bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read, whole-genome shotgun sequence data for five model organisms
Authors: Kim Kristi E. , Peluso Paul , Babayan Primo , Yeadon P. Jane , Yu Charles , Fisher William W. , Chin Chen-Shan , Rapicavoli Nicole , Rank David R. , Li Joachim , Catcheside David E. A. , Celniker Susan E. , Phillippy Adam M. , Bergman Casey M. , Landolin Jane M. 
Published: August 2014

AbstractSingle molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.
Evidence for shifts to faster growth strategies in the new ranges of invasive alien plants
Authors: Leishman Michelle R. , Cooke Julia , Richardson David M. 
Published: August 2014

Summary

Understanding the processes underlying the transition from introduction to naturalization and spread is an important goal of invasion ecology. Release from pests and pathogens in association with capacity for rapid growth is thought to confer an advantage for species in novel regions.

We assessed leaf herbivory and leaf‐level traits associated with growth strategy in the native and exotic ranges of 13 invasive plant species from 256 populations. Species were native to either the Western Cape region of South Africa, south‐western Australia or south‐eastern Australia and had been introduced to at least one of the other regions or to New Zealand. We tested for evidence of herbivore release and shifts in leaf traits between native and exotic ranges of the 13 species.

Across all species, leaf herbivory, specific leaf area and leaf area were significantly different between native and exotic ranges while there were no significant differences across the 13 species found for leaf mass, assimilation rate, dark respiration or foliar nitrogen.

Analysis at the species‐ and region‐level showed that eight out of 13 species had reduced leaf herbivory in at least one exotic region compared to its native range.

Six out of 13 species had significantly larger specific leaf area (SLA) in at least one exotic range region and five of those six species experienced reduced leaf herbivory. Increases in SLA were underpinned by increases in leaf area rather than reductions in leaf mass.

No species showed differences in the direction of trait shifts from the native range between different exotic regions. This suggests that the driver of selection on these traits in the exotic range is consistent across regions and hence is most likely to be associated with factors linked with introduction to a novel environment, such as release from leaf herbivory, rather than with particular environmental conditions.

Synthesis. These results provide evidence that introduction of a plant species into a novel environment commonly results in a reduction in the top‐down constraint imposed by herbivores on growth, allowing plants to shift towards a faster growth strategy which may result in an increase in population size and spread and consequently to invasive success.
Seasonality of precipitation interacts with exotic species to alter composition and phenology of a semi‐arid grassland
Authors: Prevéy Janet S. , Seastedt Timothy R. 
Published: August 2014

Summary

While modelling efforts suggest that invasive species will track climate changes, empirical studies are few. A relevant and largely unaddressed research question is ‘How will the presence of exotic species interact with precipitation change to alter ecosystem structure and function?’

We studied the effects of changes in seasonal timing of precipitation on species composition and resource availability in a grassland community in Colorado, USA. We examined how seasonal precipitation patterns affect the abundance of historically present (native) and recently arrived (exotic) plant species, as well as soil moisture, nitrogen and above‐ground biomass. Over 4 years, we applied four precipitation treatments based on climate model predictions for the study area: winter‐wet/summer‐ambient, winter‐wet/summer‐dry, winter‐wet/summer‐wet and winter‐dry/summer‐wet.

Cover of exotic winter‐active grasses was greater in winter‐wet treatments than in control or winter‐dry treatments. Cover of native warm‐season grasses and forbs was greatest in the winter‐dry/summer‐wet treatment, and lowest in the winter‐wet/summer‐dry treatment. These results support the expectation that increased winter precipitation benefits new arrivals, whereas increased summer precipitation benefits later‐growing native plants.

Structural equation models showed that interactive effects of increased winter precipitation and increased cover of winter‐active grasses reduced growing season soil water content and species diversity. In addition, the dominant winter‐active species, Bromus tectorum, flowered and senesced earlier in plots receiving increased winter precipitation and reduced summer precipitation, suggesting that earlier growth of winter‐active grasses decreases available soil resources and impacts later‐growing native plants. Peak above‐ground biomass was lowest in the treatment receiving reduced summer precipitation, but only in years with dry springs. Plant‐available nitrogen in spring was lower in plots receiving supplemental winter precipitation, and highest in plots with reduced winter precipitation.

Synthesis. Our results indicate that altering the seasonality of precipitation can have large direct effects on plant community composition and phenology, as well as significant indirect effects, mediated through exotic species, on plant‐available resources and plant interactions.
A novel mechanism for grazing lawn formation: large herbivore‐induced modification of the plant–soil water balance
Authors: Veldhuis Michiel P. , Howison Ruth A. , Fokkema Rienk W. , Tielens Elske , Olff Han 
Published: August 2014

Summary

Large herbivores play a key role in creating spatial heterogeneity through the formation of grazing lawns. Recent research suggests that the currently accepted nutrient‐based theory on the formation of these grazing lawns cannot universally explain their formation in all ecosystems where they are found.

