bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in ectomycorrhizal fungal community composition and declining diversity along a 2‐million‐year soil chronosequence
Authors: Albornoz Felipe E. , Teste François P. , Lambers Hans , Bunce Michael , Murray Dáithí C. , White Nicole E. , Laliberté Etienne 
Published: August 2016

AbstractEctomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co‐occurring ECM plant species (to control for host identity) in soils collected along a 2‐million‐year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal inoculum. Ectomycorrhizal fungal community composition changed and richness declined with increasing soil age; these changes were linked to pedogenesis‐driven shifts in edaphic properties, particularly pH and resin‐exchangeable and organic phosphorus. However, when differences in inoculum potential or soil abiotic properties among soil ages were removed while host identity was held constant, differences in ECM fungal communities and richness among chronosequence stages disappeared. Our results show that ECM fungal communities strongly vary during long‐term ecosystem development, even within the same hosts. However, these changes could not be attributed to short‐term fungal edaphic specialization or differences in fungal inoculum (i.e. density and composition) alone. Rather, they must reflect longer‐term ecosystem‐level feedback between soil, vegetation and ECM fungi during pedogenesis.
Body mass‐corrected molecular rate for bird mitochondrial DNA
Authors: Nabholz Benoit , Lanfear Robert , Fuchs Jérome 
Published: August 2016

AbstractMitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species’ body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.
The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi‐arid soils
Authors: Bastida Felipe , Torres Irene F. , Moreno José L. , Baldrian Petr , Ondoño Sara , Ruiz‐Navarro Antonio , Hernández Teresa , Richnow Hans H. , Starke Robert , García Carlos , Jehmlich Nico 
Published: August 2016

AbstractBiogeochemical processes and ecosystemic functions are mostly driven by soil microbial communities. However, most methods focus on evaluating the total microbial community and fail to discriminate its active fraction which is linked to soil functionality. Precisely, the activity of the microbial community is strongly limited by the availability of organic carbon (C) in soils under arid and semi‐arid climate. Here, we provide a complementary genomic and metaproteomic approach to investigate the relationships between the diversity of the total community, the active diversity and ecosystem functionality across a dissolved organic carbon (DOC) gradient in southeast Spain. DOC correlated with the ecosystem multifunctionality index composed by soil respiration, enzyme activities (urease, alkaline phosphatase and β‐glucosidase) and microbial biomass (phospholipid fatty acids, PLFA). This study highlights that the active diversity (determined by metaprotoemics) but not the diversity of the whole microbial community (evaluated by amplicon gene sequencing) is related to the availability of organic C and it is also connected to the ecosystem multifunctionality index. We reveal that DOC shapes the activities of bacterial and fungal populations in Mediterranean semi‐arid soils and determines the compartmentalization of functional niches. For instance, Rhizobales thrived at high‐DOC sites probably fuelled by metabolism of one‐C compounds. Moreover, the analysis of proteins involved in the transport and metabolism of carbohydrates revealed that Ascomycota and Basidiomycota occupied different nutritional niches. The functional mechanisms for niche specialization were not constant across the DOC gradient.
INTEGER PROGRAMMING APPROACH TO CONTROL INVASIVE SPECIES SPREAD BASED ON CELLULAR AUTOMATON MODEL
Authors: YOSHIMOTO ATSUSHI , ASANTE PATRICK , KONOSHIMA MASASHI , SUROVÝ PETER 
Published: August 2016

AbstractWe propose a new optimization model that captures the spatial dynamics of invaders by a cellular automaton model and finds the optimal solution to control its spread within a 0–1 integer programming framework. The model seeks a solution by minimizing the total costs to implement treatments for preventing the spread and damage caused by invaders’ colonization. By incorporating a cellular automaton model governed by state‐ and distance‐dependent probability rule of colonization, the model is transformed into a linear model, so that a 0–1 integer programming formulation is used to evaluate and compare an optimal allocation of treatments on colonized and uncolonized areas. The study uses a hypothetical map to show that treatments on colonized cells are more effective when implemented at the front line of the invaders, while treatments on uncolonized areas are effective when conducted with some distance or buffer zone away from the front line. These buffer zones are likely to be colonized regardless of treatment. Under annual budget limits, treatments on colonized cells are implemented first. With heterogeneity in the invaders’ dynamics, the proposed optimization model provides an optimal allocation of treatments much different from the solution with homogeneous environment. However, treatment at the front line of the invading species is always recommended.
Expression pattern of matrix metalloproteinases changes during folliculogenesis in the cat ovary
Authors: Fujihara M , Yamamizu K , Wildt DE , Songsasen N 
Published: August 2016

