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Data from: Above and belowground responses of four tundra plant functional types to deep soil heating and surface soil fertilization
1.Climate warming is faster in the Arctic than the global average. Nutrient availability in the tundra soil is expected to increase by climate warming through 1) accelerated nutrient mobilization in the surface soil layers, and 2) increased thawing depths during the growing season which increases accessibility of nutrients in the deeper soil layers. Both processes may initiate shifts in tundra vegetation composition. It is important to understand the effects of these two processes on tundra plant functional types. 2.We manipulated soil thawing depth and nutrient availability at a Northeast-Siberian tundra site to investigate their effects on above and belowground responses of four plant functional types (grasses, sedges, deciduous shrubs and evergreen shrubs). Seasonal thawing was accelerated with heating cables at ~15 cm depth without warming the surface soil, whereas nutrient availability was increased in the surface soil by adding slow-release NPK fertilizer at ~5 cm depth. A combination of these two treatments was also included. This is the first field experiment specifically investigating the effects of accelerated thawing in tundra ecosystems. 3.Deep soil heating increased the aboveground biomass of sedges, the deepest-rooted plant functional type in our study, but did not affect biomass of the other plant functional types. In contrast, fertilization increased aboveground biomass of the two dwarf shrub functional types, which both had very shallow root systems. Grasses showed the strongest response to fertilization, both above and belowground. Grasses were deep-rooted, and they showed the highest plasticity in terms of vertical root distribution, as grass root distribution shifted to deep and surface soil in response to deep soil heating and surface soil fertilization, respectively. 4.Synthesis - Our results indicate that increased thawing depth can only benefit deep-rooted sedges, while the shallow-rooted dwarf shrubs as well as flexible-rooted grasses take advantage of increased nutrient availability in the upper soil layers. Our results suggest that grasses have the highest root plasticity, which enables them to be more competitive in rapidly changing environments. We conclude that root vertical distribution strategies are important for vegetation responses to climate-induced increases in soil nutrient availability in Arctic tundra, and that future shifts in vegetation composition will depend on the balance between changes in thawing depth and nutrient availability in the surface soil.
Data from: Indirect effects of a large mammalian herbivore on small mammal populations: context-dependent variation across habitat types, mammal species and seasons
Multiple consumer species frequently co-occur in the same landscape and, through effects on surrounding environments, can interact in direct and indirect ways. These interactions can vary in occurrence and importance, and focusing on this variation is critical for understanding the dynamics of interactions among consumers. Large mammalian herbivores are important engineers of ecosystems worldwide, have substantial impacts on vegetation and can indirectly affect small-mammal populations. However, the degree to which such indirect effects vary within the same system has received minimal attention. We used a 16-year-old exclosure experiment, stratified across a heterogeneous landscape, to evaluate the importance of context-dependent interactions between tule elk (Cervus canadensis nannodes) and small mammals [deer mice (Peromyscus maniculatus), meadow voles (Microtus californicus) and harvest mice (Reithrodontymys megalotis)] in a coastal grassland in California. Effects of elk on voles varied among habitats and seasons: in open grasslands, elk reduced vole numbers during fall 2013 but not summer 2014; in Lupinus-dominated grasslands, elk reduced vole numbers during summer 2014 but not fall 2013; and in Baccharis-dominated grasslands, elk had no effect on vole numbers in either season. Effects of elk on the two mice species also varied among habitats and seasons, but often in different ways from voles and each other. In fall 2013, elk decreased mice abundances in Lupinus-dominated grasslands, but not in Baccharis-dominated or open grasslands. In summer 2014, elk decreased the abundance of harvest mice consistently across habitat types. In contrast, elk increased deer-mice numbers in open grasslands but not other habitats. Within the same heterogenous study system, the influence of elk on small mammals was strongly context dependent, varying among habitats, mammal species and seasons. We hypothesize that such variability is common in nature, and that failure to consider it may yield inaccurate findings and limit our understanding of interactions among co-occurring consumers.
