bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors
Authors: Byrne Maria , Koop Demian , Strbenac Dario , Cisternas Paula , Balogh Regina , Yang Jean Yee Hwa , Davidson Phillip L , Wray Gregory 
Published: April 2020

AbstractThe Echinodermata is characterized by a secondarily evolved pentameral body plan. While the evolutionary origin of this body plan has been the subject of debate, the molecular mechanisms underlying its development are poorly understood. We assembled a de novo developmental transcriptome from the embryo through metamorphosis in the sea star Parvulastra exigua. We use the asteroid model as it represents the basal-type echinoderm body architecture. Global variation in gene expression distinguished the gastrula profile and showed that metamorphic and juvenile stages were more similar to each other than to the pre-metamorphic stages, pointing to the marked changes that occur during metamorphosis. Differential expression and gene ontology (GO) analyses revealed dynamic changes in gene expression throughout development and the transition to pentamery. Many GO terms enriched during late metamorphosis were related to neurogenesis and signalling. Neural transcription factor genes exhibited clusters with distinct expression patterns. A suite of these genes was up-regulated during metamorphosis (e.g. Pax6, Eya, Hey, NeuroD, FoxD, Mbx, and Otp). In situ hybridization showed expression of neural genes in the CNS and sensory structures. Our results provide a foundation to understand the metamorphic transition in echinoderms and the genes involved in development and evolution of pentamery.
Isolation and characterization of Hena1 – a novelErwinia amylovorabacteriophage
Authors: Besarab Natalya V , Akhremchuk Artur E , Zlatohurska Maryna A , Romaniuk Liudmyla V , Valentovich Leonid N , Tovkach Fedor I , Lagonenko Alexander L , Evtushenkov Anatoly N 
Published: April 2020

ABSTRACTFire blight, caused by plant pathogenic bacterium Erwinia amylovora, is one of the most important diseases of Rosaceae plants. Due to the lack of effective control measures, fire blight infections pose a recurrent threat on agricultural production worldwide. Recently, bacterial viruses, or bacteriophages, have been proposed as environmentally friendly natural antimicrobial agents for fire blight control. Here, we isolated a novel bacteriophage Hena1 with activity against E. amylovora. Further analysis revealed that Hena1 is a narrow-host-range lytic phage belonging to Myoviridae family. Its genome consists of a linear 148,842 bp dsDNA (48.42% GC content) encoding 240 ORFs and 23 tRNA genes. Based on virion structure and genomic composition, Hena1 was classified as a new species of bacteriophage subfamily Vequintavirinae. The comprehensive analysis of Hena1 genome may provide further insights into evolution of bacteriophages infecting plant pathogenic bacteria.
Insights into the reason of Human-Residential Bifidobacteria (HRB) being the natural inhabitants of the human gut and their potential health-promoting benefits
Authors: Wong Chyn Boon , Odamaki Toshitaka , Xiao Jin-zhong 
Published: April 2020

ABSTRACTMembers of Bifidobacterium are among the first microbes to colonise the human gut, and certain species are recognised as the natural resident of human gut microbiota. Their presence in the human gut has been associated with health-promoting benefits and reduced abundance of this genus is linked with several diseases. Bifidobacterial species are assumed to have coevolved with their hosts and include members that are naturally present in the human gut, thus recognised as Human-Residential Bifidobacteria (HRB). The physiological functions of these bacteria and the reasons why they occur in and how they adapt to the human gut are of immense significance. In this review, we provide an overview of the biology of bifidobacteria as members of the human gut microbiota and address factors that contribute to the preponderance of HRB in the human gut. We highlight some of the important genetic attributes and core physiological traits of these bacteria that may explain their adaptive advantages, ecological fitness, and competitiveness in the human gut. This review will help to widen our understanding of one of the most important human commensal bacteria and shed light on the practical consideration for selecting bifidobacterial strains as human probiotics.
Dendroecological assessment of climate resilience of the rare and scattered forest tree species Tilia cordata Mill. in northwestern Europe
Authors: Latte Nicolas , Taverniers Philippe , de Jaegere Tanguy , Claessens Hugues 
Published: April 2020

