bluuebunny/crossref_metadata_2025_split huggingface dataset:
A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment
Authors: Li Junhua , Zhong Huanzi , Ramayo-Caldas Yuliaxis , Terrapon Nicolas , Lombard Vincent , Potocki-Veronese Gabrielle , Estellé Jordi , Popova Milka , Yang Ziyi , Zhang Hui , Li Fang , Tang Shanmei , Yang Fangming , Chen Weineng , Chen Bing , Li Jiyang , Guo Jing , Martin Cécile , Maguin Emmanuelle , Xu Xun , Yang Huanming , Wang Jian , Madsen Lise , Kristiansen Karsten , Henrissat Bernard , Ehrlich Stanislav D , Morgavi Diego P 
Published: May 2020

Abstract

Background
The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen.

Results
Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only &lt;0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes.

Conclusions
These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.
Using multicomponent ambient seismic noise cross-correlations to identify higher mode Rayleigh waves and improve dispersion measurements
Authors: Nayak Avinash , Thurber Clifford H 
Published: May 2020

SUMMARYAmbient seismic noise cross-correlation with three-component sensors yields a nine-component empirical Green's tensor, in which four components of the radial–vertical plane contain Rayleigh waves. We exploit the retrograde elliptical nature of particle motion of the fundamental mode Rayleigh wave to correct the phase of the four radial–vertical components and stack them to obtain an average fundamental mode Rayleigh-wave time-series. This technique can suppress incoherent noise and wave packets that do not follow the targeted elliptical particle motion. The same technique can be used to isolate the first higher mode Rayleigh wave that follows prograde elliptical particle motion. We first demonstrate the effectiveness of the method on synthetic waveforms and then apply it on noise cross-correlations computed in Central California. Using this method, we isolate 1st higher mode Rayleigh waves on noise cross-correlations in the Great Valley, California, which provides new phase velocity constraints for estimating velocity structure in the sedimentary basin. We also obtain improved estimates of fundamental mode Rayleigh-wave dispersion for surface-wave tomography. The waveforms stacked assuming retrograde particle motion return at least ∼20 per cent more group velocity dispersion measurements satisfying a minimum signal-to-noise ratio (SNR) criterion than the individual components for periods ∼4–18 s. For equivalent group velocity measurements, SNR for the stacked estimate of the fundamental mode Rayleigh wave is on average 40 per cent greater than that measured on the individual components at periods less than 10 s. The technique also provides an easy way to detect large errors in sensor orientation.
Marine Protection Induces Morphological Variation in the California Moray, Gymnothorax mordax
Authors: Mehta Rita S , Dale Katherine E , Higgins Benjamin A 
Published: May 2020

Synopsis
The effectiveness of marine protected areas (MPAs) on the general health and conservation of species, habitats, and community interactions is of great interest to researchers, managers, and recreationalists. However, the ecological and behavioral diversity of vertebrate predators of southern California kelp forests limits our ability to make general conclusions about MPA effectiveness across a variety of species. Identifying and studying species with extreme feeding habits or prey-capture strategies may offer greater insight into predator–prey relationships and reveal the trophic importance of an animal in the larger community. Moray eels (family Muraenidae) have been shown to have morphological and behavioral adaptations that allow them to consume large prey whole, identifying them as important predators. From 2015 to 2018, we studied the health and feeding behavior of a long-lived, elusive, and benthic kelp forest predator, the California moray eel (Gymnothorax mordax). We trapped eels inside and outside of Blue Cavern Onshore State Marine Conservation Area, an MPA on the northwest side of Santa Catalina Island, CA which prohibits the take of any species. Over 4 years, we captured 1736 eels. Overall, we found that morays were longer, older, heavier, had higher body condition, and were found in greater abundance within the MPA. Although fish comprised the majority of their summer diet, morays outside of the MPA were consuming a more diverse set of fish, while kelp bass comprised more than half of the diet for morays inhabiting the MPA. Additionally, we found that morays within the MPA had larger relative vertical gape distances (VGDs) and narrower heads. Our recapture data support the high site fidelity of morays, indicating that their diet and morphology are influenced by their local community. While the majority of morays are thriving in the MPA, as suggested by their robust sizes and longevity, high abundance appears to result in higher frequencies of cannibalism, the presence of an undescribed disease, and lower growth rates. Our results suggest that the MPA affects the life history of morays and may select for an alternative feeding strategy in which eels develop larger VGDs, smaller adductor muscles, and a specialized diet which is presumably influenced by the local environment. In addition, observations of cannibalistic behavior and species-specific disease provide us with important insight into natural factors that may still regulate populations removed from anthropogenic disturbances such as fishing.
Dynamic extracellular matrix stiffening induces a phenotypic transformation and a migratory shift in epithelial cells
Authors: Allen Shane C , Widman Jessica A , Datta Anisha , Suggs Laura J 
Published: May 2020