Data from: The effect of meal frequency in a reduced-energy regimen on the gastrointestinal and appetite hormones in patients with type 2 diabetes: a randomised crossover study
Background: Appetite and gastrointestinal hormones (GIHs) participate in energy homeostasis, feeding behavior and regulation of body weight. We demonstrated previously the superior effect of a hypocaloric diet regimen with lower meal frequency (B2) on body weight, hepatic fat content, insulin sensitivity and feelings of hunger compared to the same diet divided into six smaller meals a day (A6).Studies with isoenergetic diet regimens indicate that lower meal frequency should also have an effect on fasting and postprandial responses of GIHs.The aim of this secondary analysis was to explore the effect of two hypocaloric diet regimens on fasting levels of appetite and GIHs and on their postprandial responses after a standard meal. It was hypothesized that lower meal frequency in a reduced-energy regimen leading to greater body weight reduction and reduced hunger would be associated with decreased plasma concentrations of GIHs: gastric inhibitory peptide (GIP), glucagon-like peptide-1(GLP-1), peptide YY(PYY), pancreatic polypeptide (PP) and leptin and increased plasma concentration of ghrelin. The postprandial response of satiety hormones (GLP-1, PYY and PP) and postprandial suppression of ghrelin will be improved. Methods: In a randomized crossover study, 54 patients suffering from type 2 diabetes (T2D) underwent both regimens.The concentrations of GLP-1, GIP, PP, PYY, amylin, leptin and ghrelin were determined using multiplex immunoanalyses. Results: Fasting leptin and GIP decreased in response to both regimens with no difference between the treatments (p=0.37 and p=0.83, respectively). Fasting ghrelin decreased in A6 and increased in B2 (with difference between regimens p=0.023). Fasting PP increased in B2with no significant difference between regimens (p=0.17). Neither GLP-1 nor PYY did change in either regimen. The decrease in body weight correlated negatively with changes in fasting ghrelin (r=-0.4, p<0.043) and the postprandial reduction of ghrelin correlated positively with its fasting level (r=0.9, p<0.001). The postprandial responses of GIHs and appetite hormones were similar after both diet regimens. Conclusions: Both hypocaloric diet regimens reduced fasting leptin and GIP and postprandial response of GIP comparably. The postprandial responses of GIHs and appetite hormones were similar after both diet regimens. Eating only breakfast and lunch increased fasting plasma ghrelin more than the same caloric restriction split into six meals. The changes in fasting ghrelin correlated negatively with the decrease in body weight. These results suggest that for type 2 diabetic patients on a hypocaloric diet, eating larger breakfast and lunch may be more efficient than six smaller meals during the day.
Data from: Annotated type catalogue of the Orthalicoidea (Mollusca, Gastropoda) in the Museum für Naturkunde, Berlin
The type status is described of 96 taxa classified within the superfamily Orthalicoidea and present in the Mollusca collection of the Museum für Naturkunde der Humboldt-Universität zu Berlin. Lectotypes are designated for the following taxa: Orthalicus elegans Rolle, 1895; Bulimus maranhonensis Albers, 1854; Orthalicus nobilis Rolle, 1895; Orthalichus tricinctus Martens, 1893. Orthalicus sphinx tresmariae is introduced as new name for Zebra sphinx turrita Strebel, 1909, not Zebra quagga turrita Strebel, 1909. The following synonyms are established: Zebra crosseifischeri Strebel, 1909 = Orthalicus princeps fischeri Martens, 1893; Orthalicus isabellinus Martens, 1873 = Orthalicus bensoni (Reeve, 1849); Zebra zoniferus naesiotes Strebel, 1909 = Orthalicus undatus (Bruguière, 1789); Porphyrobaphe (Myiorthalicus) dennisoni pallida Strebel, 1909 = Hemibulimus dennisoni (Reeve, 1848); Zebra delphinus pumilio Strebel, 1909 = Orthalicus delphinus (Strebel, 1909); Orthalicus (Laeorthalicus) reginaeformis Strebel, 1909 = Corona perversa (Swainson, 1821); Bulimus (Eurytus) corticosus Sowerby III, 1895 = Plekocheilus (Eurytus) stuebeli Martens, 1885. The taxon Bulimus (Eudioptus) psidii Martens, 1877 is now placed within the family Sagdidae, tentatively in the genus Platysuccinea. Appendices are included with an index to all the types of Orthalicoidea extant (including those listed by Köhler 2007) and a partial list of letters present in the correspondence archives.
