bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community
Authors: Saunders Diane , Yoshida Kentaro , Sambles Christine , Glover Rachel , Clavijo Bernardo , Corpas Manuel , Bunting Daniel , Dong Suomeng , Rallapalli Ghanasyam , Clark Matthew D. , Swarbreck David , Ayling Sarah , Bashton Matthew , Collin Steve , Hosoya Tsuyoshi , Edwards Anne , Crossman Lisa , Etherington Graham , Win Joe , Cano Liliana , Studholme David J. , Downie J. Allan , Caccamo Mario , Kamoun Sophien , MacLean Dan 
Published: April 2014

AbstractAsh dieback is a fungal disease of ash trees caused by Hymenoscyphus pseudoalbidus that has swept across Europe in the last two decades and is a significant threat to the ash population. This emergent pathogen has been relatively poorly studied and little is known about its genetic make-up. In response to the arrival of this dangerous pathogen in the UK we took the unusual step of providing an open access database and initial sequence datasets to the scientific community for analysis prior to performing an analysis of our own. Our goal was to crowdsource genomic and other analyses and create a community analysing this pathogen. In this report on the evolution of the community and data and analysis obtained in the first year of this activity, we describe the nature and the volume of the contributions and reveal some preliminary insights into the genome and biology of H. pseudoalbidus that emerged. In particular our nascent community generated a first-pass genome assembly containing abundant collapsed AT-rich repeats indicating a typically complex genome structure. Our open science and crowdsourcing effort has brought a wealth of new knowledge about this emergent pathogen within a short time-frame. Our community endeavour highlights the positive impact that open, collaborative approaches can have on fast, responsive modern science.
Gestational diabetes mellitus and later cardiovascular disease: a Swedish population based case–control study
Authors: Fadl H , Magnuson A , Östlund I , Montgomery S , Hanson U , Schwarcz E 
Published: April 2014

ObjectiveTo identify if gestational diabetes mellitus (GDM) is a clinically useful marker of future cardiovascular disease (CVD) risk and if GDM combined with other risks (smoking, hypertension or body mass) identifies high‐risk groups.DesignPopulation‐based matched case–control study.SettingNational Swedish register data from 1991 to 2008.PopulationA total of 2639 women with a cardiovascular event and matched controls.MethodsConditional logistic regression examined associations with CVD before and after adjustment for conventional risk factors and confounders. Effect modification for the association of GDM with CVD by body mass index (BMI), smoking and chronic hypertension was assessed by stratification and interaction testing. Adjustment for diabetes post‐pregnancy evaluated its mediating role.Main outcome measuresInpatient diagnoses or causes of death identifying ischemic heart disease, ischemic stroke, atherosclerosis or peripheral vascular disease.ResultsThe adjusted odds ratios (and 95% confidence intervals) for the association of CVD with GDM are 1.51 (1.07–2.14), 2.23 (2.01–2.48) for smoking, 1.98 (1.71–2.29) for obesity and 5.10 (3.18–8.18) for chronic hypertension. In stratified analysis the association of CVD with GDM was only seen among women with BMI ≥25, with an odds ratio of 2.39 (1.39–4.10), but only women with a BMI <30 accounted for this increased risk. Adjustment for post‐pregnancy diabetes attenuated it somewhat to 1.99 (1.13–3.52).ConclusionsIn the absence of other recognised cardiovascular risk factors, such as smoking, obesity or chronic hypertension, GDM is a useful marker of raised CVD risk among women with BMI between 25 and 29.
Effects of food quality on trade‐offs among growth, immunity and survival in the greater wax mothGalleria mellonella
Authors: Krams Indrikis , Kecko Sanita , Kangassalo Katariina , Moore Fhionna R. , Jankevics Eriks , Inashkina Inna , Krama Tatjana , Lietuvietis Vilnis , Meija Laila , Rantala Markus J. 
Published: April 2014