Abstract
Soft tissue tumors, including breast cancer, become stiffer throughout disease progression. This increase in stiffness has been shown to correlate to malignant phenotype and epithelial-to-mesenchymal transition (EMT) in vitro. Unlike current models, utilizing static increases in matrix stiffness, our group has previously created a system that allows for dynamic stiffening of an alginate–matrigel composite hydrogel to mirror the native dynamic process. Here, we utilize this system to evaluate the role of matrix stiffness on EMT and metastasis both in vitro and in vivo. Epithelial cells were seen to lose normal morphology and become protrusive and migratory after stiffening. This shift corresponded to a loss of epithelial markers and gain of mesenchymal markers in both the cell clusters and migrated cells. Furthermore, stiffening in a murine model reduced tumor burden and increased migratory behavior prior to tumor formation. Inhibition of FAK and PI3K in vitro abrogated the morphologic and migratory transformation of epithelial cell clusters. This work demonstrates the key role extracellular matrix stiffening has in tumor progression through integrin signaling and, in particular, its ability to drive EMT-related changes and metastasis.
A transformation-based method for auditing the IS-A hierarchy of biomedical terminologies in the Unified Medical Language System
Authors: Zheng Fengbo , Shi Jay , Yang Yuntao , Zheng W Jim , Cui Licong 
Published: May 2020

Abstract

Objective
The Unified Medical Language System (UMLS) integrates various source terminologies to support interoperability between biomedical information systems. In this article, we introduce a novel transformation-based auditing method that leverages the UMLS knowledge to systematically identify missing hierarchical IS-A relations in the source terminologies.

Materials and Methods
Given a concept name in the UMLS, we first identify its base and secondary noun chunks. For each identified noun chunk, we generate replacement candidates that are more general than the noun chunk. Then, we replace the noun chunks with their replacement candidates to generate new potential concept names that may serve as supertypes of the original concept. If a newly generated name is an existing concept name in the same source terminology with the original concept, then a potentially missing IS-A relation between the original and the new concept is identified.

Results
Applying our transformation-based method to English-language concept names in the UMLS (2019AB release), a total of 39 359 potentially missing IS-A relations were detected in 13 source terminologies. Domain experts evaluated a random sample of 200 potentially missing IS-A relations identified in the SNOMED CT (U.S. edition) and 100 in Gene Ontology. A total of 173 of 200 and 63 of 100 potentially missing IS-A relations were confirmed by domain experts, indicating that our method achieved a precision of 86.5% and 63% for the SNOMED CT and Gene Ontology, respectively.