Data from: Multilocus microsatellite markers for molecular typing of Candida tropicalis isolates
Background: Candida tropicalis is considered to be the leading pathogen causing nosocomial fungemia and hepatosplenic fungal infections in patients with cancer, particularly those with leukemia. Microsatellite-based typing methods using sets of genetic markers have been developed and reported for population structure analysis of C. albicans, C. glabrata, and C. parapsilosis, but no studies have been published for genetic analysis of C. tropicalis. The objective of this study was to develop new microsatellite loci that have the ability to distinguish among C. tropicalis isolates. Results: DNA sequences containing over 10 bi- or tri-nucleotide repeats were selected from the C. tropicalis genome database. Thirty PCR primers sets specific for the microsatellite loci were designed and tested using eight clinically independent isolates. According to the amplification efficiency, specificity, and observed polymorphisms, eight markers were selected for further population structure analysis and molecular typing. Sixty-five independent C. tropicalis isolates were genotyped using these 8 markers. Based on these analyses, six microsatellite loci were confirmed, although two loci were found to be with unstable flanking areas. The six polymorphic loci displayed 4–22 alleles and 7–27 genotypes. The discriminatory power of the six loci ranged from 0.70 to 0.95. Genotyping results obtained by microsatellite analysis were compared to PCR-fingerprinting and multi-locus sequence typing (MLST). The comparisons showed that microsatellite analysis and MLST had the similar discriminatory power for C. tropicalis, which were more powerful than PCR-fingerprinting. Conclusions: This is the first attempt to develop new microsatellite loci for C. tropicalis. These newly developed markers will be a valuable resource for the differentiation of C. tropicalis isolates. More C. tropicalis isolates will need to be sequenced and analyzed in order to fully show the potential of these newly developed microsatellite markers.
Data from: Using greenhouse gas fluxes to define soil functional types
Aim: Soils provide key ecosystem services and directly control ecosystem functions; thus, there is a need to define the reference state of soil functionality. Most common functional classifications are vegetation-centered, such as plant functional types (PFTs), and neglect soil characteristics and processes. We propose Soil Functional Types (SFTs) as a conceptual approach to represent and describe the functionality of soils based on characteristics of their greenhouse gas (GHG) flux dynamics. Methods: We used automated measurements of CO2, CH4 and N2O soil fluxes in a forested area to define SFTs as surface areas with similar GHG dynamics. We performed mixed effects models, and independent cluster analyses of our environmental variables and SFT classifications. Results Unique groupings based on SFTs, but not environmental variables, supported the hypothesis that SFTs provide additional insights on the spatial variability of soil functionality beyond information represented by commonly measured soil parameters (e.g., soil moisture, soil temperature, litter biomass). Conclusions: This approach could complement vegetation-based functional classifications to better represent the broad range of ecosystem functions. A global application of the proposed SFT framework will only be possible if there is a community-wide effort to share data and create a global database of GHG emissions from soils.
Data from: Termite mounds differ in their importance for herbivores across savanna types, seasons and spatial scales
Herbivores do not forage uniformly across landscapes, but select for patches of higher nutrition and lower predation risk. Macrotermes mounds contain higher concentrations of soil nutrients and support grasses of higher nutritional value than the surrounding savanna matrix, attracting mammalian grazers that preferentially forage on termite mound vegetation. However, little is known about the spatial extent of such termite influence on grazing patterns and how it might differ in time and space. We measured grazing intensity in three African savanna types differing in rainfall and foliar nutrients and predicted that the functional importance of mounds for grazing herbivores would increase as the difference in foliar nutrient levels between mound and savanna matrix grasses increases and the mounds become more attractive. We expected this to occur in nutrient-poor areas and during the dry season when savanna matrix grass nutrient levels are lower. Tuft use and grass N and P content were measured along transects away from termite mounds, enabling calculation of the spatial extent of termite influence on mammalian grazing. Using termite mound densities estimated from airborne light detection and ranging (LiDAR), we further upscaled field-based results to determine the percentage of the landscape influenced by termite activity. Grasses in close proximity to termite mounds were preferentially grazed at all sites and in both seasons, but the strength of mound influence varied between savanna types and seasons. In the wet season, mounds had a relatively larger effect on grazers at the landscape scale in the nutrient-poor, wetter savanna, whereas in the dry season the pattern was reversed with more of the landscape influenced at the nutrient-rich, driest site. Our results reveal that termite mounds enhance the value of savanna landscapes for herbivores, but that their functional importance varies across savanna types and seasons.
