bluuebunny/crossref_metadata_2025 huggingface dataset:
On the variation of solar coronal rotation using SDO/AIA observations
Authors: Sharma Jaidev , Kumar Brajesh , Malik Anil K , Vats Hari Om
Published: January 2020

We report on the variability of the rotation periods of solar coronal layers with respect to temperature (or height). For this purpose, we have used observations from the Atmospheric Imaging Assembly (AIA) telescope on board the Solar Dynamics Observatory (SDO) space mission of National Aeronautics and Space Administration (NASA). The images used are at wavelengths of 94, 131, 171, 193, 211 and 335 Å during the period from 2012–2018. Analysis of solar full-disc images obtained at these wavelengths by AIA is carried out using the flux modulation method. 17 rectangular strips/bins at equal intervals of 10° (extending from 80°S to 80°N) are selected to extract a time series of extreme ultraviolet (EUV) intensity variations to obtain the autocorrelation coefficient. The peak of the Gaussian fit to the first secondary maximum in the autocorrelogram gives the synodic rotation period. Our analysis shows differential rotation with respect to latitude as well as temperature (or height). In the present study, we find that the sidereal rotation periods of different coronal layers decrease with increasing temperature (or height). The average sidereal rotation period at the lowest temperature (∼600 000 K) corresponding to AIA 171-Å, which originates from the upper transition region/quiet corona, is 27.03 days. The sidereal rotation period decreases with temperature (or height) to 25.47 days at a higher temperature (∼10 million K), corresponding to the flaring regions of the solar corona as seen in AIA 131-Å observations.
Distant foreground and the Planck-derived Hubble constant
Authors: Yershov V N , Raikov A A , Lovyagin N Yu , Kuin N P M , Popova E A
Published: January 2020

It is possible to reduce the discrepancy between the local measurement of the cosmological parameter H0 and the value derived from the Planck measurements of the cosmic microwave background (CMB) by considering contamination of the CMB by emission from some medium around distant extragalactic sources, such as extremely cold coarse-grain dust. Though being distant, such a medium would still be in the foreground with respect to the CMB, and, as any other foreground, it would alter the CMB power spectrum. This could contribute to the dispersion of CMB temperature fluctuations. By generating a few random samples of CMB with different dispersions, we have checked that the increased dispersion leads to a smaller estimated value of H0, the rest of the cosmological model parameters remaining fixed. This might explain the reduced value of the Planck-derived parameter H0 with respect to the local measurements. The signature of the distant foreground in the CMB traced by supernovae (SNe) was previously reported by the authors of this paper – we found a correlation between the SN redshifts, zSN, and CMB temperature fluctuations at the SNe locations, TSN. Here we have used the slopes of the regression lines $T_{\rm SN}\, /\, z_{\rm SN}$ corresponding to different Planck wavebands in order to estimate the possible temperature of the distant extragalactic medium, which turns out to be very low, about 5 K. The most likely ingredient of this medium is coarse-grain (grey) dust, which is known to be almost undetectable, except for the effect of dimming remote extragalactic sources.
Direct imaging of irregular satellite discs in scattered light
Authors: Nassif-Lachapelle Loic , Tamayo Daniel
Published: January 2020

Direct imaging surveys have found that long-period super-Jupiters are rare. By contrast, recent modelling of the widespread gaps in protoplanetary discs revealed by Atacama Large Millimetre Array suggests an abundant population of smaller Neptune to Jupiter-mass planets at large separations. The thermal emission from such lower-mass planets is negligible at optical and near-infrared wavelengths, leaving only their weak signals in reflected light. Planets do not scatter enough light at these large orbital distances, but there is a natural way to enhance their reflecting area. Each of the four giant planets in our Solar system hosts swarms of dozens of irregular satellites, gravitationally captured planetesimals that fill their host planets’ spheres of gravitational influence. What we see of them today are the leftovers of an intense collisional evolution. At early times, they would have generated bright circumplanetary debris discs. We investigate the properties and detectability of such irregular satellite discs (ISDs) following models for their collisional evolution from Kennedy & Wyatt (2011). We find that the scattered light signals from such ISDs would peak in the 10–100 au semimajor axis range implied by ALMA, and can render planets detectable over a wide range of parameters with upcoming high-contrast instrumentation. We argue that future instruments with wide fields of view could simultaneously characterize the atmospheres of known close-in planets, and reveal the population of long-period Neptune–Jupiter mass exoplanets inaccessible to other detection methods. This provides a complementary and compelling science case that would elucidate the early lives of planetary systems.
Fuzzy dark matter soliton cores around supermassive black holes
Authors: Davies Elliot Y , Mocz Philip
Published: January 2020

We explore the effect of a supermassive black hole (SMBH) on the density profile of a fuzzy dark matter (FDM) soliton core at the centre of a dark matter (DM) halo. We numerically solve the Schrödinger–Poisson equations, treating the black hole as a gravitational point mass, and demonstrate that this additional perturbing term has a ‘squeezing’ effect on the soliton density profile, decreasing the core radius, and increasing the central density. In the limit of large black hole mass, the solution approaches one akin to the hydrogen atom, with radius inversely proportional to the black hole mass. By applying our analysis to two specific galaxies (M87 and the Milky Way) and pairing it with known observational limits on the amount of centrally concentrated DM, we obtain a constraint on the FDM particle mass, finding that the range 10−22.12 eV ≲ m ≲ 10−22.06 eV should be forbidden (taking into account additional factors concerning the lifetime of the soliton in the vicinity of a black hole). Improved observational mass measurements of the black hole and total enclosed masses will significantly extend the lower bound on the excluded FDM mass region, while self-consistent theoretical modelling of the soliton–black hole system can extend the upper bound.
The vertical Na–O relation in the bulge globular cluster NGC 6553
Authors: Muñoz C , Villanova S , Geisler D , Cortés C C , Moni Bidin C , Cohen R E , Saviane I , Dias B , Tang B , Mauro F
Published: January 2020

