bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome and transcriptome assemblies of the kuruma shrimp,Marsupenaeus japonicus
Authors: Kawato Satoshi , Nishitsuji Koki , Arimoto Asuka , Hisata Kanako , Kawamitsu Mayumi , Nozaki Reiko , Kondo Hidehiro , Shinzato Chuya , Ohira Tsuyoshi , Satoh Noriyuki , Shoguchi Eiichi , Hirono Ikuo 
Published: August 2021

AbstractThe kuruma shrimp Marsupenaeus japonicus (order Decapoda, family Penaeidae) is an economically important crustacean that occurs in shallow, warm seas across the Indo-Pacific. Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced a draft genome assembly of M. japonicus (1.70 Gbp; 18,210 scaffolds; scaffold N50 = 234.9 kbp; 34.38% GC, 93.4% BUSCO completeness) and a complete mitochondrial genome sequence (15,969 bp). As with other penaeid shrimp genomes, the M. japonicus genome is extremely rich in simple repeats, which occupies 27.4% of the assembly. A total of 26,381 protein-coding gene models (94.7% BUSCO completeness) were predicted, of which 18,005 genes (68.2%) were assigned functional description by at least one method. We also produced an Illumina-based transcriptome shotgun assembly (40,991 entries; 93.0% BUSCO completeness) and a PacBio Iso-Seq transcriptome assembly (25,415 entries; 67.5% BUSCO completeness). We envision that the M. japonicus genome and transcriptome assemblies will serve as useful resources for the basic research, fisheries management, and breeding programs of M. japonicus.
Thermodynamically consistent model for poroelastic rocks towards tectonic and volcanic processes and earthquakes
Authors: Roubíček T 
Published: August 2021

Summary
A general-purpose model combining concepts from rational continuum mechanics, fracture and damage mechanics, plasticity, and poromechanics is devised in Eulerian coordinates, involving objective time derivatives. The model complies with mass, momentum, and energy conservation as well as entropy inequality and objectivity. It is devised to cover many diverse phenomena, specifically rupture of existing lithospheric faults, tectonic earthquakes, generation and propagation of seismic waves, birth of new tectonic faults, or volcanic activity, aseismic creep, folding of rocks, aging of rocks, long-distance saturated water transport and flow in poroelastic rocks, melting of rocks and formation of magma chambers, or solidification of magma.
Messi vs. Massi, Prior Right vs. Reputation: The Decision of the Court of Justice of the European Union and Its Assessment with Regard to the Turkish Trademark Law
Authors: Özkan ÇiĞdem YataĞan 
Published: August 2021

Abstract
The Messi case,1 which originated with the decision of the European Union Intellectual Property Office (EUIPO) in 2011 and was finalized in 2020, surprised the IP world/practitioners with the remarks of the first instance court and the Court of Justice of the European Union (CJEU) as their findings were contrary to the established case law regarding the implementation of the relative grounds of refusal. Lionel Messi was a party to the court case as the applicant of the later application for the same classes of goods; the first instance court overruled the appeal of the owner of the earlier trademark based on relative grounds, given Lionel Messi’s reputation as a famous football player and thus the reputation of his surname ‘Messi’, even though the two trademarks were considered visually and phonetically similar. It was reiterated in the court decision that the reputation of the owner of the later trademark application neutralized the likelihood of confusion with the earlier trademark. Moreover, the judgment (dated 17 September 2020) of the Tenth Chamber of the CJEU went beyond the ordinary scope of trademark law. In this study we will discuss, in the context of the Messi decision, the influence of the reputation of a later trademark on conceptual differentiation and the possible results of not adducing evidence proving the reputation of a trademark.
Projection-free nonconvex stochastic optimization on Riemannian manifolds
Authors: Weber Melanie , Sra Suvrit 
Published: August 2021

Abstract
We study stochastic projection-free methods for constrained optimization of smooth functions on Riemannian manifolds, i.e., with additional constraints beyond the parameter domain being a manifold. Specifically, we introduce stochastic Riemannian Frank–Wolfe (Fw) methods for nonconvex and geodesically convex problems. We present algorithms for both purely stochastic optimization and finite-sum problems. For the latter, we develop variance-reduced methods, including a Riemannian adaptation of the recently proposed Spider technique. For all settings, we recover convergence rates that are comparable to the best-known rates for their Euclidean counterparts. Finally, we discuss applications to two classic tasks: the computation of the Karcher mean of positive definite matrices and Wasserstein barycenters for multivariate normal distributions. For both tasks, stochastic Fw methods yield state-of-the-art empirical performance.
Testing the inferred transcription rates of a dynamic, gene network model in absolute units
Authors: Urquiza-García Uriel , Millar Andrew J 
Published: August 2021