Conclusions
Our results showed that our transformation-based method is effective in identifying missing IS-A relations in the UMLS source terminologies.
Biopesticides for Management of Bemisia tabaci MEAM1 (Hemiptera: Aleyrodidae) and Tomato Yellow Leaf Curl Virus
Authors: Smith Hugh A 
Published: May 2020

Abstract
The sweetpotato whitefly, Bemisia tabaci MEAM1 Gennadius, is a global pest of tomato, transmitting Tomato yellow leaf curl virus (TYLCV). Management of B. tabaci is challenging in part because of its ability to develop resistance to insecticides. Biopesticides include materials that control B. tabaci via mechanisms that do not select for resistance. Field experiments were conducted in the spring and fall of 2016 and 2017 at the University of Florida’s Gulf Coast Research and Education Center in west central Florida to compare biopesticides to conventional insecticides for management of B. tabaci and TYLCV. Insecticide rotations were designed in part around the concept that conventional insecticide programs should group modes of action according to 5-wk treatment intervals, corresponding to an estimated 5-wk generation time for the pest. In 2016, when tomato was treated during the first 5-wk treatment interval with either biopesticides or neonicotinoid insecticides, insecticidal soap contributed to a reduction in whitefly egg numbers and percentage TYLCV that was comparable to results achieved with dinotefuran. In contrast, egg numbers and virus incidence in plants treated with kaolin clay tended to be numerically higher than the untreated control. In spring 2017, comparisons of biopesticides and conventional ovicides/nymphicides during the second 5-wk treatment interval showed that biopesticides can provide comparable reduction in nymph numbers to conventional insecticides. While data from these trials confirm that biopesticides can reduce numbers of whitefly eggs and nymphs, they indicate that season-long programs of the biopesticides evaluated may not reduce transmission of TYLCV below economically acceptable levels.
Diversity of Calliphoridae and Mesembrinellidae (Diptera: Oestroidea) in a Mangrove, Restinga, and Forest Landscapes From a Lagoon Complex on an Atlantic Forest Coastline (Rio de Janeiro, Brazil)
Authors: Luz R T , Azevedo W T A , Silva A S , Lessa C S S , Maia V C , Aguiar V M 
Published: May 2020

AbstractDiptera Mesembrinellidae present great ecological importance as potential bioindicators and Calliphoridae stand out for their medical-sanitary importance as potential vectors of pathogens and causes of human and animal diseases such as myiasis. They beneficially aid in elucidating crimes in forensic entomology, contributing to determine the postmortem interval (PMI) and assisting in the healing process of necrotic wounds in larval therapy. This study aimed to inventory the Calliphoridae and Mesembrinellidae fauna in order to evaluate structural parameters and to apply faunal indexes in catching species in the Itaipu–Piratininga lagoon complex, in Niterói (Rio de Janeiro), Brazil. The collections were carried out monthly from September 2015 to August 2016 with fish bait (sardines) exposed for 48 h, totaling six traps installed in three physiognomies (mangrove, ombrophilous forest, and restinga). In total, 9,773 individuals were captured, divided into two families, five genera, and 11 species. Chrysomya megacephala (Fabricius, 1794) was the predominant species, while Mesembrinella bellardiana (Aldrich, 1922) was the least representative species, indicating the preservation level of this ecosystem. Ombrophilous forest was the physiognomy with greater diversity and restinga was the physiognomy with greater species dominance. The similarity index indicated greater similarity among the mangrove and restinga populations.
Connecting the structure of dark matter haloes to the primordial power spectrum
Authors: Brown Shaun T , McCarthy Ian G , Diemer Benedikt , Font Andreea S , Stafford Sam G , Pfeifer Simon 
Published: May 2020