In this article, we present a detailed chemical analysis of seven red giant members of NGC 6553 using high-resolution spectroscopy from VLT FLAMES. We obtained the stellar parameters (Teff, Log(g), vt, [Fe/H]) of these stars from the spectra, and we measured the chemical abundance for 20 elements, including light elements, iron-peak elements, α-elements, and neutron-capture elements. The metallicities in our sample stars are consistent with a homogeneous distribution. We found a mean of [Fe/H] = −0.14 ± 0.07 dex, in agreement with other studies. Using the α-elements Mg, Si, Ca, and Ti, we obtain the mean of [α/Fe] = 0.11 ± 0.05. We found a vertical relation between Na and O, characterized by a significant spread in Na and an almost non-existent spread in O. In fact, Na and Al are the only two light elements with a large intrinsic spread, which demonstrates the presence of multiple populations (MPs). An intrinsic spread in Mg is not detected in this study. The α, iron-peak, and neutron-capture elements show good agreement with the trend of the bulge field stars, indicating similar origin and evolution, in concordance with our previous studies for two other bulge globular clusters (NGC 6440 and NGC 6528).
Variations in the slope of the resolved star-forming main sequence: a tool for constraining the mass of star-forming regions
Authors: Hani Maan H , Hayward Christopher C , Orr Matthew E , Ellison Sara L , Torrey Paul , Murray Norm , Wetzel Andrew , Faucher-Giguère Claude-André
Published: January 2020

The correlation between galaxies’ integrated stellar masses and star formation rates (the ‘star formation main sequence’, SFMS) is a well-established scaling relation. Recently, surveys have found a relationship between the star formation rate (SFR) and stellar mass surface densities on kpc and sub-kpc scales (the ‘resolved SFMS’, rSFMS). In this work, we demonstrate that the rSFMS emerges naturally in Feedback In Realistic Environments 2 (FIRE-2) zoom-in simulations of Milky Way-mass galaxies. We make SFR and stellar mass maps of the simulated galaxies at a variety of spatial resolutions and star formation averaging time-scales and fit the rSFMS using multiple methods from the literature. While the absolute value of the SFMS slope (αMS) depends on the fitting method, the slope is steeper for longer star formation time-scales and lower spatial resolutions regardless of the fitting method employed. We present a toy model that quantitatively captures the dependence of the simulated galaxies’ αMS on spatial resolution and use it to illustrate how this dependence can be used to constrain the characteristic mass of star-forming clumps.
Comprehensive identification of alternative back-splicing in human tissue transcriptomes
Authors: Zhang Peng , Zhang Xiao-Ou , Jiang Tingting , Cai Lingling , Huang Xiao , Liu Qi , Li Dan , Lu Aiping , Liu Yan , Xue Wen , Zhang Peng , Weng Zhiping
Published: January 2020

Circular RNAs (circRNAs) are covalently closed RNAs derived from back-splicing of genes across eukaryotes. Through alternative back-splicing (ABS), a single gene produces multiple circRNAs sharing the same back-splice site. Although many ABS events have recently been discovered, to what extent ABS involves in circRNA biogenesis and how it is regulated in different human tissues still remain elusive. Here, we reported an in-depth analysis of ABS events in 90 human tissue transcriptomes. We observed that ABS occurred for about 84% circRNAs. Interestingly, alternative 5′ back-splicing occurs more prevalently than alternative 3′ back-splicing, and both of them are tissue-specific, especially enriched in brain tissues. In addition, the patterns of ABS events in different brain regions are similar to each other and are more complex than the patterns in non-brain tissues. Finally, the intron length and abundance of Alu elements positively correlated with ABS event complexity, and the predominant circRNAs had longer flanking introns and more Alu elements than other circRNAs in the same ABS event. Together, our results represent a resource for circRNA research—we expanded the repertoire of ABS events of circRNAs in human tissue transcriptomes and provided insights into the complexity of circRNA biogenesis, expression, and regulation.
The m6A reader YTHDF1 promotes ovarian cancer progression via augmenting EIF3C translation
Authors: Liu Tao , Wei Qinglv , Jin Jing , Luo Qingya , Liu Yi , Yang Yu , Cheng Chunming , Li Lanfang , Pi Jingnan , Si Yanmin , Xiao Hualiang , Li Li , Rao Shuan , Wang Fang , Yu Jianhua , Yu Jia , Zou Dongling , Yi Ping
Published: January 2020

