bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces
Authors: Wang Li , Josephs Emily B , Lee Kristin M , Roberts Lucas M , Rellán-Álvarez Rubén , Ross-Ibarra Jeffrey , Hufford Matthew B 
Published: April 2021

AbstractConvergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.
Role of Sex-Concordant Gene Expression in the Coevolution of Exaggerated Male and Female Genitalia in a Beetle Group
Authors: Nomura Shota , Fujisawa Tomochika , Sota Teiji 
Published: April 2021

Abstract
Some sexual traits, including genitalia, have undergone coevolutionary diversification toward exaggerated states in both sexes among closely related species, but the underlying genetic mechanisms that allow correlated character evolution between the sexes are poorly understood. Here, we studied interspecific differences in gene expression timing profiles involved in the correlated evolution of corresponding male and female genital parts in three species of ground beetle in Carabus (Ohomopterus). The male and female genital parts maintain morphological matching, whereas large interspecific variation in genital part size has occurred in the genital coevolution between the sexes toward exaggeration. We analyzed differences in gene expression involved in the interspecific differences in genital morphology using whole transcriptome data from genital tissues during genital morphogenesis. We found that the gene expression variance attributed to sex was negligible for the majority of differentially expressed genes, thus exhibiting sex-concordant expression, although large variances were attributed to stage and species differences. For each sex, we obtained co-expression gene networks and hub genes from differentially expressed genes between species that might be involved in interspecific differences in genital morphology. These gene networks were common to both sexes, and both sex-discordant and sex-concordant gene expression were likely involved in species-specific genital morphology. In particular, the gene expression related to exaggerated genital size showed no significant intersexual differences, implying that the genital sizes in both sexes are controlled by the same gene network with sex-concordant expression patterns, thereby facilitating the coevolution of exaggerated genitalia between the sexes while maintaining intersexual matching.
Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity
Authors: Lin Sheng , Chen Hua , Chen Zimin , Yang Fanli , Ye Fei , Zheng Yue , Yang Jing , Lin Xi , Sun Honglu , Wang Lingling , Wen Ao , Dong Haohao , Xiao Qingjie , Deng Dong , Cao Yu , Lu Guangwen 
Published: April 2021

Abstract
The emergence of SARS-CoV-2 infection has posed unprecedented threat to global public health. The virus-encoded non-structural protein 14 (nsp14) is a bi-functional enzyme consisting of an exoribonuclease (ExoN) domain and a methyltransferase (MTase) domain and plays a pivotal role in viral replication. Here, we report the structure of SARS-CoV-2 nsp14-ExoN domain bound to its co-factor nsp10 and show that, compared to the SARS-CoV nsp10/nsp14-full-length complex, SARS-CoV-2 nsp14-ExoN retains an integral exoribonuclease fold and preserves an active configuration in the catalytic center. Analysis of the nsp10/nsp14-ExoN interface reveals a footprint in nsp10 extensively overlapping with that observed in the nsp10/nsp16 structure. A marked difference in the co-factor when engaging nsp14 and nsp16 lies in helix-α1′, which is further experimentally ascertained to be involved in nsp14-binding but not in nsp16-engagement. Finally, we also show that nsp10/nsp14-ExoN is enzymatically active despite the absence of nsp14-MTase domain. These data demonstrate that SARS-CoV-2 nsp10/nsp14-ExoN functions as an exoribonuclease with both structural and functional integrity.
ModFOLD8: accurate global and local quality estimates for 3D protein models
Authors: McGuffin Liam J , Aldowsari Fahd M F , Alharbi Shuaa M A , Adiyaman Recep 
Published: April 2021

AbstractMethods for estimating the quality of 3D models of proteins are vital tools for driving the acceptance and utility of predicted tertiary structures by the wider bioscience community. Here we describe the significant major updates to ModFOLD, which has maintained its position as a leading server for the prediction of global and local quality of 3D protein models, over the past decade (&gt;20 000 unique external users). ModFOLD8 is the latest version of the server, which combines the strengths of multiple pure-single and quasi-single model methods. Improvements have been made to the web server interface and there has been successive increases in prediction accuracy, which were achieved through integration of newly developed scoring methods and advanced deep learning-based residue contact predictions. Each version of the ModFOLD server has been independently blind tested in the biennial CASP experiments, as well as being continuously evaluated via the CAMEO project. In CASP13 and CASP14, the ModFOLD7 and ModFOLD8 variants ranked among the top 10 quality estimation methods according to almost every official analysis. Prior to CASP14, ModFOLD8 was also applied for the evaluation of SARS-CoV-2 protein models as part of CASP Commons 2020 initiative. The ModFOLD8 server is freely available at: https://www.reading.ac.uk/bioinf/ModFOLD/.
CeLaVi: an interactive cell lineage visualization tool
Authors: Salvador-Martínez Irepan , Grillo Marco , Averof Michalis , Telford Maximilian J 
Published: April 2021

