bluuebunny/crossref_metadata_2025_split huggingface dataset:
A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes
Authors: Morgante Fabio , Carbonetto Peter , Wang Gao , Zou Yuxin , Sarkar Abhishek , Stephens Matthew 
Published: November 2022

AbstractPredicting phenotypes from genotypes is a fundamental task in quantitative genetics. With technological advances, it is now possible to measure multiple phenotypes in large samples. Multiple phenotypes can share their genetic component; therefore, modeling these phenotypes jointly may improve prediction accuracy by leveragingeffects that are shared across phenotypes. However, effects can be shared across phenotypes in a variety of ways, so computationally efficient statistical methods are needed that can accurately and flexibly capture patterns of effect sharing. Here, we describe new Bayesian multivariate, multiple regression methods that, by using flexible priors, are able to model and adapt to different patterns of effect sharing and specificity across phenotypes. Simulation results show that these new methods are fast and improve prediction accuracy compared with existing methods in a wide range of settings where effects are shared. Further, in settings where effects are not shared, our methods still perform competitively with state-of-the-art methods. In real data analyses of expression data in the Genotype Tissue Expression (GTEx) project, our methods improve prediction performance on average for all tissues, with the greatest gains in tissues where effects are strongly shared, and in the tissues with smaller sample sizes. While we use gene expression prediction to illustrate our methods, the methods are generally applicable to any multi-phenotype applications, including prediction of polygenic scores and breeding values. Thus, our methods have the potential to provide improvements across fields and organisms.Author summaryPredicting phenotypes from genotypes is a fundamental problem in quantitative genetics. Thanks to recent advances, it is increasingly feasible to collect data on many phenotypes and genome-wide genotypes in large samples. Here, we tackle the problem of predictingmultiple phenotypesfrom genotypes using a new method based on a multivariate, multiple linear regression model. Although the use of a multivariate, multiple linear regression model is not new, in this paper we introduce a flexible and computationally efficientempirical Bayesapproach based on this model. This approach uses a prior that captures how the effects of genotypes on phenotypes are shared across the different phenotypes, and then the prior is adapted to the data in order to capture the most prominent sharing patterns present in the data. We assess the benefits of this flexible Bayesian approach in simulated genetic data sets, and we illustrate its application in predicting gene expression measured in multiple human tissues. We show that our methods can outperform competing methods in terms of prediction accuracy, and the computations involved in fitting the model and making the predictions scale well to large data sets.
Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex
Authors: Jiou Jenny , Shaffer Joy M. , Bernades Natalia E. , Fung Ho Yee Joyce , Dias Juliana Kikumoto , D’Arcy Sheena , Chook Yuh Min 
Published: November 2022

AbstractPreviously we showed that the nuclear import receptor Importin-9 wraps around the H2A-H2B core to chaperone and transport it from the cytoplasm to the nucleus. However, unlike most nuclear import systems where RanGTP dissociates cargoes from their importins, RanGTP binds stably to the Importin-9•H2A-H2B complex and formation of the ternary RanGTP•Importin-9•H2A-H2B complex facilitates H2A-H2B release to the assembling nucleosome. It was unclear how RanGTP and the cargo H2A-H2B can bind simultaneously to an importin, and how interactions of the three components position H2A-H2B for nucleosome assembly. Here we show cryo-EM structures of Importin-9•RanGTP and of its yeast homolog Kap114, including Kap114•RanGTP, Kap114•H2A-H2B, and RanGTP•Kap114•H2A-H2B to explain how the conserved Kap114 binds H2A-H2B and RanGTP simultaneously and how the GTPase primes histone transfer to the nucleosome. In the ternary complex, RanGTP binds to the N-terminal repeats of Kap114 in the same manner as in the Kap114/Importin-9•RanGTP complex, and H2A-H2B binds via its acidic patch to the Kap114 C-terminal repeats much like in the Kap114/Importin-9•H2A-H2B complex. Ran binds to a different conformation of Kap114 in the ternary RanGTP•Kap114•H2A-H2B complex. Here, Kap114 no longer contacts the H2A-H2B surface proximal to the H2A docking domain that drives nucleosome assembly, positioning it for transfer to the assembling nucleosome.Significance StatementHistones and their chaperone networks are typically conserved in eukaryotes. The yeast importin Kap114 and its human homolog Importin-9 share low sequence identity, but both are primary nuclear import receptors for the core histone heterodimer H2A-H2B. Cryo-EM structures of Kap114•H2A-H2B, Kap114•RanGTP and Importin-9•RanGTP complexes show homologous structure and function for Kap114 and Importin-9. In the nucleus, RanGTP binding to Kap114/Imp9•H2A-H2B does not release H2A-H2B, but RanGTP binds to form an atypical ternary complex. Structure of the ternary RanGTP•Kap114•H2A-H2B complex explains how the GTPase and cargo bind simultaneously to Kap114 and how the presence of Ran in the complex primes H2A-H2B transfer to assembling nucleosomes.
CRISPR/Cas9-based repeat depletion for the high-throughput genotyping of complex plant genomes
Authors: Rossato Marzia , Marcolungo Luca , De Antoni Luca , Lopatriello Giulia , Bellucci Elisa , Cortinovis Gaia , Frascarelli Giulia , Nanni Laura , Bitocchi Elena , Vittori Valerio Di , Vincenzi Leonardo , Lucchini Filippo , Bett Kirstin E. , Ramsay Larissa , Konkin David James , Delledonne Massimo , Papa Roberto 
Published: November 2022

