bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance assessment of copy number microarray platforms using a spike-in experiment
Authors: Halper-Stromberg Eitan , Frelin Laurence , Ruczinski Ingo , Scharpf Robert , Jie Chunfa , Carvalho Benilton , Hao Haiping , Hetrick Kurt , Jedlicka Anne , Dziedzic Amanda , Doheny Kim , Scott Alan F. , Baylin Steve , Pevsner Jonathan , Spencer Forrest , Irizarry Rafael A. 
Published: April 2011

Abstract
Motivation: Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice.
Results: We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.
Availability: The data is available from http://rafalab.jhsph.edu/cnvcomp/.
Contact: pevsner@jhmi.edu; fspencer@jhmi.edu; rafa@jhu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Broad-Spectrum Suppression of Innate Immunity Is Required for Colonization of Arabidopsis Roots by the FungusPiriformospora indica
Authors: Jacobs Sophie , Zechmann Bernd , Molitor Alexandra , Trujillo Marco , Petutschnig Elena , Lipka Volker , Kogel Karl-Heinz , Schäfer Patrick 
Published: April 2011

AbstractPiriformospora indica is a root-colonizing basidiomycete that confers a wide range of beneficial traits to its host. The fungus shows a biotrophic growth phase in Arabidopsis (Arabidopsis thaliana) roots followed by a cell death-associated colonization phase, a colonization strategy that, to our knowledge, has not yet been reported for this plant. P. indica has evolved an extraordinary capacity for plant root colonization. Its broad host spectrum encompasses gymnosperms and monocotyledonous as well as dicotyledonous angiosperms, which suggests that it has an effective mechanism(s) for bypassing or suppressing host immunity. The results of our work argue that P. indica is confronted with a functional root immune system. Moreover, the fungus does not evade detection but rather suppresses immunity triggered by various microbe-associated molecular patterns. This ability to suppress host immunity is compromised in the jasmonate mutants jasmonate insensitive1-1 and jasmonate resistant1-1. A quintuple-DELLA mutant displaying constitutive gibberellin (GA) responses and the GA biosynthesis mutant ga1-6 (for GA requiring 1) showed higher and lower degrees of colonization, respectively, in the cell death-associated stage, suggesting that P. indica recruits GA signaling to help establish proapoptotic root cell colonization. Our study demonstrates that mutualists, like pathogens, are confronted with an effective innate immune system in roots and that colonization success essentially depends on the evolution of strategies for immunosuppression.
Dyskeratosis congenita and the DNA damage response
Authors: Kirwan Michael , Beswick Richard , Walne Amanda J. , Hossain Upal , Casimir Colin , Vulliamy Tom , Dokal Inderjeet 
Published: April 2011

SummaryDyskeratosis congenita (DC) is a heterogeneous bone marrow failure disorder with known mutations in components of telomerase and telomere shelterin. Recent work in a mouse model with a dyskerin mutation has implicated an increased DNA damage response as part of the cellular pathology, while mouse models with Terc and Tert mutations displayed a normal response. To clarify how these contradictory results might apply to DC pathology in humans, we studied the cellular phenotype in primary cells from DC patients of several genetic subtypes, focussing on T lymphocytes to remain close to the haematopoietic system. We observed novel cell cycle abnormalities in conjunction with impaired growth and an increase in apoptosis. Using flow cytometry and confocal microscopy we examined induction of the DNA damage proteins γ‐H2AX and 53BP1 and the cell cycle protein TP53 (p53). We found an increase in damage foci at telomeres in lymphocytes and an increase in the basal level of DNA damage in fibroblasts, but crucially no increased response to DNA damaging agents in either cell type. As the response to induced DNA damage was normal and levels of global DNA damage were inconsistent between cell types, DNA damage may contribute differently to the pathology in different tissues.
Timothy grass pollen extract‐induced gene expression and signalling pathways in airway epithelial cells
Authors: Röschmann K I. L. , Luiten S. , Jonker M. J. , Breit T. M. , Fokkens W. J. , Petersen A. , van Drunen C. M. 
Published: April 2011