Abstract
To increase forest resilience to global change, forest managers are often directing forest stands towards a broader diversity of tree species. The small-leaved lime (Tilia cordata Mill.), a rare and scattered species in northwestern Europe, is a promising candidate for this purpose. Its life traits suggest a high resilience to climate change and a favourable impact on forest ecosystem services. This study used a dendroecological approach to assess how lime tree radial growth had responded to the past climatic change. First, 120 lime trees from nine sites were selected in southern Belgium based on criteria adapted to the rareness of the species. Chronology quality was assessed and resulting tree-ring series were validated at site and region levels. Second, a range of dendrochronological methods was used to analyze the changes over time in the variability and long-term trends of lime tree growth and their relation to climate during the period 1955–2016. Last, behaviour of lime trees was compared with that of beech from the same region and time period. For this purpose, the same methodology was applied to an additional beech tree-ring dataset (149 trees from 13 sites). Beech is the climax tree species of the region, but is known to be drought-sensitive and has shown weaknesses in the current climate. The quality of our tree-ring series attests that dendroecological investigation using rare and scattered species is possible, opening the way to further analysis on other such lesser-known forest tree species. The analysis showed that the small-leaved lime had been resilient to the past climatic change in multiple ways. Lime growth increased during the preceding decades despite an increased frequency and intensity of stressful climatic events. Lime growth quickly recovered in the years following the stresses. The growth–climate relationships were either stable over time or had a positive evolution. The behaviour of lime contrasted strongly with that of beech. Lime performed better than beech in every analysis. Small-leaved lime is thus a serious candidate for addressing climate change challenges in the region. It should be considered by forest managers planning to improve the sustainability and resilience of their forests, in particular in vulnerable beech stands.
The Impact of Cholecystectomy on Long-Term Disease Outcomes and Quality of Life in Patients with Crohn’s Disease
Authors: Koutroumpakis Filippos , Lodhi Maham , Ahsan Maaz , Ramos Rivers Claudia , Schwartz Marc , Hashash Jana G , Babichenko Dmitriy , Tang Gong , Nagpal Tanvi , Dunn Michael , Keshavarzian Ali , Binion David G 
Published: April 2020

Abstract

Background
Cholecystectomy (CCY) is one of the most frequently performed abdominal surgeries. However, the impact of CCY in clinical settings with altered gastrointestinal physiology and anatomy, such as Crohn’s disease (CD), has not been fully characterized. We sought to investigate clinical outcomes, disease severity, and quality of life of CD patients after CCY.

Methods
We utilized a prospective, longitudinal registry of consented CD patients followed at a tertiary center. Crohn’s disease patients that had or had not undergone CCY formed the 2 study groups. The absence or presence of gallbladder was confirmed with abdominal CT scans obtained during routine care. Multiyear clinical, biochemical, and histologic data were collected and analyzed.

Results
Among 834 CD patients, 151 (18%) had undergone CCY. History of CCY was associated with higher disease activity (median Harvey-Bradshaw index; P &lt; 0.001), more years with anemia (P = 0.048), lower albumin (P = 0.001), worse quality of life (mean Short Inflammatory Bowel Disease Questionnaire; P &lt; 0.001), chronic abdominal pain (P &lt; 0.001), higher risk for incident colonic dysplasia (P = 0.011), higher rates of annual hospital admissions (P = 0.004), and opioid use (P &lt; 0.001). In multivariate analysis, CCY remained associated with higher disease activity (P &lt; 0.001), lower albumin (P = 0.008), lower quality of life (P &lt; 0.001), and more hospital admissions (P = 0.008), whereas CD patients with diseased ileum had higher risk for colonic dysplasia (P = 0.031).

Conclusions
CCY in CD patients was associated with multiple markers of disease activity and worse quality of life during multiyear follow up. This data suggests that CCY in CD patients may adversely impact the long-term clinical course.
On a Counting Theorem for Weakly Admissible Lattices
Authors: Fregoli Reynold 
Published: April 2020