Data from: Neoadjuvant and concurrent chemotherapy have varied impacts on the prognosis of patients with the ascending and descending types of nasopharyngeal carcinoma treated with intensity-modulated radiotherapy
Purpose: To compare the outcomes of patients with ascending type (T4&N0-1) and descending type (T1-2&N3) of nasopharyngeal carcinoma (NPC) treated with concurrent chemoradiotherapy (CCRT), neoadjuvant chemotherapy (NACT) + intensity-modulated radiotherapy (RT) or NACT + CCRT. Methods: Retrospective analysis of 839 patients with ascending or descending types of NPC treated at a single institution between October 2009 to February 2012. CCRT was delivered to 236 patients, NACT + RT to 302 patients, and NACT + CCRT to 301 patients. Results: The 4-year overall survival rate, distant metastasis-free survival rate, local relapse-free survival rate, nodal relapse-free survival rate, loco-regional relapse-free survival rate, and progression free survival rate were 75.2% and 73.4% (P = 0.114), 85.7% and 74.1% (P = 0.008), 88.8% and 97.1% (P = 0.013), 96.9% and 94.1% (P = 0.122), 86.9% and 91.2% (P = 0.384), 73.7% and 66.2% (P = 0.063) in ascending type and descending type. Subgroup analyses indicated that NACT + RT significantly improved distant metastasis-free survival rate and progression-free survival rate when compared with CCRT in the ascending type, and there were no significant differences between the survival curves of NACT +RT and NACT + CCRT. For descending type, there were no significant differences among the survival curves of NACT +RT, CCRT, and NACT + CCRT groups, and the survival benefit mainly came from CCRT. Conclusions: Compared with NACT + CCRT or CCRT, NACT + RT may be a reasonable approach for ascending type; Although concurrent chemotherapy was effective in descending type, NACT + CCRT may be a more appropriate strategy for descending type.
Data from: Population genetic structure within and among seasonal site types in the little brown bat (Myotis lucifugus) and the northern long-eared bat (M. septentrionalis)
During late summer and early autumn, temperate bats migrate from their summering sites to swarming sites, where mating likely occurs. However, the extent to which individuals of a single summering site migrate to the same swarming site, and vice versa, is not known. We examined the migratory connectivity between summering and swarming sites in two temperate, North American, bat species, the little brown bat (Myotis lucifugus) and the northern long-eared bat (Myotis septentrionalis). Using mitochondrial and microsatellite DNA markers, we examined population structuring within and among summering and swarming sites. Both species exhibited moderate degrees of mitochondrial DNA differentiation (little brown bat: FST(SWARMING) = 0.093, FST(SWARMING) = 0.052; northern long-eared bat: FST(SWARMING) = 0.117, FST(SWARMING) = 0.043) and little microsatellite DNA differentiation among summering and among swarming sites. Haplotype diversity was significantly higher at swarming sites than summering sites, supporting the idea that swarming sites are comprised of individuals from various summering sites. Further, pairwise analyses suggest that swarming sites are not necessarily comprised of only individuals from the most proximal summering colonies.
Data from: Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny
The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite-host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.