N 6-Methyladenosine (m6A) is the most abundant RNA modification in mammal mRNAs and increasing evidence suggests the key roles of m6A in human tumorigenesis. However, whether m6A, especially its ‘reader’ YTHDF1, targets a gene involving in protein translation and thus affects overall protein production in cancer cells is largely unexplored. Here, using multi-omics analysis for ovarian cancer, we identified a novel mechanism involving EIF3C, a subunit of the protein translation initiation factor EIF3, as the direct target of the YTHDF1. YTHDF1 augments the translation of EIF3C in an m6A-dependent manner by binding to m6A-modified EIF3C mRNA and concomitantly promotes the overall translational output, thereby facilitating tumorigenesis and metastasis of ovarian cancer. YTHDF1 is frequently amplified in ovarian cancer and up-regulation of YTHDF1 is associated with the adverse prognosis of ovarian cancer patients. Furthermore, the protein but not the RNA abundance of EIF3C is increased in ovarian cancer and positively correlates with the protein expression of YTHDF1 in ovarian cancer patients, suggesting modification of EIF3C mRNA is more relevant to its role in cancer. Collectively, we identify the novel YTHDF1-EIF3C axis critical for ovarian cancer progression which can serve as a target to develop therapeutics for cancer treatment.
Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2
Authors: Hou Linlin , Wei Yuanjie , Lin Yingying , Wang Xiwei , Lai Yiwei , Yin Menghui , Chen Yanpu , Guo Xiangpeng , Wu Senbin , Zhu Yindi , Yuan Jie , Tariq Muqddas , Li Na , Sun Hao , Wang Huating , Zhang Xiaofei , Chen Jiekai , Bao Xichen , Jauch Ralf
Published: January 2020

Some transcription factors that specifically bind double-stranded DNA appear to also function as RNA-binding proteins. Here, we demonstrate that the transcription factor Sox2 is able to directly bind RNA in vitro as well as in mouse and human cells. Sox2 targets RNA via a 60-amino-acid RNA binding motif (RBM) positioned C-terminally of the DNA binding high mobility group (HMG) box. Sox2 can associate with RNA and DNA simultaneously to form ternary RNA/Sox2/DNA complexes. Deletion of the RBM does not affect selection of target genes but mitigates binding to pluripotency related transcripts, switches exon usage and impairs the reprogramming of somatic cells to a pluripotent state. Our findings designate Sox2 as a multi-functional factor that associates with RNA whilst binding to cognate DNA sequences, suggesting that it may co-transcriptionally regulate RNA metabolism during somatic cell reprogramming.
Differential effects of phosphate binders on vitamin D metabolism in chronic kidney disease
Authors: Ginsberg Charles , Zelnick Leila R , Block Geoffrey A , Chertow Glenn M , Chonchol Michel , Hoofnagle Andrew , Kestenbaum Bryan , de Boer Ian H
Published: January 2020

Background

Phosphate binders are commonly used in the treatment of patients with hyperphosphatemia. While phosphate binders are used to lower phosphate, the effects of specific phosphate binder types on vitamin D metabolism are unknown.

Methods

We performed a secondary analysis of the Phosphate Normalization Trial in which patients with moderate to advanced chronic kidney disease were randomized to receive either placebo, sevelamer carbonate, lanthanum carbonate or calcium acetate for 9 months. We evaluated changes in serum concentrations of vitamin D metabolites including 24,25-dihydroxyvitamin D3 [24,25(OH)2D3], 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], the ratio of 24,25(OH)2D3 to 25-hydroxyvitamin D [the vitamin D metabolite ratio (VMR)] and the ratio of serum 1,25(OH)2D to 25-hydroxyvitamin D.

Results

Compared with placebo, randomization to the calcium acetate arm was associated with a 0.6 ng/mL (95% CI 0.2, 1) and 13.5 pg/ng (95% CI 5.5, 21.5) increase in 24,25(OH)2D and VMR, respectively, and a 5.2 pg/mL (95% CI 1.1, 9.4) reduction in 1,25(OH)2D. Randomization to sevelamer carbonate was associated with a 0.5 ng/mL (95% CI −0.9, −0.1) and 11.8 pg/ng (95% CI −20, −3.5) reduction in 24,25(OH)2D3 and VMR, respectively. There was no association of the sevelamer arm with the change in 1,25(OH)2D3, and randomization to lanthanum carbonate was not associated with a change in any of the vitamin D metabolites.

Conclusion

Administration of different phosphate binders to patients with moderate to severe CKD results in unique changes in vitamin D metabolism.
Impact of Genetic and Nongenetic Factors on Body Mass Index and Waist-Hip Ratio Change in HIV-Infected Individuals Initiating Antiretroviral Therapy
Authors: Barceló Catalina , Guidi Monia , Thorball Christian W , Hammer Christian , Chaouch Aziz , Scherrer Alexandra U , Hasse Barbara , Cavassini Matthias , Furrer Hansjakob , Calmy Alexandra , Haubitz Sebastian , Bernasconi Enos , Buclin Thierry , Fellay Jacques , Tarr Philip E , Csajka Chantal ,   Swiss HIV Cohort Study, Anagnostopoulos A , Battegay M , Bernasconi E , Böni J , Braun D L , Bucher H C , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Günthard H F , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Huber M , Kahlert C R , Kaiser L , Keiser O , Klimkait T , Kouyos R D , Kovari H , Ledergerber B , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner K J , Müller N , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Rudin C , Scherrer A U , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Vernazza P , Wandeler G , Weber R , Yerly S
Published: January 2020

Objective

There is limited data on abdominal obesity and the influence of genetics on weight change after antiretroviral therapy (ART) initiation. We assessed body mass index (BMI) and waist hip ration (WHR) change over time in the Swiss HIV Cohort study (SHCS).

