bluuebunny/crossref_metadata_2025_split huggingface dataset:
Half-life prediction of some neutron-rich exotic nuclei prior to peak A = 130
Authors: Shehzadi Ramoona , Nabi Jameel-Un , Farooq Fakeha 
Published: September 2022

Abstract

β-decay is amongst the key properties of nuclei required for the modeling of r-process nucleosynthesis. It also governs the flow of abundances among neighboring isotopic chains of high-mass elements. In the present work, a simple proton-neutron quasi particle random phase approximation (p–n-QRPA) model has been used for the calculation of β-decay half-lives of Rb, Sr, Y and Zr neutron-rich isotopes. For 97−103Rb, 98−107Sr, 101−109Y and 104−112Zr, where the experimental data were available, the half-life values are reproduced with reasonable accuracy. The same set of model parameters are later used to predict half-lives for few neutron-rich nuclei (104−112Rb, 108−113Sr, 110−114Y and 113−115Zr) where measured data is not available. The p–n-QRPA results (including only allowed transitions) are compared with previous calculations (allowed plus forbidden) and exhibit agreement within a factor of 2.0 when compared with the recent available experimental data.
Non-linearities in the Lyman-α forest and in its cross-correlation with dark matter halos
Authors: Givans Jahmour J. , Font-Ribera Andreu , Slosar Anže , Seeyave Louise , Pedersen Christian , Rogers Keir K. , Garny Mathias , Blas Diego , Iršič Vid 
Published: September 2022

Abstract
Three-dimensional correlations of the Lyman-α (Lyα) forest and cross correlations between the Lyα forest and quasars have been
measured on large scales, allowing a precise measurement of the baryon acoustic oscillation (BAO) feature at redshifts z > 2.
These 3D correlations are often modelled using linear perturbation theory,
but full-shape analyses to extract cosmological information beyond BAO will
require more realistic models capable of describing non-linearities present at smaller scales.
We present a measurement of the Lyα forest flux power spectrum from large
hydrodynamic simulations — the Sherwood simulations — and compare it to different
models describing the small-scale deviations from linear theory.
We confirm that the model presented in Arinyo-i-Prats et al. (2015) fits the measured
3D power up to k = 10 h Mpc-1 with an accuracy better than 5%, and show that the same
model can also describe the 1D correlations with similar precision.
We also present, for the first time, an equivalent study for the
cross-power spectrum of halos with the Lyα forest, and we discuss different challenges
we face when modelling the cross-power spectrum beyond linear scales.
We make all our measured power spectra public in https://github.com/andreufont/sherwoo_p3d.
This study is a step towards joint analyses of 1D and 3D flux correlations,
and towards using the quasar-Lyα cross-correlation beyond BAO analyses.
Second-order gauge-invariant formalism for the cosmological observables: complete verification of their gauge-invariance
Authors: Magi Matteo , Yoo Jaiyul 
Published: September 2022

Abstract
Accounting for all the relativistic effects, we have developed the fully nonlinear gauge-invariant formalism for describing the cosmological observables and presented the second-order perturbative expressions associated with light propagation and observations without choosing a gauge condition. For the first time, we have performed a complete verification of the validity of our second-order expressions by comparing their gauge-transformation properties from two independent methods: one directly obtained from their expressions in terms of metric perturbations and the other expected from their nonlinear relations. The expressions for the cosmological observables such as galaxy clustering and the luminosity distance are invariant under diffeomorphism and gauge-invariant at the observed position. We compare our results to the previous work and discuss the differences in the perturbative expressions. Our second-order gauge-invariant formalism constitutes a major step forward
in the era of precision cosmology and its applications in the future will play a crucial role for going beyond the power spectrum and probing the early universe.
Radiative pulsed L-mode operation in ARC-class reactors
Authors: Frank S.J. , Perks C.J. , Nelson A.O. , Qian T. , Jin S. , Cavallaro A. , Rutkowski A. , Reiman A. , Freidberg J.P. , Rodriguez-Fernandez P. , Whyte D. 
Published: September 2022