AbstractThe circadian clock coordinates plant physiology and development. Mathematical clock models have provided a rigorous framework to understand how the observed rhythms emerge from disparate, molecular processes. However, models of the plant clock have largely been built and tested against RNA time-series data in arbitrary, relative units. This limits model transferability, refinement from biochemical data and applications in synthetic biology. Here, we incorporate absolute mass units into a detailed model of the clock gene network in Arabidopsis thaliana. We re-interpret the established P2011 model, highlighting a transcriptional activator that overlaps the function of REVEILLE 8/LHY-CCA1-LIKE 5. The new U2020 model incorporates the repressive regulation of PRR genes, a key feature of the most detailed clock model KF2014, without greatly increasing model complexity. We tested the experimental error distributions of qRT–PCR data calibrated for units of RNA transcripts per cell and of circadian period estimates, in order to link the models to data more appropriately. U2019 and U2020 models were constrained using these data types, recreating previously described circadian behaviours with RNA metabolic processes in absolute units. To test their inferred rates, we estimated a distribution of observed, transcriptome-wide transcription rates (Plant Empirical Transcription Rates, PETR) in units of transcripts per cell per hour. The PETR distribution and the equivalent degradation rates indicated that the models’ predicted rates are biologically plausible, with individual exceptions. In addition to updated clock models, FAIR (Findable, Accessible, Interoperable, Re-usable) data resources and a software environment in Docker, this validation process represents an advance in biochemical realism for models of plant gene regulation.
Awareness, perception and the practice of COVID-19 prevention among residents of a state in the South-South region of Nigeria: implications for public health control efforts
Authors: Owhonda Golden , Maduka Omosivie , Nwadiuto Ifeoma , Tobin-West Charles , Azi Esther , Ojimah Chibianotu , Alasia Datonye , Olofinuka Ayo-Maria , Agala Vetty , Paul John Nwolim , Nria Doris , Okafor Chinenye , Ndekwu Ifeoma , Opara Chikezie , Newsom Chris 
Published: August 2021

Abstract

Background
As with any epidemic, coronavirus disease 2019 (COVID-19) has evoked panic, fear and misconceptions. The risk communication pillar of the Public Health Emergency Operations Centre is responding to the pandemic by facilitating correct and consistent information to enable the adoption of behaviours to prevent and control COVID-19. This study explored awareness, perception and practice of COVID-19 prevention among residents in Rivers State, Nigeria, during the early stages of the COVID-19 pandemic response.

Methods
This was a descriptive cross-sectional survey among 1294 adult residents across all districts of the state. It employed an interviewer-administered questionnaire. Knowledge was graded as excellent for scores of ≥80%, good for scores of 50–79% and poor for scores of &lt;50%. Respondents who washed all critical parts of their hands were categorised as adopting correct handwashing practice. Regression modelling was employed to determine predictors of knowledge and practice of COVID-19 prevention with p=0.05.

Results
The respondents were aged 18–80 y with an average age of 39.6 (SD=11.9) y. A total of 710 (54.9%) were male, 476 (36.8%) were unemployed with 685 (52.9%) having secondary education. The most common sources of information about COVID-19 were radio jingles (1102; 86.7%) and television adverts (940; 74.0%). Overall, 608 (47.0%) of the respondents had a poor knowledge of COVID-19. About 443 (34.9%) respondents believed they were unlikely to contract the virus. Only 505 (39.0%) of respondents washed all the critical parts of their hands correctly. Occupation (adjusted OR [AOR]=1.39, 95% CI 1.07 to 1.82, p=0.01), level of education (AOR=4.71, 95% CI 1.90 to 11.68, p&lt;0.001) and location (AOR=1.75, 95% CI 1.29 to 2.38; p&lt;0.001) significantly predicted respondents’ knowledge about COVID-19. The significant predictors of practice of COVID-19 were age (AOR=0.60, 95% CI 0.42 to 0.84, p=0.003), occupation (AOR=1.93, 95% CI 1.41 to 2.63, p&lt;0.001), location (AOR=2.35, 95% CI 1.65 to 3.34, p&lt;0.001) and knowledge about COVID-19 (AOR=7.75, 95% CI 5.94 to 10.11, p&lt;0.001).

