bluuebunny/crossref_metadata_2025_split huggingface dataset:
Escherichia coli amino acid auxotrophic expression host strains for investigating protein structure–function relationships
Authors: Iwasaki Toshio , Miyajima-Nakano Yoshiharu , Fukazawa Risako , Lin Myat T , Matsushita Shin-ichi , Hagiuda Emi , Taguchi Alexander T , Dikanov Sergei A , Oishi Yumiko , Gennis Robert B 
Published: November 2020

Abstract
A set of C43(DE3) and BL21(DE3) Escherichia coli host strains that are auxotrophic for various amino acids is briefly reviewed. These strains require the addition of a defined set of one or more amino acids in the growth medium, and have been specifically designed for overproduction of membrane or water-soluble proteins selectively labelled with stable isotopes, such as 2H, 13C and 15N. The strains described here are available for use and have been deposited into public strain banks. Although they cannot fully eliminate the possibility of isotope dilution and mixing, metabolic scrambling of the different amino acid types can be minimized through a careful consideration of the bacterial metabolic pathways. The use of a suitable auxotrophic expression host strain with an appropriately isotopically labelled growth medium ensures high levels of isotope labelling efficiency as well as selectivity for providing deeper insight into protein structure–function relationships.
Mating Systems of the Tree-Killing Bark Beetle Polygraphus proximus (Coleoptera: Curculionidae: Scolytinae)
Authors: Köbayashi Kenta , Takagi Etsuro 
Published: November 2020

Abstract
Polygraphus proximus Blandford (Coleoptera: Curculionidae: Scolytinae) has caused mass mortality of fir (Abies spp. (Pinaceae)) forests across large areas of Russia in the past decade. More recently, mass mortality of A. veitchii  Lindl. due to P. proximus infestation has been reported in Japan. This bark beetle species traditionally has been considered to be polygynous because their galleries have multiple gallery arms, and because harem-polygyny is common in the tribe Polygraphini. Although the mating system(s) potentially could have a marked effect on their reproductive success and population dynamics, the reproductive behavior of the tree-killing bark beetle P. proximus has not been investigated in detail in a natural setting in Japan. We, therefore, investigated the number of males and females in a gallery and the number of gallery arms in Abies species in Japan. None of the galleries examined contained more than one male, and 57.2% of the galleries had multiple gallery arms, even though only 2.8% of the galleries contained two females. The findings showed that the typical mating system employed by P. proximus is monogyny and that this species constructs multiple gallery arms in each gallery. In addition, 70.4% of galleries in which the sex of adult beetles could be determined contained no males, and 26.6% contained no females, suggesting that P. proximus males and females re-emerge.
Success of native and invasive plant congeners depends on inorganic nitrogen compositions and levels
Authors: Geng Xi-Mei , He Wei-Ming 
Published: November 2020

Abstract

Aims
Successful plant invaders usually exhibit three strategies: Jack-of-all-trades (more robust in stressful sites), Master-of-some (more responsive in favorable sites) and Jack-and-master (both robustness and responsiveness). To revisit these strategies, we examined how soil inorganic nitrogen (N) compositions and levels influence the success of native and invasive plant congeners in the context of plant communities.

Methods
We conducted an experiment involving three fixed factors: species origin, N composition and N level. Here, we selected 21 plant species (eight pairs of invasive and native congeners and five non-congeneric natives) to assemble plant communities, which were subject to nine N environments consisting of three N compositions (3:1, 2:2 and 1:3 NO3−/NH4+) and three N levels (low, medium and high N). We determined the following metrics: total biomass, relative biomass (a proxy of species success), mortality rate and mortality time.

Important Findings
Across nine N environments, native and invasive congeners exhibited similar total biomass, relative biomass and mortality time, but invaders had a marginally lower mortality rate than natives. Similar success between native and invasive congeners was linked to their similar growth and tolerance. N compositions influenced mortality time and N levels affected the total biomass and relative biomass. Importantly, species origin, N composition and N level interactively affected the total biomass, relative biomass and mortality time. These findings suggest that native and invasive plant congeners may be similarly successful across different N environments, and that inorganic N compositions and levels both contribute to plant invasion success.
Beethoven and Neefe—A Reappraisal
Authors: van der Zanden Jos 
Published: November 2020

Abstract
Deeply entrenched in Beethoven biography is the view that Christian Gottlob Neefe was the composer’s most important teacher in Bonn and that Beethoven was grateful to him. Critical writing has always vaunted Neefe’s merits in lavish terms, in sharp contradiction to the recollection of a contemporary in Bonn, his friend Franz Wegeler, who downplayed Neefe’s significance. This essay investigates the primary sources with regard to the role of Neefe in an attempt to shed light on the discrepancy. Early biographical writing is scrutinized to investigate how these early sources were presented and interpreted. Decisive were the views of Alexander Wheelock Thayer, whose authoritative biography set the standard for decades. A contextualization of Neefe’s role in musical Bonn and his leadership of the Illuminati (a branch of freemasonry), together with information on Beethoven’s trip to Holland in 1783, leads to the conclusion that Neefe’s alleged importance is a nineteenth-century construction based on uncertain evidence. The cherished notion of a close affinity between teacher and pupil is debunked as a myth that would better not be perpetuated.
On the precision of full-spectrum fitting of simple stellar populations – II. The dependence on star cluster mass in the wavelength range 0.3–5.0 µm
Authors: Goudfrooij Paul , Asa’d Randa S 
Published: November 2020