Methods

Mixed-effects models characterizing BMI and WHR change over time in 1090 SHCS participants initiating ART between 2005 and 2015 were developed and used to quantify the influence of demographics, clinical factors, and genetic background.

Results

Individuals with CD4 nadir <100 cells/µL gained 6.4 times more BMI than individuals with ≥200, and 2.8 times more WHR than individuals with ≥100 (P < .001) during the first 1.5 and 2.5 years after ART initiation, respectively. The risk of being overweight or obese after 1.5 years increased with CD4 nadir <100 cells/µL compared to 100–199 (odds ratio [OR], 2.07; 95% confidence interval [CI], 1.63–2.74) and ≥200 (OR, 1.69; 95% CI, 1.26–2.32), persisting after 10 years of ART. The risk of abdominal obesity after 2.5 years increased with CD4 nadir <100 compared to ≥100 (OR, 1.35; 95% CI, 1.17–1.54 [in men]; OR, 1.36; 95% CI, 1.18–1.57 [in women]), persisting after 10 years of ART. No significant differences were found across antiretroviral drug classes or genetic scores.

Conclusions

The risk of general and abdominal obesity increased with CD4 nadir <100 cells/µL. Based on our results, including the genetic background would not improve obesity predictions in HIV-infected individuals.
CGRP Plasma Levels Decrease in Classical Trigeminal Neuralgia Patients Treated with Botulinum Toxin Type A: A Pilot Study
Authors: Zhang Yi , Lian Yajun , Zhang Haifeng , Xie Nanchang , Chen Yuan
Published: January 2020

Objective

The aim of this study was to investigate the changes of calcitonin gene-related peptide (CGRP) plasma levels in patients with classical trigeminal neuralgia (TN) and if plasma CGRP concentrations could be used to predict the response to botulinum toxin type A (BTX-A).

Methods

Forty-seven patients with classical TN were recruited and treated with BTX-A. A patient was considered a responder when the visual analog scale (VAS) score and number of episodes were reduced by at least 50% compared with baseline data. Matched healthy subjects with no headache history served as controls. CGRP levels were measured by the enzyme-linked immunosorbent assay.

Results

A total of 45 patients and 30 healthy controls completed the study. Plasma CGRP concentrations after treatment with BTX-A (median [interquartile range {IQR}] = 28.86 [14.75–61.23] pg/mL) were significantly lower than before treatment (median [IQR] = 55.38 [22.59–71.67] pg/mL, P < 0.001). Plasma CGRP concentrations in responders after treatment with BTX-A (median [IQR] = 28.02 [12.78–57.28] pg/mL) were significantly lower than before treatment (median [IQR] = 50.57 [24.30–70.09] pg/mL, P < 0.001). In nonresponders, there were no significant differences between the levels before and after treatment (P = 0.938). Age, gender, VAS score, taking/not taking carbamazepine, and the number of trigeminal nerve branches involved had no significant influence on the median difference between plasma CGRP concentrations. The concentration of CGRP before treatment was not predictive of the treatment result.

Conclusions

CGRP levels decrease significantly in patients with classical TN after treatment with BTX-A. Plasma levels of CGRP cannot be used to predict the response to BTX-A. This study indicates that CGRP is likely to be involved in the pathophysiology of classical TN. Moreover, the analgesic mechanism of BTX-A may be related to the inhibition of CGRP release.
Practical and measurable definitions of care coordination, care management, and case management
Authors: Williams Mark D
Published: January 2020

Integrated behavioral health is a population-based approach that acknowledges the chronic nature of most mental illnesses and the need for services beyond those delivered in face-to-face visits. These services have been referred to by different and confusing names with over 40 definitions of care coordination concepts in the literature. Kilbourne et al. in a recent article in this journal divided these tasks into three groups: care coordination, care management and case management with associated definitions provided as used in the veterans affairs system. In this commentary, while drawing on over a decade of experience in implementing care management models in the Mayo clinic system of care, I will suggest we need to be even more specific with these definitions. I propose these terms be linked to critical and measurable tasks in the management of chronic conditions, thus allowing those administrating or researching these interventions to better assess fidelity, processes and outcomes when a model is applied to a population of patients with chronic conditions in an integrated setting.
Potential of ToxCast Data in the Safety Assessment of Food Chemicals
Authors: Punt Ans , Firman James , Boobis Alan , Cronin Mark , Gosling John Paul , Wilks Martin F , Hepburn Paul A , Thiel Anette , Fussell Karma C
Published: January 2020

