bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches
Authors: Kosakovsky Pond Sergei L , Wisotsky Sadie R , Escalante Ananias , Magalis Brittany Rife , Weaver Steven 
Published: October 2020

AbstractA number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.
Phosphorylation of Msx1 promotes cell proliferation through the Fgf9/18-MAPK signaling pathway during embryonic limb development
Authors: Yang Yenan , Zhu Xiaoli , Jia Xiang , Hou Wanwan , Zhou Guoqiang , Ma Zhangjing , Yu Bin , Pi Yan , Zhang Xumin , Wang Jingqiang , Wang Gang 
Published: October 2020

AbstractMsh homeobox (Msx) is a subclass of homeobox transcriptional regulators that control cell lineage development, including the early stage of vertebrate limb development, although the underlying mechanisms are not clear. Here, we demonstrate that Msx1 promotes the proliferation of myoblasts and mesenchymal stem cells (MSCs) by enhancing mitogen-activated protein kinase (MAPK) signaling. Msx1 directly binds to and upregulates the expression of fibroblast growth factor 9 (Fgf9) and Fgf18. Accordingly, knockdown or antibody neutralization of Fgf9/18 inhibits Msx1-activated extracellular signal-regulated kinase 1/2 (Erk1/2) phosphorylation. Mechanistically, we determined that the phosphorylation of Msx1 at Ser136 is critical for enhancing Fgf9 and Fgf18 expression and cell proliferation, and cyclin-dependent kinase 1 (CDK1) is apparently responsible for Ser136 phosphorylation. Furthermore, mesenchymal deletion of Msx1/2 results in decreased Fgf9 and Fgf18 expression and Erk1/2 phosphorylation, which leads to serious defects in limb development in mice. Collectively, our findings established an important function of the Msx1-Fgf-MAPK signaling axis in promoting cell proliferation, thus providing a new mechanistic insight into limb development.
KinaseMD: kinase mutations and drug response database
Authors: Hu Ruifeng , Xu Haodong , Jia Peilin , Zhao Zhongming 
Published: October 2020

Abstract
Mutations in kinases are abundant and critical to study signaling pathways and regulatory roles in human disease, especially in cancer. Somatic mutations in kinase genes can affect drug treatment, both sensitivity and resistance, to clinically used kinase inhibitors. Here, we present a newly constructed database, KinaseMD (kinase mutations and drug response), to structurally and functionally annotate kinase mutations. KinaseMD integrates 679 374 somatic mutations, 251 522 network-rewiring events, and 390 460 drug response records curated from various sources for 547 kinases. We uniquely annotate the mutations and kinase inhibitor response in four types of protein substructures (gatekeeper, A-loop, G-loop and αC-helix) that are linked to kinase inhibitor resistance in literature. In addition, we annotate functional mutations that may rewire kinase regulatory network and report four phosphorylation signals (gain, loss, up-regulation and down-regulation). Overall, KinaseMD provides the most updated information on mutations, unique annotations of drug response especially drug resistance and functional sites of kinases. KinaseMD is accessible at https://bioinfo.uth.edu/kmd/, having functions for searching, browsing and downloading data. To our knowledge, there has been no systematic annotation of these structural mutations linking to kinase inhibitor response. In summary, KinaseMD is a centralized database for kinase mutations and drug response.
ConjuPepDB: a database of peptide–drug conjugates
Authors: Balogh Balázs , Ivánczi Márton , Nizami Bilal , Beke-Somfai Tamás , Mándity István M 
Published: October 2020

Abstract
Peptide–drug conjugates are organic molecules composed of (i) a small drug molecule, (ii) a peptide and (iii) a linker. The drug molecule is mandatory for the biological action, however, its efficacy can be enhanced by targeted delivery, which often also reduces unwanted side effects. For site-specificity the peptide part is mainly responsible. The linker attaches chemically the drug to the peptide, but it could also be biodegradable which ensures controlled liberation of the small drug. Despite the importance of the field, there is no public comprehensive database on these species. Herein we describe ConjuPepBD, a freely available, fully annotated and manually curated database of peptide drug conjugates. ConjuPepDB contains basic information about the entries, e.g. CAS number. Furthermore, it also implies their biomedical application and the type of chemical conjugation employed. It covers more than 1600 conjugates from ∼230 publications. The web-interface is user-friendly, intuitive, and useable on several devices, e.g. phones, tablets, PCs. The webpage allows the user to search for content using numerous criteria, chemical structure and a help page is also provided. Besides giving quick insight for newcomers, ConjuPepDB is hoped to be also helpful for researchers from various related fields. The database is accessible at: https://conjupepdb.ttk.hu/.
Potential benefits of dietary seaweeds as protection against COVID-19
Authors: Tamama Kenichi 
Published: October 2020