Abstract
A new ARC-class, highly-radiative, pulsed, L-mode, burning plasma scenario is developed and evaluated as a candidate for future tokamak reactors. Pulsed inductive operation alleviates the stringent current drive requirements of steady-state reactors, and operation in L-mode affords ELM-free access to

∼
90
%

core radiation fractions, significantly reducing the divertor power handling requirements. In this configuration the fusion power density can be maximized despite L-mode confinement by utilizing high-field to increase plasma densities and current. This allows us to obtain high gain in robust scenarios in compact devices with P
fus > 1000 MW despite low confinement. We demonstrate the feasibility of such scenarios here; first by showing that they avoid violating 0D tokamak limits, and then by performing self-consistent integrated simulations of flattop operation including neoclassical and turbulent transport, magnetic equilibrium, and radiofrequency current drive models. Finally we examine the potential effect of introducing negative triangularity with a 0D model. Our results show high-field radiative pulsed L-mode scenarios are a promising alternative to the typical steady state advanced tokamak scenarios which have dominated tokamak reactor development.
Complete dynamical evaluation of the characteristic polynomial of binary quantum graphs
Authors: Harrison J M , Hudgins T 
Published: September 2022

Abstract
We evaluate the variance of coefficients of the characteristic polynomial for binary quantum graphs using a dynamical approach. This is the first example where a spectral statistic can be evaluated in terms of periodic orbits for a system with chaotic classical dynamics without taking the semiclassical limit, which here is the limit of large graphs. The variance depends on the sizes of particular sets of primitive pseudo orbits (sets of distinct primitive periodic orbits): the set of primitive pseudo orbits without self-intersections and the sets of primitive pseudo orbits with a fixed number of self-intersections, all of which consist of two arcs of the pseudo orbit crossing at a single vertex. To show other pseudo orbits do not contribute we give two arguments. The first is based on a reduction of the variance formula from a sum over pairs of primitive pseudo orbits to a sum over pseudo orbits where no bonds are repeated. The second employs a parity argument for the Lyndon decomposition of words. For families of binary graphs, in the semiclassical limit, we show the pseudo orbit formula approaches a universal constant independent of the coefficient of the polynomial. This is obtained by counting the total number of primitive pseudo orbits of a given length.
dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data
Authors: Xu Yu , Chen Jiaxing , Lyu Aiping , Cheung William K , Zhang Lu 
Published: September 2022

AbstractTime-course single-cell RNA sequencing (scRNA-seq) data have been widely used to explore dynamic changes in gene expression of transcription factors (TFs) and their target genes. This information is useful to reconstruct cell-type-specific gene regulatory networks (GRNs). However, the existing tools are commonly designed to analyze either time-course bulk gene expression data or static scRNA-seq data via pseudo-time cell ordering. A few methods successfully utilize the information from multiple time points while also considering the characteristics of scRNA-seq data. We proposed dynDeepDRIM, a novel deep learning model to reconstruct GRNs using time-course scRNA-seq data. It represents the joint expression of a gene pair as an image and utilizes the image of the target TF–gene pair and the ones of the potential neighbors to reconstruct GRNs from time-course scRNA-seq data. dynDeepDRIM can effectively remove the transitive TF–gene interactions by considering neighborhood context and model the gene expression dynamics using high-dimensional tensors. We compared dynDeepDRIM with six GRN reconstruction methods on both simulation and four real time-course scRNA-seq data. dynDeepDRIM achieved substantially better performance than the other methods in inferring TF–gene interactions and eliminated the false positives effectively. We also applied dynDeepDRIM to annotate gene functions and found it achieved evidently better performance than the other tools due to considering the neighbor genes.
Artificial intelligence-driven prediction of multiple drug interactions
Authors: Chen Siqi , Li Tiancheng , Yang Luna , Zhai Fei , Jiang Xiwei , Xiang Rongwu , Ling Guixia 
Published: September 2022