We developed and investigated an alternative hypothesis on grazing lawn formation and maintenance based on herbivore effects on the plant–soil water balance. We propose that large herbivores change the soil water balance in grazing lawns through defoliation and soil compaction, causing a shift in vegetation composition towards a drought‐tolerant plant community.

Investigating this idea in a tropical savanna, we indeed found profound differences in grazing lawn soil properties and water balance. In particular, defoliation increased soil temperatures and potential evaporation rates while soil compaction increased bulk density and decreased water infiltration rates, especially on fine‐textured soils. Soil moisture was therefore generally much lower in grazing lawns than in adjacent bunch grass areas.

Furthermore, we found that grazing lawn species show drought‐tolerant traits, with higher leaf sodium levels, suggesting evolutionary adaptation to these herbivore‐induced dry conditions. However, leaf water potentials did not differ between grazing lawn and bunch grass species.

Synthesis. This study shows that large herbivores might form grazing lawns through previously underestimated effects on water balance. Thus, future studies on large herbivore effects on vegetation should increasingly focus on additional pathways of soil compaction and defoliation. While nutrient‐based processes driving grazing lawn formation may operate during the wet season in savannas, we suggest that water balance‐based processes are additionally important during the dry season.
Spoilage by Alicyclobacillus Bacteria in Juice and Beverage Products: Chemical, Physical, and Combined Control Methods
Authors: Tianli Yue , Jiangbo Zhang , Yahong Yuan 
Published: August 2014

AbstractAlicyclobacillus is a genus of spoilage bacteria causing contamination of juices and other beverage products that cannot easily be contaminated by other microbes because of their high acid contents. During the last 4 decades since the first species of Alicyclobacillus was isolated in 1967, Alicyclobacillus has become a major concern to the global juice and beverage industries, and many promising methods have been developed and applied to control them. After introducing the history and general characteristics of Alicyclobacillus, as well as their heat resistance and spoilage, this review focuses on the control methods against Alicyclobacillus, including chemical and physical methods and combined methods. All these control methods show inhibitory or killing effects against Alicyclobacillus to some extent and, moreover, some of them have been put to use in the juice and beverage industries for decades and shown to be quite effective, although further developments can be achieved and new methods are constantly being established and investigated. Although it is difficult to compare the effects with one another among these methods because of the different experimental conditions in different reports, some of them, such as the treatments of nisin and high hydrostatic pressure, are well studied and proved to have extensive application prospect. The inhibitory factors, test strains and media, and especially the detailed experimental conditions and main results of these control methods are summarized here. The limitations of some methods mainly relating to the changes of products’ sensory qualities are also presented.
Traditional Fermented Foods and Beverages from a Microbiological and Nutritional Perspective: The Colombian Heritage
Authors: Chaves‐López Clemencia , Serio Annalisa , Grande‐Tovar Carlos David , Cuervo‐Mulet Raul , Delgado‐Ospina Johannes , Paparella Antonello 
Published: August 2014

AbstractFermentation has been used for preserving foods for centuries prior to the invention of pasteurization and sterilization, and every culture has a variety of fermented products as part of its diet. This paper reviews the diversity of fermented foods and beverages from Latin America; these fermented products are produced by traditional methods that exploit mixed cultures of various nonpathogenic microorganisms. Fermented foods covered in this review include maize, cassava, palm sap, sugar cane juice, cocoa, and milk. We explore the history of some Colombian fermented foods and beverages, which are today part of the tradition of some ethnic groups, and evaluate their technology, microbiology, the presence of some nutritional factors, and safety concerns. To the best of our knowledge, this is the 1st systematic review on Colombian fermented beverages and foods, and we believe that it may contribute to valorize these products that are still part of the Latin America tradition.
Interactions of Foodborne Pathogens with Free‐living Protozoa: Potential Consequences for Food Safety
Authors: Vaerewijck Mario J.M. , Baré Julie , Lambrecht Ellen , Sabbe Koen , Houf Kurt 
Published: August 2014

AbstractFree‐living protozoa (FLP) are ubiquitous in natural ecosystems where they play an important role in the reduction of bacterial biomass and the regeneration of nutrients. However, it has been shown that some species such as Acanthamoeba castellanii, Acanthamoeba polyphaga, and Tetrahymena pyriformis can act as hosts of pathogenic bacteria. There is a growing concern that FLP might contribute to the maintenance of bacterial pathogens in the environment. In addition to survival and/or replication of bacterial pathogens in FLP, resistance to antimicrobial agents and increased virulence of bacteria after passage through protozoa have been reported. This review presents an overview of FLP in food‐associated environments and on foods, and discusses bacterial interactions with FLP, with focus on the foodborne pathogens Campylobacter jejuni, Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes. The consequences of these microbial interactions to food safety are evaluated.
A Guidance Document on the Best Practices in Food Traceability
Authors: Zhang Jianrong , Bhatt Tejas 
Published: August 2014