AbstractThe resources available to an individual in any given environment are finite, and variation in life history traits reflect differential allocation of these resources to competing life functions. Nutritional quality of food is of particular importance in these life history decisions. In this study, we tested trade‐offs among growth, immunity and survival in 3 groups of greater wax moth (Galleria mellonella) larvae fed on diets of high and average nutritional quality. We found rapid growth and weak immunity (as measured by encapsulation response) in the larvae of the high‐energy food group. It took longer to develop on food of average nutritional quality. However, encapsulation response was stronger in this group. The larvae grew longer in the low‐energy food group, and had the strongest encapsulation response. We observed the highest survival rates in larvae of the low‐energy food group, while the highest mortality rates were observed in the high‐energy food group. A significant negative correlation between body mass and the strength of encapsulation response was found only in the high‐energy food group revealing significant competition between growth and immunity only at the highest rates of growth. The results of this study help to establish relationships between types of food, its nutritional value and life history traits ofG. mellonellalarvae.
Antibacterial Activity of Essential Oils of Edible Spices, Ocimum canum and Xylopia aethiopica
Authors: Vyry Wouatsa N. A. , Misra Laxminarain , Venkatesh Kumar R. 
Published: April 2014

AbstractThe essential oils of 2 Cameroonian spices, namely, Xylopia aethiopica and Ocimum canum, were chemically investigated and screened for their antibacterial activity. The essential oils were analyzed by means of GC, GC/MS, and NMR. X. aethiopica oil contained myrtenol (12%), a monoterpenoid in highest concentration. The essential oil of O. canum belonged to the known linalool (44%) rich chemotype. The results of the antibacterial screening against the food spoiling bacteria revealed a significant and broad spectrum of activity for these essential oils. The present material of X. aethiopica, which is having myrtenol in relatively higher concentration, has shown moderate antibacterial activity. The bioassay‐guided fractionation of Ocimum canum oil through flash chromatography showed that minor compounds, namely, α‐terpineol, chavicol, chavibetol, and trans‐p‐mentha‐2,8‐dien‐ol, significantly contributed for the overall activity observed. Hence, these results evidenced the possible potential of the essential oil of O. canum as a suitable antibacterial for controlling food‐borne pathogens whereas the X. aethiopica oil has moderate possibility.Practical ApplicationThere is a strong global demand for the microbe‐free, safe, and healthy foods. In this study, we showed that the essential oil of O. canum (wild basil) can be used as antibacterial for food items. Also, we showed that a value addition in the antibacterial potential of O. canum oil can be done by processing the essential oil through flash chromatographic separations.
Hairy cell leukemia presenting initially with symptoms of Behçet's disease
Authors: Oksuz Mustafa Ferhat , Coskun Belkis Nihan , Tufan Ayse Nur , Orucoglu Nurdan , Dalkilic Ediz , Öztürk Nazlıoğlu Hülya , Pehlivan Yavuz 
Published: April 2014

AbstractVasculitis is relatively uncommon in lymphoproliferative disease and may predate the diagnosis of lymphoproliferative disease. Many vasculitides have been associated with hairy cell leukemia (HCL), including polyarteritis nodosa (PAN) and leukocytoclastic vasculitis. We herein report a case whose initial presentation was like Behçet's disease (BD) (arthritis, oral and genital ulcerations, papulopustular skin lesions) in addition to pancytopenia, but turned out to have HCL. Because of the overlap between their symptoms, like oral ulcerations, skin lesions, arthritis and constitutional findings, HCL and BD may mimic each other. We should keep in mind other reasons for vasculitis such as lymphoproliferative disease, especially whose who have hematological abnormalities such as pancytopenia.
Field trial on removal of petroleum‐hydrocarbon pollutants using a microbial consortium for bioremediation and rhizoremediation
Authors: Pizarro‐Tobías Paloma , Niqui José L. , Roca Amalia , Solano Jennifer , Fernández Matilde , Bastida Felipe , García Carlos , Ramos Juan L. 
Published: April 2014