ContentsMatrix metalloproteinase (MMP) has been implicated as having roles in ovarian folliculogenesis. Here, we determined the expression pattern of six MMPs (MMP1, MMP2, MMP3, MMP7, MMP9 and MMP13) and their endogenous tissue inhibitor, TIMP1, during cat follicle growth. Different developmental stage follicles were mechanically isolated and gene expression analysed by real‐time qPCR while MMP1, 2, 9 and 13 localization was determined by immunohistochemistry. With the exception of MMP13, the amount of MMP mRNA was lowest in primordial follicles and increased thereafter. Peak levels were detected in early antral follicles for MMP1 (72.2‐fold increase above primordial follicle amount), MMP2 (10‐fold), MMP3 (57‐fold) and MMP9 (2.8‐fold). MMP7 transcripts increased 2‐fold by the primary follicle stage and then plateaued. MMP13 mRNA peaked in primary follicles (2.5‐fold) and was lower in more advanced counterparts. TIMP1 sharply increased (6‐fold) in secondary follicles and gradually declined in the later stages. MMP1 and MMP9 expression were expressed in the granulosa cells of all follicle stages. MMP2 was immunoreactive in early and antral follicles, especially at granulosa cells adjacent to the antral cavity. By contrast, the MMP13 was weakly detected in primary follicles onward. In summary, there are distinctive and consistent changes in MMPs and TIMP1 expression during follicle development, suggesting that these enzymes play one or more roles in cat folliculogenesis. In particular, high mRNA and protein expression levels of MMP1 and MMP2, especially at the antral stage, indicate that these enzymes likely are involved in antrum formation and expansion.
It's a Sin—Contraceptive Use, Religious Beliefs, and Long‐run Economic Development
Authors: Prettner Klaus , Strulik Holger 
Published: August 2016

AbstractThis study presents a novel theory on the interaction of social norms, fertility, education, and their joint impact on long‐run economic development. The theory takes into account that sexual intercourse is utility enhancing and that the use of modern contraceptives potentially conflicts with prevailing social norms (religious beliefs). The theory motivates the existence of two steady states. At the traditional steady state, the economy stagnates, fertility is high, education is minimal, and the population sustains a norm according to which modern contraceptives are not used. At the modern steady state, the population has abandoned traditional beliefs, modern contraceptives are used, fertility is low and education and economic growth are high. Social dynamics explain why both equilibria are separated by a saddlepoint‐equilibrium (a separatrix), i.e. why it is so hard to transit from the traditional regime to the modern regime.
More‐than‐Active Food Citizens: A Longitudinal and Comparative Study of Alternative and Conventional Eaters
Authors: Carolan Michael 
Published: August 2016

AbstractThis article has multiple aims: (1) to understand, with the help of descriptive statistics, how eaters engaged within various alternative foodscapes compare to more conventional eaters when asked questions about things like their interest in local politics, whether they volunteer, and their reasons for buying local foods; (2) to map, with the help of descriptive statistics, changes in how individuals respond to questions after being “exposed” to certain alternative foodscape experiences; (3) and to understand, with the help of practice theory and qualitative data, why individuals might think and behave differently after being exposed to these alternative doings and sayings, findings that lead to a discussion about how aspects of these alternative foodscapes engender the making of more‐than‐active citizens. A research team studied individuals in Colorado who had recently begun participating in one of the following practices: (1) drop‐off community‐supported agriculture (CSA), (2) CSA volunteer membership, (3) farmers’ market, and (4) member‐owned food cooperative. Researchers surveyed participants and resurveyed them two years later, at which time sampled eaters were also engaged in an extensive qualitative interview, with a total of 119 personal interviews conducted. In addition, the team conducted a phone survey (n = 106) of randomly selected residents in Colorado to represent conventional eaters.
Effect of floorball training on blood lipids, body composition, muscle strength, and functional capacity of elderly men
Authors: Vorup J. , Pedersen M. T. , Melcher P. S. , Dreier R. , Bangsbo J. 
Published: August 2016

