bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-level genome assembly of Aristolochia contorta provides insights into the biosynthesis of benzylisoquinoline alkaloids and aristolochic acids
Authors: Cui Xinyun , Meng Fanqi , Pan Xian , Qiu Xiaoxiao , Zhang Sixuan , Li Caili , Lu Shanfa 
Published: February 2022

Abstract
Aristolochic acids (AAs) and their derivatives are present in multiple Aristolochiaceae species that have been or are being used as medicinal materials. During the past decades, AAs have received increasing attention because of their nephrotoxicity and carcinogenicity. Elimination of AAs from medicinal materials using biotechnological approaches is important for improving medication safety. However, it has not been achieved because of the limited information available on AA biosynthesis. Here, we report a high-quality, reference-grade genome assembly of the AA-containing vine Aristolochia contorta. The total size of the assembly is 209.27 Mb, and it is assembled into 7 pseudochromosomes. Synteny analysis, Ks distribution, and 4DTv suggest an absence of whole-genome duplication (WGD) events in Aristolochia contorta after the angiosperm-wide WGD. Based on genomic, transcriptomic, and metabolic data, pathways and candidate genes were proposed for benzylisoquinoline alkaloid (BIA) and AA biosynthesis in A. contorta. Five O-methyltransferase genes, including AcOMT1–3, AcOMT5, and AcOMT7, were cloned and functionally characterized. The results provide a high-quality reference genome for AA-containing species of Aristolochiaceae. They lay a solid foundation for further elucidation of AA biosynthesis and regulation and for the molecular breeding of Aristolochiaceae medicinal materials.
Jasmonic acid biosynthetic genesTgLOX4andTgLOX5are involved in daughter bulb development in tulip (Tulipa gesneriana)
Authors: Sun Qi , Zhang Bei , Yang Chaolong , Wang Weiliang , Xiang Lin , Wang Yanping , Chan Zhulong 
Published: February 2022

AbstractTulip bulbs are modified underground stems that originate from axillary meristems of mother bulb scales. Hormones, including jasmonic acids (JAs), play key roles in the regulation of tulip bulb development. Here, we compared variations in daughter bulb development through transcriptomic profiling analysis and characterized the functions of JA biosynthesis-related genes during daughter bulb enlargement. The results showed that tulip cultivars exhibited contrasting bulb size variations. Transcriptomic analyses revealed that genes involved in plant hormones and development, including the two lipoxygenase genes TgLOX4 and TgLOX5, showed significant changes in expression following tulip bulb growth. Ectopic overexpression of TgLOX4 and TgLOX5 in Arabidopsis enhanced endogenous JA content, improved plant growth, and increased lateral root numbers. Silencing of these two genes in tulip repressed the growth of daughter bulbs. Furthermore, exogenous JA treatment promoted tulip bulb growth, whereas the JA biosynthesis inhibitor sodium diethyldithiocarbamate (DIECA) inhibited this process. This study offers supporting evidence for the involvement of tulip TgLOX4 and TgLOX5 in the regulation of daughter bulb growth and development.
ROS1 promotes low temperature-induced anthocyanin accumulation in apple by demethylating the promoter of anthocyanin-associated genes
Authors: Yu Lujia , Sun Yuying , Zhang Xi , Chen Mengchen , Wu Ting , Zhang Jie , Xing Yifan , Tian Ji , Yao Yuncong 
Published: February 2022

AbstractLow temperature can affect the growth and development of plants through changes in DNA demethylation patterns. Another known effect of low temperature is the accumulation of anthocyanin pigments. However, it is not known whether the two phenomena are linked, specifically whether DNA demethylation participates in anthocyanin accumulation in response to low-temperature stress. The ROS1 gene is involved in plant DNA demethylation and influences methylation levels in response to low-temperature stress. In this study, using RNA sequencing, we detected the transcription levels of MdROS1, as well as those of anthocyanin biosynthesis-related genes, correlate with the anthocyanin content in apple (Malus domestica), at low temperature. Genomic bisulfite sequencing showed that the methylation levels of the promoters of the anthocyanin-related genes MdCHS, MdCHI, MdF3′H, MdANS, MdUFGT, and MdMYB10 decreased in apple leaves after low-temperature treatment. Similar expression and methylation results were found in apple fruit. Transiently silencing MdROS1 in the leaves and fruit of apple cultivars inhibited the accumulation of anthocyanins and led to decreased expression of anthocyanin biosynthetic genes, and the opposite results were detected in MdROS1-overexpressing leaves and fruit. A promoter binding assay showed that the conserved RRD-DME domains of MdROS1 bind directly to the promoters of MdF3′H and MdUFGT. Taken together, these results suggest that ROS1 affects the anthocyanin biosynthetic pathway by decreasing the methylation level of anthocyanin-related gene promoters, thereby increasing their expression and increasing anthocyanin accumulation.
Forum: A Coup At the Capitol? Conceptualizing Coups and Other Antidemocratic Actions
Authors: Powell Jonathan M , Ben Hammou Salah , Smith Amy Erica , Borba Lucas , Kinney Drew Holland , Chacha Mwita , De Bruin Erica 
Published: February 2022