Abstract
We give a precise estimate for the number of lattice points in certain bounded subsets of $\mathbb{R}^{n}$ that involve “hyperbolic spikes” and occur naturally in multiplicative Diophantine approximation. We use Wilkie’s o-minimal structure $\mathbb{R}_{\exp }$ and expansions thereof to formulate our counting result in a general setting. We give two different applications of our counting result. The 1st one establishes nearly sharp upper bounds for sums of reciprocals of fractional parts and thereby sheds light on a question raised by Lê and Vaaler, extending previous work of Widmer and of the author. The 2nd application establishes new examples of linear subspaces of Khintchine type thereby refining a theorem by Huang and Liu. For the proof of our counting result, we develop a sophisticated partition method that is crucial for further upcoming work on sums of reciprocals of fractional parts over distorted boxes.
Maternal supplementation of energy and protein, but not methionine hydroxy analog, enhanced postnatal growth and response to vaccination in Bos indicus-influenced beef offspring
Authors: Moriel Philipe , Vedovatto Marcelo , Palmer Elizabeth A , Oliveira Rhaiza A , Silva Hiran Marcelo , Ranches Juliana , Vendramini Joao M B 
Published: April 2020

Abstract
A 2-yr study evaluated the growth and postvaccination immune response of beef calves born from heifers offered no supplementation or pre- and postpartum supplementation of sugarcane molasses + urea with or without methionine hydroxy analog (MHA). On day 0 of each year (57 ± 5 d prepartum), Brangus crossbred beef heifers (n = 36/yr; 20 to 22 mo of age) were stratified by their initial body weight (BW; 396 ± 24.1 kg) and body condition score (BCS; 5.6 ± 0.43) and randomly allocated into 1 of 12 bahiagrass (Paspalum notatum) pastures (3 heifers/pasture). Treatments were randomly assigned to pastures (4 pastures/treatment/yr) and consisted of no supplementation (NOSUP) and supplementation of sugarcane molasses + urea (7.2 kg of DM/heifer/wk) with (MOL+) or without (MOL−) fortification with 105 g/heifer/wk of MHA. Treatments were provided from 57 ± 5 d prepartum until 17 ± 5 d postpartum (day 0 to 74). On day 74, all heifer-calf pairs were combined and managed as a single group until the end of the breeding season (day 237). Calves were early weaned at 89 ± 5 d of age (day 147), limit-fed at 3.5% of BW (DM basis) in drylot until day 201, and vaccinated against respiratory disease pathogens on days 160 and 188. Prepartum BCS on day 44 did not differ (P = 0.26) between MOL+ and MOL− heifers but both groups had greater (P &lt; 0.0001) BCS than NOSUP heifers. Plasma concentrations of l-methionine on day 44 were the greatest (P ≤ 0.04) for MOL+ heifers and did not differ (P = 0.40) between NOSUP vs. MOL− heifers. Calf birth BW did not differ (P = 0.13) among treatments. Calf average daily gain (ADG) from birth to day 201 did not differ (P ≥ 0.17) between MOL+ vs. MOL− calves, but both groups had greater (P ≤ 0.05) ADG from birth to day 201 than NOSUP calves. Calf postvaccination plasma concentrations of glucose, cortisol, and haptoglobin did not differ among treatments (P ≥ 0.13). However, plasma concentrations of IGF-1 on day 167 and the overall positive vaccine seroconversion did not differ (P ≥ 0.18) between MOL− and MOL+ calves, but both were greater (P ≤ 0.04) compared with NOSUP calves. Hence, maternal supplementation of sugarcane molasses + urea increased BCS at calving and offspring BW gain and response to vaccination against respiratory pathogens compared with no maternal supplementation. MHA inclusion into maternal supplements effectively increased maternal plasma l-methionine concentrations but did not enhance maternal BCS at calving and offspring growth and postvaccination immune response.
The Effect of Anthropization on Sarcophagidae (Diptera: Calyptratae) Community Structure: An Assessment on Different Types of Habitats in the Humid Chaco Ecoregion of Argentina
Authors: Dufek Matias I , Larrea Dario D , Damborsky Miryam P , Mulieri Pablo R 
Published: April 2020

