Miracle-dz/UniFAR-FTUs huggingface dataset:
Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov.

Bacterial strains KIS82-1(T) and GRS42(T) were isolated from soil and from sap of Acer mono, respectively, in the Republic of Korea. Both strains were aerobic, Gram-stain-positive, mesophilic, rod-shaped and motile. Phylogenetically, both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS82-1(T) showed the highest similarity to those of Frondihabitans peucedani RS-15(T) (97.6%), Frigoribacterium mesophilum MSL-08(T) (97.2%) and Labedella gwakjiensis KSW2-17(T) (97.0%), while strain GRS42(T) showed the highest 16S rRNA gene sequence similarity to Frondihabitans peucedani RS-15(T) (98.7%), Frondihabitans cladoniiphilus CafT13(T) (98.4%), Frondihabitans australicus E1HC-02(T) (98.2%) and Frigoribacterium faeni 801(T) (97.3%). The 16S rRNA gene sequence similarity between GRS42(T) and KIS82-1(T) was 97.0%. Phylogenetic trees indicated that strain GRS42(T) was firmly grouped into the genus Frondihabitans, while strain KIS82-1(T) did not show a clear affiliation to any genus within the family Microbacteriaceae. Strain KIS82-1(T) showed type B1β peptidoglycan with 2,4-diamino-L-butyric acid as the diamino acid. It had MK-11, MK-10 and MK-12 as respiratory quinones, anteiso-C(15 : 0), iso-C(16: 0) and iso-C(14 : 0) as major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid as predominant polar lipids. The peptidoglycan of strain GRS42(T) was of type B2β with D-ornithine as the diamino acid. The strain contained MK-8, MK-9 and MK-7 as respiratory quinones, summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c) as major cellular fatty acid and diphosphatidylglycerol, phosphatidylglycerol and three unknown glycolipids as predominant polar lipids. Strain GRS42(T) revealed low DNA-DNA hybridization (<50% relatedness) with closely related strains. Based on the data obtained in the present polyphasic taxonomic study, we propose that strain KIS82-1(T) represents a novel genus and species and that strain GRS42(T) represents a novel species in the family Microbacteriaceae. The genus Galbitalea gen. nov. is proposed, with strain KIS82-1(T) ( = KACC 15520(T) = NBRC 108727(T)) as the type strain of the type species, Galbitalea soli sp. nov. Strain GRS42(T) ( = KACC 15521(T) = NBRC 108728(T)) is proposed as the type strain of Frondihabitans sucicola sp. nov.
Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the mussel Mytilus edulis

Genome scans of population differentiation identify candidate loci for adaptation but provide little information on how selection has influenced the genetic structure of these loci. Following a genome scan, we investigated the nature of the selection responsible for the outlying differentiation observed between populations of the marine mussel Mytilus edulis at a leucine/arginine polymorphism (L31R) in the antimicrobial peptide MGD2. We analysed DNA sequence polymorphisms, allele frequencies and population differentiation of polymorphisms closely linked to L31R, and pairwise and third‐order linkage disequilibria. An outlying level of population differentiation was observed at L31R only, while no departure from panmixia was observed at linked loci surrounding L31R, as in most of the genome. Selection therefore seems to affect L31R directly. Three hypotheses can explain the lack of differentiation in the chromosomal region close to L31R: (i) hitchhiking has occurred but migration and recombination subsequently erased the signal, (ii) selection was weak enough and recombination strong enough to limit the hitchhiking effect to a very small chromosomal region or (iii) selection acted on a pre‐existing polymorphism (i.e. standing variation) at linkage equilibrium with its background. Linkage equilibrium was observed between L31R and linked polymorphisms in every population analysed, as expected under the three hypotheses. However, linkage disequilibrium was observed in some populations between pairs of loci located upstream and downstream to L31R, generating a complex pattern of third‐order linkage disequilibria which is best explained by the hypothesis of selection on a pre‐existing polymorphism. We hypothesise that selection could be either balanced, maintaining alleles at different frequencies depending on the pathogen community encountered locally by mussels, or intermittent, resulting in sporadic fluctuations in allele frequency.
Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria.