Conclusions
Broadcast media has a pivotal role to play in risk communication for behavioural change for the control of current and future epidemics in this population.
Characterization of Enterobacter cloacae and Citrobacter freundii species complex isolates with decreased susceptibility to cephalosporins from United States hospitals and activity of ceftazidime/avibactam and comparator agents
Authors: Sader Helio S , Mendes Rodrigo E , Doyle Timothy B , Davis Andrew P , Castanheira Mariana 
Published: August 2021

Abstract

Objectives
To evaluate the antimicrobial susceptibility and resistance mechanisms to β-lactams among Enterobacter cloacae and Citrobacter freundii from United States medical centres.

Methods
2571 E. cloacae and 1008 C. freundii species complex isolates were consecutively collected from 77 medical centres and susceptibility tested by broth microdilution method. Isolates displaying MIC values ≥16 mg/L for ceftazidime or ≥2 mg/L for cefepime (n = 914) were tested for β-lactamase-encoding genes using whole genome sequencing.

Results
Overall susceptibility to ceftazidime and cefepime were 73.9% and 91.2% among E. cloacae and 74.2% and 93.5% among C. freundii, respectively. Sixty-three isolates harboured a carbapenemase gene, including 56 blaKPC, 2 blaNMC-A, and 5 metallo-β-lactamase genes. Among non-carbapenemase producers, 121 isolates had at least one ESBL-encoding gene, mainly blaSHV (81) or blaCTX-M (61), and 15 had a transferable AmpC gene, mainly blaDHA-1 (8) or blaFOX-5 (6). Carbapenemase, ESBL, or transferable AmpC-encoding genes were not identified among 718 of 914 (78.6%) isolates sequenced. The most active agents against isolates with a decreased susceptibility to ceftazidime and/or cefepime were ceftazidime/avibactam (MIC50/90, 0.5/1 mg/L; 99.3% susceptible), amikacin (MIC50/90, 1/4 mg/L; 99.5% susceptible), and meropenem (MIC50/90, 0.06/0.5 mg/L; 92.9% susceptible). The isolates resistant to ceftazidime/avibactam were the five MBL producers and one E. cloacae isolate with a reduced expression of OmpF and overexpression of AcrAB-TolC.

Conclusions
Hyperproduction of chromosomal AmpC appears to be the most common mechanism of resistance to ceftazidime and/or cefepime in E. cloacae and C. freundii. Ceftazidime/avibactam remained highly active against most isolates showing decreased susceptibility to ceftazidime and/or cefepime.
Methane emissions and δ13C composition from beef steers consuming increasing proportions of sericea lespedeza hay on bermudagrass hay diets
Authors: van Cleef Flavia O S , Dubeux José C B , Naumann Harley D , Santos Erick R S , Sollenberger Lynn E , Vendramini João M B , Ruiz-Moreno Martin , Ciriaco Francine M , DiLorenzo Nicolas 
Published: August 2021

Abstract
An experiment was conducted to evaluate the effects of different proportions of ‘Au Grazer’ sericea lespedeza [SL, Lespedeza cuneata (Dum. Cours.) G. Don], a legume rich in condensed tannins (CT), on nutrient intake and digestibility, and to estimate methane (CH4) emissions and 13C isotopic composition (δ13CCH4) from beef steers consuming a forage-based diet. Twenty-five Angus-crossbred steers were distributed in a randomized complete block design (344 ± 48 kg initial BW), and randomly assigned to one of five treatments: 0SL, 25SL, 50SL, 75SL, and 100SL, diets containing 0%, 25%, 50%, 75%, and 100% of SL hay, respectively, mixed with ‘Tifton-85’ bermudagrass hay (Cynodon spp.). The study was carried out for two experimental periods of 21-d each. The statistical model included the fixed effect of treatment and random effects of block, experimental period, and their interaction. Apparent total tract digestibility of crude protein, neutral detergent fiber, and acid detergent fiber was linearly decreased (P &lt; 0.001) by the inclusion of SL. No effects were observed for total CH4 emissions per day, nor for CH4 relative to organic matter intake or digestible organic matter with the inclusion of SL. However, emission of CH4 in relation to intake of CT was affected by treatment (P &lt; 0.001). A linear (P &lt; 0.001) decrease and a quadratic effect (P &lt; 0.001) were observed for δ13C of diets and gas, respectively, in which diets and enteric CH4 with greater inclusion of SL were more depleted in 13C. Moreover, the difference in δ13C between diets and gas (Δδ13C) had a linear decrease (P = 0.001) with the inclusion of SL. The model developed to predict the C3 proportions in the enteric CH4 fitted to predicted values (P &lt; 0.0001). Therefore, greater proportions of SL resulted in lesser CH4 emission when CT intake was considered and the isotopic composition from enteric CH4 was able to predict the contribution of SL in the emissions.
Autophagy in sexual plant reproduction: new insights
Authors: Zhou Xuemei , Zhao Peng , Sun Meng-Xiang 
Published: August 2021

