and gene expression data to build computational models of these networks. These functional networks are underpinned by the correlated expression of a core set of 161 genes. In this set, genes coding for ion channels and other synaptic functions such as neurotransmitter release dominate.Science, this issue p.1241
Development and Evaluation of an Enterovirus D68 Real-Time Reverse Transcriptase PCR Assay
Authors: Wylie Todd N. , Wylie Kristine M. , Buller Richard S. , Cannella Maria , Storch Gregory A. 
Published: June 2015

ABSTRACT
We have developed and evaluated a real-time reverse transcriptase PCR (RT-PCR) assay for the detection of human enterovirus D68 (EV-D68) in clinical specimens. This assay was developed in response to the unprecedented 2014 nationwide EV-D68 outbreak in the United States associated with severe respiratory illness. As part of our evaluation of the outbreak, we sequenced and published the genome sequence of the EV-D68 virus circulating in St. Louis, MO. This sequence, along with other GenBank sequences from past EV-D68 occurrences, was used to computationally select a region of EV-D68 appropriate for targeting in a strain-specific RT-PCR assay. The RT-PCR assay amplifies a segment of the VP1 gene, with an analytic limit of detection of 4 copies per reaction, and it was more sensitive than commercially available assays that detect enteroviruses and rhinoviruses without distinguishing between the two, including three multiplex respiratory panels approved for clinical use by the FDA. The assay did not detect any other enteroviruses or rhinoviruses tested and did detect divergent strains of EV-D68, including the first EV-D68 strain (Fermon) identified in California in 1962. This assay should be useful for identifying and studying current and future outbreaks of EV-D68 viruses.
Context-Dependent Cleavage of the Capsid Protein by the West Nile Virus Protease Modulates the Efficiency of Virus Assembly
Authors: VanBlargan Laura A. , Davis Kaitlin A. , Dowd Kimberly A. , Akey David L. , Smith Janet L. , Pierson Theodore C. 
Published: June 2015

ABSTRACT

The molecular mechanisms that define the specificity of flavivirus RNA encapsulation are poorly understood. Virions composed of the structural proteins of one flavivirus and the genomic RNA of a heterologous strain can be assembled and have been developed as live attenuated vaccine candidates for several flaviviruses. In this study, we discovered that not all combinations of flavivirus components are possible. While a West Nile virus (WNV) subgenomic RNA could readily be packaged by structural proteins of the DENV2 strain 16681, production of infectious virions with DENV2 strain New Guinea C (NGC) structural proteins was not possible, despite the very high amino acid identity between these viruses. Mutagenesis studies identified a single residue (position 101) of the DENV capsid (C) protein as the determinant for heterologous virus production. C101 is located at the P1′ position of the NS2B/3 protease cleavage site at the carboxy terminus of the C protein. WNV NS2B/3 cleavage of the DENV structural polyprotein was possible when a threonine (Thr101 in strain 16681) but not a serine (Ser101 in strain NGC) occupied the P1′ position, a finding not predicted by
in vitro
protease specificity studies. Critically, both serine and threonine were tolerated at the P1′ position of WNV capsid. More extensive mutagenesis revealed the importance of flanking residues within the polyprotein in defining the cleavage specificity of the WNV protease. A more detailed understanding of the context dependence of viral protease specificity may aid the development of new protease inhibitors and provide insight into associated patterns of drug resistance.

IMPORTANCE
West Nile virus (WNV) and dengue virus (DENV) are mosquito-borne flaviviruses that cause considerable morbidity and mortality in humans. No specific antiflavivirus therapeutics are available for treatment of infection. Proteolytic processing of the flavivirus polyprotein is an essential step in the replication cycle and is an attractive target for antiviral development. The design of protease inhibitors has been informed by insights into the molecular details of the interactions of proteases and their substrates. In this article, studies of the processing of WNV and DENV capsid proteins by the WNV protease identified an unexpected contribution of the sequence surrounding critical residues within the cleavage site on protease specificity. This demonstration of context-dependent protease cleavage has implications for the design of chimeric flaviviruses, new therapeutics, and the interpretation of flavivirus protease substrate specificity studies.
The impact of time-window bias on the assessment of the long-term effect of medication adherence: the case of secondary prevention after myocardial infarction
Authors: Di Martino Mirko , Kirchmayer Ursula , Agabiti Nera , Bauleo Lisa , Fusco Danilo , Perucci Carlo Alberto , Davoli Marina 
Published: June 2015

ObjectivesTime-window bias was described in case–control studies and led to a biased estimate of drug effect. No studies have measured the impact of this bias on the assessment of the effect of medication adherence on health outcomes. Our goals were to estimate the association between adherence to drug therapies after myocardial infarction (MI) and the incidence of a new MI, and to quantify the error that would have been produced by a time-window bias.SettingThis is a population-based study. Data were obtained from the Regional Health Information Systems of the Lazio Region in Central Italy (around 5 million inhabitants).ParticipantsPatients discharged after MI in 2006–2007 were enrolled in the cohort and followed through 2009.Outcome measureThe study outcome was reinfarction: either mortality, or hospital admission for MI, whichever occurred first.DesignA nested case–control study was performed. Controls were selected using both time-dependent and time-independent sampling. Adherence to antiplatelets, β-blockers, ACE inhibitors/angiotensin receptor blockers (ACEI/ARBs) and statins was calculated using the proportion of days covered (PDC).ResultsA total of 6880 patients were enrolled in the cohort. Using time-dependent sampling, a protective effect was detected for all study drugs. Conversely, using time-independent sampling, the beneficial effect was attenuated, as in the case of antiplatelet agents and statins, or completely masked, as in the case of ACEI/ARBs and β-blockers. For ACEI/ARBs, the time-dependent approach produced ORs of 0.83 (95% CI 0.57 to 1.21) and 0.72 (0.55 to 0.95), respectively, for ‘0.5<PDC≤0.75’ and ‘PDC>0.75’ versus ‘0≤PDC≤0.5’. Using the time-independent approach, the ORs were 0.96 (0.65 to 1.43) and 1.00 (0.76 to 1.33), respectively.ConclusionsA time-independent definition of a time-dependent exposure introduces a bias when the length of follow-up varies with the outcome. The persistence of time-related biases in peer-reviewed papers strongly suggests the need for increased awareness of this methodological pitfall.