Miracle-dz/UniFAR-FTUs huggingface dataset:
Anoxybacillus vitaminiphilus sp. nov., a strictly aerobic and moderately thermophilic bacterium isolated from a hot spring.

A strictly aerobic, Gram-stain-positive, motile and spore-forming bacterium, strain 3nP4(T), was isolated from the Puge hot spring located in the south-western geothermal area of China. Strain 3nP4(T) grew at 38-66 °C (optimum 57-60 °C), at pH 6.0-9.3 (optimum 7.0-7.5) and with 0-4 % (w/v) NaCl (optimum 0-0.5 %). Phylogenetic analysis of 16S rRNA gene sequences, as well as DNA-DNA relatedness values, indicated that the isolate represents a novel species of the genus Anoxybacillus, related most closely to Anoxybacillus voinovskiensis DSM 12111(T). Strain 3nP4(T) had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid as major polar lipids and iso-C15 : 0 and iso-C17 : 0 as major fatty acids, which are both typical chemotaxonomic characteristics of the genus Anoxybacillus. The mean DNA G+C content of strain 3nP4(T) was 39.2±0.95 mol% (HPLC). A distinctive characteristic of the novel isolate was its extreme reliance on vitamin mixture or yeast extract for growth. Based on data from this taxonomic study using a polyphasic approach, strain 3nP4(T) is considered to represent a novel species of the genus Anoxybacillus, for which the name Anoxybacillus vitaminiphilus sp. nov. is proposed. The type strain is 3nP4(T) ( = CGMCC 1.8979(T) = JCM 16594(T)).
Prospective implementation of a standardized screening protocol for deep venous thrombosis in abdominal surgical oncology patients

Venous thromboembolism (VTE) remains a major cause of perioperative morbidity and mortality despite implementation of prophylaxis guidelines. We sought to identify risk factors for occult deep venous thrombosis (DVT) following abdominal surgery for cancer and measure the clinical impact of a prospectively implemented standardized postoperative DVT screening protocol.
Who knows what: An exploration of the infant feeding message environment and intracultural differences in Port‐au‐Prince, Haiti

Worldwide, mothers with young children receive many messages about infant feeding. Some messages are generated by health providers and others by the households, communities, and social contexts in which women live. We aimed to determine the scope of infant feeding messages in urban Haiti and to examine intracultural differences in salience of these messages and their alignment with international guidelines. We applied the method of free listing with 13 health workers and 15 human immunodeficiency virus (HIV)-infected and 15 HIV-uninfected mothers with infants 0-6 months old at Groupe Haïtien d'Etude du Sarcome de Kaposi et des Infections Opportunistes in Port-au-Prince, Haiti. Participants listed all messages women receive about infant feeding and specifically about HIV and infant feeding. Message salience was determined by frequency of mention and recall order; messages were coded for key themes. For all groups, the World Health Organization infant feeding recommendations were salient, especially those related to exclusive breastfeeding. Messages across all groups focused on infant health outcomes, with less emphasis on maternal outcomes. Cultural beliefs were also elicited and showed higher salience for mothers than health workers, particularly for consequences of poor maternal nutrition. Health workers' free lists were poorly correlated to those of mothers, whereas those of mothers were highly correlated, regardless of HIV status. Inasmuch as many salient messages were culturally generated, and differences existed between mothers and health workers, we conclude that it is important for health workers to acknowledge the broader infant feeding message environment, and discrepancies within that environment, to address successes and failures in the messages reaching mothers, given potential consequences for mothers' breastfeeding behaviours.
Ocular Irritation Following Frequent Applications of Cyclosporinea