Abstract
Autophagy is a mechanism by which damaged or unwanted cells are degraded and their constituents recycled. Over the past decades, research focused on autophagy has expanded from yeast to mammals and plants, and the core machinery regulating autophagy appears to be conserved. In plants, autophagy has essential roles in responses to stressful conditions and also contributes to normal development, especially in the context of reproduction. Here, based on recent efforts to understand the roles and molecular mechanisms underlying autophagy, we highlight the specific roles of autophagy in plant reproduction and provide new insights for further studies.
The Role of Israel in American Haredi Life
Authors: Krakowski Moshe , Rand Elana Riback , Brooks Suzanne 
Published: August 2021

Abstract
This article examines the role of Israel in the daily lives of American haredim in both Yeshivish and Hasidic communities. Evidence drawn from over 25 interviews with yeshivish and hasidic lay leaders, school administrators, magazine publishers, and community members presents a nuanced portrait of attitudes toward, and ideologies regarding, the State of Israel. Although historically and sociologically Zionism has been seen as a key issue distinguishing modern and haredi Jewish communities, this distinction may lie more at the level of ideological affirmation, rather than actual behavior, knowledge, or belief.
WALLABY pre-pilot survey: H i content of the Eridanus supergroup
Authors: For B-Q , Wang J , Westmeier T , Wong O I , Murugeshan C , Staveley-Smith L , Courtois H M , Pomarède D , Spekkens K , Catinella B , McQuinn K B W , Elagali A , Koribalski B S , Lee-Waddell K , Madrid J P , Popping A , Reynolds T N , Rhee J , Bekki K , Dènes H , Kamphuis P , Verdes-Montenegro L 
Published: August 2021

ABSTRACT
We present observations of the Eridanus supergroup obtained with the Australian Square Kilometre Array Pathfinder (ASKAP) as part of the pre-pilot survey for the Widefield ASKAP L-band Legacy All-sky Blind surveY (WALLABY). The total number of detected H i sources is 55, of which 12 are background galaxies not associated with the Eridanus supergroup. Two massive H i clouds are identified and large H i debris fields are seen in the NGC 1359 interacting galaxy pair, and the face-on spiral galaxy NGC 1385. We describe the data products from the source finding algorithm and present the basic parameters. The presence of distorted H i morphology in all detected galaxies suggests ongoing tidal interactions within the subgroups. The Eridanus group has a large fraction of H i-deficient galaxies as compared to previously studied galaxy groups. These H i-deficient galaxies are not found at the centre of the group. We find that galaxies in the Eridanus supergroup do not follow the general trend of the atomic gas fraction versus stellar mass scaling relation, which indicates that the scaling relation changes with environmental density. In general, the majority of these galaxies are actively forming stars.
Plasma properties, switchback patches, and low α-particle abundance in slow Alfvénic coronal hole wind at 0.13 au
Authors: Woolley Thomas , Matteini Lorenzo , McManus Michael D , Berčič Laura , Badman Samuel T , Woodham Lloyd D , Horbury Timothy S , Bale Stuart D , Laker Ronan , Stawarz Julia E , Larson Davin E 
Published: August 2021