AbstractSeveral regulatory agencies around the world are involved in rulemaking to improve the traceability of foods. Given the complexity of the global food system, guidance on improving traceability practices across the entire food industry is a challenge. A review of the current regulations and best practices indicates that “one back, one forward” is the minimum traceability requirement. There are also no uniform requirements across different food sectors, supply chains, or countries for collection of Critical Tracking Events (CTEs) and Key Data Elements (KDEs). There is a need for standardized and harmonized requirements across all food sectors compared with developing specialized rules and mandates, including exceptions, for specific foods. This document presents food traceability best practices guidance and it addresses the unknowns and gaps in understanding and the broad applicability of a CTE–KDE framework. It applies this framework to 6 food sectors as bakery, dairy, meat and poultry, processed foods, produce, and seafood. An analysis of similarities and differences across these sectors is conducted to determine broader applicability to other foods. Fifty‐five experts from 11 countries were involved in developing this guidance. This guidance document is intended for regulatory agencies and the food industry. Regulators will find it useful in developing regulations and/or guidance applicable to most foods. Industry will find the minimum criteria that are necessary to manage a proper food traceability system, with the understanding that companies can choose to exceed the minimum level of criteria established. This guidance is intended to serve as a step toward consistent baseline requirements for food traceability.
Homeland Heroes: Migrants and Soldiers in the Neoliberal Era
Authors: Brigden Noelle Kateri , Vogt Wendy A. 
Published: August 2014

AbstractThis paper examines the dynamic relationship between neoliberalism and nationalism through the counterintuitive comparison of journeys travelled by US citizens as they enlist in the military and by unauthorized Central Americans as they migrate to the United States. We argue that, however different the context and content of their decisions and their lives, Central American migrants and US soldiers are both connected within a larger political economy. We complicate the idea of migrants and soldiers as purely rational economic actors, but we also reject the idea, imputed onto migrants and soldiers by neoliberal states, that they are naturally nationalistic actors. Migrants and soldiers embody a neoliberal subjectivity produced through processes of violence, capital accumulation and militarization. Yet, as we examine throughout this paper, their construction as homeland heroes within the national imaginary masks the ways their labor and their mobility serve the institutionalization of neoliberal statecraft.
Audio spectrum analysis of umbilical artery Doppler ultrasound signals applied to a clinical material
Authors: Thuring Ann , Brännström K.Jonas , Jansson Tomas , Maršál Karel 
Published: August 2014

AbstractAnalysis of umbilical artery flow velocity waveforms characterized by pulsatility index (PI) is used to evaluate fetoplacental circulation in high‐risk pregnancies. However, an experienced sonographer may be able to further differentiate between various timbres of Doppler audio signals. Recently, we have developed a method for objective audio signal characterization; the method has been tested in an animal model. In the present pilot study, the method was for the first time applied to human pregnancies. Doppler umbilical artery velocimetry was performed in 13 preterm fetuses before and after two doses of 12 mg betamethasone. The auditory measure defined by the frequency band where the spectral energy had dropped 15 dB from its maximum level (MAXpeak‐15 dB), increased two days after betamethasone administration (p = 0.001) parallel with a less pronounced decrease in PI (p = 0.04). The new auditory parameter MAXpeak‐15 dB reflected the changes more sensitively than the PI did.
Mode of delivery and subsequent reproductive patterns. A national follow‐up study
Authors: Fussing‐Clausen Caroline , Geirsson Reynir T. , Hansen Thomas , Rasmussen Steen , Lidegaard Øjvind , Hedegaard Morten 
Published: August 2014

AbstractObjectiveTo investigate associations between mode of delivery and subsequent reproductive outcomes.DesignCohort study.PopulationWomen with term singleton live births from 1987 to 2009.SettingDenmark, birth registration data.MethodsWomen with a first singleton delivery after 37 weeks were followed until the end of 2010, from a first birth to include subsequent live births. We used Cox's proportional hazards model stratified by parity to compare the likelihood for subsequent delivery according to mode of delivery at first and later births, estimating maternal age effects and lag time to next delivery.Main outcome measureLikelihood of a subsequent live‐born child by previous delivery mode.ResultsWe identified 642 052 women with a first delivery. Compared with women with a non‐instrumental vaginal delivery, delivering a child by elective cesarean section implied a 23% (95% CI 0.76–0.787) decreased likelihood for subsequent delivery. Emergency cesarean section meant 16% fewer (95% CI 0.84–0.85), and vaginal instrumental delivery 4% fewer subsequent deliveries (95% CI 0.95–0.96). Hazard ratios were largely unchanged after controlling for parity and year of birth. Small age‐trends were seen, with hazard ratios affected by maternal age at birth. Delivery mode at first birth affected marginally the time lag until next birth.ConclusionsFecundity, measured as likelihood of a successive live‐born child, varied with mode of delivery at the first and also subsequent births. A first or later delivery by cesarean section implied decreased likelihood of subsequent delivery compared with women with a first vaginal birth.
Maternal age and serum concentration of human chorionic gonadotropin in early pregnancy
Authors: Haavaldsen Camilla , Fedorcsak Peter , Tanbo Tom , Eskild Anne 
Published: August 2014