Tox21 and ToxCast are high-throughput in vitro screening programs coordinated by the U.S. National Toxicology Program and the U.S. Environmental Protection Agency, respectively, with the goal of forecasting biological effects in vivo based on bioactivity profiling. The present study investigated whether mechanistic insights in the biological targets of food-relevant chemicals can be obtained from ToxCast results when the chemicals are grouped according to structural similarity. Starting from the 556 direct additives that have been identified in the ToxCast database by Karmaus et al. [Karmaus, A. L., Trautman, T. D., Krishan, M., Filer, D. L., and Fix, L. A. (2017). Curation of food-relevant chemicals in ToxCast. Food Chem. Toxicol. 103, 174–182.], the results showed that, despite the limited number of assays in which the chemical groups have been tested, sufficient results are available within so-called “DNA binding” and “nuclear receptor” target families to profile the biological activities of the defined chemical groups for these targets. The most obvious activity identified was the estrogen receptor-mediated actions of the chemical group containing parabens and structurally related gallates, as well the chemical group containing genistein and daidzein (the latter 2 being particularly active toward estrogen receptor β as a potential health benefit). These group effects, as well as the biological activities of other chemical groups, were evaluated in a series of case studies. Overall, the results of the present study suggest that high-throughput screening data could add to the evidence considered for regulatory risk assessment of food chemicals and to the evaluation of desirable effects of nutrients and phytonutrients. The data will be particularly useful for providing mechanistic information and to fill data gaps with read-across.
Experimental translocations to low predation lead to non-parallel increases in relative brain size
Authors: Mitchell David J. , Vega-Trejo Regina , Kotrschal Alexander
Published: January 2020

Predation is a near ubiquitous factor of nature and a powerful selective force on prey. Moreover, it has recently emerged as an important driver in the evolution of brain anatomy, though population comparisons show ambiguous results with considerable unexplained variation. Here, we test the reproducibility of reduced predation on evolutionary trajectories of brain evolution. We make use of an introduction experiment, whereby guppies (
Poecilia reticulata
) from a single high predation stream were introduced to four low predation streams. After 8–9 years of natural selection in the wild and two generations of common garden conditions in the laboratory, we quantified brain anatomy. Relative brain region sizes did not differ between populations. However, we found a general increase and striking variation in relative brain size of introduced populations, which varied from no change to a 12.5% increase in relative brain weight, relative to the ancestral high predation population. We interpret this as evidence for non-parallel evolution, which implies a weak or inconsistent association of relative brain size with fitness in low predation sites. The evolution of brain anatomy appears sensitive to unknown environmental factors, or contingent on either chance events or historical legacies of environmental change.
Partitioning colony size variation into growth and partial mortality
Authors: Madin Joshua S. , Baird Andrew H. , Baskett Marissa L. , Connolly Sean R. , Dornelas Maria A.
Published: January 2020

Body size is a trait that broadly influences the demography and ecology of organisms. In unitary organisms, body size tends to increase with age. In modular organisms, body size can either increase or decrease with age, with size changes being the net difference between modules added through growth and modules lost through partial mortality. Rates of colony extension are independent of body size, but net growth is allometric, suggesting a significant role of size-dependent mortality. In this study, we develop a generalizable model of partitioned growth and partial mortality and apply it to data from 11 species of reef-building coral. We show that corals generally grow at constant radial increments that are size independent, and that partial mortality acts more strongly on small colonies. We also show a clear life-history trade-off between growth and partial mortality that is governed by growth form. This decomposition of net growth can provide mechanistic insights into the relative demographic effects of the intrinsic factors (e.g. acquisition of food and life-history strategy), which tend to affect growth, and extrinsic factors (e.g. physical damage, and predation), which tend to affect mortality.
Evolutionary dynamics in the dispersal of sign languages
Authors: Power Justin M. , Grimm Guido W. , List Johann-Mattis
Published: January 2020

The evolution of spoken languages has been studied since the mid-nineteenth century using traditional historical comparative methods and, more recently, computational phylogenetic methods. By contrast, evolutionary processes resulting in the diversity of contemporary sign languages (SLs) have received much less attention, and scholars have been largely unsuccessful in grouping SLs into monophyletic language families using traditional methods. To date, no published studies have attempted to use language data to infer relationships among SLs on a large scale. Here, we report the results of a phylogenetic analysis of 40 contemporary and 36 historical SL manual alphabets coded for morphological similarity. Our results support grouping SLs in the sample into six main European lineages, with three larger groups of Austrian, British and French origin, as well as three smaller groups centring around Russian, Spanish and Swedish. The British and Swedish lineages support current knowledge of relationships among SLs based on extra-linguistic historical sources. With respect to other lineages, our results diverge from current hypotheses by indicating (i) independent evolution of Austrian, French and Spanish from Spanish sources; (ii) an internal Danish subgroup within the Austrian lineage; and (iii) evolution of Russian from Austrian sources.
The biomolecular characterization of a finger ring contextually dated to the emergence of the Early Neolithic from Syltholm, Denmark
Authors: Trolle Jensen Theis Zetner , Mackie Meaghan , Taurozzi Alberto John , Lanigan Liam Thomas , Gundelach Carsten , Olsen Jesper , Sørensen Søren Anker , Collins Matthew James , Sørensen Mikkel , Schroeder Hannes
Published: January 2020

We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterize the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS). We conclude that the ring was made from long bone or antler due to the presence of osteons (Haversian canals). Subsequent ZooMS analysis of collagen I and II indicated that it was made fromAlces alcesorCervus elaphusmaterial. We then used LC-MS/MS analysis to refine our species identification, confirming that the ring was made fromCervus elaphus, and to examine the rest of the proteome. This study demonstrates the potential of ancient proteomics for species identification of prehistoric artefacts made from osseous material.
Numerical simulation on fracturing behaviour of hard roofs at different levels during extra-thick coal seam mining
Authors: Gao Rui , Huo Bingjie , Xia Hongchun , Meng Xiangbin
Published: January 2020