Risk for excessive anticoagulation during hemodialysis is associated with type of vascular access and bedside coagulation testing: Results of a cross-sectional study
<p>Anonymized dataset of the cross-sectional study assessing (i) heparin dosing within a prevalent hemodialysis cohort, (ii) the anticoagulant effects of the heparinization strategy and (iii) identifying predictive factors of the heparin dosing regimen.</p>
Linking socioeconomic inequalities and type 2 diabetes through obesity and lifestyle factors among Mexican adults: a structural equations modeling approach
<p><strong>Objective. </strong>To assess the association between type 2 diabetes (DM2) and socioeconomic inequalities, mediated by the contribution of body mass index (BMI), physical activity (PA), and diet (diet-DII). <strong>Materials and methods</strong>. We conducted a cross-sectional analysis using data of adults participating in the Diabetes Mellitus Survey of Mexico City. Socioeconomic and demographic characteristics as well as height and weight, dietary intake, leisure time activity and the presence of DM2 were measured. We fitted a structural equation model (SEM) with DM2 as the main outcome, and BMI, diet-DII and PA served as mediator variables between socioeconomic inequalities index (SII) and DM2. <strong>Results. </strong>The prevalence of DM2 was 13.6%. From the fitted SEM, each standard deviation increases in the SII was associated with increased scores of DM2 (β=0.174, <em>P</em><0.001). <strong>Conclusion. </strong>The results in the present study show how high scores in the index of SII may influence the presence of DM2.</p>
Data from: A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs
Muscle development and lipid accumulation in muscle critically affect meat quality in livestock. Yet, the underlying genetic factors for myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western breeds and Korean native pigs (KNPs) and a joint linkage-linkage disequilibrium analysis, we here identified a 488.1-kb region on porcine chromosome 12 that affects both reddish meat color (a*) and IMF. In this critical region, only the MYH3 gene, encoding myosin heavy chain 3, was found to be preferentially overexpressed in the skeletal muscle in KNPs. Subsequently, MYH3-transgenic mice demonstrated that this gene controls both myofiber-type specification and adipogenesis in skeletal muscle. We discovered a structural variant in the promotor/regulatory region of MYH3 for which Q allele carriers exhibited significantly higher values of a* and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation and co-transfection assays showed the structural variant in the 5'-UTR of MYH3 abrogated binding of the myogenic regulatory factors (MYF5, MYOD, MYOG, and MRF4). The allele distribution of the MYH3 among worldwide pig populations indicated that the MYH3 Q allele is of Asian origin and likely predates domestication. In conclusion, we identified a functional regulatory sequence variant in the porcine MYH3 that provides novel insights into the genetic basis of the regulation of myofiber type ratios and associated changes in IMF in pigs. The MYH3 variant can play an important role to improve pork quality in current breeding programs.
Data from: The Life Aquatic: an association between habitat type and skin thickness in snakes
An aquatic animal faces challenges not encountered by its terrestrial counterparts, promoting adaptive responses in multiple traits. For example, a thicker dermis might protect snakes when they are pushed against sharp objects by water currents, and might enable a snake to shed fouling organisms attached to its skin. We thus predicted that marine snakes should have thicker skin than terrestrial species; and that smaller sea snakes should have relatively thicker skin (because absolute, not relative, thickness determines vulnerability to fouling). Measurements of 192 snakes of 44 species supported those predictions. Many (but not all) sea snakes have skins 50% thicker than those of terrestrial and amphibious snake species, representing multiple independent evolutionary origins of thicker skin (in acrochordids, and Laticauda sea kraits, and both main clades of hydrophiine sea snakes). Marine snakes showed different allometries of skin thickness than did their terrestrial counterparts; larger snakes had thicker skin within and among species of amphibious and terrestrial snakes, but larger aquatic snake species had thinner skin than did smaller taxa. Interspecific variation in skin thickness was primarily due to increased collagen in the deep dermis, a physical barrier well-suited to protecting against physical injury and to resisting penetration by epibionts.