Abstract
The coronavirus disease 2019 (COVID-19) pandemic in Japan is not as disastrous as it is in other Western countries, possibly because of certain lifestyle factors. One such factor might be the seaweed-rich diet commonly consumed in Japan. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which binds to angiotensin-converting enzyme 2 (ACE2) on the cell surface and downregulates ACE2, likely elevating the ratio of angiotensin-converting enzyme (ACE) to ACE2. The overreaction of the immune system, combined with the cytokine storm and ACE dominance, is purported to cause the condition of COVID-19 patients to deteriorate rapidly. Dietary seaweeds contain numerous components, including ACE inhibitory peptides, soluble dietary fibers (eg, fucoidan, porphyran), omega-3 fatty acids, fucoxanthin, fucosterol, vitamins D3 and B12, and phlorotannins. These components exert antioxidant, anti-inflammatory, and antiviral effects directly as well as indirectly through prebiotic effects. It is possible that ACE inhibitory components could minimize the ACE dominance caused by SARS-CoV-2 infection. Thus, dietary seaweeds might confer protection against COVID-19 through multiple mechanisms. Overconsumption of seaweeds should be avoided, however, as seaweeds contain high levels of iodine.
Introduction to Israeli Politics and Society
Authors: Hazan Reuven Y. , Dowty Alan , Hofnung Menachem , Rahat Gideon 
Published: October 2020

Abstract
Few countries receive as much attention as Israel and are at the same time as misunderstood. The Oxford Handbook of Israeli Politics and Society brings together the leading Israeli and international figures in order to offer the most wide-ranging treatment available of an intriguing country. This chapter tackles the issue of Israeli exceptionalism, arguing against those who shy away from assessing Israel in a comparative perspective—whether for reasons of complexity or because of a political agenda. Israel is indeed different, for many reasons, but it possesses enough similarities in its democratic political institutions and social makeup that to truly understand the country, scholars need to employ a comparative analytical perspective. The chapter argues that Israeli politics and society are comparable, that comparison will improve the ability to assess Israel, and that Israel can contribute to theory building and testing in comparative politics. The chapter then outlines the sections and summarizes the main features of each chapter in this handbook.
Religion, Society, and Politics in Israel
Authors: Cohen Asher 
Published: October 2020

Abstract
This chapter focuses on four main aspects of relations among religion, society, and the state. The first section describes religion–state relations in Israel in comparison to the models prevalent in Western democracies. The second section categorizes the components of Jewish society in Israel by attitude toward tradition and religion. The third section focuses on the political system, with a look at the distribution of political parties based on religion and state and on models of accommodational and crisis politics. The fourth section examines two key disputes involving relations among religion, society, and the state: the public nature of the Jewish Sabbath as an expression of the struggle over the public space and the question of the boundaries of the Jewish collective, known in Israel as “who is a Jew.” After seventy years of existence, Israel still wrestles with a wide range of unresolved issues pertaining to religion, society, and state, reflecting an inability to reach stable and consensual solutions.
The Jewish Ethnic Divide and Ethnic Politics in Israel
Authors: Smooha Sammy 
Published: October 2020

Abstract
Ethnic differences are commonly reflected in governing elites, public policies, political parties, voting, and intergroup conflicts. This is true of Jews in Israel despite the strong assimilationist ideology and lack of legitimacy of ethnicity and ethnic politics. Notwithstanding increasing assimilation, decreasing ethnic inequalities, and diminishing discrimination, Jews in Israel are still markedly divided by ethnicity, social class, religious observance, subculture, geographic concentration, and collective memory. The political divide between the Right and the Center-Left is grounded in both class and ethnicity. The bases of the right-wing parties are non-dominant and low-socioeconomic-status Jews, Mizrahim, Russian immigrants, the National Religious, the ultra-Orthodox, and offspring of the Revisionists, who are more nationalistic and less liberal than the economically better off and Ashkenazi supporters of the Center-Left. The political Right represents its supporters’ illiberal views well and grants them a feeling of being at home in Israel and some preferential treatment as Jews. The demographic predominance of its supporters gives the Right a lead in vying for power, makes Israel more Jewish than democratic, and reduces the chances of peacemaking with the Palestinians.
Gender in Israel
Authors: Itzkovitch-Malka Reut 
Published: October 2020