ABSTRACT
A large body of work based on collisionless cosmological N-body simulations going back over two decades has advanced the idea that collapsed dark matter (DM) haloes have simple and approximately universal forms for their mass density and pseudo-phase-space density (PPSD) distributions. However, a general consensus on the physical origin of these results has not yet been reached. In the present study, we explore to what extent the apparent universality of these forms holds when we vary the initial conditions (i.e. the primordial power spectrum of density fluctuations) away from the standard CMB-normalized case, but still within the context of lambda cold dark matter with a fixed expansion history. Using simulations that vary the initial amplitude and shape, we show that the structure of DM haloes retains a clear memory of the initial conditions. Specifically, increasing (lowering) the amplitude of fluctuations increases (decreases) the concentration of haloes and, if pushed far enough, the density profiles deviate strongly from the NFW form that is a good approximation for the CMB-normalized case. Although, an Einasto form works well. Rather than being universal, the slope of the PPSD (or pseudo-entropy) profile steepens (flattens) with increasing (decreasing) power spectrum amplitude and can exhibit a strong halo mass dependence. Our results therefore indicate that the previously identified universality of the structure of DM haloes is mostly a consequence of adopting a narrow range of (CMB-normalized) initial conditions for the simulations. Our new suite provides a useful test-bench against which physical models for the origin of halo structure can be validated.
The mergers in Abell 2256: displaced gas and its connection to the radio-emitting plasma
Authors: Breuer J P , Werner N , Mernier F , Mroczkowski T , Simionescu A , Clarke T E , ZuHone J A , Di Mascolo L 
Published: May 2020

ABSTRACT
We present the results of deep Chandra and XMM–Newton X-ray imaging and spatially resolved spectroscopy of Abell 2256, a nearby (z = 0.058) galaxy cluster experiencing multiple mergers and displaying a rich radio morphology dominated by a large relic. The X-ray data reveal three subclusters: (i) the ‘main cluster’; (ii) the remnant of an older merger in the east of the cluster with an ∼600 kpc-long tail; (iii) a bright, bullet-like, low-entropy infalling system, with a large line-of-sight velocity component. The low-entropy system displays a 250 kpc-long cold front with a break and an intriguing surface brightness decrement. Interestingly, the infalling gas is not co-spatial with bright galaxies and the radio-loud brightest cluster galaxy of the infalling group appears dissociated from the low-entropy plasma by ∼50 kpc in projection, to the south of the eastern edge of the cold front. Assuming that the dark matter follows the galaxy distribution, we predict that it is also significantly offset from the low-entropy gas. Part of the low-frequency radio emission near the cold front might be revived by magnetic field amplification due to differential gas motions. Using analytical models and numerical simulations, we investigate the possibility that the supersonic infall of the subcluster generates a large-scale shock along our line of sight, which can be detected in the X-ray temperature map but is not associated with any clear features in the surface brightness distribution.
Simulating the outer layers of rapidly rotating stars
Authors: Robinson F J , Tanner J , Basu S 
Published: May 2020

ABSTRACT
This paper presents the results of a set of radiative hydrodynamic simulations of convection in the near-surface regions of a rapidly rotating star. The simulations use microphysics consistent with stellar models, and include the effects of realistic convection and radiative transfer. We find that the overall effect of rotation is to reduce the strength of turbulence. The combination of rotation and radiative cooling creates a zonal velocity profile in which the motion of fluid parcels near the surface is independent of rotation. Their motion is controlled by the strong up and down flows generated by radiative cooling. The fluid parcels in the deeper layers, on the other hand, are controlled by rotation.
Intensity and time series of extreme solar-terrestrial storm in 1946 March
Authors: Hayakawa Hisashi , Ebihara Yusuke , Pevtsov Alexei A , Bhaskar Ankush , Karachik Nina , Oliveira Denny M 
Published: May 2020