ABSTRACT Purpose. Previous studies have shown that repetitive administrations of Cyclosporine A (CsA) eye drops to the rabbit eye caused a long-lasting miosis, accompanied by conjunctival hyperemia, anterior humor flare, and fibrin formation in the anterior chamber. The aim of the present study was to clarify the mechanism of these findings. Methods. One drop of 0.1% CsA eye drops was applied once or six times every 30 minutes for 2.5 hours. The eyes were examined by slit-lamp microscope, and IOP and anterior humor flare were measured prior to the studies and at 0, 1, 3, 6, 12, and 24 hours after administration of CsA or vehicle. While anterior chamber aqueous flare was increasing, aqueous humor and anterior segment of the eye were taken and analyzed. The entry of plasma proteins into the aqueous humor was studied by using Evans blue dye. Result. Conjunctival hyperemia, anterior humor flare and IOP rise miosis and fibrin formation in the anterior chamber were shown after six CsA administration ipsilaterally during 1–12 hours after the final administration. All of these observations were inhibited by pretreatment of indomethacin. While miosis was appearing, Evans blue dye penetrated the nonpigmented layer of the ciliary epithelium and the iris vessels. Calcitonin gene-related peptide (CGRP) was detected (184.1 ± 84.6 pg/mL), and CsA levels (891.6 ± 153.0 ng/mL) in anterior uvea exceeded the trough level. Conclusions. These results suggest that CsA can cause disruption of the blood-aqueous barrier with leaking from vessels in the ciliary processes and the iris, which are probably secondary effects of the irritation response releasing CGRP.
A coupled phylogeographical and species distribution modelling approach recovers the demographical history of a Neotropical seasonally dry forest tree species

We investigated here the demographical history of Tabebuia impetiginosa (Bignoniaceae) to understand the dynamics of the disjunct geographical distribution of South American seasonally dry forests (SDFs), based on coupling an ensemble approach encompassing hindcasting species distribution modelling and statistical phylogeographical analysis. We sampled 17 populations (280 individuals) in central Brazil and analysed the polymorphisms at chloroplast (trnS‐trnG, psbA‐trnH, and ycf6‐trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. Phylogenetic analyses based on median‐joining network showed no haplotype sharing among population but strong evidence of incomplete lineage sorting. Coalescent analyses showed historical constant populations size, negligible gene flow among populations, and an ancient time to most recent common ancestor dated from ~4.7 ± 1.1 Myr BP. Most divergences dated from the Lower Pleistocene, and no signal of important population size reduction was found in coalescent tree and tests of demographical expansion. Demographical scenarios were built based on past geographical range dynamic models, using two a priori biogeographical hypotheses (‘Pleistocene Arc’ and ‘Amazonian SDF expansion’) and on two additional hypotheses suggested by the palaeodistribution modelling built with several algorithms for distribution modelling and palaeoclimatic data. The simulation of these demographical scenarios showed that the pattern of diversity found so far for T. impetiginosa is in consonance with a palaeodistribution expansion during the last glacial maximum (LGM, 21 kyr BP), strongly suggesting that the current disjunct distribution of T. impetiginosa in SDFs may represent a climatic relict of a once more wide distribution.
Genome‐wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout

Little is known of the genetic basis of migration despite the ecological benefits migratory species provide to their communities and their rapid global decline due to anthropogenic disturbances in recent years. Using next‐generation sequencing of restriction‐site‐associated DNA (RAD) tags, we genotyped thousands of single nucleotide polymorphisms (SNPs) in two wild populations of migratory steelhead and resident rainbow trout (Oncorhynchus mykiss) from the Pacific Northwest of the United States. One population maintains a connection to the sea, whereas the other population has been sequestered from its access to the ocean for more than 50 years by a hydropower dam. Here we performed a genome‐wide association study to identify 504 RAD SNP markers from several genetic regions that were associated with the propensity to migrate both within and between the populations. Our results corroborate those in previous quantitative trait loci studies and provide evidence for additional loci associated with this complex migratory life history. Our results suggest a complex multi‐genic basis with several loci of small effect distributed throughout the genome contributing to migration in this species. We also determined that despite being sequestered for decades, the landlocked population continues to harbour genetic variation associated with a migratory life history and ATPase activity. Furthermore, we demonstrate the utility of genotyping‐by‐sequencing and how RAD‐tag SNP data can be readily compared between studies to investigate migration within this species.
Mhc‐linked survival and lifetime reproductive success in a wild population of great tits