Cite this as: K. I. L. Röschmann, S. Luiten, M. J. Jonker, T. M. Breit, W. J. Fokkens, A. Petersen and C. M. van Drunen, Clinical & Experimental Allergy, 2011 (41) 830–841.SummaryBackground
Grass pollen allergy is one of the most common allergies worldwide and airborne allergens are the major cause of allergic rhinitis. Airway epithelial cells (AECs) are the first to encounter and respond to aeroallergens and are therefore interesting targets for the development of new therapeutics. Our understanding of the epithelial contribution to immune responses is limited as most studies focus on only a few individual genes or proteins.Objective
To describe in detail the Timothy grass pollen extract (GPE)‐induced gene expression in AECs.Methods
NCI‐H292 cells were exposed to GPE for 24 h, and isolated RNA and cell culture supernatants were used for microarray analysis and multiplex ELISA, respectively.Results
Eleven thousand and seven hundred fifty‐eight transcripts were affected after exposure to GPE, with 141 genes up‐regulated and 121 genes down‐regulated by more than threefold. The gene ontology group cell communication was among the most prominent categories. Network analysis revealed that a substantial part of regulated genes are related to the cytokines IL‐6, IL‐8, IL‐1A, and the transcription factor FOS. After analysing significantly regulated signalling pathways, we found, among others, epidermal growth factor receptor 1, IL‐1, Notch‐, and Wnt‐related signalling members. Unexpectedly, we found Jagged to be down‐regulated and an increased release of IL‐12, in line with a more Th1‐biased response induced by GPE.Conclusion and Clinical Relevance
Our data show that the stimulation of AECs with GPE results in the induction of a broad response on RNA and protein level by which they are able to affect the initiation and regulation of local immune responses. Detailed understanding of GPE‐induced genes and signalling pathways will allow us to better define the pathogenesis of the allergic response and to identify new targets for treatment.
The Tool for Understanding Residents’ Needs as Individual Persons (TURNIP): construction and initial testing
Authors: Edvardsson David , Fetherstonhaugh Deirdre , Nay Rhonda 
Published: April 2011

Aims and objectives.  To construct and evaluate an intervention tool for increasing the person‐centredness of care in residential aged care services.Background.  Providing care that is person‐centred and evidence‐based is increasingly being regarded as synonymous with best quality aged care. However, consensus about how person‐centred care should be defined, operationalised and implemented has not yet been reached.Design.  Literature reviews, expert consultation (n = 22) and stakeholder interviews (n = 67) were undertaken to develop the Tool for Understanding Residents’ Needs as Individual Persons (TURNIP).Methods.  Statistical estimates of validity and reliability were employed to evaluate the tool in an Australian convenience sample of aged care staff (n = 220).Results.  The 39 item TURNIP conceptualised person‐centred care into five dimensions: (1) the care environment, (2) staff members’ attitudes towards dementia, (3) staff members’ knowledge about dementia, (4) the care organisation and (5) the content of care provided. Psychometric testing indicated satisfactory validity and reliability, as shown for example in a total Cronbach’s alpha of 0·89.Conclusions.  The TURNIP adds to current literature on person‐centred care by presenting a rigorously developed intervention tool based on an explicit conceptual structure that can inform the design, employment and communication of clinical interventions aiming to promote person‐centred care.Relevance to clinical practice.  The TURNIP contains clinically relevant items that are ready to be applied in clinical aged care. The tool can be used as a base for clinical interventions applying discussions in aged care organisations about the quality of current care and how to increase person‐centredness of the care provided.
Absence of nucleoid occlusion effector Noc impairs formation of orthogonal FtsZ rings during Staphylococcus aureus cell division
Authors: Veiga Helena , Jorge Ana M. , Pinho Mariana G. 
Published: April 2011