A thermophilic, aerobic, Gram-stain-positive bacterium (strain PM5(T)), which formed mycelia of irregularly branched filaments and produced multiple exospores per cell, was isolated from a geothermally heated biofilm. Strain PM5(T) grew at 40-65 °C and pH 4.1-8.0, with optimal growth at 55 °C and pH 6.0. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PM5(T) belonged to the class Ktedonobacteria, and was related most closely to Thermogemmatispora onikobensis ONI-1(T) (97.7 % similarity) and Thermogemmatispora foliorum ONI-5(T) (96.1 %). Morphological features and fatty acid profiles (major fatty acids: iso-C17 : 0, iso-C19 : 0 and 12,17-dimethyl C18 : 0) supported the affiliation of strain PM5(T) to the genus Thermogemmatispora. Strain PM5(T) oxidized carbon monoxide [CO; 10±1 nmol h(-1) (mg protein)(-1)], but did not grow with CO as a sole carbon and energy source. Results from analyses of related strains indicated that the capacity for CO uptake occurred commonly among the members of the class Ktedonobacteria; 13 of 14 strains tested consumed CO or harboured coxL genes that potentially enabled CO oxidation. The results of DNA-DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain PM5(T) from the two recognized species of the genus Thermogemmatispora. Strain PM5(T) differed from Thermogemmatispora onikobensis ONI-1(T) in its production of orange pigment, lower temperature optimum, hydrolysis of casein and starch, inability to grow with mannitol, xylose or rhamnose as sole carbon sources, and utilization of organic acids and amino acids. Strain PM5(T) is therefore considered to represent a novel species, for which the name Thermogemmatispora carboxidivorans sp. nov. is proposed. The type strain is PM5(T) ( = DSM 45816(T) = ATCC BAA-2534(T)).
The gravity of pollination: integrating at‐site features into spatial analysis of contemporary pollen movement

Pollen‐mediated gene flow is a major driver of spatial genetic structure in plant populations. Both individual plant characteristics and site‐specific features of the landscape can modify the perceived attractiveness of plants to their pollinators and thus play an important role in shaping spatial genetic variation. Most studies of landscape‐level genetic connectivity in plants have focused on the effects of interindividual distance using spatial and increasingly ecological separation, yet have not incorporated individual plant characteristics or other at‐site ecological variables. Using spatially explicit simulations, we first tested the extent to which the inclusion of at‐site variables influencing local pollination success improved the statistical characterization of genetic connectivity based upon examination of pollen pool genetic structure. The addition of at‐site characteristics provided better models than those that only considered interindividual spatial distance (e.g. IBD). Models parameterized using conditional genetic covariance (e.g. population graphs) also outperformed those assuming panmixia. In a natural population of Cornus florida L. (Cornaceae), we showed that the addition of at‐site characteristics (clumping of primary canopy opening above each maternal tree and maternal tree floral output) provided significantly better models describing gene flow than models including only between‐site spatial (IBD) and ecological (isolation by resistance) variables. Overall, our results show that including interindividual and local ecological variation greatly aids in characterizing landscape‐level measures of contemporary gene flow.
Energy Expenditure on Breathing during Anaesthesia

Measurements of carbon dioxide production were carried out on 20 patients undergoing arthroplastic operation of the hip joint, under halothane anaesthesia supplemented with lumbar plexus block. Compared to spontaneous respiration, the carbon dioxide production during controlled ventilation, with and without muscular relaxation, showed a decrease of 19% and 12%, respectively.
Baculovirus‐induced tree‐top disease: how extended is the role of egt as a gene for the extended phenotype?

Many parasites alter host behaviour to enhance their chance of transmission. Recently, the ecdysteroid UDP‐glucosyl transferase (egt) gene from the baculovirus Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) was identified to induce tree‐top disease in L. dispar larvae. Infected gypsy moth larvae died at elevated positions (hence the term tree‐top disease), which is thought to promote dissemination of the virus to lower foliage. It is, however, unknown whether egt has a conserved role among baculoviruses in inducing tree‐top disease. Here, we studied tree‐top disease induced by the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in two different host insects, Trichoplusia ni and Spodoptera exigua, and we investigated the role of the viral egt gene therein. AcMNPV induced tree‐top disease in both T. ni and S. exigua larvae, although in S. exigua a moulting‐dependent effect was seen. Those S. exigua larvae undergoing a larval moult during the infection process died at elevated positions, while larvae that did not moult after infection died at low positions. For both T. ni and S. exigua, infection with a mutant AcMNPV lacking egt did not change the position where the larvae died. We conclude that egt has no highly conserved role in inducing tree‐top disease in lepidopteran larvae. The conclusion that egt is a ‘gene for an extended phenotype’ is therefore not generally applicable for all baculovirus–host interactions. We hypothesize that in some baculovirus–host systems (including LdMNPV in L. dispar), an effect of egt on tree‐top disease can be observed through indirect effects of egt on moulting‐related climbing behaviour.
Lysobacter panacisoli sp. nov., isolated from ginseng soil.

