bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genomic and epigenetic maps of human centromeres
Authors: Altemose Nicolas , Logsdon Glennis A. , Bzikadze Andrey V. , Sidhwani Pragya , Langley Sasha A. , Caldas Gina V. , Hoyt Savannah J. , Uralsky Lev , Ryabov Fedor D. , Shew Colin J. , Sauria Michael E.G. , Borchers Matthew , Gershman Ariel , Mikheenko Alla , Shepelev Valery A. , Dvorkina Tatiana , Kunyavskaya Olga , Vollger Mitchell R. , Rhie Arang , McCartney Ann M. , Asri Mobin , Lorig-Roach Ryan , Shafin Kishwar , Aganezov Sergey , Olson Daniel , de Lima Leonardo Gomes , Potapova Tamara , Hartley Gabrielle A. , Haukness Marina , Kerpedjiev Peter , Gusev Fedor , Tigyi Kristof , Brooks Shelise , Young Alice , Nurk Sergey , Koren Sergey , Salama Sofie R. , Paten Benedict , Rogaev Evgeny I. , Streets Aaron , Karpen Gary H. , Dernburg Abby F. , Sullivan Beth A. , Straight Aaron F. , Wheeler Travis J. , Gerton Jennifer L. , Eichler Evan E. , Phillippy Adam M. , Timp Winston , Dennis Megan Y. , O’Neill Rachel J. , Zook Justin M. , Schatz Michael C. , Pevzner Pavel A. , Diekhans Mark , Langley Charles H. , Alexandrov Ivan A. , Miga Karen H. 
Published: July 2021

AbstractExisting human genome assemblies have almost entirely excluded highly repetitive sequences within and near centromeres, limiting our understanding of their sequence, evolution, and essential role in chromosome segregation. Here, we present an extensive study of newly assembled peri/centromeric sequences representing 6.2% (189.9 Mb) of the first complete, telomere-to-telomere human genome assembly (T2T-CHM13). We discovered novel patterns of peri/centromeric repeat organization, variation, and evolution at both large and small length scales. We also found that inner kinetochore proteins tend to overlap the most recently duplicated subregions within centromeres. Finally, we compared chromosome X centromeres across a diverse panel of individuals and uncovered structural, epigenetic, and sequence variation at single-base resolution across these regions. In total, this work provides an unprecedented atlas of human centromeres to guide future studies of their complex and critical functions as well as their unique evolutionary dynamics.One-sentence summaryDeep characterization of fully assembled human centromeres reveals their architecture and fine-scale organization, variation, and evolution.
Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous
Authors: Ghezelayagh Ava , Harrington Richard C. , Burress Edward D. , Campbell Matthew A. , Buckner Janet C. , Chakrabarty Prosanta , Glass Jessica R. , Tyler McCraney W. , Unmack Peter J. , Thacker Christine E. , Alfaro Michael E. , Friedman Sarah T. , Ludt William B. , Cowman Peter F. , Friedman Matt , Price Samantha A. , Dornburg Alex , Faircloth Brant C. , Wainwright Peter C. , Near Thomas J. 
Published: July 2021

AbstractSpiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species1–3. It is believed that this dominance resulted from explosive lineage and phenotypic diversification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event4. It remains unclear, however, if living acanthomorph diversity is the result of a punctuated burst or gradual accumulation of diversity following the K-Pg. We assess these hypotheses with a time-calibrated phylogeny inferred using ultraconserved elements from a sampling of species that represent over 91% of all acanthomorph families, as well as an extensive body shape dataset of extant species. Our results indicate that several million years after the end-Cretaceous, acanthomorphs underwent a prolonged and significant expansion of morphological disparity primarily driven by changes in body elongation, and that acanthomorph lineages containing the bulk of the living species diversity originated throughout the Cenozoic. These acanthomorph lineages radiated into distinct regions of morphospace and retained their iconic phenotypes, including a large group of laterally compressed reef fishes, fast-swimming open-ocean predators, bottom-dwelling flatfishes, seahorses, and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of a post K-Pg adaptive radiation in which rates of lineage diversification were decoupled from periods of high phenotypic disparity.
An atlas of the Norway spruce needle seasonal transcriptome
Authors: Bag Pushan , Lihavainen Jenna , Delhomme Nicolas , Riquelme Thomas , Robinson Kathryn M , Jansson Stefan 
Published: July 2021

SummaryBoreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 – June 30), cell walls, organelles etc. were formed, and this developmental program heavily influenced the transcriptome, explained by over represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July-August), autumn (September-October), winter (November-February) and spring (March-April), where over represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.Significance statementThe development of Norway spruce needles and their annual cycle of biochemical activities (photosynthesis in the summer, adaptation and survival of the harsh boreal winter) is not well understood. We use deep RNA sequencing to profile the transcriptome over the season, and show how the dataset could be used to give information about “what needles do” over the year, and are here making the dataset available for the scientific community.Graphical abstract
A drug candidate for treating adverse reactions caused by pathogenic antibodies inducible by COVID-19 virus and vaccines
Authors: Wang Huiru , Wu Xiancong , Zhang Yuekai , Chen Qiuchi , Dai Lin , Chen Yuxing , Liu Xiaoling 
Published: July 2021

SummaryIn a recent study, we reported that certain anti-spike antibodies of COVID-19 and SARS-CoV viruses can have a pathogenic effect through binding to sick lung epithelium cells and misleading immune responses to attack self-cells. We termed this new pathogenic mechanism “Antibody Dependent Auto-Attack” (ADAA). This study explores a drug candidate for prevention and treatment of such ADAA-based diseases. The drug candidate is a formulation comprising N-acetylneuraminic acid methyl ester (NANA-Me), an analog of N-acetylneuraminic acid. NANA-Me acts through a unique mechanism of action (MOA) which is repairment of the missing sialic acid on sick lung epithelium cells. This MOA can block the antibodies’ binding to sick cells, which are vulnerable to pathogenic antibodies. Our in vivo data showed that the formulation significantly reduced the sickness and deaths caused by pathogenic anti-spike antibodies. Therefore, the formulation has the potential to prevent and treat the serious conditions caused by pathogenic antibodies during a COVID-19 infection. In addition, the formulation has potential to prevent and treat the adverse reactions of COVID-19 vaccines because the vaccines can induce similar antibodies, including pathogenic antibodies. The formulation will be helpful in increasing the safety of the vaccines without reducing the vaccine’s efficacy. Compared to existing antiviral drugs, the formulation has a unique MOA of targeting receptors, broad spectrum of indications, excellent safety profile, resistance to mutations, and can be easily produced.
Practical expedients and theoretical flaws: the IASB's legitimacy strategy during the COVID-19 pandemic
Authors: Moscariello Nicola , Pizzo Michele 
Published: July 2021

PurposeGrounded in the legitimacy theory and framed within the context of European Union’s (EU's) endorsement process, this paper analyses the International Accounting Standards Board’s (IASB's) response to the COVID-19 crisis and the impact of its practical expedient COVID-19-Related Rent Concession on the IASB's output legitimacy.Design/methodology/approachThis study uses a qualitative process-tracing approach and combines inductive historical narratives and deductive reasoning to draw theoretical implications concerning the COVID-19 crisis' impact on the standard-setting process.FindingsThe paper shows a growing reliance on practical expedients in International Financial Reporting Standards (IFRS) to maintain the IASB's output legitimacy. While introducing some theoretical flaws, practical expedients increase the standards' flexibility and strengthen the IASB's ability to respond to the European political bodies' concerns. Indeed, an analysis of the IASB's response to the COVID-19 outbreak reveals the role practical expedients might play not only in reducing (ex ante) new IFRS transition costs but also in dealing (ex-post) with the broader economic impact of unexpected systemic crises to limit criticisms and controversies surrounding IFRS.Originality/valueThis study reveals a causal relationship between the rise of the European public good criterion in the EU endorsement process and the wider use of practical expedients in IFRS. An analysis of the latest amendment to IFRS 16 in response to the COVID-19 crisis also confirms the role of practical expedients in strengthening the acceptance of IFRS in an increasingly complex economic reality and sheds some light on the new strategies adopted by the IASB to preserve its legitimacy in the EU.
On copula moment: empirical likelihood based estimation method
Authors: Abdelli Jihane , Brahimi Brahim 
Published: July 2021

PurposeIn this paper, the authors applied the empirical likelihood method, which was originally proposed by Owen, to the copula moment based estimation methods to take advantage of its properties, effectiveness, flexibility and reliability of the nonparametric methods, which have limiting chi-square distributions and may be used to obtain tests or confidence intervals. The authors derive an asymptotically normal estimator of the empirical likelihood based on copula moment estimation methods (ELCM). Finally numerical performance with a simulation experiment of ELCM estimator is studied and compared to the CM estimator, with a good result.Design/methodology/approachIn this paper we applied the empirical likelihood method which originally proposed by Owen, to the copula moment based estimation methods.FindingsWe derive an asymptotically normal estimator of the empirical likelihood based on copula moment estimation methods (ELCM). Finally numerical performance with a simulation experiment of ELCM estimator is studied and compared to the CM estimator, with a good result.Originality/valueIn this paper we applied the empirical likelihood method which originally proposed by Owen 1988, to the copula moment based estimation methods given by Brahimi and Necir 2012. We derive an new estimator of copula parameters and the asymptotic normality of the empirical likelihood based on copula moment estimation methods.
Extension of the unsymmetric 8-node hexahedral solid element US-ATFH8 to geometrically nonlinear analysis
Authors: Li Zhi , Cen Song , Li Chenfeng 
Published: July 2021