SummaryThe Gram‐positive pathogen Staphylococcus aureus divides by synthesizing the septum in three orthogonal planes over three consecutive division cycles. This process has to be tightly coordinated with chromosome segregation to avoid bisection of the nucleoid by the septum. Here we show that deletion of the nucleoid occlusion effector Noc in S. aureus results in the formation of Z‐rings over the nucleoid, as well as in DNA breaks, indicating that Noc has an important role as an antiguillotine checkpoint that prevents septa from forming over the DNA. Furthermore, Noc deleted cells show multiple Z‐rings which are no longer placed in perpendicular planes. We propose that the axis of chromosome segregation has a role in determining the placement of the division septum. This is achieved via the action of Noc which restricts the placement of the division septum to one of an infinite number of potential division planes that exist in S. aureus.
New insights into riboswitch regulation mechanisms
Authors: Bastet Laurène , Dubé Audrey , Massé Eric , Lafontaine Daniel A. 
Published: April 2011

SummaryRiboswitches are genetic elements located in non‐coding regions of some messenger RNAs (mRNAs) that are present in all three domains of life. The binding of ligands to riboswitches induces conformational changes in the mRNA molecule, resulting in modulation of gene transcription, or RNA splicing, translation or stability. This mechanism of regulation is particularly widespread in bacteria and allows a direct response to various metabolic changes. A large number of riboswitches have been discovered in the last few years, suggesting the existence of a huge diversity of regulatory ligands and genetic mechanisms of regulation. This review focuses on recent discoveries in riboswitch regulatory mechanisms as well as current outstanding challenges.
Dissecting the complete lipoprotein biogenesis pathway in Streptomyces scabies
Authors: Widdick David A. , Hicks Matthew G. , Thompson Benjamin J. , Tschumi Andreas , Chandra Govind , Sutcliffe Iain C. , Brülle Juliane K. , Sander Peter , Palmer Tracy , Hutchings Matthew I. 
Published: April 2011

SummaryFollowing translocation, bacterial lipoproteins are lipidated by lipoprotein diacylglycerol transferase (Lgt) and cleaved of their signal peptides by lipoprotein signal peptidase (Lsp). In Gram‐negative bacteria and mycobacteria, lipoproteins are further lipidated by lipoprotein N‐acyl transferase (Lnt), to give triacylated lipoproteins. Streptomyces are unusual amongst Gram‐positive bacteria because they export large numbers of lipoproteins via the twin arginine protein transport (Tat) pathway. Furthermore, some Streptomyces species encode two Lgt homologues and all Streptomyces species encode two homologues of Lnt. Here we characterize lipoprotein biogenesis in the plant pathogen Streptomyces scabies and report that lgt and lsp mutants are defective in growth and development while only moderately affected in virulence. Lipoproteins are lost from the membrane in an S. scabies lgt mutant but restored by expression of Streptomyces coelicolor lgt1 or lgt2 confirming that both encode functional Lgt enzymes. Furthermore, lipoproteins are N‐acylated in Streptomyces with efficient N‐acylation dependent on Lnt1 and Lnt2. However, deletion of lnt1 and lnt2 has no effect on growth, development or virulence. We thus present a detailed study of lipoprotein biogenesis in Streptomyces, the first study of Lnt function in a monoderm bacterium and the first study of bacterial lipoproteins as virulence factors in a plant pathogen.
ZmMKK4, a novel group C mitogen‐activated protein kinase kinase in maize (Zea mays), confers salt and cold tolerance in transgenic Arabidopsis
Authors: KONG XIANGPEI , PAN JIAOWEN , ZHANG MAOYING , XING XIN , ZHOU YAN , LIU YANG , LI DAPENG , LI DEQUAN 
Published: April 2011

ABSTRACTMitogen‐activated protein kinase (MAPK) cascades are signalling modules that transduce extracellular signalling to a range of cellular responses. Plant MAPK cascades have been implicated in development and stress response. In this study, we isolated a novel group C MAPKK gene, ZmMKK4, from maize. Northern blotting analysis revealed that the ZmMKK4 transcript expression was up‐regulated by cold, high salt and exogenous H2O2, but down‐regulated by exogenous abscisic acid (ABA). Over‐expression of ZmMKK4 in Arabidopsis conferred tolerance to cold and salt stresses by increased germination rate, lateral root numbers, plant survival rate, chlorophyll, proline and soluble sugar contents, and antioxidant enzyme [peroxidase (POD), catalase (CAT)] activities compared with control plants. Furthermore, ZmMKK4 enhanced a 37 kDa kinase activity after cold and salt stresses. RT‐PCR analysis revealed that the transcript levels of stress‐responsive transcription factors and functional genes were higher in ZmMKK4‐over‐expressing plants than in control plants. In addition, ZmMKK4 protein is localized in the nucleus. Taken together, these results indicate that ZmMKK4 is a positive regulator of salt and cold tolerance in plants.
Auxin modulates the enhanced development of root hairs in Arabidopsis thaliana (L.) Heynh. under elevated CO2
Authors: NIU YAOFANG , JIN CHONGWEI , JIN GULEI , ZHOU QINGYAN , LIN XIANYONG , TANG CAIXIAN , ZHANG YONGSONG 
Published: April 2011