Floorball training consists of intense repeated exercise and may offer a motivating and social stimulating team activity in elderly individuals. However, the effect of floorball training in elderly adults on physiological adaptations important for health is not known. Thus, this study examined the effect of floorball training on blood lipids, muscle strength, body composition, and functional capacity of men aged 65–76 years. Thirty‐nine recreational active men were randomized into a floorball group (FG;n = 22) or petanque group (PG;n = 17), in which training was performed 1 h twice a week for 12 weeks. InFGandPG, average heart rate (HR) during training was 80% and 57%, respectively, of maximalHR. InFG, plasma low‐density lipoprotein (LDL) cholesterol and triglycerides were 11% and 8% lower (P < 0.05), respectively. Insulin resistance determined by homeostatic model assessment (HOMA‐IR) was reduced (P < 0.05) by 18%.HRduring submaximal cycling was 5% lower (P < 0.05), and maximal voluntary contraction force was 8% higher (P < 0.05). Total and visceral fat content was lowered (P < 0.05) by 5% and 14%, respectively,HRat rest was 8% lower (P < 0.05) and performance in four different functional capacity tests were better (P < 0.05) after compared to before the training period. No changes were observed inPG. In conclusion, 12 weeks of floorball training resulted in a number of favorable effects important for health and functional capacity, suggesting that floorball training can be used as a health‐promoting activity in elderly men.
On the Importance of Family, Morality, Masculine, and Feminine Honor for Theory and Research
Authors: Rodriguez Mosquera Patricia M. 
Published: August 2016

AbstractThis paper presents an approach to honor as multifaceted. In this approach, honor is defined as having four different facets, or honor codes: morality‐based honor, family honor, masculine honor, and feminine honor. The honor‐as‐multifaceted approach has generated much psychological research examining the importance of each honor code across different cultural and social groups. An overview of this research shows that that the different honor codes exert a powerful influence on a variety of group processes, including collective action, in‐group identification, the definition of gendered roles within the family, in‐group responses to threats to collective honor, intergroup attitudes, and value change within groups. The paper discusses how defining and measuring honor as multifaceted ‐rather than as an unitary construct‐ provides a fuller understanding of honor's role in group life.
Comparison of two apheresis systems during hematopoietic progenitor stem cell collections at a tertiary medical center
Authors: Li Yanchun , Li Jie , Reeves Hollie M. , Reyes Ramil , Maitta Robert W. 
Published: August 2016

BACKGROUNDThe Spectra Optia is a newer apheresis system developed based on the COBE Spectra platform. COBE Spectra requires more manual control, while Spectra Optia offers greater automation. The purpose of this study was to compare the two systems during hematopoietic progenitor stem cell (HPSC) collections.STUDY DESIGN AND METHODSA retrospective review of 41 collections performed in 26 subjects at a tertiary medical center between June 1, 2013, and December 31, 2013, was conducted, 11 with the Spectra Optia and 30 with the COBE Spectra. Six patients underwent two consecutive daily collections, first on the Spectra Optia followed by the COBE Spectra.RESULTSProcedure run time with the Spectra Optia was considerably longer than with the COBE Spectra (283 ± 11 min vs. 217 ± 2 min, respectively; p < 0.01). Mean CD34+ cell yields with the Spectra Optia were comparable with those of the COBE Spectra. Products collected with the Spectra Optia had less red blood cell contamination. However, platelet (PLT) attrition was greater with the Spectra Optia. Similar results were obtained in patients who were collected on consecutive days in both systems.CONCLUSIONCollections with the Spectra Optia take longer and lead to greater PLT losses during HPSC collections.
RT‐qPCR for the diagnosis of dermatophilosis in horses
Authors: Frank Linda A. , Kania Stephen A. , Weyant Ellie 
Published: August 2016

BackgroundDermatophilus congolensis causes a crusting dermatitis that affects horses. Diagnosis requires the identification of the organism with cytological evaluation of crust samples. This method can lack sensitivity in chronic cases.Hypothesis/ObjectivesTo develop a probe‐based real time quantitative polymerase chain reaction (RT‐qPCR) test to assist with the diagnosis of dermatophilosis in horses.AnimalsTwenty six privately owned horses and seven horses from a research colony were used.MethodsCrust samples, collected from 14 horses with suspected dermatophilosis and 12 horses with crusting skin disease not characteristic of dermatophilosis, were evaluated by cytological evaluation and RT‐qPCR; the latter was also performed on hair samples collected from seven healthy horses.ResultsCytological evaluation revealed organisms consistent with Dermatophilus congolensis from nine horses with suspected dermatophilosis, with only a few organisms seen from five samples. Cytological evaluation of all other crusts was negative for Dermatophilus. Other bacterial organisms were detected on cytological evaluation from 15 samples. RT‐qPCR for Dermatophilus was positive from 11 crusts, whereas all other samples were negative. Two samples were cytologically negative but RT‐qPCR positive for Dermatophilus. No samples were cytologically positive but RT‐qPCR negative for Dermatophilus.ConclusionResults of this study show that RT‐qPCR may be a more sensitive and easier method than cytological evaluation for the diagnosis of dermatophilosis in horses.
Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization
Authors: Capel Elena , Zomer Aldert L. , Nussbaumer Thomas , Bole Christine , Izac Brigitte , Frapy Eric , Meyer Julie , Bouzinba-Ségard Haniaa , Bille Emmanuelle , Jamet Anne , Cavau Anne , Letourneur Franck , Bourdoulous Sandrine , Rattei Thomas , Nassif Xavier , Coureuil Mathieu 
Published: August 2016