Abstract
When a drug is administered to exert its efficacy, it will encounter multiple barriers and go through multiple interactions. Predicting the drug-related multiple interactions is critical for drug development and safety monitoring because it provides foundations for practical, safe compatibility and rational use of multiple drugs. With the progress of artificial intelligence (AI) technology, a variety of novel prediction methods for single interaction have emerged and shown great advantages compared to the traditional, expensive and time-consuming laboratory research. To promote the comprehensive and simultaneous predictions of multiple interactions, we systematically reviewed the application of AI in drug–drug, drug–food (excipients) and drug–microbiome interactions. We began by outlining the model methods, evaluation indicators, algorithms and databases commonly used to build models for three types of drug interactions. The models based on the metabolic enzyme P450, drug similarity and drug targets have empathized among the machine learning models of drug–drug interactions. In particular, we discussed the limitations of current approaches and identified potential areas for future research. It is anticipated the in-depth review will be helpful for the development of the next-generation of systematic prediction models for simultaneous multiple interactions.
Full-text chemical identification with improved generalizability and tagging consistency
Authors: Kim Hyunjae , Sung Mujeen , Yoon Wonjin , Park Sungjoon , Kang Jaewoo 
Published: September 2022

Abstract
Chemical identification involves finding chemical entities in text (i.e. named entity recognition) and assigning unique identifiers to the entities (i.e. named entity normalization). While current models are developed and evaluated based on article titles and abstracts, their effectiveness has not been thoroughly verified in full text. In this paper, we identify two limitations of models in tagging full-text articles: (1) low generalizability to unseen mentions and (2) tagging inconsistency. We use simple training and post-processing methods to address the limitations such as transfer learning and mention-wise majority voting. We also present a hybrid model for the normalization task that utilizes the high recall of a neural model while maintaining the high precision of a dictionary model. In the BioCreative VII NLM-Chem track challenge, our best model achieves 86.72 and 78.31 F1 scores in named entity recognition and normalization, significantly outperforming the median (83.73 and 77.49 F1 scores) and taking first place in named entity recognition. In a post-challenge evaluation, we re-implement our model and obtain 84.70 F1 score in the normalization task, outperforming the best score in the challenge by 3.34 F1 score.
Database URL: https://github.com/dmis-lab/bc7-chem-id
Trends in Assortative Mating and Offspring Outcomes
Authors: Bratsberg Bernt , Markussen Simen , Raaum Oddbjørn , Røed Knut , Røgeberg Ole 
Published: September 2022

Abstract
We study assortative mating of Norwegian parents over five decades and its consequences for offspring outcomes. Parents are characterised by the earnings decile of their parents (the offspring's grandparents) as an indicator of social class. While assortative mating has remained stable across decades, parenthood has become more skewed toward the higher classes. Examining the influence on offspring education and employment, we find that the marginal effect of one parent's class is smaller the higher is the class of the other. Overall, mating trends have contributed to slight improvements in average education and employment and reduced inequality in the offspring generation.
LiveLighter® ‘Junk Food’ mass media campaign increases behavioural strategies to reduce consumption
Authors: Morley Belinda , Nuss Tegan , Gascoyne Claudia , Dixon Helen , Wakefield Melanie 
Published: September 2022

