bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking deep learning methods for predicting CRISPR/Cas9 sgRNA on- and off-target activities
Authors: Zhang Guishan , Luo Ye , Dai Xianhua , Dai Zhiming 
Published: September 2023

Abstract
In silico design of single guide RNA (sgRNA) plays a critical role in clustered regularly interspaced, short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. Continuous efforts are aimed at improving sgRNA design with efficient on-target activity and reduced off-target mutations. In the last 5 years, an increasing number of deep learning-based methods have achieved breakthrough performance in predicting sgRNA on- and off-target activities. Nevertheless, it is worthwhile to systematically evaluate these methods for their predictive abilities. In this review, we conducted a systematic survey on the progress in prediction of on- and off-target editing. We investigated the performances of 10 mainstream deep learning-based on-target predictors using nine public datasets with different sample sizes. We found that in most scenarios, these methods showed superior predictive power on large- and medium-scale datasets than on small-scale datasets. In addition, we performed unbiased experiments to provide in-depth comparison of eight representative approaches for off-target prediction on 12 publicly available datasets with various imbalanced ratios of positive/negative samples. Most methods showed excellent performance on balanced datasets but have much room for improvement on moderate- and severe-imbalanced datasets. This study provides comprehensive perspectives on CRISPR/Cas9 sgRNA on- and off-target activity prediction and improvement for method development.
Structome: a tool for the rapid assembly of datasets for structural phylogenetics
Authors: Malik Ashar J , Langer Desiree , Verma Chandra S , Poole Anthony M , Allison Jane R 
Published: September 2023

Abstract

Summary
Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed that allows users to rapidly identify protein structures similar to a query protein and to assemble datasets useful for structure-based phylogenetics. Structome was created by clustering ∼94% of the structures in RCSB PDB using 90% sequence identity and representing each cluster by a centroid structure. Structure similarity between centroid proteins was calculated, and annotations from PDB, SCOP, and CATH were integrated. To illustrate utility, an H3 histone was used as a query, and results show that the protein structures returned by Structome span both sequence and structural diversity of the histone fold. Additionally, the pre-computed nexus-formatted distance matrix, provided by Structome, enables analysis of evolutionary relationships between proteins not identifiable using searches based on sequence similarity alone. Our results demonstrate that, beginning with a single structure, Structome can be used to rapidly generate a dataset of structural neighbours and allows deep evolutionary history of proteins to be studied.

Availability and Implementation
Structome is available at: https://structome.bii.a-star.edu.sg.
Justifying the Unjustifiable: Russia’s Aggression against Ukraine, International Law, and Carl Schmitt’s “Theory of the Greater Space” (“Großraumtheorie”)
Authors: Hilpold Peter 
Published: September 2023

Abstract
Russia’s aggression against Ukraine has been accompanied by attempts to justify this blatant violation of international law with reference to the accepted exceptions to the prohibition of the use of force. These attempts had to fail from the outset as the necessary preconditions were not given. More pernicious is, however, the endeavor to find a justification in an “alternative” system of international law. The respective arguments echo considerations popular in the first half of the 20th century, such as Carl Schmitt’s “theory of the greater space” and the “theory of encirclement”. To accept a revival of such arguments, even only in part, risks undermining the very basics of modern international law. Ultimately, to allow this “obsession with territory” (Georges Scelle) to unfold would not even be in Russia’s interest as it would deflect from this country’s real economic and societal problems that need urgent action.
Annual wages in the Kingdom of the Two Sicilies from 1800 to 1860 and the beginning of the Italian regional divide
Authors: Fiore Melacrinis Francesco M S 
Published: September 2023