Abstract
Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking cell divisions using live microscopy, or by deducing the history of cells using molecular recorders. A cell lineage on its own, however, is simply a description of cell divisions as branching events. A major goal of current research is to integrate this description of cell relationships with information about the spatial distribution and identities of the cells those divisions produce. Visualizing, interpreting and exploring these complex data in an intuitive manner requires the development of new tools. Here we present CeLaVi, a web-based visualization tool that allows users to navigate and interact with a representation of cell lineages, whilst simultaneously visualizing the spatial distribution, identities and properties of cells. CeLaVi’s principal functions include the ability to explore and manipulate the cell lineage tree; to visualise the spatial distribution of cell clones at different depths of the tree; to colour cells in the 3D viewer based on lineage relationships; to visualise various cell qualities on the 3D viewer (e.g. gene expression, cell type) and to annotate selected cells/clones. All these capabilities are demonstrated with four different example data sets. CeLaVi is available at http://www.celavi.pro.
SynLeGG: analysis and visualization of multiomics data for discovery of cancer ‘Achilles Heels’ and gene function relationships
Authors: Wappett Mark , Harris Adam , Lubbock Alexander L R , Lobb Ian , McDade Simon , Overton Ian M 
Published: April 2021

AbstractAchilles’ heel relationships arise when the status of one gene exposes a cell's vulnerability to perturbation of a second gene, such as chemical inhibition, providing therapeutic opportunities for precision oncology. SynLeGG (www.overton-lab.uk/synlegg) identifies and visualizes mutually exclusive loss signatures in ‘omics data to enable discovery of genetic dependency relationships (GDRs) across 783 cancer cell lines and 30 tissues. While there is significant focus on genetic approaches, transcriptome data has advantages for investigation of GDRs and remains relatively underexplored. SynLeGG depends upon the MultiSEp algorithm for unsupervised assignment of cell lines into gene expression clusters, which provide the basis for analysis of CRISPR scores and mutational status in order to propose candidate GDRs. Benchmarking against SynLethDB demonstrates favourable performance for MultiSEp against competing approaches, finding significantly higher area under the Receiver Operator Characteristic curve and between 2.8-fold to 8.5-fold greater coverage. In addition to pan-cancer analysis, SynLeGG offers investigation of tissue-specific GDRs and recovers established relationships, including synthetic lethality for SMARCA2 with SMARCA4. Proteomics, Gene Ontology, protein-protein interactions and paralogue information are provided to assist interpretation and candidate drug target prioritization. SynLeGG predictions are significantly enriched in dependencies validated by a recently published CRISPR screen.
Single-cell transcriptome and genome analyses of pituitary neuroendocrine tumors
Authors: Cui Yueli , Li Chao , Jiang Zhenhuan , Zhang Shu , Li Qingqing , Liu Xixi , Zhou Yuan , Li Runting , Wei Liudong , Li Lianwang , Zhang Qi , Wen Lu , Tang Fuchou , Zhou Dabiao 
Published: April 2021

Abstract

Background
Pituitary neuroendocrine tumors (PitNETs) are the second most common intracranial tumor. We lacked a comprehensive understanding of the pathogenesis and heterogeneity of these tumors.

Methods
We performed high-precision single-cell RNA sequencing for 2679 individual cells obtained from 23 surgically resected samples of the major subtypes of PitNETs from 21 patients. We also performed single-cell multi-omics sequencing for 238 cells from 5 patients.

Results
Unsupervised clustering analysis distinguished all tumor subtypes, which was in accordance with the classification based on immunohistochemistry and provided additional information. We identified 3 normal endocrine cell types: somatotrophs, lactotrophs, and gonadotrophs. Comparisons of tumor and matched normal cells showed that differentially expressed genes of gonadotroph tumors were predominantly downregulated, while those of somatotroph and lactotroph tumors were mainly upregulated. We identified novel tumor-related genes, such as AMIGO2, ZFP36, BTG1, and DLG5. Tumors expressing multiple hormone genes showed little transcriptomic heterogeneity. Furthermore, single-cell multi-omics analysis demonstrated that the tumor had a relatively uniform pattern of genome with slight heterogeneity in copy number variations.