AbstractThe term “coup” has been used to describe a diverse range of events. Although recent decades have seen the academic study of coups focus on an increasingly narrow type of military intervention in politics, the general public, governments, and international organizations frequently apply the coup label to a broader set of antidemocratic actions. This was dramatically illustrated after the overrunning of the US Capitol Building on January 6, 2021, when discussions of the event led to debates about whether or not it constituted a coup. More than a mere matter of semantics, describing an event as a coup can have analytical, normative, and practical implications. The scholars in this forum explore the challenges inherent in distinguishing coups from other types of antidemocratic actions, highlight gaps between academic and popular conceptions of the term, and identify ways in which scholars can productively contribute to public debates around contentious events.
Nutritional and physico-chemical implications of avocado meal as a novel dietary fiber source in an extruded canine diet
Authors: Dainton Amanda N , He Fei , Bingham Tanner W , Sarlah David , Detweiler Katelyn B , Mangian Heather J , de Godoy Maria Regina Cattai 
Published: February 2022

Abstract
This study assessed the effects of a diet containing avocado meal (AMD), an underutilized by-product avocado oil processing, on apparent total tract digestibility (ATTD) and fecal fermentative end-products when compared with beet pulp (BPD) and cellulose (CD) diets targeting 15% total dietary fiber (TDF). The concentration of persin, a natural fungicidal toxin present in avocado, was also determined on several parts of the fruit and avocado meal. Nine intact female beagles (4.9 ± 0.6 yr and 11.98 ± 1.76 kg) were randomly grouped in a 3 × 3 replicated Latin square design. Periods were 14 d long, with 10 d of adaptation followed by 4 d of total fecal and urine collection for apparent total tract digestibility (ATTD) calculations. Fresh fecals were analyzed for fermentative end-products. The BPD (87.0 g/d) caused higher (P &lt; 0.05) fecal output (as-is basis) than AMD (62.3 g/d) and CD (58.0 g/d). Fecal score for the BPD (3.1) was greater (P &lt; 0.05) than for AMD (2.8) or CD (2.6). Acid-hydrolyzed fat ATTD was lower (P &lt; 0.05) for the BPD (94.1%) than for the AMD (95.5%) and CD (95.7%). Crude protein ATTD was greater (P &lt; 0.05) for the CD (88.5%) than the AMD (82.2%) or BPD (83.7%). Dogs fed AMD (49.9%) or BPD (51.0%) exhibited greater (P &lt; 0.05) TDF ATTD than CD. The fermentative profile for the AMD (233.4, 70.9, 8.8, and 12.0 μmole/g DM, respectively) was similar (P &gt; 0.05) to the CD (132.9, 61.7, 7.5, and 9.5 μmole/g DM, respectively) profile, with lower (P &lt; 0.05) concentrations of acetate and propionate and higher (P &lt; 0.05) concentrations of isovalerate and indoles compared to the BPD. Dogs fed AMD (47.0 μmole/g DM) or BPD (54.2 μmole/g DM) exhibited similar (P &gt; 0.05) fecal butyrate concentrations greater (P &lt; 0.05) than for CD (24.7 μmole/g DM). Given these results, avocado meal appears to be an adequate dietary fiber source when compared with traditional fiber sources used in canine diets. No health adverse effects were observed in dogs fed extruded diet containing as much as 18% of avocado meal (as-is basis).
Unsupervised network traffic anomaly detection with deep autoencoders
Authors: Dutta Vibekananda , Pawlicki Marek , Kozik Rafał , Choraś Michał 
Published: February 2022