Abstract
This study presents new urban and rural annual wage series for the South of Italy before the unification. The use of annual wages overcomes the intrinsic biases of daily wages and mirrors the effective living standards of unskilled workers making regional comparisons more reliable. The comparisons with existing analogous series for the centre and the north of the country show a divide at the time of Italy’s unification in line with the majoritarian view expressed in earlier studies. However, unexpected convergence trends emerge at the urban level, mostly before 1840. Instead, rural areas consistently displayed divergence that has been worsening since 1850.
Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community
Authors: Leale Alanna , Auxier Ben , Smid Eddy J , Schoustra Sijmen 
Published: September 2023

Abstract
The influence of community diversity, which can be measured at the level of metabolic guilds, on community function is a central question in ecology. Particularly, the long-term temporal dynamic between a community's function and its diversity remains unclear. We investigated the influence of metabolic guild diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types, such as yeast, on community functionality and bacterial community compositions over repeated propagation cycles amounting to ∼100 generations. The starting richness of metabolic guilds had a repeatable effect on bacterial community compositions, metabolic profiles, and acidity. The influence of a single metabolic guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together suggest an unexpected niche division between yeast and bacterial communities and evidence ecological selection on the microbial communities in our system.
Leveraging genomic redundancy to improve inference and alignment of orthologous proteins
Authors: Singleton Marc , Eisen Michael 
Published: September 2023

Abstract
Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work, we implemented several improvements to the traditional methodology that more fully leverage the redundancy of closely related genomes and the organization of their annotations. Two highlights include the application of the more flexible k-clique percolation algorithm for identifying clusters of orthologous proteins and the development of a novel technique for removing poorly supported regions of alignments with a phylogenetic hidden Markov model (phylo-HMM). In making the latter, we wrote a fully documented Python package Homomorph that implements standard HMM algorithms and created a set of tutorials to promote its use by a wide audience. We applied the resulting pipeline to a set of 33 annotated Drosophila genomes, generating 22,813 orthologous groups and 8,566 high-quality alignments.
Using Liquid Chromatography—Isotope Ratio Mass Spectrometry for Detection of Economically Motivated Adulteration of Maple Syrup
Authors: Mantha Madhavi , Kubachka Kevin M , Urban John R , Brueggemeyer Jana L , Kaine Lisa A , Patton Reagan A 
Published: September 2023

Abstract

Background
Maple syrup is a sought-after commodity, and used as a condiment and a sweetener. Also, it is an active target of economically motivated adulteration (EMA), similar to other foods such as lemon juice and honey.

Objective
This study is aimed to detect low cost sugar adulteration in maple syrup via an internal standard method using malic acid through solid-phase extraction (SPE) and LC with isotope ratio mass spectrometric detection (LC–IRMS).

Methods
In this work, an optimized SPE sample preparation procedure was used for the isolation of organic acids from maple syrup. Using LC–IRMS, malic acid was separated from other organic acids and the δ13C value of malic acid was determined. Eleven maple syrup samples, domestic or imported from Canada, were evaluated for 13C/12C ratios (δ13C values) using combustion module—cavity ring down spectrometry (CM-CRDS) and compared to the δ13C values obtained from well-established elemental analyzer–isotope ratio mass spectrometry (EA–IRMS) methods. The δ13C values of isolated malic acid analyzed by SPE–LC–IRMS were used as internal standards and compared to the δ13C values of bulk maple syrup; difference (δ13Csugars − δ13Cmalic acid) values greater than 3.6‰ are indicative of low-cost sugar adulteration.

Results
Overall, the results obtained from SPE–LC–IRMS provided a faster, novel analysis approach for determining low-cost sugar adulteration in maple syrup for regulatory purposes. This method also provided lower detectable limits of adulteration versus current literature reports using bulk analysis and comparable detection limits to Tremblay and co-workers who utilized an internal standard method.

Conclusion
SPE–LC–IRMS is a robust method that can be used for detecting adulteration in maple syrup samples for regulatory purposes.