Conclusions
Our single-cell transcriptome and single-cell multi-omics analyses provide novel insights into the characteristics and heterogeneity of these complex neoplasms for the identification of biomarkers and therapeutic targets.
Household saving, health, and healthcare utilization in Japan
Authors: Alzuabi Raslan , Brown Sarah , Gray Daniel , Harris Mark N , Spencer Christopher 
Published: April 2021

AbstractWe explore the effects of health and healthcare utilization on household saving and financial portfolios using data from the Japanese Household Panel Survey and the Keio Household Panel Survey. Poor psychological well-being is found to be associated with lower levels of savings and smaller financial portfolios, whereas associations with poor physical health are largely absent. Significantly, our findings do not support the hypothesis that poorer physical health is associated with savings accumulation. In contrast, healthcare utilization in the form of hospital visits, hospitalization, and health screening is associated with greater savings and larger financial portfolios. This suggests that healthcare-based incentives to accumulate savings and financial wealth are related to channels associated with investment in health.
A Written Constitution: A Case Not Made
Authors: Murkens Jo Eric Khushal 
Published: April 2021

Abstract
Whether the UK needs a written constitution is a staple of British constitutional debates. Over the years, the fault lines have shifted from whether to incorporate a Bill of Rights to much deeper disagreement with respect to the people and the central power of the state. In this article I neither endorse the conservative case against a written constitution nor argue for the existing constitution to be codified. Instead, I first assess the content of various proposals for a written constitution. I then problematise the process of constitution making by asking not whether the UK constitution should be codified, but by relating the constitution to the people as the authors and to the state as its object.
Intraoperative Seizure Detection During Active Resection of Glioblastoma Through a Novel Hollow Circular Electrocorticography Array
Authors: Domingo Ricardo A , Vivas-Buitrago Tito , De Biase Gaetano , Middlebrooks Erik H , Bechtle Perry S , Sabsevitz David S , Quiñones-Hinojosa Alfredo , Tatum William O 
Published: April 2021

Abstract

BACKGROUND AND IMPORTANCE
Data supporting the use of electrocorticography (ECoG) monitoring during electrical stimulation in awake craniotomies for resection of supratentorial neoplasms is robust, but its applicability during active resection is often limited by the inability to keep the array in place. Given the known survival benefit of gross total resection in glioma surgery, novel approaches to surgical monitoring are warranted to maximize safe resection and optimize surgical outcomes in patients with glioblastoma.

CLINICAL PRESENTATION
A 68-yr-old right-handed woman presented to the emergency department with confusion. Imaging studies revealed a bifrontal intra-axial brain lesion. She underwent a left-sided awake craniotomy procedure with cortical and subcortical mapping. During surgical resection, multiple electrographic seizures were detected on continuous ECoG monitoring with a customized 22-channel high-density hollow circular array. She remained without clinical evidence of seizures at 3 mo after surgery.

CONCLUSION
We report a unique case of serial electrographic seizures detected during continuous intraoperative ECoG monitoring during active surgical resection of a glioblastoma using a novel circular hollow array during an awake craniotomy. The use of continuous ECoG monitoring during active resection may provide additional data, with potential influence in outcomes for patients undergoing resection of high-grade glial neoplasms.
Depth Electrode Guided Anterior Insulectomy: 2-Dimensional Operative Video
Authors: Mandel Mauricio , Lamsam Layton , Farooque Pue , Spencer Dennis , Damisah Eyiyemisi 
Published: April 2021

Abstract
The insula is well established as an epileptogenic area.
1
Insular epilepsy surgery demands precise anatomic knowledge
2-4
and tailored removal of the epileptic zone with careful neuromonitoring.
5
We present an operative video illustrating an intracranial electroencephalogram (EEG) depth electrode guided anterior insulectomy.
We report a 17-yr-old right-handed woman with a 4-yr history of medically refractory epilepsy. The patient reported daily nocturnal ictal vocalization preceded by an indescribable feeling. Preoperative evaluation was suggestive of a right frontal-temporal onset, but the noninvasive results were discordant. She underwent a combined intracranial EEG study with a frontal-parietal grid, with strips and depth electrodes covering the entire right hemisphere. Epileptiform activity was observed in contact 6 of the anterior insula electrode. The patient consented to the procedure and to the publication of her images.
A right anterior insulectomy was performed. First, a portion of the frontal operculum was resected and neuronavigation was used for the initial insula localization. However, due to unreliable neuronavigation (ie, brain shift), the medial and anterior borders of the insular resection were guided by the depth electrode reference. The patient was discharged 3 d after surgery with no neurological deficits and remains seizure free.
We demonstrate that depth electrode guided insular surgery is a safe and precise technique, leading to an optimal outcome.
Fair Housing
Authors: Korver-Glenn Elizabeth 
Published: April 2021