SummaryPetroleum waste sludges are toxic and dangerous that is why environmental protection agencies have declared their treatment top priority. Physicochemical treatments are expensive and environmentally unfriendly, while alternative biological treatments are less costly but, in general, work at a slower pace. An in situ bioremediation and rhizoremediation field‐scale trial was performed in an area contaminated with oil refinery sludge under semiarid climate. The bioremediation and rhizoremediation treatments included the use of an artificial consortium made up of plant growth‐promoting rhizobacteria and polycyclic aromatic hydrocarbon‐degrading bacteria, and the combined use of the mentioned consortium along with pasture plants respectively. Rhizoremediation revealed that the development of vegetation favoured the evolution of indigenous microbiota with potential to remove petroleum wastes. This was inferred as the decline of total petroleum hydrocarbons 7 months after the biological treatment.
Nurse‐plant effects on the seed biology and germination of desert annuals
Authors: Sotomayor Diego A. , Lortie Christopher J. , Lamarque Laurent J. 
Published: April 2014

AbstractNurse‐plants generally have positive effects on understorey species by creating more suitable conditions for stress‐intolerant plants relative to open micro‐habitats. However, long‐term effects of this plant–plant facilitation system have been rarely examined. Seeds of five desert annual species from Atiquipa coastal desert in Southern Peru were used to examine whether different microenvironmental conditions under the nurse‐plants Caesalpinia spinosa Molina (Kuntze) lead to differences in seed biology and germinability of annual plants relative to open, canopy‐free conditions. Seeds collected from plants associated with nurse‐plants were predicted to be (i) larger due to more favourable growing conditions, (ii) more viable and with greater germination rates, (iii) less variable in size and viability due to reduced environmental heterogeneity, and (iv) to germinate faster to avoid apparent competition with other annuals. Seed attribute measurements and germination trials in growth chambers were used to test these predictions. Although the plant abundance of only 2 of 5 species was strongly facilitated by the nurse‐plant, no significant differences were found in seed mass, viability or relative variability between understorey and open micro‐habitats for any of the species. Contrary to our predictions, final seed germination rates of seeds from open micro‐habitats were higher, and the open micro‐habitat treatment was more favourable for germination of seeds from both open and understorey environments. Taken together, these results suggest that plant–plant facilitation does not necessarily affect seed biology traits. Further studies addressing larger distribution ranges and/or density gradients of understorey species will illuminate the potential evolutionary effects of nurse‐plants.
Recommendations for the standardization of clinical outcomes used in allergen immunotherapy trials for allergic rhinoconjunctivitis: an EAACI Position Paper
Authors: Pfaar O. , Demoly P. , Gerth van Wijk R. , Bonini S. , Bousquet J. , Canonica G. W. , Durham S. R. , Jacobsen L. , Malling H. J. , Mösges R. , Papadopoulos N. G. , Rak S. , Rodriguez del Rio P. , Valovirta E. , Wahn U. , Calderon M. A. 
Published: April 2014

AbstractBackgroundAllergen immunotherapy (AIT) has been thoroughly documented in randomized controlled trials (RCTs). It is the only immune‐modifying and causal treatment available for patients suffering from IgE‐mediated diseases such as allergic rhinoconjunctivitis, allergic asthma and insect sting allergy. However, there is a high degree of clinical and methodological heterogeneity among the endpoints in clinical studies on AIT, for both subcutaneous and sublingual immunotherapy (SCIT and SLIT). At present, there are no commonly accepted standards for defining the optimal outcome parameters to be used for both primary and secondary endpoints.MethodsAs elaborated by a Task Force (TF) of the European Academy of Allergy and Clinical Immunology (EAACI) Immunotherapy Interest Group, this Position Paper evaluates the currently used outcome parameters in different RCTs and also aims to provide recommendations for the optimal endpoints in future AIT trials for allergic rhinoconjunctivitis.ResultsBased on a thorough literature review, the TF members have outlined recommendations for nine domains of clinical outcome measures. As the primary outcome, the TF recommends a homogeneous combined symptom and medication score (CSMS) as a simple and standardized method that balances both symptoms and the need for antiallergic medication in an equally weighted manner. All outcomes, grouped into nine domains, are reviewed.ConclusionA standardized and globally harmonized method for analysing the clinical efficacy of AIT products in RCTs is required. The EAACI TF highlights the CSMS as the primary endpoint for future RCTs in AIT for allergic rhinoconjunctivitis.
Governing the Commercial Streets of the City: New Terrains of Disinvestment and Gentrification in Toronto's Inner Suburbs
Authors: Rankin Katharine N. , McLean Heather 
Published: April 2014