In fully mechanized caving mining of extra-thick coal seams, the movement range of overburden is wide, resulting in the breakage of multilayer hard roofs in overlying large spaces. However, the characteristics, morphology and impact effect of hard roofs at different levels are different and unclear. In this study, a secondary development was used in the numerical simulation software ABAQUS, and the caving of rock strata in the finite-element software was realized. The bearing stress distribution, fracturing morphology and impact energy characteristics of hard roofs at different levels were studied to reflect the action and difference of hard roof failure on the working face; thus, revealing the mechanism of the strong ground pressure in stopes, and providing a theoretical basis for the safe and efficient mining of extra-thick coal seams with hard roofs.
Limited thermal plasticity and geographical divergence in the ovipositor of
Drosophila suzukii
Authors: Varón-González Ceferino , Fraimout Antoine , Delapré Arnaud , Debat Vincent , Cornette Raphaël
Published: January 2020

Phenotypic plasticity has been repeatedly suggested to facilitate adaptation to new environmental conditions, as in invasions. Here, we investigate this possibility by focusing on the worldwide invasion of
Drosophila suzukii
: an invasive species that has rapidly colonized all continents over the last decade. This species is characterized by a highly developed ovipositor, allowing females to lay eggs through the skin of ripe fruits. Using a novel approach based on the combined use of scanning electron microscopy and photogrammetry, we quantified the ovipositor size and three-dimensional shape, contrasting invasive and native populations raised at three different developmental temperatures. We found a small but significant effect of temperature and geographical origin on the ovipositor shape, showing the occurrence of both geographical differentiation and plasticity to temperature. The shape reaction norms are in turn strikingly similar among populations, suggesting very little difference in shape plasticity among invasive and native populations, and therefore rejecting the hypothesis of a particular role for the plasticity of the ovipositor in the invasion success. Overall, the ovipositor shape seems to be a fairly robust trait, indicative of stabilizing selection. The large performance spectrum rather than the flexibility of the ovipositor would thus contribute to the success of
D. suzukii
worldwide invasion.
Thermus thermamylovorans sp. nov., isolated from a hot spring
Authors: Ming Hong , Zhao Zhuo-li , Ji Wei-li , Ding Chen-Long , Cheng Li-jiao , Niu Ming-ming , Li Meng , Yi Bing-fang , Xia Ting-ting , Nie Guo-xing
Published: January 2020

A novel thermophilic bacterium, designated CFH 72773T was isolated from the enrichment of a Jinze hot spring sample which was collected from Dientan town, Tengchong county, Yunnan province, south-western PR China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and non-sporulating. The taxonomic position of the strain was investigated by using a polyphasic approach. Growth occurred at 37–75 °C, pH 6.0–8.0 and with 0–2.0 % (w/v) NaCl. Comparison of the 16S rRNA gene sequences indicated the strain represented a member of the genus

Thermus

and showed close relationships to the type strains

Thermus caliditerrae

YIM 77925T (96.3 % similarity) and

Thermus igniterrae

RF-4T (96.2 % similarity). The whole genome of CFH 72773T consisted of 2.25 Mbp and the DNA G+C content was 69.5 mol%. A total of 2262 genes, including a variety of enzymes for chemolithotrophy and anerobic respiration, were predicted. The strain had a unique negative oxidase activity and could hydrolyze starch at high temperature. Furthermore, various genes related to methane, sulfur, fumarate and nitrate metabolism were found, all these indicated that it is worth studying the novel strain. The predominant menaquinone is MK-8. The predominant cellular fatty acids included iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The major polar lipids were comprised of aminophospholipid, glycolipid and two phospholipids. On the basis of low ANI values, different phenotypic and chemotaxonomic characters and phylogenetic analysis, we made a proposal that strain CFH 72773T represents a novel member of the genus

Thermus

, for which the name Thermus thermamylovorans sp. nov. is proposed. The type strain is CFH 72773T (=CCTCC AB2018244T=KCTC 43129T).
Natrialba swarupiae sp. nov., a halophilic archaeon isolated from a hypersaline lake in India
Authors: Kajale Swapnil , Deshpande Neelima , Pali Snigdha , Shouche Yogesh , Sharma Avinash
Published: January 2020

A haloarchaeal strain (ESP3B_9T) was isolated from the salt pan of Sambhar salt lake, Rajasthan, India. Cells were coccoid, non-motile, Gram-stain-negative and formed reddish-pink pigmented colonies. The strain was aerobic, able to grow at 35–55 °C (optimum, 40 °C), in 20–35 % (25 %) NaCl and pH 8–10 (pH 9). Mg2+not required for growth. The cells were lysed in distilled water and the minimum NaCl concentration that prevented cell lysis was 5 % w/v. The 16S rRNA gene sequence similarities between strain ESP3B_9TandNatrialba hulunbeirensisJCM 10989TandNatrialba magadiiATCC 43099Twere 96.53 and 96.25 % respectively. The similarities of the RNA polymerase subunit B gene between strain ESP3B_9TandN. hulunbeirensisJCM 10989TandN. magadiiATCC 43099Twere 84.47 and 84.9 % respectively. Genome sequencing revealed a genome size of 4.20 Mbp with DNA G+C content of 62.5 mol%. The major polar lipids were phosphotidylglycerol and phosphatidylglycerol phosphate methyl esters with minor amounts of unidentified lipids. The results of polyphasic analysis determined that strain ESP3B_9Trepresents a novel species of the genusNatrialba, for which the nameNatrialba swarupiaesp. nov. is proposed. The type strain is ESP3B_9T(MCC 3419T=JCM 33002T=KCTC 4279T=CGMCC 1.16737T).
Saccharothrix deserti sp. nov., an actinomycete isolated from desert soil
Authors: Liu Jinjuan , Sun Yong , Liu Jinrong , Wu Yunjian , Cao Chengliang , Li Rongpeng , Jiang Jihong
Published: January 2020