Major histocompatibility complex (Mhc) genes are frequently used as a model for adaptive genetic diversity. Although associations between Mhc and disease resistance are frequently documented, little is known about the fitness consequences of Mhc variation in wild populations. Further, most work to date has involved testing associations between Mhc genotypes and fitness components. However, the functional diversity of the Mhc, and hence the mechanism by which selection on Mhc acts, depends on how genotypes map to the functional properties of Mhc molecules. Here, we test three hypotheses that relate Mhc diversity to fitness: (i) the maximal diversity hypothesis, (ii) the optimal diversity hypothesis and (iii) effect of specific Mhc types. We combine mark–recapture methods with analysis of long‐term breeding data to investigate the effects of Mhc class I functional diversity (Mhc supertypes) on individual fitness in a wild great tit (Parus major) population. We found that the presence of three different Mhc supertypes was associated with three different components of individual fitness: survival, annual recruitment and lifetime reproductive success (LRS). Great tits possessing Mhc supertype 3 experienced higher survival rates than those that did not, whereas individuals with Mhc supertype 6 experienced higher LRS and were more likely to recruit offspring each year. Conversely, great tits that possessed Mhc supertype 5 had reduced LRS. We found no evidence for a selective advantage of Mhc diversity, in terms of either maximal or optimal supertype diversity. Our results support the suggestion that specific Mhc types are an important determinant of individual fitness.
Genome sequence of dwarf birch (Betula nana) and cross‐species RAD markers

New sequencing technologies allow development of genome‐wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridization. We present a de novo reference genome sequence assembly, from 66× short read coverage, of Betula nana (dwarf birch) – a diploid that is the keystone woody species of subarctic scrub communities but of conservation concern in Britain. We also present 100 bp PstI RAD markers for B. nana and closely related Betula tree species. Assembly of RAD markers in 15 individuals by alignment to the reference B. nana genome yielded 44–86k RAD loci per individual, whereas de novo RAD assembly yielded 64–121k loci per individual. Of the loci assembled by the de novo method, 3k homologous loci were found in all 15 individuals studied, and 35k in 10 or more individuals. Matching of RAD loci to RAD locus catalogues from the B. nana individual used for the reference genome showed similar numbers of matches from both methods of RAD locus assembly but indicated that the de novo RAD assembly method may overassemble some paralogous loci. In 12 individuals hetero‐specific to B. nana 37–47k RAD loci matched a catalogue of RAD loci from the B. nana individual used for the reference genome, whereas 44–60k RAD loci aligned to the B. nana reference genome itself. We present a preliminary study of allele sharing among species, demonstrating the utility of the data for introgression studies and for the identification of species‐specific alleles.
Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates

We propose a two‐step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade‐off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC‐type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.
Multidisciplinary Pain Management

The realization that chronic pain and acute pain might have different mechanisms has led to important developments in both research and patients’ care. Basic research paradigms that focus upon long-term changes in tissues and the nervous system have led to useful models for chronic pain. Clinical research has shown that strategies effective for acute pain often fail in patients with chronic pain and that there is utility in the cognitive-behavioral approach to the management of patients with chronic pain. We discuss the history and implementation of comprehensive multidisciplinary pain diagnosis and treat-ment. We conclude with a review of the data on outcomes and cost-effectiveness for multidisciplinary pain management.
A Medium Viscous Acrylic Cement Enhances Uniformity of CementFilling and Reduces Leakage in Cancellous Bone Augmentation

Vertebroplasty is an efficient procedure to treat osteoporotic vertebral fractures. Cement leakage is considered to be the most severe complication during vertebroplasty. At high cement viscosities, the risk of leakage is reduced. However, injection forces are highly increased, requiring the use of high force injection systems with the lack in tactile force feedback. Therefore, an acrylic cement was developed showing medium initial viscosity and which still allows to be manually applied using syringes. An established model favoring leakage was used to observe the filling pattern and leaked cement mass. The method used included the simulation of body temperature, and all materials submitted are approved medical products. When applied just after preparation, the medium viscous cement resulted in good cement filling and less cement leakage than low viscosity cement. The added clinical value of the new cement is that the waiting time for the physician will be shortened to zero minutes without compromising the safety for the procedure.
The role of continental shelf width in determining freshwater phylogeographic patterns in south‐eastern Australian pygmy perches (Teleostei: Percichthyidae)

Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South‐eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of river coalescence during low sea levels. Our specific hypothesis is that the degree of phylogeographic divergence between coastal river basins should correspond to the continental shelf width of each region. This predicts that genetic divergences between river basins should be lowest in regions with a wider continental shelf and that regions with similar continental shelf width should have similar genetic divergences. Pygmy perches (Nannoperca australis and Nannoperca ‘flindersi’) in south‐eastern Australia provide an ideal opportunity to test these biogeographic hypotheses. Phylogeographic patterns were examined based on range‐wide sampling of 82 populations for cytochrome b and 23 polymorphic allozyme loci. Our results recovered only limited support for our continental shelf width hypothesis, although patterns within Bass clade were largely congruent with reconstructed low sea‐level drainage patterns. In addition, we identified several instances of drainage divide crossings, typically associated with low elevational differences. Our results demonstrate high levels of genetic heterogeneity with important conservation implications, especially for declining populations in the Murray–Darling Basin and a highly restricted disjunct population in Ansons River, Tasmania.
Uncovering symbiont‐driven genetic diversity across North American pea aphids