Highlights
SPE-LC-IRMS is a faster, novel analysis approach for determining C4 adulteration in maple syrup with lower detection limits.
Integrating single-cell and spatial transcriptomics reveals endoplasmic reticulum stress-related CAF subpopulations associated with chordoma progression
Authors: Zhang Tao-Lan , Xia Chao , Zheng Bo-Wen , Hu Hai-Hong , Jiang Ling-Xiang , Escobar David , Zheng Bo-Yv , Chen Tian-Dong , Li Jing , Lv Guo-Hua , Huang Wei , Yan Yi-Guo , Zou Ming-Xiang 
Published: September 2023

Abstract

Background
With cancer-associated fibroblasts (CAFs) as the main cell type, the rich myxoid stromal components in chordoma tissues may likely contribute to its development and progression.

Methods
Single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, bulk RNA-seq, and multiplexed quantitative immunofluorescence (QIF) were used to dissect the heterogeneity, spatial distribution, and clinical implication of CAFs in chordoma.

Results
We sequenced here 72 097 single cells from 3 primary and 3 recurrent tumor samples, as well as 3 nucleus pulposus samples as controls using scRNA-seq. We identified a unique cluster of CAF in recurrent tumors that highly expressed hypoxic genes and was functionally enriched in endoplasmic reticulum stress (ERS). Pseudotime trajectory and cell communication analyses showed that this ERS-CAF subpopulation originated from normal fibroblasts and widely interacted with tumoral and immune cells. Analyzing the bulk RNA-seq data from 126 patients, we found that the ERS-CAF signature score was associated with the invasion and poor prognosis of chordoma. By integrating the results of scRNA-seq with spatial transcriptomics, we demonstrated the existence of ERS-CAF in chordoma tissues and revealed that this CAF subtype displayed the most proximity to its surrounding tumor cells. In subsequent QIF validation involving 105 additional patients, we confirmed that ERS-CAF was abundant in the chordoma microenvironment and located close to tumor cells. Furthermore, both ERS-CAF density and its distance to tumor cells were correlated with tumor malignant phenotype and adverse patient outcomes.

Conclusions
These findings depict the CAF landscape for chordoma and may provide insights into the development of novel treatment approaches.
The value of arterial spin labelling (ASL) perfusion MRI in the assessment of post-treatment progression in adult glioma: A systematic review and meta-analysis.
Authors: Alsulami Tamadur A , Hyare Harpreet , Thomas David L , Golay Xavier 
Published: September 2023

Abstract

Background
The distinction between viable tumor and therapy-induced changes is crucial for the clinical management of patients with gliomas. This study aims to quantitatively assess the efficacy of arterial spin labeling (ASL) biomarkers, including relative cerebral blood flow (rCBF) and absolute cerebral blood flow (CBF), for the discrimination of progressive disease (PD) and treatment-related effects.

Methods
Eight articles were included in the synthesis after searching the literature systematically. Data have been extracted and a meta-analysis using the random-effect model was subsequently carried out. Diagnostic accuracy assessment was also performed.

Results
This study revealed that there is a significant difference in perfusion measurements between groups with PD and therapy-induced changes. The rCBF yielded a standardized mean difference (SMD) of 1.25 [95% CI 0.75, 1.75] (p &lt; .00001). The maximum perfusion indices (rCBFmax and CBFmax) both showed equivalent discriminatory ability, with SMD of 1.35 [95% CI 0.78, 1.91] (p &lt; .00001) and 1.56 [95% CI 0.79, 2.33] (p &lt; .0001), respectively. Similarly, accuracy estimates were comparable among ASL-derived metrices. Pooled sensitivities [95% CI] were 0.85 [0.67, 0.94], 0.88 [0.71, 0.96], and 0.93 [0.73, 0.98], and pooled specificities [95% CI] were 0.83 [0.71, 0.91], 0.83 [0.67, 0.92], 0.84 [0.67, 0.93], for rCBF, rCBFmax and CBFmax, respectively. Corresponding HSROC area under curve (AUC) [95% CI] were 0.90 [0.87, 0.92], 0.92 [0.89, 0.94], and 0.93 [0.90, 0.95].