Abstract
Contemporary Artificial Intelligence methods, especially their subset-deep learning, are finding their way to successful implementations in the detection and classification of intrusions at the network level. This paper presents an intrusion detection mechanism that leverages Deep AutoEncoder and several Deep Decoders for unsupervised classification. This work incorporates multiple network topology setups for comparative studies. The efficiency of the proposed topologies is validated on two established benchmark datasets: UNSW-NB15 and NetML-2020. The results of their analysis are discussed in terms of classification accuracy, detection rate, false-positive rate, negative predictive value, Matthews correlation coefficient and F1-score. Furthermore, comparing against the state-of-the-art methods used for network intrusion detection is also disclosed.
Do the ‘conventional’ grounds for refusal also apply to EU certification marks? The Fifth Board of Appeal of EUIPO says yes
Authors: Ringelhann Axel Paul 
Published: February 2022

Abstract
Boards of Appeal of EUIPO, Cases R 1410/2019-5, Manuka honey; R 2110/2019-5, Bio-Mineralwasser I and R 2112/2019-5, bio mineralwasser (fig.) II, 27 October 2021
The Fifth Board of Appeal of the European Union Intellectual Property Office (EUIPO) held that EU certification mark applications are, like any other EU trade mark (EUTM) application, assessed on all general grounds of refusal laid down in Article 7(1) of the EU Trade Mark Regulation 2017/1001 (EUTMR). However, when assessing the general grounds of refusal, the specific function of certification must always be kept in mind. In three different cases, the Fifth Board of EUIPO decided that the certification marks Manuka honey and Bio-Mineralwasser (as word and figurative mark) are non-distinctive and descriptive.
Taxonomic versus ecological prey traits among arthropodophagous bats: implications for surveying trophic partitioning patterns
Authors: Segura-Trujillo Cintya A , Álvarez-Castañeda Sergio Ticul , Castañeda-Rico Susette , Maldonado Jesús E 
Published: February 2022

AbstractSpecies can coexist spatially and temporally by partitioning the niche space and forming complex assemblages made up of different species that share the prey resource. Chiroptera is the second most species-rich mammalian order and about 75% of bat species feed on arthropods, which makes these bats a good model group for studying complex trophic interactions. Next-generation parallel sequencing techniques allow a detailed analysis of arthropod resource partitioning patterns in bats. However, previous studies have not reached a consensus on the concordance between diet composition, habitat use, and segregation of trophic resources in bats. We analyzed diet composition in terms of taxonomy of the insect prey, and the prey characteristics. Feces of 16 bat species were examined in the Mexican Neotropics. We carried out a SIMPER (similarity percentage) test, nonmetric multidimensional scaling, and principal component analyses to identify general segregation patterns of trophic resources in relation to the habitat-use guild of bats and computed Pianka’s niche overlap index between species and Levin’s index to estimate the niche width of each species. Bats from the same locality tend to partition their diet, with a niche overlap ranging between 0.5 and 0.8. The highest values were found between species with different foraging behaviors. We suggest that future bat diet studies should incorporate the ecological and taxonomic information of arthropod prey to better understand the trophic interactions with bats.
Origin of young accreting neutron stars in high-mass X-ray binaries in supernova remnants
Authors: Khokhriakova A D , Popov S B 
Published: February 2022

ABSTRACT
Recently, several accreting neutron stars (NSs) in X-ray binary systems inside supernova remnants have been discovered. They represent a puzzle for the standard magnetorotational evolution of NSs, as their ages (≲105 yr) are much shorter than the expected duration of Ejector and Propeller stages preceding the onset of wind accretion. To explain appearance of such systems, we consider rotational evolution of NSs with early fallback accretion and asymmetry in forward/backward transitions between Ejector and Propeller stages (so-called hysteresis effect proposed by V. Shvartsman in 1970). It is shown that after a successful fallback episode with certain realistic values of the initial spin period, stellar wind properties, and magnetic field, a young NS may not enter the Ejector stage during its evolution which results in a relatively rapid initiation of accretion within the lifetime of a supernova remnant. For a standard magnetic field ∼1012 G and initial spin period ∼0.1–0.2 s accretion rate ≳1014–1015 g s−1 is enough to avoid the Ejector stage.
Forward and back: kinematics of the Palomar 5 tidal tails
Authors: Kuzma P B , Ferguson A M N , Varri A L , Irwin M J , Bernard E J , Tolstoy E , Peñarrubia J , Zucker D B 
Published: February 2022