AbstractObjectiveTo study whether maternal age is associated with serum concentration of human chorionic gonadotropin in early pregnancy.DesignCross‐sectional study.SettingOslo University Hospital in Oslo, Norway.PopulationAll vital pregnancies in gestational week 8 conceived by in vitro fertilization between February 1996 and February 2013 (n = 4472).MethodsSerum concentrations of human chorionic gonadotropin were measured on day 12 after embryo transfer/day 16 following ovulation induction. Trends in geometric means of human chorionic gonadotropin concentrations by maternal age group were tested by linear regression analysis. We also studied the association of maternal age (years) with log‐transformed human chorionic gonadotropin concentrations, and adjustments were made for number of embryos transferred, method of in vitro fertilization and year (period) of embryo transfer.Main outcome measureSerum concentration of human chorionic gonadotropin.ResultsGeometric mean concentrations of human chorionic gonadotropin decreased with increasing maternal age (p = 0.024, test for trend by weighted linear regression). Also, we estimated a significant negative association of maternal age with log‐transformed human chorionic gonadotropin concentrations (adjusted regression coefficient −0.011, standard error 0.003, p < 0.001).ConclusionsSerum concentrations of human chorionic gonadotropin in very early pregnancy decreased with maternal age. Since human chorionic gonadotropin is synthesized in trophoblast cells only, the lower human chorionic gonadotropin concentrations in women of advanced age may reflect functional impairment or delayed proliferation of trophoblast cells in early pregnancy in these women.
B‐type natriuretic peptide measurement for early diagnosis of acute pulmonary edema during pregnancy
Authors: Seror Jeremy , Lefevre Guillaume , Berkane Nathalie , Richard Frederic , Bornes Marie , Uzan Serge , Berkane Nadia 
Published: August 2014

AbstractCalcium‐channel blockers administered to pregnant women as tocolytic agents can cause acute pulmonary edema. The first signs of this severe complication can be atypical and so delay introduction of appropriate therapy. We describe three cases in whom B‐type natriuretic peptide measurements proved to be relevant in early diagnosis and monitoring of pregnant women with acute pulmonary edema. B‐type natriuretic peptide measurement in this setting could contribute to timely diagnosis and improve follow‐up.
General, but not abdominal, overweight increases odds of asthma among Norwegian adolescents: the Young‐HUNT study
Authors: Egan Kathryn B. , Ettinger Adrienne S. , DeWan Andrew T. , Holford Theodore R. , Holmen Turid Lingaas , Bracken Michael B. 
Published: August 2014

AbstractAimThe aim of this analysis was to examine the association between asthma and general and abdominal weight status, defined by age‐ and sex‐specific cut‐offs for body mass index (BMI) and waist circumference (WC) in adolescents.MethodsParticipants aged 12–19 years in the Young‐HUNT (YH) Study (YH1 1995–1997: n = 8222; YH3 2006–2008: n = 7403) completed self‐administered questionnaires in school as part of a series of cross‐sectional, population‐based studies conducted in Nord‐Trøndelag, Norway. Weight, height and WC were measured. Adjusted odds ratios (ORs) and 95% Confidence Intervals (CI) for asthma, defined by self‐reported physician diagnosis, were calculated. Potential effect modifiers evaluated included sex and pubertal development status (PDS).ResultsAsthma was reported by 11.8% of the adolescents in YH1 and 17.0% in YH3. Asthma odds significantly increased for adolescents with general (OR = 1.33; 95%CI: 1.13, 1.56), but not abdominal, overweight and increased for adolescents with general (OR = 1.34; 95%CI: 1.02, 1.75) or abdominal obesity (OR = 1.36; 95%CI: 1.16, 1.60). Underweight had no association with asthma regardless of weight assessment type, and PDS did not meaningfully influence the associations between asthma and weight.ConclusionOverweight and obesity both increased the odds of asthma in 12–19 year‐old Norwegians. WC did not add further information to that already provided by BMI to improve our understanding of the association between asthma and weight.