ABSTRACTRoot hairs may play a critical role in nutrient acquisition of plants grown under elevated CO2. This study investigated how elevated CO2 enhanced the development of root hairs in Arabidopsis thaliana (L.) Heynh. The plants under elevated CO2 (800 µL L−1) had denser and longer root hairs, and more H‐positioned cells in root epidermis than those under ambient CO2 (350 µL L−1). The elevated CO2 increased auxin production in roots. Under elevated CO2, application of either 1‐naphthoxyacetic acid (1‐NOA) or N‐1‐naphthylphthalamic acid (NPA) blocked the enhanced development of root hairs. The opposite was true when the plants under ambient CO2 were treated with 1‐naphthylacetic acid (NAA), an auxin analogue. Furthermore, the elevated CO2 did not enhance the development of root hairs in auxin‐response mutants, axr1‐3, and auxin‐transporter mutants, axr4‐1, aux1‐7 and pin1‐1. Both elevated CO2 and NAA application increased expressions of caprice, triptychon and rho‐related protein from plants 2, and decreased expressions of werewolf, GLABRA2, GLABRA3 and the transparent testa glabra 1, genes related to root‐hair development, while 1‐NOA and NPA application had an opposite effect. Our study suggests that elevated CO2 enhanced the development of root hairs in Arabidopsis via the well‐characterized auxin signalling and transport that modulate the initiation of root hairs and the expression of its specific genes.
Intermittent preventive treatment of malaria in pregnancy: at the crossroads of public health policy
Authors: Chico R. Matthew , Chandramohan Daniel 
Published: April 2011

SummaryThe intermittent preventive treatment of malaria in pregnancy (IPTp) with sulphadoxine‐pyrimethamine (SP) has been a key component of the focused antenatal care package for nearly a decade, reducing the burden of low birthweight attributable to malaria in sub‐Saharan Africa. However, SP has lost parasite sensitivity in many sub‐Saharan locations during the same period, rendering its beneficial effect in IPTp debatable. Malaria transmission has also declined in some epidemiological settings. There is no evidence to suggest, however, that the risk of malaria in pregnancy without preventive measures has declined in the same locations. Thus, the urgency to identify efficacious drugs and/or new strategies to prevent malaria in pregnancy remains as great as ever. We summarise the results of recently published SP‐IPTp studies from areas of high drug resistance and/or low malaria transmission. We also present the evidence for mefloquine and azithromycin‐based combinations (ABCs), two leading drug options to replace SP in IPTp. We discuss optimal dosing for ABCs and their likely protection against several sexually transmitted and reproductive tract infections. We also summarise data from a diagnosis‐based alternative to IPTp known as the intermittent screening and treatment (IST) for malaria. Clinical and operational research is urgently needed to compare birth outcomes achieved by IPTp with ABCs vs. IST using an efficacious antimalarial therapy.
Evidence of assurance enhancing the quality of voluntary environmental disclosures: an empirical analysis
Authors: Moroney Robyn , Windsor Carolyn , Aw Yong Ting 
Published: April 2011