AbstractSarcophagidae (Diptera) are of great interest from a veterinary, medical, and forensic viewpoint, and are potential bioindicators for environmental impact assessments. In this study, we evaluated changes in abundance, species richness, and diversity of flesh flies in different habitat types in the Humid Chaco ecoregion of South America: 1) anthropized habitats: urban, cattle farm, and alfalfa crop, and 2) natural habitats: savanna and forest. We hypothesized that sarcophagid fly community parameters are affected by the anthropization and that spatial turnover will contribute more to the overall beta diversity than nestedness between habitats. In each habitat, samplings were conducted monthly from March 2015 to February 2016 in 25 sites, 5 per habitat, totaling 300 independent samples at the end of the study. We collected 5,790 Sarcophagidae (55 species). Community parameters of Sarcophagidae were evaluated and compared. The ecological effects of anthropization and habitat type were observed in the present study. As expected, our results showed the highest abundance, species richness, and diversity in the savanna and forest habitats (natural), whereas the lowest values were registered in the urban and alfalfa crop habitats, supporting the hypotheses of anthropization as the main driver of diversity loss. In addition, sarcophagid assemblages differed between all habitats and the overall dissimilarity was structured by spatial turnover. The main conclusion of this research is that flesh fly community structure is greatly affected by anthropization and habitat type, and this would be related to canopy cover and microclimate conditions of each environment.
Using Digital Image Analysis to Quantify Small Arthropod Vectors
Authors: Parker Christine , Meador Morgan , Hoover Jeffrey P 
Published: April 2020

Abstract
Quantifying arthropod vectors can be a time-consuming process. Here, we describe a technique to count large samples of small arthropods using ImageJ. ImageJ is an open source image processing software, produced by the National Institutes of Health, with a straightforward interface that has proven useful in quantifying small organisms (i.e., cells, pollen, eggs). In 2017, we deployed CDC light traps baited with carbon dioxide among seven sites to capture black flies (Diptera: Simuliidae). Samples of the captured specimens were photographed, and then quantified manually and automatically, using ImageJ. We compared the accuracy of three types of automated counts to manual counts of black flies using an information-theoretic approach. We found that changing the particle size produced counts closest to those obtained by manual counts. Even over a large range of values, from tens to thousands of flies, our automated counts were often identical to and almost always within 5% of the manual counts. When different, automated counts were usually slightly less than manual counts, and thus conservative estimates. This automated technique is simple, repeatable, requires minimal training, and can reduce the time needed to quantify small arthropods such as black flies.
The mass of our Galaxy from satellite proper motions in the Gaia era
Authors: Fritz T K , Di Cintio A , Battaglia G , Brook C , Taibi S 
Published: April 2020

ABSTRACT
We use Gaia DR2 systemic proper motions of 45 satellite galaxies to constrain the mass of the Milky Way using the scale-free mass estimator of Watkins et al. (2010). We first determine the anisotropy parameter β, and the tracer satellites’ radial density index γ to be β = $-0.67^{+0.45}_{-0.62}$ and γ = 2.11 ± 0.23. When we exclude possible former satellites of the Large Magellanic Cloud, the anisotropy changes to β = $-0.21^{+0.37}_{-0.51}$. We find that the index of the Milky Way’s gravitational potential α, which is dependent on the mass itself, is the parameter with the largest impact on the mass determination. Via comparison with cosmological simulations of Milky Way-like galaxies, we carried out a detailed analysis of the estimation of the observational uncertainties and their impact on the mass estimator. We found that the mass estimator is biased when applied naively to the satellites of simulated Milky Way haloes. Correcting for this bias, we obtain for our Galaxy a mass of $0.58^{+0.15}_{-0.14}\times 10^{12}$ M⊙ within 64 kpc, as computed from the inner half of our observational sample, and $1.43^{+0.35}_{-0.32}\times 10^{12}$ M⊙ within 273 kpc, from the full sample; this latter value extrapolates to a virial mass of $M_\mathrm{vir\, \Delta =97}=1.51^{+0.45}_{-0.40} \times 10^{12}\,{\rm M}_{\odot }$ corresponding to a virial radius of Rvir = 308 ± 29 kpc. This value of the Milky Way mass lies in-between other mass estimates reported in the literature, from various different methods.
Simulations of gas sloshing induced by a newly discovered gas poor substructure in galaxy cluster Abell 1644
Authors: Doubrawa L , Machado R E G , Laganá T F , Lima Neto G B , Monteiro-Oliveira R , Cypriano E S 
Published: April 2020