Data from: Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae)
Soil gradients are known to be an important driver of divergent natural selection in plant populations. Neotropical trees have the highest diversity on earth and it is not uncommon to find soil specialist congeners distributed parapatrically. Nevertheless very little is known about the role that edaphic heterogeneity plays in the origin and maintenance of tropical tree diversity. We predict that the mosaic of different soils in the lowland Amazon rainforest play a major role in generating and maintaining genetic variation in tropical tree populations through ecological divergence. This study examines genetic and morphological differentiation in the tropical tree Protium subserratum populations growing on the mosaic of white-sand, brown-sand and clay soil types distributed parapatrically throughout the western Amazon basin. We use nuclear microsatellites and vegetative characters to answer four major questions: (1) Are populations phenotypically and genetically differentiated across all three habitat types? (2) Can we detect a signature of natural selection over drift divergence among populations on different soil types? (3) What is the extent of hybridization and introgression across habitat types? (4) What is the relative importance of spatial distance and soil type in structuring P. subserratum tree populations and influencing migration rates among populations? We found significant morphological variation in populations across the three soil types. Higher levels of genetic differentiation and lower levels of gene flow were observed between adjacent populations found on different soil types than between geographically distant populations on the same soil type. Comparisons of phenotypic and neutral genetic variation among soil specialist populations suggest a role for natural selection in population divergence and a small number of hybrid individuals were detected between soil ecotypes showing that gene flow among populations may be occurring at a low frequency. Our results suggest that edaphic specialization in P. subserratum populations has occurred across multiple soil boundaries. While we cannot discern which factors caused initial divergence our results do suggest that natural selection is plays an important role in maintaining the integrity of populations across ecological boundaries and that edaphic specialization may be a general mechanism that promotes and maintains Amazonian tree diversity.
Data from: Recovery from bleaching is mediated by threshold densities of background thermo-tolerant symbiont types in a reef-building coral
Sensitive molecular analyses show that most corals host a complement of Symbiodinium genotypes that includes thermo-tolerant types in low abundance. While tolerant symbiont types are hypothesized to facilitate tolerance to temperature and recovery from bleaching, empirical data on their distribution and relative abundance in corals under ambient and stress conditions are still rare. We quantified visual bleaching and mortality of coral hosts, along with relative abundance of C- and D-type Symbiodinium cells in 82 Acropora millepora colonies from three locations on the Great Barrier Reef transplanted to a central inshore site over a 13 month period. Our analyses reveal dynamic change in symbiont associations within colonies and among populations over time. Coral bleaching and declines in C- but not D-type symbionts were observed in transplanted corals. Survival and recovery of 25% of corals from one population was associated with either initial D-dominance or an increase in D-type symbionts that could be predicted by a minimum pre-stress D : C ratio of 0.003. One-third of corals from this population became D dominated at the bleached stage despite no initial detection of this symbiont type, but failed to recover and died in mid to late summer. These results provide a predictive threshold minimum density of background D-type symbionts in A. millepora, above which survival following extreme thermal stress is increased.
Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.
Data from: Phylogeny of Mycoplasma bovis isolates from Hungary based on multi locus sequence typing and multiple-locus variable-number tandem repeat analysis
Background: Mycoplasma bovis is an important pathogen causing pneumonia, mastitis and arthritis in cattle worldwide. As this agent is primarily transmitted by direct contact and spread through animal movements, efficient genotyping systems are essential for the monitoring of the disease and for epidemiological investigations. The aim of this study was to compare and evaluate the multi locus sequence typing (MLST) and the multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) through the genetic characterization of M. bovis isolates from Hungary. Results: Thirty one Hungarian M. bovis isolates grouped into two clades by MLST. Two strains had the same sequence type (ST) as reference strain PG45, while the other twenty nine Hungarian isolates formed a novel clade comprising five subclades. Isolates originating from the same herds had the same STs except for one case. The same isolates formed two main clades and several subclades and branches by MLVA. One clade contained the reference strain PG45 and three isolates, while the other main clade comprised the rest of the strains. Within-herd strain divergence was also detected by MLVA. Little congruence was found between the results of the two typing systems. Conclusions: MLST is generally considered an intermediate scale typing method and it was found to be discriminatory among the Hungarian M. bovis isolates. MLVA proved to be an appropriate fine scale typing tool for M. bovis as this method was able to distinguish closely related strains isolated from the same farm. We recommend the combined use of the two methods for the genotyping of M. bovis isolates. Strains have to be characterized first by MLST followed by the fine scale typing of identical STs with MLVA.