PurposeThe purpose of this paper is to extend a recent unsymmetric 8-node, 24-DOF hexahedral solid element US-ATFH8 with high distortion tolerance, which uses the analytical solutions of linear elasticity governing equations as the trial functions (analytical trial function) to geometrically nonlinear analysis.Design/methodology/approachBased on the assumption that these analytical trial functions can still properly work in each increment step during the nonlinear analysis, the present work concentrates on the construction of incremental nonlinear formulations of the unsymmetric element US-ATFH8 through two different ways: the general updated Lagrangian (UL) approach and the incremental co-rotational (CR) approach. The key innovation is how to update the stresses containing the linear analytical trial functions.FindingsSeveral numerical examples for 3D structures show that both resulting nonlinear elements, US-ATFH8-UL and US-ATFH8-CR, perform very well, no matter whether regular or distorted coarse mesh is used, and exhibit much better performances than those conventional symmetric nonlinear solid elements.Originality/valueThe success of the extension of element US-ATFH8 to geometrically nonlinear analysis again shows the merits of the unsymmetric finite element method with analytical trial functions, although these functions are the analytical solutions of linear elasticity governing equations.
A three-dimensional dental model restoration method based on tooth feature contours
Authors: Yang Shuai , Zhao Wenjie , Ke Yongzhen , Liu Jiaying , Xue Yongjiang 
Published: July 2021

Purpose
Due to the inability to directly apply an intra-oral image with esthetic restoration to restore tooth shape in the computer-aided design system, this paper aims to propose a method that can use two-dimensional contours obtained from the image for the three-dimensional dental mesh model restoration.

Design/methodology/approach
First, intra-oral image and smiling image are taken from the patient, then teeth shapes of the images are designed based on esthetic restoration concepts and the pixel coordinates of the teeth’s contours are converted into the vertex coordinates in the three-dimensional space. Second, the dental mesh model is divided into three parts – active part, passive part and fixed part – based on the teeth’s contours of the mesh model. Third, the vertices from the teeth’s contours of the dental model are matched with ones from the intra-oral image and with the help of matching operation, the target coordinates of each vertex in the active part can be calculated. Finally, the Laplacian-based deformation algorithm and mesh smoothing algorithm are performed.

Findings
Benefitting from the proposed method, the dental mesh model with esthetic restoration can be quickly obtained based on the intra-oral image that is the result of doctor-patient communication. Experimental results show that the quality of restoration meets clinical needs, and the typical time cost of the method is approximately one second. So the method is both time-saving and user-friendly.

Originality/value
The method provides the possibility to design personalized dental esthetic restoration solutions rapidly.
What effect did the Green Credit Policy have on China's energy or emission intensive firms?
Authors: Zhang Qin , Xu Li , Wang Keying , Shi Xunpeng 
Published: July 2021

PurposeThe role of energy or emission intensive firms face contradictory demands from advancing economic development and environmental improvement and protection and thus require appropriate policy interventions to balance the two needs. China's “Green Credit” policy that restricts loans to energy or emission intensive firms provides an example to study the impact of these kinds of policy intervention.Design/methodology/approachUsing the data of all A-share listed companies in Shanghai and Shenzhen stock exchanges, our paper empirically analyzes the impact of the Green Credit Policy on performance of these energy or emission intensive firms.Findings(1) Using difference-in-difference (DID) and propensity score matching (PSM)-DID method and the dynamic effect method, we found that from 2012 to 2015, the Green Credit Policy had an inhibiting effect on the performance of energy or emission intensive firms. This inhibiting effect was gradually weakened in 2016, and it turned into a positive promoting effect in 2017; (2) The performance's change of these firms around 2015 showed that Green Credit promoted the green transformation and upgrading of these firms; (3) Loans were helpful to the performance of energy or emission intensive firms to some extent, but government subsidies were not significant.Originality/valueThe results suggest that the government, banks and other institutions should dynamically assess the implementation results of the Green Credit Policy on energy or emission intensive firms.
Social business and social innovation: the Brazilian experience
Authors: Comini Graziella Maria , Fischer Rosa Maria , D'Amario Edison Quirino 
Published: July 2021