ABSTRACT
The Parker Solar Probe (PSP) mission presents a unique opportunity to study the near-Sun solar wind closer than any previous spacecraft. During its fourth and fifth solar encounters, PSP had the same orbital trajectory, meaning that solar wind was measured at the same latitudes and radial distances. We identify two streams measured at the same heliocentric distance (∼0.13 au) and latitude (∼–$3{_{.}^{\circ}}5$) across these encounters to reduce spatial evolution effects. By comparing the plasma of each stream, we confirm that they are not dominated by variable transient events, despite PSP’s proximity to the heliospheric current sheet. Both streams are consistent with a previous slow Alfvénic solar wind study once radial effects are considered, and appear to originate at the Southern polar coronal hole boundary. We also show that the switchback properties are not distinctly different between these two streams. Low α-particle abundance (∼0.6 per cent) is observed in the encounter 5 stream, suggesting that some physical mechanism must act on coronal hole boundary wind to cause α-particle depletion. Possible explanations for our observations are discussed, but it remains unclear whether the depletion occurs during the release or the acceleration of the wind. Using a flux tube argument, we note that an α-particle abundance of ∼0.6 per cent in this low-velocity wind could correspond to an abundance of ∼0.9 per cent at 1 au. Finally, as the two streams roughly correspond to the spatial extent of a switchback patch, we suggest that patches are distinct features of coronal hole wind.
AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation inArabidopsis thaliana
Authors: Wang Qianwen , Bao Xiucong , Chen Shengjie , Zhong Huan , Liu Yaqin , Zhang Li , Xia Yiji , Kragler Friedrich , Luo Ming , Li Xiang David , Lam Hon-Ming , Zhang Shoudong 
Published: August 2021

AbstractPericentromeric DNA, consisting of high-copy-number tandem repeats and transposable elements, is normally silenced through DNA methylation and histone modifications to maintain chromosomal integrity and stability. Although histone deacetylase 6 (HDA6) has been known to participate in pericentromeric silencing, the mechanism is still yet unclear. Here, using whole genome bisulfite sequencing (WGBS) and chromatin immunoprecipitation-sequencing (ChIP-Seq), we mapped the genome-wide patterns of differential DNA methylation and histone H3 lysine 18 acetylation (H3K18ac) in wild-type and hda6 mutant strains. Results show pericentromeric CHG hypomethylation in hda6 mutants was mediated by DNA demethylases, not by DNA methyltransferases as previously thought. DNA demethylases can recognize H3K18ac mark and then be recruited to the chromatin. Using biochemical assays, we found that HDA6 could function as an ‘eraser’ enzyme for H3K18ac mark to prevent DNA demethylation. Oxford Nanopore Technology Direct RNA Sequencing (ONT DRS) also revealed that hda6 mutants with H3K18ac accumulation and CHG hypomethylation were shown to have transcriptionally active pericentromeric DNA.
ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network
Authors: Wang Ziye , Li Shuo , You Ronghui , Zhu Shanfeng , Zhou Xianghong Jasmine , Sun Fengzhu 
Published: August 2021

Abstract
Antibiotic resistance in bacteria limits the effect of corresponding antibiotics, and the classification of antibiotic resistance genes (ARGs) is important for the treatment of bacterial infections and for understanding the dynamics of microbial communities. Although several methods have been developed to classify ARGs, none of them work well when the ARGs diverge from those in the reference ARG databases. We develop a novel method, ARG-SHINE, for ARG classification. ARG-SHINE utilizes state-of-the-art learning to rank machine learning approach to ensemble three component methods with different features, including sequence homology, protein domain/family/motif and raw amino acid sequences for the deep convolutional neural network. Compared with other methods, ARG-SHINE achieves better performance on two benchmark datasets in terms of accuracy, macro-average f1-score and weighted-average f1-score. ARG-SHINE is used to classify newly discovered ARGs through functional screening and achieves high prediction accuracy. ARG-SHINE is freely available at https://github.com/ziyewang/ARG_SHINE.
CONSULT: accurate contamination removal using locality-sensitive hashing
Authors: Rachtman Eleonora , Bafna Vineet , Mirarab Siavash 
Published: August 2021

Abstract
A fundamental question appears in many bioinformatics applications: Does a sequencing read belong to a large dataset of genomes from some broad taxonomic group, even when the closest match in the set is evolutionarily divergent from the query? For example, low-coverage genome sequencing (skimming) projects either assemble the organelle genome or compute genomic distances directly from unassembled reads. Using unassembled reads needs contamination detection because samples often include reads from unintended groups of species. Similarly, assembling the organelle genome needs distinguishing organelle and nuclear reads. While k-mer-based methods have shown promise in read-matching, prior studies have shown that existing methods are insufficiently sensitive for contamination detection. Here, we introduce a new read-matching tool called CONSULT that tests whether k-mers from a query fall within a user-specified distance of the reference dataset using locality-sensitive hashing. Taking advantage of large memory machines available nowadays, CONSULT libraries accommodate tens of thousands of microbial species. Our results show that CONSULT has higher true-positive and lower false-positive rates of contamination detection than leading methods such as Kraken-II and improves distance calculation from genome skims. We also demonstrate that CONSULT can distinguish organelle reads from nuclear reads, leading to dramatic improvements in skim-based mitochondrial assemblies.