Data from: When the going gets tough: behavioral type dependent space use in the sleepy lizard changes as the season dries
Understanding space use remains a major challenge for animal ecology, with implications for species interactions, disease spread, and conservation. Behavioural type (BT) may shape the space use of individuals within animal populations. Bolder or more aggressive individuals tend to be more exploratory and disperse further. Yet, to date we have limited knowledge on how space use other than dispersal depends on BT. To address this question we studied BT-dependent space-use patterns of sleepy lizards (Tiliqua rugosa) in southern Australia. We combined high-resolution global positioning system (GPS) tracking of 72 free-ranging lizards with repeated behavioural assays, and with a survey of the spatial distributions of their food and refuge resources. Bayesian generalized linear mixed models (GLMM) showed that lizards responded to the spatial distribution of resources at the neighbourhood scale and to the intensity of space use by other conspecifics (showing apparent conspecific avoidance). BT (especially aggressiveness) affected space use by lizards and their response to ecological and social factors, in a seasonally dependent manner. Many of these effects and interactions were stronger later in the season when food became scarce and environmental conditions got tougher. For example, refuge and food availability became more important later in the season and unaggressive lizards were more responsive to these predictors. These findings highlight a commonly overlooked source of heterogeneity in animal space use and improve our mechanistic understanding of processes leading to behaviourally driven disease dynamics and social structure.
Data from: How self-stigma affects patient activation in persons with type 2 diabetes
<p><span><span><span><b><span>Objectives</span></b></span></span></span></p> <p><span><span><span><span>Self-stigma is associated with lower patient activation levels for self-care in persons with type 2 diabetes mellitus (T2DM). However, the causal pathway linking self-stigma with patient activation for self-care has not been shown. In order to determine how self-stigma affects patient activation for self-care, we tested a two-path hypothetical model both directly and as mediated by self-esteem and self-efficacy.</span></span></span></span></p> <p><span><span><span><b><span>Design</span></b></span></span></span></p> <p><span><span><span><span>A cross-sectional study</span></span></span></span></p> <p><span><span><span><b><span>Setting</span></b></span></span></span></p> <p><span><span><span><span>2 university hospitals, 1 general hospital, and 1 clinic in Japan</span></span></span></span></p> <p><span><span><span><b><span>Participants</span></b></span></span></span></p> <p><span><span><span><span>T2DM outpatients receiving treatment (n = 209) completed a self-administered questionnaire comprising the Self-Stigma Scale, Patient Activation Measure, Rosenberg Self-Esteem Scale, General Self-Efficacy Scale, Patient Health Questionnaire, hemoglobin A1c test, age, sex, and BMI.</span></span></span></span></p> <p><span><span><span><b><span>Primary and Secondary Outcome Measures</span></b></span></span></span></p> <p><span><span><span><span>Self-stigma levels were measured by using the Self-Stigma Scale. Patient activation levels were measured by the Patient Activation Measure.</span></span></span></span></p> <p><span><span><span><b><span>Results</span></b></span></span></span></p> <p><span><span><span><span>Path analysis showed a strong relationship between self-stigma and patient activation (χ<sup>2 </sup>= 27.55, <i>p</i> = 0.120; GFI = 0.97; AGFI = 0.94; CFI = 0.98; RMSEA = 0.04). Self-stigma had a direct effect on patient activation (β = −0.20; <i>p</i> = 0.002). Indirectly, self-stigma affected patient activation along two paths (β = 0.31; <i>p</i> < 0.001) by reducing self-esteem (β = −0.22; p < 0.001) and self-efficacy (β = −0.36; p < 0.001).</span></span></span></span></p> <p><span><span><span><b><span>Conclusions</span></b></span></span></span></p> <p><span>Due to the cross-sectional design of the study, longitudinal changes between all the variables cannot be established. However, the findings indicate that self-stigma affected patient activation for self-care, both directly and as mediated by self-esteem and self-efficacy. Interventions that increase self-esteem and self-efficacy may decrease self-stigma in T2DM patients, thus increasing patient activation for self-care.</span></p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.