ABSTRACTThe tidal tails of Palomar 5 (Pal 5) have been the focus of many spectroscopic studies in an attempt to identify individual stars lying along the stream and characterize their kinematics. The well-studied trailing tail has been explored out to a distance of 15○ from the cluster centre, while less than 4° have been examined along the leading tail. In this paper, we present results of a spectroscopic study of two fields along the leading tail that we have observed with the AAOmega spectrograph on the Anglo-Australian telescope. One of these fields lies roughly 7○ along the leading tail, beyond what has been previously been explored spectroscopically. Combining our measurements of kinematics and line strengths with Pan-STARRS1 photometric data and Gaia EDR3 astrometry, we adopt a probabilistic approach to identify 16 stars with a high probability of belonging to the Pal 5 stream. Eight of these stars lie in the outermost field and their sky positions confirm the presence of ‘fanning’ in the leading arm. We also revisit previously published radial velocity studies and incorporate Gaia EDR3 astrometry to remove interloping field stars. With a final sample of 109 bona fide Pal 5 cluster and tidal stream stars, we characterize the 3D kinematics along the the full extent of the system. We provide this catalogue for future modeling work.
The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: cosmological implications from multitracer BAO analysis with galaxies and voids
Authors: Zhao Cheng , Variu Andrei , He Mengfan , Forero-Sánchez Daniel , Tamone Amélie , Chuang Chia-Hsun , Kitaura Francisco-Shu , Tao Charling , Yu Jiaxi , Kneib Jean-Paul , Percival Will J , Shan Huanyuan , Zhao Gong-Bo , Burtin Etienne , Dawson Kyle S , Rossi Graziano , Schneider Donald P , de la Macorra Axel 
Published: February 2022

ABSTRACT
We construct cosmic void catalogues with the dive void finder upon SDSS BOSS DR12 and eBOSS DR16 galaxy samples with BAO reconstruction, and perform a joint BAO analysis using different types of galaxies and the corresponding voids. The BAO peak is evident for the galaxy–galaxy, galaxy–void, and void–void correlation functions of all data sets, including the ones cross-correlating LRG and ELG samples. Two multitracer BAO fitting schemes are tested, one combining the galaxy and void correlation functions with a weight applied to voids, and the other using a single BAO dilation parameter for all clustering measurements. Both methods produce consistent results with mock catalogues, and on average ∼10 per cent improvements of the BAO statistical uncertainties are observed for all samples, compared to the results from galaxies alone. By combining the clustering of galaxies and voids, the uncertainties of BAO measurements from the SDSS data are reduced by 5–15 per cent, yielding 0.9 per cent, 0.8 per cent, 1.1 per cent, 2.3 per cent, and 2.9 per cent constraints on the distance $D_{_{\rm V}}(z)$, at effective redshifts 0.38, 0.51, 0.70, 0.77, and 0.85, respectively. When combined with BAO measurements from SDSS MGS, QSO, and Lyα samples, as well as the BBN results, we obtain $H_0 = 67.58 \pm 0.91\, {\rm km}\, {\rm s}^{-1}\, {\rm Mpc}^{-1}$, Ωm = 0.290 ± 0.015, and $\Omega _\Lambda h^2 = 0.3241 \pm 0.0079$ in the flat-ΛCDM framework, where the 1σ uncertainties are around 6 per cent, 6 per cent, and 17 per cent smaller respectively, compared to constraints from the corresponding anisotropic BAO measurements without voids and LRG–ELG cross-correlations.
Connecting galaxy evolution in clusters with their radial profiles and phase space distribution: results from the IllustrisTNG hydrodynamical simulations
Authors: Dacunha Tara , Belyakov Matthew , Adhikari Susmita , Shin Tae-hyeon , Goldstein Samuel , Jain Bhuvnesh 
Published: February 2022

ABSTRACT
We study the population of galaxies around galaxy clusters in the hydrodynamic simulation suite IllustrisTNG 300-1 to study the signatures of their evolutionary history on observable properties. We measure the radial number density profile, phase space distribution, and splashback radius for galaxies of different masses and colours over the redshift range z = 0−1. The three primary physical effects which shape the galaxy distribution within clusters are the galaxy quenching, angular momentum distribution, and dynamical friction. We find three distinct populations of galaxies by applying a Gaussian mixture model to their distribution in colour and mass. They have distinct evolutionary histories and leave distinct signatures on their distribution around cluster haloes. We find that low-mass red galaxies show the most concentrated distribution in clusters and the largest splashback radius, while high-mass red galaxies show a less concentrated distribution and a smaller splashback radius. Blue galaxies, which mostly quench into the low-mass red population, have the shallowest distribution within the clusters, with those on radial orbits quenched rapidly before reaching pericentre. Comparison with the distribution of galaxies from the Dark Energy Survey survey around Sunyaev–Zeldovich clusters from the Atacama Cosmology Telescope and South Pole Telescope surveys shows evidence for differences in galaxy evolution between simulations and data.
AstroSat detection of a quasi-periodic oscillation at ∼42 Hz in Cygnus X-2
Authors: Chhangte Vanzarmawii , Roy Jayashree , Misra Ranjeev , Zadeng Lalthakimi 
Published: February 2022