A Gram-stain-positive, aerobic actinomycete, designated strain BMP B8144T, was isolated from desert soil, in Xinjiang province, northwest China. The isolate produced scanty aerial mycelium and fragmented substrate mycelium on most tested media. Cell-wall hydrolysates contained meso-diaminopimelic acid, galactose and mannose. The diagnostic phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylhydroxylethanolamine, phosphatidylinositol, and phosphatidylinositol mannosides. The major fatty acids included iso-C16 : 0, C17 : 1
ω8c and iso-C15 : 0. The predominant menaquinones were MK-9(H4) and MK-10(H4). The DNA G+C content was 70.4 mol% (genome). Based on the 16S rRNA gene sequence analysis on EzBioCloud server, strain BMP B8144T showed the closest similarities to

Saccharothrix lopnurensis

YIM LPA2hT (98.9 %) and ‘

Saccharothrix yanglingensis

’ Hhs.015 (98.6 %). However, it can be distinguished from the closest strains based on the low levels of DNA–DNA relatedness (59.3±1.8 and 47.9±2.3 %, respectively). A combination of morphological, chemotaxonomic and phylogenetic characteristics, strain BMP B8144T represents a novel species of the genus

Saccharothrix

, for which the name Saccharothrix deserti sp. nov. is proposed. The type strain is BMP B8144T (=CGMCC 4.7490T=KCTC 49001T).
Paenibacillus paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis
Authors: Wang Min , Jiang Xing-Wang , Tang Shu-Kun , Zhi Xiao-Yang , Yang Ling-Ling
Published: January 2020

A Gram-reaction-positive, endospore-forming and rod-shaped bacterial strain, designated py1325T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan Province, PR China, and subjected to a polyphasic taxonomic characterization. It grew optimally with 0–1 % NaCl (w/v), at pH 7 and at 30 °C. The major respiratory quinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acid was anteiso-C15 : 0. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. The results of 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to

Paenibacillus luteus

R-3T (99.0 %),

Paenibacillus sinopodophylli

CCTCC AB 2016047T (97.9 %),

Paenibacillus castaneae

DSM 19417T (97.5 %) and

Paenibacillus endophyticus

LMG 27297T (97.2 %). The digital DNA–DNA hybridization and average
nucleotide identity values between py1325T and these species ranged 20.6–53.3 % and 79.9–93.6 %. The G+C content of the genomic DNA was 47.7 mol%. According to the phylogenetic, phenotypic and chemotaxonomic evidence, strain py1325T clearly represents a novel species of the genus

Paenibacillus

, for which the name Paenibacillus paridis sp. nov. is proposed. The type strain is py1325T (=CCTCC AB 2015220T=LMG 29068T).
Honey bee queen production: Canadian costing case study and profitability analysis
Authors: Bixby Miriam , Hoover Shelley E. , McCallum Robyn , Ibrahim Abdullah , Ovinge Lynae , Olmstead Sawyer , Pernal Stephen F. , Zayed Amro , Foster Leonard J. , Guarna M. Marta
Published: January 2020

The recent decline in honey bee (Hymenoptera: Apidae) colony health worldwide has had a significant impact on the beekeeping industry as well as on pollination-dependent crop sectors in North America and Europe. The pollinator crisis has been attributed to many environmental and anthropological factors including less nutrient rich agricultural monocultures, pesticide exposure, new parasite and pathogen infestations as well as beekeeper management and weather. Canadian beekeepers have indicated that issues with honey bee queens are the most significant factor affecting their colony health. In Canada, beekeepers manage colony losses by relying on the importation of foreign bees, particularly queens from warmer climates, to lead new replacement colonies. Unfortunately, the risks associated with imported queens include the introduction of new and potentially resistant pests and diseases, undesirable genetics including bees with limited adaptations to Canada’s unique climate and bees negatively affected by transportation. Importing a large proportion of our queens each year also creates an unsustainable dependency on foreign bee sources, putting our beekeeping and pollination sectors at an even greater risk in the case of border closures and restrictions. Increasing the domestic supply of queens is one mitigation strategy that could provide Canadian beekeepers, farmers and consumers with a greater level of agricultural stability through locally bred, healthier queens. Our study is the first rigorous analysis of the economic feasibility of Canadian queen production. We present the costs of queen production for three case study operations across Canada over two years as well as the profitability implications. Our results show that for a small to medium sized queen production operation in Canada, producing queen cells and mated queens can be profitable. Using a mated queen market price ranging from $30 to $50, a producer selling mated queens could earn a profit of between $2 and $40 per queen depending on price and the cost structure of his operation. If the producer chose to rear queens for his own operation, the cost savings would also be significant as imported queen prices continue to rise. Our case studies reveal that there is potential for both skilled labour acquisition over time in queen production as well as cost savings from economies of scale. Our queen producers also reduced their production costs by re-using materials year to year. Domestic queen production could be one viable strategy to help address the current pollinator crisis in Canada.
Hybrid dynamic pharmacophore models as effective tools to identify novel chemotypes for anti-TB inhibitor design: A case study with Mtb-DapB
Authors: Choudhury Chinmayee , Bhardwaj Anshu
Published: January 2020