Abstract
The LiveLighter® 2016 ‘Junk Food’ campaign ran for 5 weeks in Western Australia (WA) and urged adults to reduce their junk food consumption to avoid weight gain and associated chronic disease. A cohort design assessed campaign impact on knowledge, beliefs and behaviour. Pre-campaign (n = 1501) and post-campaign (n = 737) telephone surveys of WA adults aged 25–49 were undertaken. A post-campaign-only sample (n = 501) controlled for pre-test effects. The campaign reached 57% of respondents and increased knowledge of the link between overweight and non-alcoholic fatty liver disease (78% cf. 87%; P &lt; 0.01). Following campaign activity, respondents were more likely to avoid purchasing food from settings depicted in the advertisements (fast food outlets: 63% cf. 77%; service stations: 82% cf. 93%; vending machines: 87% cf. 96%; all P &lt; 0.001), particularly among pre-campaign consumers of fast food and salty snacks (≤2 times/week). Weight-loss self-efficacy increased among adults with higher body weight and campaign exposure (89% cf. 97%; P &lt; 0.01), and there was no increased endorsement of overweight stereotypes among the full sample. Support for fiscal disincentives and nutritional disclosure policies increased among healthy weight adults. LiveLighter® positively influenced knowledge, beliefs and behaviours, along with attitudes towards policies to encourage healthy eating, supporting LiveLighter® as an advocacy campaign.
Inactivation of BoORP3a, an oxysterol-binding protein, causes a low wax phenotype in ornamental kale
Authors: Zhang Simeng , Zhou Fuhui , Liu Zheng , Feng Xin , Li Yashu , Zhu Pengfang 
Published: September 2022

Abstract
Identifying genes associated with wax deposition may contribute to the genetic improvement of ornamental kale. Here, we characterized a candidate gene for wax contents, BoORP3a, encoding an oxysterol-binding protein. We sequenced the BoORP3a gene and coding sequence from the high-wax line S0835 and the low-wax line F0819, which revealed 12 single nucleotide polymorphisms between the two lines, of which six caused five amino acids substitutions. BoORP3a appeared to be relatively well conserved in Brassicaceae, as determined by a phylogenetic analysis, and localized to the endoplasmic reticulum and the nucleus. To confirm the role of BoORP3a in wax deposition, we generated three orp3a mutants in a high-wax kale background via CRISPR/Cas9-mediated genome editing. Importantly, all three mutants exhibited lower wax contents and glossy leaves. Overall, these data suggest that BoORP3a may participate in cuticular wax deposition in ornamental kale.
The banana genome hub: a community database for genomics in the Musaceae
Authors: Droc Gaëtan , Martin Guillaume , Guignon Valentin , Summo Marilyne , Sempéré Guilhem , Durant Eloi , Soriano Alexandre , Baurens Franc-Christophe , Cenci Alberto , Breton Catherine , Shah Trushar , Aury Jean-Marc , Ge Xue-Jun , Harrison Pat Heslop , Yahiaoui Nabila , D’Hont Angélique , Rouard Mathieu 
Published: September 2022

AbstractThe Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources—planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.
Distance-quality trade-off and choice of family planning provider in urban Pakistan
Authors: Hussain Imtiaz , Nausheen Sidrah , Rizvi Arjumand , Ansari Uzair , Baz Mir , Zehra Kaneez , Yameen Sahar , Hackett Kristy , Lassi Zohra , Canning David , Shah Iqbal , Soofi Sajid Bashir 
Published: September 2022

ABSTRACT

Background
There is limited evidence between contraceptive use, availability of commodities and distance to the facility in developing countries. Distance to the facility is an essential determinant of contraceptive use. Still, women may not seek family planning services from the nearest facility and may be prepared to travel the farthest distance to receive quality family planning services.

Methods
We analyzed women's survey data linked to health facility data and applied an alternate specific conditional logit model to examine the distance a woman is prepared to travel and the quality of services offered by facilities in urban areas in Karachi, Pakistan.

Results
This study analyzed data from 336 women and 28 facilities and identified that the mean distance to the nearest facility was 0.44 km; the chosen facility was, on average, 5 km away. Women preferred facilities that offered a range of contraceptive methods and additional services provided by female healthcare providers only. Furthermore, on average, women are willing to travel a further 1.7 km for a facility that offers more family planning methods, 1.4 km for a facility that offers additional health services and 11 km for a facility that offers services delivered by female healthcare providers.