ABSTRACTHigh-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genomewide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches for genotyping are progressively replacing traditional genotyping methods due to the lower ascertainment bias. However, genome-wide genotyping based on sequencing becomes expensive in species with large genomes and a high proportion of repetitive DNA. Here we describe the use of CRISPR/Cas9 technology to deplete repetitive elements in the 3.76-Gb genome of lentil (Lens culinaris), 84% consisting of repeats, thus concentrating the sequencing data on coding and regulatory regions (single-copy regions). We designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats and excluding repetitive regions overlapping annotated genes and putative regulatory elements based on ATAC-Seq data. The novel depletion method removed ∼40% of reads mapping to repeats, increasing those mapping to single-copy regions by ∼2.6-fold. When analyzing 25 million fragments, this repeat-to-single-copy shift in the sequencing data increased the number of genotyped bases of ∼10-fold compared to non-depleted libraries. In the same condition, we were also able to identify ∼12-fold more genetic variants in the single-copy regions and increased the genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed due to low coverage. The method performed similarly regardless of the multiplexing level, type of library or genotypes, including different cultivars and a closely-related species (L. orientalis). Our results demonstrated that CRISPR/Cas9-driven repeat depletion focuses sequencing data on meaningful genomic regions, thus improving high-density and genome-wide genotyping in large and repetitive genomes.
Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration
Authors: Wei Ke-Hsuan , Lin I-Ting , Chowdhury Kaushik , Liu Kuan-Ting , Ko Tai-Ming , Chang Yao-Ming , Yang Kai-Chien , Lai Shih-Lei 
Published: November 2022

AbstractZebrafish exhibit a robust ability to regenerate their hearts following injury, and the immune system plays a key role in this process. We previously showed that delaying macrophage recruitment by clodronate liposome (CL) treatment compromises neutrophil resolution and heart regeneration, even when the infiltrating macrophage number was restored within the first-week post injury (Lai et al., 2017). Here, we examined the molecular mechanisms underlying the cardiac repair of regenerative PBS-control hearts vs. non-regenerative CL-treated hearts. Bulk transcriptomic analyses revealed that CL-treated hearts exhibited disrupted inflammatory resolution and energy metabolism during cardiac repair. Temporal single-cell profiling of inflammatory cells in regenerative vs. non-regenerative conditions further identified heterogenous macrophages and neutrophils with distinct infiltration dynamics, gene expression, and cellular crosstalk. Among them, two residential macrophage subpopulations were enriched in regenerative hearts and barely recovered in non-regenerative hearts. Early CL treatment at 8 days or even 1 month before cryoinjury led to the depletion of resident macrophages without affecting the circulating macrophage recruitment to the injured area. Strikingly, these resident macrophage-deficient zebrafish still exhibited compromised neovascularization and scar resolution. Our results characterized the inflammatory cells of the zebrafish injured hearts and identified key resident macrophage subpopulations prerequisite for successful heart regeneration.
Online modeling of environmental constraint region for complex-shaped parts assembly
Authors: Gan Shuai , Liu Yang , Chen Ziyu 
Published: November 2022

Purpose
The paper aims to propose a method to build environmental constraint region online in complex-shaped peg-in-hole assembly tasks.

Design/methodology/approach
Compared with conventional way which using computer-aided design (CAD) models of assembly parts to construct the environmental constraint region offline, the paper provides an online approach that consists of three aspects: modeling assembly parts through visual recognition, decomposing complex shapes into multiple primitive convex shapes and a numerical algorithm to simulate the peg-in-hole insertion contact. Besides, a contrast experiment is performed to validate the feasibility and effectiveness of the method.

Findings
The experiment result indicates that online construction takes less time than the offline way under the same task conditions. Furthermore, due to the CAD models of the parts are not required to be known, the method proposed in the paper has a broader application in most assembly scenarios.