ABSTRACT
Major solar eruptions occasionally cause magnetic superstorms on the Earth. Despite their serious consequences, the low frequency of their occurrence provides us with only limited cases through modern instrumental observations, and the intensities of historical storms before the coverage of the Dst index have been only sporadically estimated. Herein, we examine a solar-terrestrial storm that occurred in 1946 March and quantitatively evaluate its parameters. During the ascending phase of Solar Cycle 18, two moderate sunspot groups caused a major flare. The H α flaring area was recorded to be ≥600–1200 millionths of solar hemisphere, suggesting that this was an M- or X-class flare in soft X-ray intensity. Upon this eruption, a rapid interplanetary coronal mass ejection (ICME) with an average speed of ≈1590 km s−1 was launched. Based on measurements in four known mid-latitude and relatively complete magnetograms, the arrival of this extreme ICME caused a magnetic superstorm, which caused an initial phase with the H-component amplitude of ≥80 nT, followed by a main phase whose intensity was reconstructed as ≤−512 nT using most negative Dst* estimates. Meanwhile, the equatorial boundary of the auroral oval extended down to ≤41${^{\circ}_{.}}$8 in invariant latitude and formed a corona aurora in Watheroo, Australia. Interestingly, during this magnetic superstorm, larger magnetic disturbances were recorded at dusk and near the dip equator on the dayside. Its cause may be associated with a strong westward equatorial electrojet and field-aligned current, in addition to the contribution from the storm-time ring current.
A prominent environmental endocrine disruptor, 4-nonylphenol, promotes endometriosis development via plasmacytoid dendritic cells
Authors: Sharma Pooja , Tseng Hsin-Han , Lee Jo-Yu Lynn , Tsai Eing-Mei , Suen Jau-Ling 
Published: May 2020

Abstract
Endometriosis is an estrogen-dependent chronic inflammatory disease and is associated etiologically with environmental endocrine disruptor (EED) exposure. 4-nonylphenol (NP), a widely found EED, has weak estrogenic activity and modulates plasmacytoid dendritic cell (pDC) function in vitro and in vivo. We aimed to elucidate the immunomodulatory effect of NP on the development of endometriosis, particularly focusing on pDCs. This study established a surgically induced endometriosis murine model (C57BL/6) under conditions of NP treatment that are relevant to the level and route of human exposure. Multi-parametric flow cytometry was used for analysis of infiltrated immune cell subsets in lesions. The results showed that NP exposure significantly promoted endometriotic lesion growth, survival and angiogenesis development of lesions as well as pDC accumulation in the lesions in mice. Adoptive transfer of NP-conditioned pDCs into mice significantly enhanced lesion development and local pDC infiltration, whereas NP-conditioned conventional dendritic cells did not affect lesion growth. In vitro functional analysis showed that NP-conditioned pDCs in lesions expressed high levels of CD36, a scavenger receptor and NP-conditioned splenic pDCs secreted an enhanced level of IL-10 in response to apoptotic cell recognition in a CD36-dependent manner. Furthermore, we observed that local treatment with blocking antibodies against IL-10 and CD36 on the day of surgery significantly inhibited lesion development. NP exposure also altered the estrous cycle in mice. The results suggest that chronic and low-dose exposure to NP enhances endometriotic lesion growth by altering pDC homeostasis and function. This study has important implications for understanding the environment-innate immunity interaction in human endometriosis.
Activation and inhibition of nonsense-mediated mRNA decay control the abundance of alternative polyadenylation products
Authors: Kishor Aparna , Fritz Sarah E , Haque Nazmul , Ge Zhiyun , Tunc Ilker , Yang Wenjing , Zhu Jun , Hogg J Robert 
Published: May 2020

AbstractAlternative polyadenylation (APA) produces transcript 3′ untranslated regions (3′UTRs) with distinct sequences, lengths, stabilities and functions. We show here that APA products include a class of cryptic nonsense-mediated mRNA decay (NMD) substrates with extended 3′UTRs that gene- or transcript-level analyses of NMD often fail to detect. Transcriptome-wide, the core NMD factor UPF1 preferentially recognizes long 3′UTR products of APA, leading to their systematic downregulation. Counteracting this mechanism, the multifunctional RNA-binding protein PTBP1 regulates the balance of short and long 3′UTR isoforms by inhibiting NMD, in addition to its previously described modulation of co-transcriptional polyadenylation (polyA) site choice. Further, we find that many transcripts with altered APA isoform abundance across multiple tumor types are controlled by NMD. Together, our findings reveal a widespread role for NMD in shaping the outcomes of APA.