A novel bacterial strain, designated CJ29(T), was isolated from ginseng soil of Anseong in South Korea. Cells of strain CJ29(T) were Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile. Strain CJ29(T) grew optimally at 28-30 °C and pH 7.0. Based on 16S rRNA gene sequence analysis, strain CJ29(T) was shown to belong to the genus Lysobacter within the class Gammaproteobacteria and was related most closely to Lysobacter soli DCY21(T) (98.5% similarity) and Lysobacter niastensis GH41-7(T) (98.2%). DNA-DNA relatedness between strain CJ29(T) and its closest relatives was below 55.6%. The predominant cellular fatty acids of strain CJ29(T) were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major isoprenoid quinone was ubiquinone 8 (Q-8). The G+C content of the genomic DNA was 65.6 mol%. Phenotypic, genotypic and phylogenetic characteristics strongly supported the differentiation of strain CJ29(T) from related species of the genus Lysobacter. On the basis of data from this polyphasic taxonomic study, strain CJ29(T) is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter panacisoli sp. nov. is proposed. The type strain is CJ29(T) ( = KACC 17502(T) = JCM 19212(T)).
Demographic inferences using short‐read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus

Approximate Bayesian computation (ABC) is a powerful tool for model‐based inference of demographic histories from large genetic data sets. For most organisms, its implementation has been hampered by the lack of sufficient genetic data. Genotyping‐by‐sequencing (GBS) provides cheap genome‐scale data to fill this gap, but its potential has not fully been exploited. Here, we explored power, precision and biases of a coalescent‐based ABC approach where GBS data were modelled with either a population mutation parameter (θ) or a fixed site (FS) approach, allowing single or several segregating sites per locus. With simulated data ranging from 500 to 50 000 loci, a variety of demographic models could be reliably inferred across a range of timescales and migration scenarios. Posterior estimates were informative with 1000 loci for migration and split time in simple population divergence models. In more complex models, posterior distributions were wide and almost reverted to the uninformative prior even with 50 000 loci. ABC parameter estimates, however, were generally more accurate than an alternative composite‐likelihood method. Bottleneck scenarios proved particularly difficult, and only recent bottlenecks without recovery could be reliably detected and dated. Notably, minor‐allele‐frequency filters – usual practice for GBS data – negatively affected nearly all estimates. With this in mind, we used a combination of FS and θ approaches on empirical GBS data generated from the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing support for a population split before the last glacial maximum followed by asymmetrical migration and a high Arctic bottleneck. Overall, this study evaluates the potential and limitations of GBS data in an ABC‐coalescence framework and proposes a best‐practice approach.
Spectrum sharing and power allocation in multiple-in multiple-out cognitive radio networks via pricing

In the cognitive radio (CR) networks consisting of selfish users competing for spectrum resources, the social optimum is usually not achieved at the Nash equilibrium (NE) of the power control game, since selfish users are only interested in their own benefit. In this study with the aim of improving the NE efficiency, the authors extend the pricing concept to a multi-channel multiple-in multiple-out (MIMO) CR scenario and propose two iterative algorithms for power control and channel allocation in such systems. Specially, the authors consider both linear and non-linear pricing methods and derive the optimal pricing factor for both scenarios and prove the existence and uniqueness of the NE. Simulation results prove the outstanding performance of the proposed MIMO cognitive system considering price-based power control over the non-price-based MIMO cognitive systems.
Actinophytocola sediminis sp. nov., an actinomycete isolated from a marine sediment.

A novel actinomycete strain, designated YIM M13705(T), was isolated from a marine sediment sample of the South China Sea and its characteristics were determined by a polyphasic approach. The slowly growing, Gram-stain-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, and no diffusible pigment was produced on the media tested. At maturity, spore chains were formed on aerial hyphae and substrate mycelium was not fragmented. Whole-cell hydrolysates of the strain contained meso-diaminopimelic acid and galactose, glucose, ribose and rhamnose. The predominant menaquinones were MK-9(H4) and MK-10(H2). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and ninhydrin-positive phosphoglycolipids. The major fatty acid was iso-C(16 : 0). The G+C content of the genomic DNA was 68.2 mol%. On the basis of 16S rRNA gene sequence, the strain was shown to be most closely related to species of the genus Actinophytocola. DNA-DNA hybridization relatedness values (<70%) of the isolate with its closest neighbour Actinophytocola xinjiangensis QAIII60(T) supported classification of the isolate as a representative of a novel species. On the basis of phylogenetic analysis, and phenotypic and genotypic data, it is concluded that the new isolate belongs to a novel species of the genus Actinophytocola, for which the name Actinophytocola sediminis sp. nov. (type strain YIM M13705(T) = DSM 45939(T) = BCRC 16956(T)) is proposed.
Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora.