ABSTRACT
Collision events lead to peculiar morphologies in the intracluster gas of galaxies clusters. That seems to be the case of Abell 1644, a nearby galaxy cluster, composed of three main structures: the southern cluster that exhibits a spiral-like morphology, A1644S; the northern cluster seen in X-ray observations, A1644N1; and the recently discovered substructure, A1644N2. By means of N-body hydrodynamical simulations, we attempt to reconstruct the dynamical history of this system. These simulations resulted in two specific scenarios: (i) The collision between A1644S and A1644N2. Our best model has an inclination between the merger plane and the plane of the sky of 30°, and reaches the best morphology 1.6 Gyr after the pericentric passage. At this instant A1644N2 is gas poor, becoming nearly undetectable in X-ray emission. This model shows a good agreement with observations; (ii) The collision between A1644S and A1644N1. This approach did not give rise to results as satisfactory as the first scenario, due to great disturbances in density and mismatching temperature maps. As a complementary study, we perform a three-cluster simulation using as base the best-fitting model to reproduce the current state of A1644 with the three main structures. This scenario presented a good agreement to the global morphology of the observations. Thus, we find that the more likely scenario is a collision between A1644S and the newly discovered A1644N2, where A1644N1 may be present as long as it does not greatly interfere in the formation of the spiral feature.
Spatial distribution of quasi-biennial oscillations in high-latitude solar activity
Authors: Deng L H , Fei Y , Deng H , Mei Y , Wang F 
Published: April 2020

ABSTRACT
Quasi-biennial oscillations (QBOs) are considered to be a fundamental mode of solar magnetic activity at low latitudes (≤50°). However, the evolutionary aspect and the hemispheric distribution of solar QBOs at high latitudes (≥60°) are rarely studied. Here, we apply a relatively novel time-frequency analysis technique, called the synchrosqueezed wavelet transform, in order to extract the main components of the polar faculae in the Northern and Southern hemispheres for the time interval from 1951 August to 1998 December. We note the following. (i) Apart from the 22-yr Hale cycle, the 17-yr extended activity cycle and the 11-yr Schwabe cycle, QBOs have been estimated as a prominent time-scale of solar magnetic activity at high latitudes. (ii) The QBOs of the polar faculae are coherent in the two hemispheres, but the temporal (phase) and the spatial (amplitude) variations of solar QBOs occur unevenly on both hemispheres. (iii) For the 11-yr period mode, this begins in the Northern hemisphere three months earlier than in the Southern hemisphere. Moreover, the spatial and temporal distributions of the hemispheric QBOs differ from those of the 11-yr Schwabe cycle mode in the two hemispheres. Our findings could be helpful to improve our knowledge of the physical origin of the spatial distribution of solar QBOs at high latitudes, and could also provide more constraints on solar dynamo models introduced to characterize the different components of the solar magnetic activity cycle.
Detection of Na, K, and H2O in the hazy atmosphere of WASP-6b
Authors: Carter Aarynn L , Nikolov Nikolay , Sing David K , Alam Munazza K , Goyal Jayesh M , Mikal-Evans Thomas , Wakeford Hannah R , Henry Gregory W , Morrell Sam , López-Morales Mercedes , Smalley Barry , Lavvas Panayotis , Barstow Joanna K , García Muñoz Antonio , Gibson Neale P , Wilson Paul A 
Published: April 2020

ABSTRACT
We present new observations of the transmission spectrum of the hot Jupiter WASP-6b both from the ground with the Very Large Telescope FOcal Reducer and Spectrograph (FORS2) from 0.45 to 0.83 μm, and space with the Transiting Exoplanet Survey Satellite from 0.6 to 1.0 μm and the Hubble Space Telescope (HST) Wide Field Camera 3 from 1.12 to 1.65 μm. Archival data from the HST Space Telescope Imaging Spectrograph (STIS) and Spitzer are also re-analysed on a common Gaussian process framework, of which the STIS data show a good overall agreement with the overlapping FORS2 data. We also explore the effects of stellar heterogeneity on our observations and its resulting implications towards determining the atmospheric characteristics of WASP-6b. Independent of our assumptions for the level of stellar heterogeneity we detect Na i, K i, and H2O absorption features and constrain the elemental oxygen abundance to a value of [O/H] ≃ −0.9 ± 0.3 relative to solar. In contrast, we find that the stellar heterogeneity correction can have significant effects on the retrieved distributions of the [Na/H] and [K/H] abundances, primarily through its degeneracy with the sloping optical opacity of scattering haze species within the atmosphere. Our results also show that despite this presence of haze, WASP-6b remains a favourable object for future atmospheric characterization with upcoming missions such as the James Webb Space Telescope.