Conclusions
The findings highlight the quality measures women prioritize over distance and consider essential when choosing a family planning facility.
Combined synchronization and superovulation treatments negatively impact embryo viability possibly by the downregulation of WNT/β-catenin and Notch signaling genes in the porcine endometrium
Authors: Gonzalez-Ramiro Henar , Parrilla Inmaculada , Miquel Cambra Josep , Gonzalez-Plaza Alejandro , Antonia Gil Maria , Cuello Cristina , Martinez Emilio A , Rodriguez-Martinez Heriberto , Martinez Cristina A 
Published: September 2022

Abstract
The combination of estrus synchronization and superovulation treatments introduces molecular modifications whose effects are yet to be disclosed. Here, reproductive parameters and gene expression changes in ovaries and endometrium were explored on day 6 after artificial insemination (AI), when synthetic progestin altrenogest (ALT) was combined with gonadotropins. Sows were administered ALT for 7 d beginning on the day of weaning and superovulated with equine chorionic gonadotropin (eCG) 24 h later and human chorionic gonadotropins (hCG) at the onset of estrus (SS-7 group; n = 6). The controls were either superovulated sows with eCG 24 h postweaning and hCG at the onset of estrus (SC group; n = 6) or sows with postweaning spontaneous estrus (NC group; n = 6). Ovary examination and embryo and tissue collection were performed in all sows via laparotomy on day 6 post-AI. RNA-Seq was conducted to analyze differentially expressed genes (DEGs) between groups. Statistical analysis of the reproductive parameters was conducted with ANOVA and Tukey post hoc tests. DEGs were analyzed with an ANOVA (fold changes ≥2 or ≤2, P value &lt;0.05). Hormonal treatments almost doubled (P &lt; 0.03) the number of corpora lutea (39.8 ± 10.2 and 38.3 ± 11.1 in SS-7 and SC sows, respectively) compared with that in the NC group (23.1 ± 3.8). In contrast, embryo viability significantly decreased (P &lt; 0.003) in response to SS-7 treatment (75.1% ± 15.2%) compared to SC and NC groups (93.8 ± 7.6% and 91.8 ± 6.9%, respectively). RNA-Seq analyses revealed 675 and 1,583 DEGs in the SS-7 group compared to both SC and NC groups in endometrial and ovarian samples, respectively. Interestingly, many genes with key roles in the Wnt/β-catenin and Notch signaling pathways were differentially expressed in SS-7 sows relative to SC and NC groups (e.g., Ctnnb1, Myc, Gli3, Scyl2, Ccny, Daam1, Ppm1n, Rbpj, and Usp8). A key finding in this study was the downregulation of β-catenin (Ctnnb1) gene expression in the SS-7 endometrium, suggesting that this treatment influences embryo–uterine dialogue by triggering a cascade of events leading to embryo maldevelopment. These data explain the proliferative defects in SS-7 embryos and suggest a novel mechanism of a porcine embryo–maternal crosstalk.
Six principles for working effectively with landowners to advance bird conservation
Authors: Lindell Catherine A , Dayer Ashley A 
Published: September 2022

Abstract
Private land management is an essential component of bird conservation. How private landowners manage their farms, rangelands, forests, and yards, influences the resources and hazards birds encounter, with associated impacts on bird abundance. We describe 6 principles, based on recent research, that conservation practitioners should incorporate into their bird conservation efforts with landowners: (1) use social and natural science and stakeholder input to decide how and where to work; (2) tailor strategies to local ecological and social conditions; (3) build relationships and support landowner interests; (4) reduce barriers to participation; (5) offer a menu of options to support landowner conservation behavior; and (6) promote persistence of landowner conservation behavior. These principles emphasize the importance of recognizing the considerations of landowners, customizing interventions to local conditions, and making interventions as easy to implement as possible. Developing relationships with landowners, along with a diverse menu of conservation interventions, takes time and effort but should improve both the uptake and persistence of conservation practices on private lands.