AbstractThis paper explores the commercial shopping street as a site of racialized class struggle. The argument builds around the study of a disinvested inner‐suburban neighbourhood in Toronto, which furnishes an ideal case through which to achieve the paper's objectives of, first, identifying commercial space as an important site of contestation over competing suburban futures; second, delineating how processes of racialization inform the economies of commercial gentrification and urban renewal; and third, highlighting the epistemological and theoretical insights that emerge when research is conducted collaboratively, among academic, community, and activist groupings. The paper argues that such commercial spaces play a key role in making the city accessible to vulnerable and marginalized groups. Two competing planning agendas centred on reordering commercial space, meanwhile, spell the almost‐certain demise of such arrangements: a “real estate” vision featuring new condominium developments, and a new urbanist resistance favouring “green” and “creative” alternatives. Our engagements with precarious, predominantly immigrant‐owned businesses and community‐based researchers reveal the complicity of both modes of development planning with processes of displacement and structural racism. Specifying these dynamics as “racialized class projects” opens up space for intervention and organizing.
Disparity Despite Diversity: SocialInjustice in New York City's Urban Agriculture System
Authors: Reynolds Kristin 
Published: April 2014

AbstractMany studies have documented the benefits of urban agriculture, including increased food access, job creation, educational opportunities, and green space. A focus on its social benefits has fed an association of urban agriculture with social justice, yet there is a distinction between alleviating symptoms of injustice (such as disparate access to food or environmental amenities) and disrupting structures that underlie them. Despite its positive impacts, urban agriculture systems may reinforce inequities that practitioners and supporters aim to address. This paper reports findings from a 2‐year study of urban agriculture in New York City, which found race‐ and class‐based disparities among practitioners citywide. Using the lens of critical race theory, it argues that a failure to examine urban agriculture's role in either supporting or dismantling unjust structures may perpetuate an inequitable system. The paper concludes with recommendations for urban agriculture supporters and scholars to help advance social justice at structural levels.
An evaluation of inferential procedures for adaptive clinical trial designs with pre‐specified rules for modifying the sample size
Authors: Levin Gregory P. , Emerson Sarah C. , Emerson Scott S. 
Published: April 2014

SummaryMany papers have introduced adaptive clinical trial methods that allow modifications to the sample size based on interim estimates of treatment effect. There has been extensive commentary on type I error control and efficiency considerations, but little research on estimation after an adaptive hypothesis test. We evaluate the reliability and precision of different inferential procedures in the presence of an adaptive design with pre‐specified rules for modifying the sampling plan. We extend group sequential orderings of the outcome space based on the stage at stopping, likelihood ratio statistic, and sample mean to the adaptive setting in order to compute median‐unbiased point estimates, exact confidence intervals, and P‐values uniformly distributed under the null hypothesis. The likelihood ratio ordering is found to average shorter confidence intervals and produce higher probabilities of P‐values below important thresholds than alternative approaches. The bias adjusted mean demonstrates the lowest mean squared error among candidate point estimates. A conditional error‐based approach in the literature has the benefit of being the only method that accommodates unplanned adaptations. We compare the performance of this and other methods in order to quantify the cost of failing to plan ahead in settings where adaptations could realistically be pre‐specified at the design stage. We find the cost to be meaningful for all designs and treatment effects considered, and to be substantial for designs frequently proposed in the literature.
A pathway EM‐algorithm for estimating vaccine efficacy with a non‐monotone validation set
Authors: Yang Yang , Halloran M. Elizabeth , Chen Yanjun , Kenah Eben 
Published: April 2014