Conclusion
These results suggest that ASL quantitative biomarkers, particularly rCBFmax and CBFmax, have the potential to discriminate between glioma progression and therapy-induced changes.
Anti-EGFR Antibodies in the Management of Advanced Colorectal Cancer
Authors: Kasi Pashtoon Murtaza , Afable Manuel Geroy , Herting Cameron , Lukanowski Mariusz , Jin Zhaohui 
Published: September 2023

Abstract
Colorectal cancer is the third most common cancer worldwide, and incidence is rising in younger individuals. Anti-EGFR antibodies, including cetuximab and panitumumab, have been incorporated into standard-of-care practice for patients with advanced disease. Herein, we review the molecular characteristics of these agents and the trials that lead to their approvals. Further, we discuss clinical implications of data regarding biomarkers that dictate treatment selection, different dosing strategies, and side effect management. Finally, we look towards the future and describe contexts in which these agents are currently being investigated clinically with a focus on combinations with MAPK-targeted therapies and immunotherapy. Overall, this review provides historical context, current clinical usage, and future directions for anti-EGFR antibodies in advanced colorectal cancer.
Introduction
Authors: Huddy Leonie , Sears David O. , Levy Jack S. , Jerit Jennifer 
Published: September 2023

Abstract
This chapter serves as an introduction to the Oxford Handbook of Political Psychology. It provides an overview of the field, focusing on key theories, topics, and empirical approaches. The chapter begins by defining political psychology as the behavior of individuals within a specific political system. This is followed by a lengthy discussion on the major intellectual underpinnings of political psychology in biopolitics, personality, cognitive and affective psychology, and intergroup relations. These approaches are often contrasted with a rational approach to human behavior and help to explain why human political behavior often falls short of the democratic ideal. The chapter concludes with a discussion of the volume’s organization and an overview of its specific chapters.
The Psychological and Social Foundations of Ideological Belief Systems
Authors: Federico Christopher M. , Malka Ariel 
Published: September 2023

Abstract
Defining ideology as a system of functionally interconnected political attitudes and beliefs, we review evidence concerning (1) the nature and origins of ideology in mass publics and (2) the social and interpersonal nature of the motives underlying ideological coherence. One key conclusion that we draw is that the links between psychological attributes and subsets of ideological attitudes sometimes appear to be organic and functional but other times appear to be conditional on how the relevant attitudes are packaged with other attitudes into socially constructed ideologies. A second key conclusion is that the social motives that induce citizens to pull diverse attitudes into ideological alignment may also, in polarized contexts, induce people to adopt non-political identities and self-perceptions that are congruent with ideological stereotypes. We recommend a focus on the implications of these processes for polarization and democratic stability.
Personality Approaches to Political Behavior
Authors: Bakker Bert N. 
Published: September 2023

Abstract
Whether personality is relevant for political behavior is a question that has a long tradition in political psychology. This chapter provides a comprehensive overview of the state-the-art evidence on the association between personality and political behavior of citizens and politicians. In particular, this chapter focuses on the association between personality and political ideology, voting behavior, political loyalties, political participation, political engagement, and news consumption. The chapter concludes by outlining a research agenda for the next generation of research with attention to the assumed causal effects of personality on political “outcomes.” Future research is also encouraged to adopt open science practices that will increase transparency, replicability, and ultimately the field’s credibility.
The Gaze from Below
Authors: Pérez Efrén O. , Vicuña Bianca V. 
Published: September 2023