Abstract
By regularly acting out racialized organizational routines and interpreting ostensibly neutral routines through the lens of racist ideas comprising the racist market rubric, real estate professionals separate people and neighborhoods by race. In doing so, these race and racism brokers ensure that the most housing market opportunities and resources are reserved for White individuals and neighborhoods. Their actions exclude individuals and neighborhoods of color from such opportunities. This chapter describes the author’s policy recommendations for interrupting such housing market racism. These recommendations are directed toward governmental, real estate, and fair housing agencies and organizations rather than toward individual professionals. Broadly, the chapter’s recommendations focus on how to monitor housing market professionals (particularly housing developers and appraisers), prosecute violations of fair housing law, and directly intervene in organizational routines that implicitly or explicitly enable racist interpretations of individuals and neighborhoods. These recommendations return to the fundamental point of this book: Racial segregation is not a natural or neutral feature of urban landscapes.
Introduction
Authors: Elfring Tom , Klyver Kim , van Burg Elco 
Published: April 2021

Abstract
This chapter introduces the entrepreneurship-as-networking perspective. The authors argue that a focus on the social-interactive aspects and action orientation of entrepreneurship is needed. They contribute an integrated account in which the entrepreneur’s agency is combined with a greater emphasis on the social environment. The importance of social relations and the associated interactions between entrepreneurs and their environment give insight into key entrepreneurial processes. These are (a) the origins of opportunities, (b) how entrepreneurs access resources and subsequently mobilize and deploy them, and (c) the ways entrepreneurs build legitimacy, facilitating them to act on perceived new combinations and thereby exploit their potential.
Legitimizing through entrepreneurial networking
Authors: Elfring Tom , Klyver Kim , van Burg Elco 
Published: April 2021

Abstract
This chapter presents an entrepreneurship-as-networking perspective on new venture legitimacy. New ventures are more likely to survive and perform when various audiences and stakeholders perceive their activities as legitimate. This is especially true when new ventures are pursuing something novel and innovative. Therefore, it is crucial for new ventures to gain legitimacy. In this chapter, viewing legitimacy predominantly as a process and concurrently distinguishing processes related to types of legitimacy, the authors theorize how entrepreneurs incorporate various audiences and their judgments into their active networking, thus shaping the legitimacy process. The interactions between various audiences and the entrepreneur take form through different legitimacy strategies—that is, identity-seeking strategies, associative strategies, and networking strategies—resulting in legitimacy judgments by audiences. Under conditions of high uncertainty, the legitimacy judgment as the outcome of the social interactions is co-created by audiences and entrepreneurs and is diffused outside local networks to the broader society through distributed brokerage.
Distributive and Relational Equality
Authors: Schemmel Christian 
Published: April 2021

Abstract
This chapter develops the expressive perspective on justice on which the overall argument of the book for liberal relational equality is based. It shows that the way social and political institutions treat individuals and groups is of irreducible importance to justice, and that this consideration cannot be satisfactorily accounted for by more traditional distributive theories of egalitarian justice, which focus on according individuals equal shares of justice-relevant goods; paradigmatically goods such as resources, (opportunity for welfare), or basic capabilities. It makes a case for the special relevance for justice of the attitudes expressed by institutions in the treatment of those subject to their power, as that expression constitutes its meaning. That meaning is particularly salient where the treatment gives rise to, or shores up, power and status hierarchies between different individuals and groups.
Social Status, Self-Respect, and Opportunity
Authors: Schemmel Christian 
Published: April 2021

Abstract
This chapter extends the requirements of liberal relational egalitarianism by way of an account of esteem-based norms of social status, analysing three kinds of injustices that such norms can engender or constitute. First, they can enable or aggravate domination. Second, they can harm self-respect. However, a closer analysis of self-respect and its crucial role for individual autonomy reveals that not all inegalitarian status norms can be classified as threats to self-respect without threatening precisely that role. Third, they can be unjust simply by depriving individuals of significant social opportunities, because losing such opportunities due to norm-coordinated, self-sustaining disesteem by others is a threat to one’s equal standing in social cooperation not present when they are foreclosed in other ways. This is an independent rationale for combating these norms which is fully accessible to liberals, and does better at capturing the distinct evil of status hierarchy than rival views.
Parents’ Expectations of Religious Congregations
Authors: Smith Christian , Adamczyk Amy 
Published: April 2021

Abstract
Church leaders, youth ministers, and volunteers are likely curious about the extent to which parents find congregations useful in transmitting religious beliefs and behaviors. This chapter explores how parents use religious congregations to transmit religious belief. The chapter discusses why parents tend to feel that they, rather than their congregations, are primarily responsible for passing on religious faith. Many parents select their congregations for fairly practical reasons, they have a lot of confidence in their own understanding of religion, and they want to be involved in all aspects of their child’s life, including religious development. This chapter also unpacks what parents see as the most valuable contributions that congregations provide for their children. These include the congregation’s role in providing religious education, making religion fun for their children, and transmitting cultural traditions.