Antimicrobial resistance (AMR) is one of the most serious global public health threats as it compromises the successful treatment of deadly infectious diseases like tuberculosis. New therapeutics are constantly needed but it takes a long time and is expensive to explore new biochemical space. One way to address this issue is to repurpose the validated targets and identify novel chemotypes that can simultaneously bind to multiple binding pockets of these targets as a new lead generation strategy. This study reports such a strategy, dynamic hybrid pharmacophore model (DHPM), which represents the combined interaction features of different binding pockets contrary to the conventional approaches, where pharmacophore models are generated from single binding sites. We have considered Mtb-DapB, a validated mycobacterial drug target, as our model system to explore the effectiveness of DHPMs to screen novel unexplored compounds. Mtb-DapB has a cofactor binding site (CBS) and an adjacent substrate binding site (SBS). Four different model systems of Mtb-DapB were designed where, either NADPH/NADH occupies CBS in presence/absence of an inhibitor 2, 6-PDC in the adjacent SBS. Two more model systems were designed, where 2, 6-PDC was linked to NADPH and NADH to form hybrid molecules. The six model systems were subjected to 200ns molecular dynamics simulations and trajectories were analyzed to identify stable ligand-receptor interaction features. Based on these interactions, conventional pharmacophore models (CPM) were generated from the individual binding sites while DHPMs were created from hybrid-molecules occupying both binding sites. A huge library of 15, 63,764 publicly available molecules were screened by CPMs and DHPMs. The screened hits obtained from both types of models were compared based on their Hashed binary molecular fingerprints and 4-point pharmacophore fingerprints using Tanimoto, Cosine, Dice and Tversky similarity matrices. Molecules screened by DHPM exhibited significant structural diversity, better binding strength and drug like properties as compared to the compounds screened by CPMs indicating the efficiency of DHPM to explore new chemical space for anti-TB drug discovery. The idea of DHPM can be applied for a wide range of mycobacterial or other pathogen targets to venture into unexplored chemical space.
CASSPER: A Semantic Segmentation based Particle Picking Algorithm for Single Particle Cryo-Electron Microscopy
Authors: George Blesson , Assaiya Anshul , Roy Robin Jacob , Kembhavi Ajit , Chauhan Radha , Paul Geetha , Kumar Janesh , Philip Ninan Sajeeth
Published: January 2020

Single-particle cryo-electron microscopy has emerged as the method of choice for structure determination of proteins and protein complexes. However, particle identification and selection which is a prerequisite for achieving high-resolution still poses a major bottleneck for automating the steps of structure determination. Here, we present a generalised deep learning tool, CASSPER, for the automated detection and isolation of protein particles in transmission microscope images. This deep learning tool uses Semantic Segmentation and a collection of visually prepared training samples to capture the differences in the transmission intensities of protein, ice, carbon and other impurities found in the micrograph. CASSPER is the first method to do pixel level classification and completely eliminates the need of manual particle picking. Integration of Contrast Limited Adaptive Histogram Equalization (CLAHE) in CASSPER enables high-fidelity particle detection even in micrographs with variable ice thickness and contrast. In addition, our generalized model for cross molecule picking works with high efficiency on unseen datasets and can potentially pick particles on-the-fly, thereby, enabling automation of data processing.
Immunohistochemical Characterization of Phosphorylated Ubiquitin in the Mouse Hippocampus
Authors: Kataoka Kosuke , Bilkei-Gorzo Andras , Zimmer Andreas , Asahi Toru
Published: January 2020

Mitochondrial autophagy (mitophagy) is an essential and evolutionarily conserved process that maintains mitochondrial integrity via the removal of damaged or superfluous mitochondria in eukaryotic cells. Phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (PINK1) and Parkin promote mitophagy and function in a common signaling pathway. PINK1-mediated ubiquitin phosphorylation at Serine 65 (Ser65-pUb) is a key event in the efficient execution of PINK1/Parkin-dependent mitophagy. However, few studies have used immunohistochemistry to analyze Ser65-pUb in the mouse. Here, we examined the immunohistochemical characteristics of Ser65-pUb in the mouse hippocampus. Some hippocampal cells were Ser65-pUb positive, whereas the remaining cells expressed no or low levels of Ser65-pUb. PINK1 deficiency resulted in a decrease in the density of Ser65-pUb-positive cells, consistent with a previous hypothesis based onin vitroresearch. Interestingly, Ser65-pUb-positive cells were detected in hippocampi lacking PINK1 expression. The CA3 pyramidal cell layer and the dentate gyrus (DG) granule cell layer exhibited significant reductions in the density of Ser65-pUb-positive cells in PINK1-deficient mice. Moreover, Ser65-pUb immunoreactivity colocalized predominantly with neuronal markers. These findings suggest that Ser65-pUb may serve as a biomarker ofin situPINK1 signaling in the mouse hippocampus; however, the results should be interpreted with caution, as PINK1 deficiency downregulated Ser65-pUb only partially.