A facultatively alkaliphilic actinomycete strain, designated EGI 80088(T), was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088(T) formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5%) were anteiso-C(15 : 0), iso-C(15 : 0), summed feature 4 (iso-C(17 : 1)I/anteiso-C(17 : 1)B), iso-C(16 : 0) and anteiso-C(17 : 0). The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088(T) was 70.6 mol%. EGI 80088(T) showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246(T) (98.5%). The DNA-DNA relatedness value of the strain EGI 80088(T) and H. alba YIM 93246(T) was 59.3±5.2%. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA-DNA hybridization data, strain EGI 80088(T) represents a novel species of the genus Haloactinopolyspora, for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088(T) = BCRC 16946(T) = JCM 19128(T)) is proposed. The description of the genus Haloactinopolyspora has also been emended.
Sun skink landscape genomics: assessing the roles of micro‐evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Incorporating genomic data sets into landscape genetic analyses allows for powerful insights into population genetics, explicitly geographical correlates of selection, and morphological diversification of organisms across the geographical template. Here, we utilize an integrative approach to examine gene flow and detect selection, and we relate these processes to genetic and phenotypic population differentiation across South‐East Asia in the common sun skink, Eutropis multifasciata. We quantify the relative effects of geographic and ecological isolation in this system and find elevated genetic differentiation between populations from island archipelagos compared to those on the adjacent South‐East Asian continent, which is consistent with expectations concerning landscape fragmentation in island archipelagos. We also identify a pattern of isolation by distance, but find no substantial effect of ecological/environmental variables on genetic differentiation. To assess whether morphological conservatism in skinks may result from stabilizing selection on morphological traits, we perform FST–PST comparisons, but observe that results are highly dependent on the method of comparison. Taken together, this work provides novel insights into the manner by which micro‐evolutionary processes may impact macro‐evolutionary scale biodiversity patterns across diverse landscapes, and provide genomewide confirmation of classic predictions from biogeographical and landscape ecological theory.
Methanohalophilus levihalophilus sp. nov., a slightly halophilic, methylotrophic methanogen isolated from natural gas-bearing deep aquifers, and emended description of the genus Methanohalophilus.

A mesophilic, slightly halophilic, obligately methylotrophic, methanogenic archaeon, designated strain GTA13(T), was isolated from natural gas-bearing confined aquifers in the Minami-Kanto gas field, Japan. The cells were non-motile, slightly irregular cocci, 0.7-1.0 µm in diameter and occurred singly, in pairs or as small aggregates. The cells grew with tri- or dimethylamine but not with H2/CO2, formate, acetate, methanol or dimethyl sulphide. Vitamins, sodium and magnesium were required for growth. Optimal growth occurred at pH 7.0-7.5, 35 °C, 0.35-0.40 M NaCl and 15-50 mM MgCl2. The NaCl range for growth was 0.2-1.3 M. The DNA G+C content was 43.7 mol%. Strain GTA13(T) showed highest levels of 16S rRNA gene sequence similarity with Methanohalophilus portucalensis FDF-1(T) (96.4% sequence similarity) and Methanohalophilus halophilus DSM 3094(T) (96.0%). On the basis of physiological and phylogenetic features, strain GTA13(T) is considered to represent a novel species of the genus Methanohalophilus, for which the name Methanohalophilus levihalophilus sp. nov. is proposed. The type strain is GTA13(T) ( = NBRC 110099(T) = DSM 28452(T)). An emended description of the genus Methanohalophilus is also proposed.
Association of angiotensin I converting enzyme polymorphism as genetic risk factor in benign prostatic hyperplasia and prostate cancer.

INTRODUCTION Angiotensin I converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism is one of the genetic factors found to be related with prostate cancer (PC). We investigated the association between grade and stage of disease, age of diagnosis, vascular or perineural invasion, prediagnostic plasma prostate specific antigen (PSA) levels, and PC risk with I/D polymorphism of the ACE gene. MATERIALS AND METHODS We recruited 206 subjects in this study, including 95 patients with PC and 111 patients with benign prostatic hyperplasia. RESULTS The odds ratio between II and DD polymorphisms (reference) was 1.38. It means that the presence of the II polymorphism increased the risk of cancer more than 38% compared with DD polymorphism although still it was not statistically significant. The mean of total PSA in the patients with the II genotype was 20 ng/L more than that in those who had DD polymorphism. The odds ratio (OR) between the D allele and PC development was 1.16, indicating that this allele increased the risk of cancer about 16%. CONCLUSION We found no association between the ACE polymorphism and cancer risk, overall or by grade, stage, or age of diagnosis. The difference in results for ACE polymorphisms between studies may be minimized by using larger study groups.