PurposeThe aim of this article is to contribute to the field of social businesses, particularly considering the dimension of social innovation.Design/methodology/approachThe authors adopted a qualitative approach, whose purpose is to gather in-depth insights into a problem to understand its contextual elements and interrelations. The authors used an exploratory descriptive design and a multiple case study, which allows the identification of similarities and differences in the research subjects. They developed a scale that enables the classification of the operation logic of the social businesses analyzed.FindingsIt became evident that social businesses present a few differences in their modus operandi: those based on a social logic are more concerned with the generation of socio-environmental value, however with small-scale innovation; in contrast, social business guided by a market logic do not intend to generate socio-environmental value in different dimensions and are more concerned with the wider range of their innovations.Research limitations/implicationsThis research analyzed social businesses from a founder and manager perspective and did not comprise all stakeholders. The purpose of this study was not to measure the effective impact generated by innovation, but to understand its potential to generate socio-environmental value.Practical implicationsThe generation of socio-environmental value and the strategies to expand practices of social innovation are associated with the operation logic of social business.Originality/valueThe created scale allowed the classification of social businesses in terms of operation logic (greater emphasis on market or social aspects) and proposes a few dimensions to evaluate a socio-environmental innovation.
The predictive validity of entrance scores and short-term performance for long-term success in engineering education
Authors: Abdelfattah Faisal A. , Obeidat Omar S. , Salahat Yousef A. , BinBakr Maha B. , Al Sultan Adam A. 
Published: July 2021

PurposeThis study examined predictors of cumulative grade point average (GPA) from entrance scores and successive performance during students' academic work in university engineering programs.Design/methodology/approachScores from high school coursework, the General Ability Test and the Achievement Test were examined to determine if these factors and annual successive GPAs were predictors of long-term GPA. The sample consisted of 2,031 students registered in university engineering programs during the 2013–2019 period.FindingsCorrelations were significant between entrance scores and the preparatory year GPA but not with cumulative GPA. Also, correlations were significant between year-1 GPA to year-3 GPA and the graduation GPA. Adjacent year GPA is the better predictor of later GPA. More importantly, GPA at the time of graduation is well predicted by GPAs throughout years of study within engineering programs after controlling for entrance scores. Girls outperform boys in their entrance scores and GPAs. Hence, girls are likely to obtain higher cumulative GPAs.Research limitations/implicationsThe implications of the study findings could help university faculty and administrators to understand the role of current entrance scores in predicting academic achievement of engineering students. In addition, the results could serve as a foundation to review weights of entrance scores for future developments and revisions. The findings of the study are limited to admission data for engineering students during the 2013–2019 period. Other disciplines may show a different pattern of relationships among the studied variables.Practical implicationsThe study findings have useful practical implications for admitting and monitoring student progress at engineering education programs. Results may help program curriculum development specialists and committees in designing admission criteria.Social implicationsAdministrators and faculty members are advised to consider entrance scores when providing counseling and monitoring throughout students' program-year progress. More attention should be devoted to university performance when interest is focused on later or graduation CGPA, with less emphasis on entrance scores.Originality/valueThe existed previous studies explored factors that influence the student performance in engineering programs. This study documents the role of admission criteria and successive GPAs in predicting the student graduation CGPA in engineering programs. Relationships between factors are crucial for engineering program revisions and policymaking.
Rethinking interaction in social distancing times: implications for business-to-business companies
Authors: Runfola Andrea , Milanesi Matilde , Guercini Simone 
Published: July 2021

Purpose
This paper aims to investigate how the COVID-19 pandemic has affected the interaction in a business-to-business (BtoB) setting and the emerging relational dynamics. The COVID-19 pandemic is having a strong impact on BtoB markets in terms of the stop of production, the difficulty of coping with payments, restrictions on the flows of people and goods within national and international markets. The paper discusses that the effects of worldwide lockdowns, social distancing and other related restrictions undermine one of the salient features of business relationships, namely interaction.

Design/methodology/approach
The paper relies on a qualitative interpretivist approach based on the data collected from in-depth interviews with key informants and secondary sources. The fashion industry is taken as an emblematic case, given the relevance of BtoB relationships, especially those between global fashion brands and their suppliers, and the dramatic impact of the pandemic.

Findings
The paper shows four effects in terms of relational dynamics. The freezing effect is the maintaining of interaction at minimum operating levels capable of ensuring survival for both interacting actors. The ripple effect can be conceived as a negative effect of the pandemic related to the weakening of the freezing effects in interactions along the supply chain. The rebound effect is a sudden increase in interactive processes among existing relationships. The vicious effect is a negative effect of the pandemic on the interaction that refers to the decay of existing interaction and their ending.

Originality/value
This study fits into the current period of the COVID-19 pandemic to stress the role of interaction involving people and businesses as a key to restart. The paper suggests managerial implications to respond to the pandemic in the short term and to set the basis for future opportunities.