Abstract
This chapter traces, identifies, and characterizes the main features of the gender division in Israeli society and politics. It addresses questions relevant to the status of women, as well as the LGBTQ community, and assesses the magnitude of gender inequality in the various societal, cultural, and political arenas. While substantial progress has been made in improving the status of women in Israel, there is still a long road ahead before Israel can achieve true gender equality. In order for such equality to become a reality, genuine change is in order: a focus on the substantive outputs of the Knesset and the government; an emphasis on gender mainstreaming practices; and widespread feminist activity in formal politics, meant to inject critical feminist views into the political system and alter existing gender relations.
Conceptualizing Palestinian Politics in Israel in the Shadow of the Arab Spring
Authors: Jamal Amal 
Published: October 2020

Abstract
This chapter examines the debates about the conceptualization and practices of resistance in Palestinian society in Israel. It does so in light of two important developments that have had major repercussions for this homeland minority: the social and political upheavals in the Arab Spring states on the one hand and the growing nationalist extremism in Israel, culminating in the passing of the nation-state law in 2018 and the delegitimization of the Joint List in the 2019–2020 elections, on the other. Examining the debates taking place about resistance helps us understand how political subjects active in this community define themselves and others and the meaning and implications of such definitions. Furthermore, it assists in demonstrating how Palestinians in Israel utilize the opportunities inherent in their institutional environment and the tools provided by that environment to facilitate an alternative political ethos that will guarantee it full civil equality and human dignity.
Public Opinion in Israel
Authors: Hermann Tamar 
Published: October 2020

Abstract
In Israel, as in many other countries, the impact of public opinion on national policymaking has increased dramatically over the last few decades. In fact, public opinion has practically developed into one of the prime political inputs in Israel. This chapter argues that this increased impact, which could have contributed to improving the Israeli democracy, is in fact often undermined by the increasing overlapping of the main cleavages within Israel: between the political Right and Left, between Jews and Arabs, and between religious and secular Israelis. This extreme overlapping has severely eroded the national consensus and accelerated the emergence of deep disagreements in public opinion over strategic issues, such as the nature of the state (Jewish? Democratic?), the main challenges facing the nation (including the best way of dealing with the protracted Israeli–Palestinian conflict), and the desired collective future.
The Judicial Branch in Israel
Authors: Hofnung Menachem , Wattad Mohammed S. 
Published: October 2020

Abstract
The contemporary perception of Israel’s judiciary as an independent branch does not coincide with Israel’s first government’s perception after establishing the first Supreme Court. To a great extent the executive branch deemed the court its long arm. Until the mid-1950s judges were appointed by the government, and questions of conflicts of interest and political affiliation—in the wide sense of the term—were not compelling. However, since the 1990s the court’s power of judicial review and the legitimacy of its decisions have become issues of heated public debate. Consequently, the process of appointing justices to the court has become subject to very strict public and political scrutiny. This chapter asks whether the Israeli judiciary truly constitutes a third independent branch of government. This is relevant considering the continuous attempts to change the existing balance of power, aiming to limit the court’s capacity to apply universal judicial doctrines and legal standards to executive and legislative decisions.
The Electoral System of Israel
Authors: Shugart Matthew S. 
Published: October 2020

Abstract
The electoral system of Israel is an “extreme” example of proportional representation because of its use of a single nationwide district. This feature has been a constant since 1949, while secondary features, such as legal thresholds and the proportional seat-allocation formula, have changed and had an impact on degrees of proportionality. The party system is highly fragmented, as expected in extreme proportional systems. By applying the Seat Product Model to indices of election outcomes, it is possible to determine whether Israel’s system is more or less fragmented and proportional than expected for its institutional design. This chapter reports that the long-term average outputs are about as expected, but they have fluctuated over time. Some of these fluctuations reflect changes in the secondary features of the system, while others are the results of political factors independent of the institutions.
Parties and the Party System of Israel
Authors: Hazan Reuven Y. 
Published: October 2020

Abstract
Both the parties and the party system of Israel have undergone significant changes during the last seventy years. This chapter begins by delineating the transformation of the political parties in Israel, from classic mass parties to a plethora of types that coexist somewhat uneasily, and from parties focused on domestic socioeconomic issues to ones dominated by foreign policy and security concerns. It then shifts to its main focus, assessing the changes in the party system. The chapter argues two points: first, that while the Israeli parties were extremely volatile, the party blocs were surprisingly stable; and second, that while the Israeli party system exhibited two very stable periods during the first fifty years—albeit with a short, transformative interim phase—during the last twenty-five years it has exhibited accelerated change and instability.
Israel’s Policy in and toward the West Bank and the Gaza Strip
Authors: Barak Oren 
Published: October 2020