ABSTRACT
We report the results of AstroSat observations of Cygnus X-2 during 2016 February. The source’s power density spectrum generated using Large Area X-ray Proportional Counter (LAXPC) data revealed the presence of a prominent quasi-periodic oscillation (QPO) at ∼42 Hz with broad-band continuum noise at lower frequencies at ∼10 Hz. The large effective area of LAXPC at ≳30 keV allowed for an unprecedented study of the energy dependence of the QPO and the broad noise continuum. The fractional rms increases with energy, and its shape is similar for both the QPO and the continuum noise, suggesting a common radiative origin. However, while the QPO exhibits hard time-lags, with the high-energy photons lagging the low ones by a few milliseconds, the continuum noise shows the opposite behaviour. The photon spectrum from Soft X-ray Imaging Telescope and LAXPC in 0.7–30 keV band comprises the soft component from a disc and a hard Comptonized component from a hot corona. While the energy dependence of the rms shows that the QPO and the continuum noise variability are dominated by the Comptonized component, the change in sign of the time-lag suggests that the dynamic origin of the QPO may be in the disc while the noise continuum may originate from the corona.
Cobalt oxide (Co3O4) nanoparticles induced genotoxicity in Chinese hamster lung fibroblast (V79) cells through modulation of reactive oxygen species
Authors: Lugun Onila , Singh Jagreeti , Thakur Ravindra Singh , Pandey Alok Kumar 
Published: February 2022

Abstract
Incessant production, pervasive applications in different fields, and eventually unintended exposure of cobalt oxide nanoparticles (Co3O4 NPs) lead to rise in their toxicity studies toward human health. However, the information regarding the potential toxicity mechanisms of Co3O4 NPs especially genotoxicity is still sparse with missing interconnections. So far, only solitary reports on Co3O4 NPs are at hand, bearing witness to reactive oxygen species (ROS)-mediated DNA damage in lung cells. To address this, we evaluated the Co3O4 NP-induced cytotoxic and genotoxic potential in Chinese hamster lung fibroblast cell line (V79). Our preliminary results demonstrate that Co3O4 NPs at concentrations of 20–100 µg/ml induced moderate mortality after 24-h exposure. However, these low concentrations caused a significant reduction in various organelles’ activity in a concentration-dependent manner. Mitochondrial activity and membrane potential were found to be compromised due to NP exposure in a concentration-dependent manner. The study affirms that Co3O4 NPs inhibited lysosomal activity in V79 cells. In addition to this, Co3O4 NPs are also found to stimulate free oxygen radical generation. Genotoxicity studies revealed a potent and dose-dependent effect of non-cytotoxic concentrations of Co3O4 NPs in the induction of DNA lesions. Interestingly, N-acetylcysteine, a free oxygen radical scavenger (5, 10 mM, pretreatment) inhibited the progression of free oxygen radicals and induction of Co3O4 NP-mediated DNA lesions. This suggests the ROS-mediated genotoxic potential of Co3O4 NPs.
RadD is a RecA-dependent accessory protein that accelerates DNA strand exchange
Authors: Bonde Nina J , Romero Zachary J , Chitteni-Pattu Sindhu , Cox Michael M 
Published: February 2022

Abstract
In rapidly growing cells, with recombinational DNA repair required often and a new replication fork passing every 20 min, the pace of RecA-mediated DNA strand exchange is potentially much too slow for bacterial DNA metabolism. The enigmatic RadD protein, a putative SF2 family helicase, exhibits no independent helicase activity on branched DNAs. Instead, RadD greatly accelerates RecA-mediated DNA strand exchange, functioning only when RecA protein is present. The RadD reaction requires the RadD ATPase activity, does not require an interaction with SSB, and may disassemble RecA filaments as it functions. We present RadD as a new class of enzyme, an accessory protein that accelerates DNA strand exchange, possibly with a helicase-like action, in a reaction that is entirely RecA-dependent. RadD is thus a DNA strand exchange (recombination) synergist whose primary function is to coordinate closely with and accelerate the DNA strand exchange reactions promoted by the RecA recombinase. Multiple observations indicate a uniquely close coordination of RadD with RecA function.