Originality/value
With the improvement of customization and complexity of manufactured parts, the assembly of complex-shaped parts has drawn greater attention of many researchers. The assembly methods based on attractive region in environment (ARIE) have shown great performance to achieve high-precision manipulation with low-precision systems. The construction of environmental constraint region serves as an essential part of ARIE-based theory, directly affect the formulation and application of assembly strategies.
IFRS for SMEs adoption, corporate governance, and quality of financial statements: evidence from Dominican Republic and El Salvador
Authors: Sassi Nesrine , Damak-Ayadi Salma 
Published: November 2022

PurposeThe purpose of this study is to examine the indirect relationship between the mandatory adoption of International Financial Reporting Standards for small and medium-sized enterprises (IFRS for SMEs) and the corporate governance index (CGI) by checking the mediating effect of the quality of financial statements (QFS) on this relationship.Design/methodology/approachThe main objective of the IFRS for SMEs standard is to meet the specific needs of SMEs in transition and developing economies. Here, the authors used the structural equation method to investigate SMEs in countries that mandate the application of IFRS for SMEs for the years 2010 (pre-adoption) and 2016 (post-adoption). The final sample covered two emerging countries: the Dominican Republic and El Salvador.FindingsThe results show a positive association between the adoption of IFRS for SMEs, CGI and QFS. Furthermore, the findings confirm that the relationship between IFRS for SMEs adoption and CGI is under the control of the QFS.Originality/valueThis study provides standard setters and managers of SMEs with an overview of the importance of QFS on the significance of this relationship in emerging countries. The study contributes to the literature by examining the indirect relationship between IFRS for SMEs and CGI and building a CGI that integrates a set of governance practices linked to SMEs.
Pufferfish versus lionfish: comparing risks for Turkish marine economics
Authors: Kaplan Merve , Yildirim Seda , Yildirim Durmus Cagri 
Published: November 2022

PurposeThis study aims to explore the risk level of pufferfish and lionfish by comparing them among Turkish marines. In addition, this study focuses on comparing pufferfish with lionfish to determine which one is more dangerous for marine economics in Türkiye.Design/methodology/approachThis study employs descriptive content analysis to give some qualitative evidence for the related literature. As a sample case, Türkiye was selected in the context of being a country in the Mediterranean Basin. By reviewing recent news, reports and publications, this study firstly will conclude how invasive alien marine species affect Turkish marines. Then, pufferfish and lionfish will be compared together to determine the risk level of these species for Turkish marine economics.FindingsAs a result of descriptive findings, it is seen that captured fishery has been declined in Turkey recently due to many factors including climate change, global warming, overfishing, environmental pollution and attack of invasive alien species. Pufferfish and lionfish are seen as the most spread marine species in Turkish marines. When comparing pufferfish with lionfish, it is seen that pufferfish is more dangerous than lionfish for Turkish marine economics.Research limitations/implicationsThis study provides descriptive and original findings as a result of comparison of pufferfish and lionfish due to their impact on Turkish marine economy. It is thought to give useful importation for the fight against invasive alien marine species in the Mediterranean Basin. Future studies can investigate different invasive alien marine species and their impacts on marine economics in the Mediterranean Basin.Practical implicationsBased on the Turkish cases, it is determined that there should be different policies for fight against invasive alien marine species in the Mediterranean Sea. Each marine species has different impacts on seafood market. Some of marine species can be consumed as a seafood product but some of them can't be consumed that policy makers should develop other strategies such as catching them to reduce their population in the local marines.Social implicationsThe spread of invasive alien marine species is still continuing in the Mediterranean Basin. Each country has been affected by the attack of invasive alien marine species. To keep sustainable seafood market and marine economics, countries should both implement common policies and develop policies specific to threats in their own countries.Originality/valueThis study reveals key points in the rise of invasive alien marine species in Turkish marines at first. The main contribution of this study is to be a recent sample for a country which is under attack by invasive alien marine species by giving a comparison of pufferfish and lionfish.
Hydraulic traits are not robust predictors of tree species stem growth during a severe drought in a wet tropical forest
Authors: Smith‐Martin Chris M. , Muscarella Robert , Ankori‐Karlinsky Roi , Delzon Sylvain , Farrar Samuel L. , Salva‐Sauri Melissa , Thompson Jill , Zimmerman Jess K. , Uriarte María 
Published: November 2022

Abstract

Severe droughts have led to lower plant growth and high mortality in many ecosystems worldwide, including tropical forests. Drought vulnerability differs among species, but there is limited consensus on the nature and degree of this variation in tropical forest communities. Understanding species‐level vulnerability to drought requires examination of hydraulic traits since these reflect the different strategies species employ for surviving drought.