Abstract
This chapter grapples with the political psychology of minority status by focusing on the attitudes and actions expressed by groups who are subordinated based on race, gender, sexual orientation, or other stigmatized attributes. We call on political psychologists to develop more unified theories that study the growing array of subordinated groups, with the goal of isolating the psychological mechanisms behind their politics. We model one response to this call by drawing on social identity theory and its offshoots to illuminate some of the cognitive and affective roots of minority status and its implications for inter- and intra-group behavior in politics. We discuss the micro-foundations of minority group formation, the structural roots of minority status, and, most critically, the connections between minority status and political attitudes and behavior. We conclude by discussing three broad areas where scholars can use these insights to (re)invigorate debates in studies of minority group politics.
Social Movements and the Dynamics of Collective Action
Authors: van Stekelenburg Jacquelien , Gaidytė Teodora 
Published: September 2023

Abstract
In this chapter, we propose a framework to study the political psychology of collective action participation. We first introduce the dynamics of collective action, which are decomposed into the dynamics of demand, supply, and mobilization. The dynamics of demand are about people and their motives. The dynamics of supply are about organizations and their appeals. The dynamics of mobilization concern the convergence of demand and supply. In the mobilization section, we specifically consider how classic social capital factors such as social trust and embeddedness in organizations and more recent developments of virtualization influence who does or does not participate in protest activity. Subsequently we discuss how the social and political psychological processes of politicization, polarization, and radicalization hinder or spur participation in collective action. Finally, we show how perceptions of the political context influence the decision to protest or not, focusing on socio-economic, political, and cultural contextual factors. In doing so, we provide an overview of what social and political psychology, combined with other disciplines, has to offer to the study of social movements and collective action, where we stand, and where we think the lacunas are. We end with a discussion of the challenges by those who study social movement participation.
Migration and Multiculturalism
Authors: Green Eva G. T. , Staerklé Christian 
Published: September 2023

Abstract
This chapter provides an overview of research on migration and multiculturalism from the perspective of political psychology. The first part outlines some historical benchmarks of modern migration and briefly presents two key notions of a psychological approach to migration—assimilation and multiculturalism—in their historical context. The second part summarizes research on the psychological dynamics involved in the migrant experience, in particular the interactionist and complex nature of migrant identities, acculturation in receiving societies, and intergroup approaches to acculturation and multiculturalism. The third part analyzes the role of threat regarding immigrants and immigration in the reactions of majority populations in receiving societies. The fourth part presents multilevel research on the effects of contextual factors on attitudes toward immigration held by national majority groups. In the conclusion, ongoing and future challenges for research on migration and multiculturalism are outlined.
Emotion and Political Psychology
Authors: Kushner Gadarian Shana , Brader Ted 
Published: September 2023

Abstract
For many years political psychology and scholars of politics in general neglected the study of emotion. Whatever the reasons for neglect, it no longer holds true. Emotions are best understood as reactions to signals about the significance that circumstances hold for an individual’s goals and well-being. The source of those signals can be external or internal. The chapter reviews major theoretical approaches and questions of methodology in the study of emotion. The remainder of the chapter focuses heavily on research into the causes of politically relevant emotions and their consequences for political behavior across a wide variety of settings. The chapter also draws attention to the ways in which elite actors attempt to manipulate emotions of citizens to further their political goals.
Foreign Policy Decision-Making The Psychological Dimension
Authors: Levy Jack S. 
Published: September 2023

Abstract
This chapter combines a general introduction to psychological approaches to international relations, with a particular focus on models of judgment and decision-making in foreign policy. It surveys the leading concepts, theories, findings, and methodologies associated with the major psychological approaches to foreign policy, and identifies questions that require further exploration. After an examination of the growing influence of political psychology in the IR field, the chapter turns to the beliefs and images of political leaders and the traits and prior experiences that shape them. It explores theories of information processing and belief change, including cognitive biases, motivated reasoning, and other impediments to rational Bayesian updating. The chapter then surveys a number of alternative models of decision-making. These include prospect theory – with its key concepts of reference dependence, loss aversion, and variable risk orientation – and models of intertemporal choice, temporal construal, groupthink, and crisis decision-making.