Heritable genetic variation is required for evolution, and while typically encoded within nuclear and organellar genomes, several groups of invertebrates harbour heritable microbes serving as additional sources of genetic variation. Hailing from the symbiont‐rich insect order Hemiptera, pea aphids (Acyrthosiphon pisum) possess several heritable symbionts with roles in host plant utilization, thermotolerance and protection against natural enemies. As pea aphids vary in the numbers and types of harboured symbionts, these bacteria provide heritable and functionally important variation within field populations. In this study, we quantified the cytoplasmically inherited genetic variation contributed by symbionts within North American pea aphids. Through the use of Denaturing Gradient Gel Electrophoresis (DGGE) and 454 amplicon pyrosequencing of 16S rRNA genes, we explored the diversity of bacteria harboured by pea aphids from five populations, spanning three locations and three host plants. We also characterized strain variation by analysing 16S rRNA, housekeeping and symbiont‐associated bacteriophage genes. Our results identified eight species of facultative symbionts, which often varied in frequency between locations and host plants. We detected 28 cytoplasmic genotypes across 318 surveyed aphids, considering only the various combinations of secondary symbiont species infecting single hosts. Yet the detection of multiple Regiella insecticola, Hamiltonella defensa and Rickettsia strains, and diverse bacteriophage genotypes from H. defensa, suggest even greater diversity. Combined, these findings reveal that heritable bacteria contribute substantially to genetic variation in A. pisum. Given the costs and benefits of these symbionts, it is likely that fluctuating selective forces play a role in the maintenance of this diversity.
Approximate Bayesian estimation of extinction rate in the Finnish Daphnia magna metapopulation

Approximate Bayesian computation (ABC) is useful for parameterizing complex models in population genetics. In this study, ABC was applied to simultaneously estimate parameter values for a model of metapopulation coalescence and test two alternatives to a strict metapopulation model in the well‐studied network of Daphnia magna populations in Finland. The models shared four free parameters: the subpopulation genetic diversity (θS), the rate of gene flow among patches (4Nm), the founding population size (N0) and the metapopulation extinction rate (e) but differed in the distribution of extinction rates across habitat patches in the system. The three models had either a constant extinction rate in all populations (strict metapopulation), one population that was protected from local extinction (i.e. a persistent source), or habitat‐specific extinction rates drawn from a distribution with specified mean and variance. Our model selection analysis favoured the model including a persistent source population over the two alternative models. Of the closest 750 000 data sets in Euclidean space, 78% were simulated under the persistent source model (estimated posterior probability = 0.769). This fraction increased to more than 85% when only the closest 150 000 data sets were considered (estimated posterior probability = 0.774). Approximate Bayesian computation was then used to estimate parameter values that might produce the observed set of summary statistics. Our analysis provided posterior distributions for e that included the point estimate obtained from previous data from the Finnish D. magna metapopulation. Our results support the use of ABC and population genetic data for testing the strict metapopulation model and parameterizing complex models of demography.
SEROLOGICAL SCREENING FOR INFECTIOUS CATTLE DISEASES: II. ASSOCIATION BETWEEN PREVALENCE AND LEVEL OF ELISA RESPONSE

A herd of cattle (Holstein-Zebu crosses) was screened every two months by ELISA during a period of two years for IgG antibodies against 19 infectious disease agents. Two hundred and ninety five sera were collected from 157 young animals (0-4 months of age), 1037 sera from 292 developing animals (4-36 months of age) and 1468 sera from 259 producing animals (> 36 months of age). The results indicate that the difference in ELISA between positive and negative tests is associated with the overall prevalence of positive tests. When the prevalence of positive tests is low the difference between positive and negative tests is greater than when the prevalence is intermediate or high. This means that ELISA, presumably other serological tests for IgG antibodies, is more reliable at low disease (antibody) prevalence. This will tend to offset the declining predictive value of positive tests at low prevalence and may contribute to the successful use of serological tests in disease eradication.