AbstractIn response to investor and public concerns about harm to the environment, companies are increasingly disclosing environmental information. To enhance the quality of corporate environmental disclosures in a largely voluntary context, various stakeholders are also demanding independent assurance. This study uses a stakeholder‐agency theoretical perspective to examine whether the quality of voluntary environmental disclosures is enhanced when assured. This study also examines the difference in the quality of voluntary environmental disclosures when assurance is provided by either professional accountant assurers or private consultants. Our sample comprises listed companies voluntarily disclosing environmental information in stand‐alone reports, annual reports, and websites. We use an index based upon the Global Reporting Initiative (GRI) to measure the quality of company environmental reporting. Results of this matched pairs study show that the quality of voluntary environmental disclosures scores significantly higher for assured companies than unassured companies. For assured companies, the quality is no different when assured by accountants or consultants. Additional analysis provides preliminary evidence that experience improves the quality of environmental disclosures.
A Multilevel Modelling Approach to Investigating the Predictive Validity of Editorial Decisions: Do the Editors of a High Profile Journal Select Manuscripts that are Highly Cited After Publication?
Authors: Bornmann Lutz , Mutz Rüdiger , Marx Werner , Schier Hermann , Daniel Hans-Dieter 
Published: April 2011

SummaryScientific journals must deal with the following questions concerning the predictive validity of editorial decisions. Is the best scientific work selected from submitted manuscripts? Does selection of the best manuscripts also mean selecting papers that after publication show top citation performance within their fields? Taking the journal Angewandte Chemie International Edition as an example, this study proposes a new methodology for investigating whether manuscripts that are most worthy of publication are in fact selected validly. First, the influence on citation of the accepted and rejected but then published elsewhere manuscripts was appraised on the basis of percentile impact classes scaled in a subfield of chemistry and, second, the association between the decisions on selection and the influence on citation of the manuscripts was determined by using a multilevel logistic regression for ordinal categories. This approach has many advantages over methodologies that were used in previous research studies on the predictive validity of editorial selection decisions.
Small Area Estimation Using a Reweighting Algorithm
Authors: Tanton Robert , Vidyattama Yogi , Nepal Binod , McNamara Justine 
Published: April 2011

SummaryThe paper describes a method of small area estimation which uses a reweighting algorithm to reweight survey data to a number of known totals (benchmarks) for small areas. The method has so far been used to estimate small area poverty rates and housing stress. The method gives poverty rates for small areas that are similar to those available from the 2006 Australian census, when the same definition of poverty was used. Various methods of validating the poverty rates have been used, including aggregating the poverty rates to a larger area and comparing them with official Australian Bureau of Statistics estimates from a survey, and applying the spatial microsimulation to larger areas and comparing with official Australian Bureau of Statistics survey results. Both these tests show that the estimates are comparable and fairly robust for most states in Australia.
Diversity of predaceous arthropods in the almond tree canopy in Northeastern Portugal: A methodological approach
Authors: BENHADI‐MARIN Jacinto , PEREIRA José A. , BARRIENTOS José A. , BENTO Albino , SANTOS Sónia A. P. 
Published: April 2011

AbstractThe almond tree is an economically important crop in Mediterranean regions. However, knowledge about the biodiversity of natural enemies that may be useful as biocontrol agents is scarce. The objectives of this work were: (i) to study the diversity of predaceous arthropods; and (ii) to establish a suitable sampling protocol for arthropods of the almond tree canopy. Between April and October of 2007 and 2008, 25 randomly selected trees were sampled in an organic almond grove located in the north‐east of Portugal using the beating technique. The specimens collected were counted and identified and the sampling protocol was established by using the accumulation curves and the seasonal richness peaks of the most abundant groups of natural enemies. A total of 1856 and 1301 arthropods were captured, respectively, in 2007 and 2008, where Araneae, Coccinellidae and Formicidae were the most abundant groups. A total of 14 families and 29 species of spiders were identified as Linyphiidae, Philodromidae, Thomisidae, Araneidae and Oxyopidae, the five most abundant families in both years. In the Coccinellidae and Formicidae communities 15 and 13 species were identified, respectively. According to taxa accumulation curves, the minimum sampling effort that provided a reliable picture of the biodiversity was established in 11 samples. Moreover, considering the seasonal richness distribution, it would be advisable to concentrate the sampling period from the beginning of July to the harvesting of almonds. This protocol might generate accurate replicate samples to estimate species richness when the effect of agricultural management is studied.