Here, we examined hydraulic traits and growth reductions during a severe drought for 12 common woody species in a wet tropical forest community in Puerto Rico to ask: Q1. To what extent can hydraulic traits predict growth declines during drought? We expected that species with more hydraulically vulnerable xylem and narrower safety margins (SMP50) would grow less during drought. Q2. How does species successional association relate to the levels of vulnerability to drought and hydraulic strategies? We predicted that early‐ and mid‐successional species would exhibit more acquisitive strategies, making them more susceptible to drought than shade‐tolerant species. Q3. What are the different hydraulic strategies employed by species and are there trade‐offs between drought avoidance and drought tolerance? We anticipated that species with greater water storage capacity would have leaves that lose turgor at higher xylem water potential and be less resistant to embolism forming in their xylem (P50).

We found a large range of variation in hydraulic traits across species; however, they did not closely capture the magnitude of growth declines during drought. Among larger trees (≥10 cm diameter at breast height—DBH), some tree species with high xylem embolism vulnerability (P50) and risk of hydraulic failure (SMP50) experienced substantial growth declines during drought, but this pattern was not consistent across species. We found a trade‐off among species between drought avoidance (capacitance) and drought tolerating (P50) in this tropical forest community. Hydraulic strategies did not align with successional associations. Instead, some of the more drought‐vulnerable species were shade‐tolerant dominants in the community, suggesting that a drying climate could lead to shifts in long‐term forest composition and function in Puerto Rico and the Caribbean.

Read the free Plain Language Summary for this article on the Journal blog.
Below‐ground net primary productivity stability in response to a nitrogen addition gradient in an alpine meadow
Authors: Ma Fangfang , Chen Weinan , Wang Jinsong , Tian Dashuan , Zhou Qingping , Niu Shuli 
Published: November 2022

Abstract

Temporal stability of ecosystem productivity is important for providing reliable ecosystem services under global changes. Great efforts have been made to explore the response of above‐ground net primary productivity (ANPP) stability to nitrogen (N) enrichment, yet how it affects below‐ground net primary productivity (BNPP) stability remains elusive, which hinders a comprehensive understanding of ecosystem stability from the view of a whole system.

Here, using a field manipulative experiment with six N addition rates (0, 2, 4, 8, 16, 32 g N m−2 year−1), we explored the response patterns and drivers of BNPP stability in the topsoil (0–20 cm) and subsoil (20–40 cm) in the alpine meadow.

The results showed that BNPP stability at both soil depths showed a unimodal response to increasing N addition rates. Specifically, for both the topsoil and subsoil, low‐level N addition significantly promoted BNPP stability, while high doses of N addition had no significant impact on BNPP stability, suggesting that current low level of N deposition likely benefits the stable provision of below‐ground functioning. Furthermore, dominant species stability and species richness contributed most to the changes in BNPP stability in the topsoil, whereas only dominant species stability was the dominant driver of BNPP stability in the subsoil.

This study is among the first to illuminate the main mechanisms underlying the responses of BNPP stability to N enrichment at various soil depths, which will advance our current understanding of N addition effects on below‐ground processes and benefit the sustainable provision of ecosystem functioning in the context of atmospheric N deposition.

Read the free Plain Language Summary for this article on the Journal blog.
An effective scheme of joint migration inversion in the pseudo‐time domain
Authors: Qu Shan , Verschuur Dirk Jacob 
Published: November 2022

AbstractTraditional full‐waveform inversion is a non‐linear and ill‐posed inversion problem. To reduce the non‐linearity of it, joint migration inversion (joint migration inversion) was proposed as an alternative. Joint migration inversion tries to minimize the mismatch between measured and modelled reflection data. One key feature of joint migration inversion is its parameterization: two separate parameters, reflectivity (for the amplitudes of reflected events) and propagation velocity (for the phase effects). This separation helps to reduce the non‐linearity of the inversion. During joint migration inversion, with the velocity being updated, the reflectors in the updated image are also shifting in depth accordingly, this phenomenon is called depth–velocity ambiguity. This interaction between the two parameters during inversion is desired to keep the image time consistent with the measured data but may lead to non‐robustness of joint migration inversion due to the presence of local minima. Therefore, we propose a more robust joint migration inversion scheme, which parameterizes the models with vertical time, termed pseudo‐time joint migration inversion. In pseudo‐time, the updates of velocity will not result in the associated vertical location changes of reflectors in the estimated image. Instead, the reflectors are mainly getting more focused. One limitation is that the depth‐pseudo‐time conversion process assumes a simple linear relationship between depth and pseudo‐time, which might cause some artefacts in the converted models when there exist strong lateral velocity variations. One subsequent round of depth joint migration inversion is recommended to resolve this issue. We demonstrate the effectiveness of our proposed method with a two‐dimensional synthetic example in an extreme scenario, where the initial velocity model is homogeneous, a realistic offshore two‐dimensional synthetic example, a two‐dimensional field example from the Vøring basin in Norway and a simple three‐dimensional synthetic example. In all examples, pseudo‐time joint migration inversion manages to recover more reasonable updates in the inverted velocity and invert more focused reflectors in the inverted image, compared to depth joint migration inversion.