SummaryHere, we consider time‐to‐event data where individuals can experience two or more types of events that are not distinguishable from one another without further confirmation, perhaps by laboratory test. The event type of primary interest can occur only once. The other types of events can recur. If the type of a portion of the events is identified, this forms a validation set. However, even if a random sample of events are tested, confirmations can be missing nonmonotonically, creating uncertainty about whether an individual is still at risk for the event of interest. For example, in a study to estimate efficacy of an influenza vaccine, an individual may experience a sequence of symptomatic respiratory illnesses caused by various pathogens over the season. Often only a limited number of these episodes are confirmed in the laboratory to be influenza‐related or not. We propose two novel methods to estimate covariate effects in this survival setting, and subsequently vaccine efficacy. The first is a pathway expectation‐maximization (EM) algorithm that takes into account all pathways of event types in an individual compatible with that individual's test outcomes. The pathway EM iteratively estimates baseline hazards that are used to weight possible event types. The second method is a non‐iterative pathway piecewise validation method that does not estimate the baseline hazards. These methods are compared with a previous simpler method. Simulation studies suggest mean squared error is lower in the efficacy estimates when the baseline hazards are estimated, especially at higher hazard rates. We use the pathway EM‐algorithm to reevaluate the efficacy of a trivalent live‐attenuated influenza vaccine during the 2003–2004 influenza season in Temple‐Belton, Texas, and compare our results with a previously published analysis.
Cardiovascular event risk dynamics over time in older patients on dialysis: A generalized multiple‐index varying coefficient model approach
Authors: Estes Jason P. , Nguyen Danh V. , Dalrymple Lorien S. , Mu Yi , Şentürk Damla 
Published: April 2014

SummaryAmong patients on dialysis, cardiovascular disease and infection are leading causes of hospitalization and death. Although recent studies have found that the risk of cardiovascular events is higher after an infection‐related hospitalization, studies have not fully elucidated how the risk of cardiovascular events changes over time for patients on dialysis. In this work, we characterize the dynamics of cardiovascular event risk trajectories for patients on dialysis while conditioning on survival status via multiple time indices: (1) time since the start of dialysis, (2) time since the pivotal initial infection‐related hospitalization, and (3) the patient's age at the start of dialysis. This is achieved by using a new class of generalized multiple‐index varying coefficient (GM‐IVC) models. The proposed GM‐IVC models utilize a multiplicative structure and one‐dimensional varying coefficient functions along each time and age index to capture the cardiovascular risk dynamics before and after the initial infection‐related hospitalization among the dynamic cohort of survivors. We develop a two‐step estimation procedure for the GM‐IVC models based on local maximum likelihood. We report new insights on the dynamics of cardiovascular events risk using the United States Renal Data System database, which collects data on nearly all patients with end‐stage renal disease in the United States. Finally, simulation studies assess the performance of the proposed estimation procedures.
Nonpharmacologic Approaches for Pain Management During Labor Compared with Usual Care: A Meta‐Analysis
Authors: Chaillet Nils , Belaid Loubna , Crochetière Chantal , Roy Louise , Gagné Guy‐Paul , Moutquin Jean Marie , Rossignol Michel , Dugas Marylène , Wassef Maggy , Bonapace Julie 
Published: April 2014

AbstractObjectivesTo assess the effects of nonpharmacologic approaches to pain relief during labor, according to their endogenous mechanism of action, on obstetric interventions, maternal, and neonatal outcomes.Data sourceCochrane library, Medline, Embase, CINAHL and the MRCT databases were used to screen studies from January 1990 to December 2012.Study selectionAccording to Cochrane criteria, we selected randomized controlled trials that compared nonpharmacologic approaches for pain relief during labor to usual care, using intention‐to‐treat method.ResultsNonpharmacologic approaches, based on Gate Control (water immersion, massage, ambulation, positions) and Diffuse Noxious Inhibitory Control (acupressure, acupuncture, electrical stimulation, water injections), are associated with a reduction in epidural analgesia and a higher maternal satisfaction with childbirth. When compared with nonpharmacologic approaches based on Central Nervous System Control (education, attention deviation, support), usual care is associated with increased odds of epidural OR 1.13 (95% CI 1.05–1.23), cesarean delivery OR 1.60 (95% CI 1.18–2.18), instrumental delivery OR 1.21 (95% CI 1.03–1.44), use of oxytocin OR 1.20 (95% CI 1.01–1.43), labor duration (29.7 min, 95% CI 4.5–54.8), and a lesser satisfaction with childbirth. Tailored nonpharmacologic approaches, based on continuous support, were the most effective for reducing obstetric interventions.ConclusionNonpharmacologic approaches to relieve pain during labor, when used as a part of hospital pain relief strategies, provide significant benefits to women and their infants without causing additional harm.