Abstract
This chapter discusses Israel’s policy in and toward the West Bank (and East Jerusalem) and the Gaza Strip from the Six-Day War (1967), when Israel occupied these areas, to the present. Although the focus here is on the political-security realm, other spheres (e.g., economic, social, and cultural-discursive) are also addressed. The first part of the chapter discusses Israel’s policy in and vis-à-vis the Territories in the first decade after 1967, which in retrospect was the policy’s formative period. It then examines the four decades that followed, identifying elements of continuity and change in Israel’s policy. This is followed by a discussion of the major challenges to Israel’s policy since 1967: the first Palestinian intifada, the Israeli–Palestinian peace process, the second intifada, and Israel’s withdrawal from the Gaza Strip. The concluding section tries to assess the cumulative impact of Israel’s policy in and toward the Territories.
Israel and the Arab World
Authors: Rabinovich Itamar 
Published: October 2020

Abstract
This chapter traces and analyzes the course of the Arab–Israeli conflict from its early days to the present. What began as a Jewish–Arab conflict in and over Palestine developed in 1948 into a larger conflict between Israel and the Arab world. The conflict festered in the 1950s and culminated in the war of June 1967. That war had two major contradictory results. First, it provided Israel with bargaining chips for negotiating peace with Arab countries that lost territory in the Six-Day War. Most significantly, this led to the signing of the Israeli–Egyptian peace treaty in 1979. But second, it also encumbered Israel with the West Bank, the Gaza Strip, and the lingering control of a large Palestinian population. To a great extent the larger Arab–Israeli conflict was telescoped into the Israeli–Palestinian conflict in its present form. In recent years two other contradictory developments have been shaping the Israeli–Arab landscape. The return of Iran and Turkey into the Middle Eastern arena has added an important Islamic dimension to the conflict. But Iran’s quest for regional hegemony and the exacerbation of Sunni–Shiite tensions in the Middle East have had a moderating effect on the attitude of the Sunni Arab states toward Israel.
Political Culture and Israeli Politics
Authors: Ariely Gal 
Published: October 2020

Abstract
This chapter provides a broad overview of the political culture in Israel. It begins by discussing whether a single Israeli political culture can indeed be identified. It then surveys the principal factors that shape political culture and the key changes from the early days of nation-building attempts to Israel’s current, more multicultural character. Making use of a cultural-value map, the chapter then addresses the question of whether Israel’s political culture is indeed “Western” and compares the principal Israeli political orientations with those of other societies. Finally, it analyzes aspects of system support and democratic norms via the use of national and cross-national survey data. The analysis presented concludes that Israeli political culture is dominated by countervailing forces that create a combination of assertive and allegiant forms of citizenship.
Political History of Israel
Authors: Shapira Anita 
Published: October 2020

Abstract
This chapter discusses the internal political development of the Jewish community in Palestine and, after 1948, of the State of Israel. The rise of popular politics in the early 1930s culminated in the hegemony of the Left, which was the predominant power in Israeli politics from 1933 until 1977. The predominant leader was David Ben Gurion, who retired in 1963. The Left was mostly pragmatic, with a social democratic agenda that emphasized the role of the state in the economy and culture, promoting a narrative that glorified the predominance of the Left in nation- and state-building. In 1977 there was a change of direction: the right-wing opposition won the elections. The government now moved toward a free enterprise economy and a new narrative, which emphasized the question of Greater Israel as the focal point of government and state interest. The clash between Left and Right in Israel was no longer centered on questions of economy and society but rather on external policy. Growing polarization between Left and Right, Ashkenazi Jews and Mizrahim (Middle Eastern Jews), Orthodox and secular, and Israeli Arabs and Israeli Jews has typified Israel politics in the last two decades.
Arab Citizens in the “Jewish” State of Israel
Authors: Galnoor Itzhak 
Published: October 2020

Abstract
Israel’s Declaration of Independence proclaims full equality for all of Israel’s citizens and calls upon members of the Arab nation “to participate in the upbuilding of the State on the basis of full and equal citizenship.” This pledge has not been kept. On the one hand, the government is using its majority to legislate laws that undermine the status and legitimacy of the Arab citizens. On the other, since 2007 the same government has been investing a great deal of money in improving the economic conditions in the Arab localities. The tenuous relationship between Jews and Arabs is under constant pressure. Nonetheless, a change has begun to surface tacitly in the official state policy toward Arab citizens, recognizing the justification of equality, in economic terms. The three subsequent Knesset elections held in 2019–2020 strengthened the political representation and clout of the Arab citizens; however, the discriminating barrier, preventing their recognition as legitimate partners in the government coalition, has not been removed.