ABSTRACT

Neisseria meningitidis
is a leading cause of bacterial meningitis and septicemia, affecting infants and adults worldwide.
N. meningitidis
is also a common inhabitant of the human nasopharynx and, as such, is highly adapted to its niche. During bacteremia,
N. meningitidis
gains access to the blood compartment, where it adheres to endothelial cells of blood vessels and causes dramatic vascular damage. Colonization of the nasopharyngeal niche and communication with the different human cell types is a major issue of the
N. meningitidis
life cycle that is poorly understood. Here, highly saturated random transposon insertion libraries of
N. meningitidis
were engineered, and the fitness of mutations during routine growth and that of colonization of endothelial and epithelial cells in a flow device were assessed in a transposon insertion site sequencing (Tn-seq) analysis. This allowed the identification of genes essential for bacterial growth and genes specifically required for host cell colonization. In addition, after having identified the small noncoding RNAs (sRNAs) located in intergenic regions, the phenotypes associated with mutations in those sRNAs were defined. A total of 383 genes and 8 intergenic regions containing sRNA candidates were identified to be essential for growth, while 288 genes and 33 intergenic regions containing sRNA candidates were found to be specifically required for host cell colonization.

IMPORTANCE
Meningococcal meningitis is a common cause of meningitis in infants and adults.
Neisseria meningitidis
(meningococcus) is also a commensal bacterium of the nasopharynx and is carried by 3 to 30% of healthy humans. Under some unknown circumstances,
N. meningitidis
is able to invade the bloodstream and cause either meningitis or a fatal septicemia known as purpura fulminans. The onset of symptoms is sudden, and death can follow within hours. Although many meningococcal virulence factors have been identified, the mechanisms that allow the bacterium to switch from the commensal to pathogen state remain unknown. Therefore, we used a Tn-seq strategy coupled to high-throughput DNA sequencing technologies to find genes for proteins used by
N. meningitidis
to specifically colonize epithelial cells and primary brain endothelial cells. We identified 383 genes and 8 intergenic regions containing sRNAs essential for growth and 288 genes and 33 intergenic regions containing sRNAs required specifically for host cell colonization.
New patient-reported experience measure for children with allergic disease: development, validation and results from integrated care
Authors: Gore C , Griffin R , Rothenberg T , Tallett A , Hopwood B , Sizmur S , O'Keeffe C , Warner J O 
Published: August 2016

ObjectivesTo develop and validate a new allergy-specific patient-reported experience measure (PREM) for children and their parents, and to collect feedback in an integrated care setting.DesignTwo allergy-specific PREMs were produced using focus groups, cognitive testing, two prospective validation studies (collaboration: Royal College of Paediatrics and Child Health, Picker Institute Europe, Imperial College/London): ‘Your Allergy Care’, for children aged 8–16 years; ‘Your Child's Allergy Care’, for parents of children aged 0–7 years.SettingCommunity event, primary/secondary/tertiary allergy care settings.Main outcome measuresPerformance of PREMs in validation study; reported experience of allergy care.Participants687 children with allergic conditions and their parents/carers.ResultsIn total, 687 questionnaires were completed; 503/687 (253 child; 250 parent) for the final survey. In both surveys, demographic variations were not associated with differences in results. Although 71% of patients reported one or more allergic conditions (food allergy/eczema/hay fever/asthma), 62% required multiple visits before receiving final diagnosis. Overall, patient experience was good for communication with patient/parent, competence and confidence in ability, and 73% felt looked after ‘very well’ and 23% ‘quite well’. Areas for improvement included communication with nurseries/schools, more information on side effects, allergic conditions and allergen/irritant avoidance. Allergy care in primary/emergency care settings was associated with higher problem-scores (worse experience) than in specialist clinics.ConclusionsThese new PREMs will allow allergy-specific patient experience reporting for children and parents and help identification of priority areas for improvement and commissioning of care. Efforts towards better allergy care provision must be targeted at primary and emergency care settings and underpinned by improving communication between healthcare providers and the community.