ABSTRACT
In this second paper of a series on the accuracy and precision of the determination of age and metallicity of simple stellar populations (SSPs) by means of the full-spectrum fitting technique, we study the influence of star cluster mass through stochastic fluctuations of the number of stars near the top of the stellar mass function, which dominate the flux in certain wavelength regimes depending on the age. We consider SSP models based on the Padova isochrones, spanning the age range $7.0 \le \mbox{log(age/yr}) \le 10.1$. Simulated spectra of star clusters in the mass range 104 ≤ M/M⊙ &lt; 106 are compared with SSP model spectra to determine best-fitting ages and metallicities using a full-spectrum fitting routine in four wavelength regimes: the blue optical (0.35–0.70 µm), the red optical (0.6–1.0 µm), the near-infrared (near-IR; 1.0–2.5 µm), and the mid-IR (2.5–5.0 µm). We compare the power of each wavelength regime in terms of both the overall precision of age and metallicity determination and its dependence on cluster mass. We also study the relevance of spectral resolution in this context by utilizing two different spectral libraries (BaSeL and BT-Settl). We highlight the power of the mid-IR regime in terms of identifying young massive clusters in dusty star-forming regions in distant galaxies. The spectra of the simulated star clusters and SSPs are made available online to enable follow-up studies by the community.
Influence of a quasi-molecular mechanism of recombination on the formation of hydrogen in the early Universe
Authors: Kereselidze Tamaz , Noselidze Irakli , Ogilvie John F 
Published: November 2020

ABSTRACT
In the framework of a quasi-molecular approach, the formation of hydrogen atom in the pre-recombination period of evolution of the Universe is analysed quantitatively. Calculations in an adiabatic multilevel representation enable estimates of probabilities of radiative transitions. The quasi-molecular mechanism of recombination allows the formation of hydrogen molecular ion, ${\mathrm{ H}_2}^+$, in its ground state. The probability of this process is comparable with the probability of the creation of atomic hydrogen. The participation of a second proton in the recombination increases the binding energy of an electron and decreases the rate of recombination of hydrogen.
dearseq: a variance component score test for RNA-seq differential analysis that effectively controls the false discovery rate
Authors: Gauthier Marine , Agniel Denis , Thiébaut Rodolphe , Hejblum Boris P 
Published: November 2020

AbstractRNA-seq studies are growing in size and popularity. We provide evidence that the most commonly used methods for differential expression analysis (DEA) may yield too many false positive results in some situations. We present dearseq, a new method for DEA that controls the false discovery rate (FDR) without making any assumption about the true distribution of RNA-seq data. We show that dearseq controls the FDR while maintaining strong statistical power compared to the most popular methods. We demonstrate this behavior with mathematical proofs, simulations and a real data set from a study of tuberculosis, where our method produces fewer apparent false positives.
Clinical, histopathologic and molecular features of idiopathic and diabetic nodular mesangial sclerosis in humans
Authors: Eadon Michael T , Lampe Sam , Baig Mirza M , Collins Kimberly S , Melo Ferreira Ricardo , Mang Henry , Cheng Ying-Hua , Barwinska Daria , El-Achkar Tarek M , Schwantes-An Tae-Hwi , Winfree Seth , Temm Constance J , Ferkowicz Michael J , Dunn Kenneth W , Kelly Katherine J , Sutton Timothy A , Moe Sharon M , Moorthi Ranjani N , Phillips Carrie L , Dagher Pierre C ,   for the Kidney Precision Medicine Project
Published: November 2020

Abstract

Background
Idiopathic nodular mesangial sclerosis, also called idiopathic nodular glomerulosclerosis (ING), is a rare clinical entity with an unclear pathogenesis. The hallmark of this disease is the presence of nodular mesangial sclerosis on histology without clinical evidence of diabetes mellitus or other predisposing diagnoses. To achieve insights into its pathogenesis, we queried the clinical, histopathologic and transcriptomic features of ING and nodular diabetic nephropathy (DN).

Methods
All renal biopsy reports accessioned at Indiana University Health from 2001 to 2016 were reviewed to identify 48 ING cases. Clinical and histopathologic features were compared between individuals with ING and DN (n = 751). Glomeruli of ING (n = 5), DN (n = 18) and reference (REF) nephrectomy (n = 9) samples were isolated by laser microdissection and RNA was sequenced. Immunohistochemistry of proline-rich 36 (PRR36) protein was performed.

Results
ING subjects were frequently hypertensive (95.8%) with a smoking history (66.7%). ING subjects were older, had lower proteinuria and had less hyaline arteriolosclerosis than DN subjects. Butanoate metabolism was an enriched pathway in ING samples compared with either REF or DN samples. The top differentially expressed gene, PRR36, had increased expression in glomeruli 248-fold [false discovery rate (FDR) P = 5.93 × 10−6] compared with the REF and increased 109-fold (FDR P = 1.85 × 10−6) compared with DN samples. Immunohistochemistry revealed a reduced proportion of cells with perinuclear reaction in ING samples as compared to DN.

Conclusions
Despite similar clinical and histopathologic characteristics in ING and DN, the uncovered transcriptomic signature suggests that ING has distinct molecular features from nodular DN. Further study is warranted to understand these relationships.
Tracing Choreography
Authors: Ritter Julia M. 
Published: November 2020

AbstractChapter 1 contextualizes choreography as integral to, yet invisibilized within, immersive performance. The chapter's focus is the thematic concerns of choreography in Western dance history, specifically the intentionality with which it is created, the portability of its concepts outside of the realm of formal dance, and its resulting ubiquity across domains in the twenty-first century. Deployed by European aristocrats in the sixteenth and seventeenth centuries as a practice for reinforcing structures of ritual and power when assigning societal roles, choreography as a term emerged alongside the professionalization of dance in the eighteenth and nineteenth centuries. In the mid-twentieth century, choreography became a tacitly borrowed resource for creators of physical theater. In the twenty-first century, choreography is seen as an expanded practice, having surged beyond the bounds of dance to the point that it can be used to organize the behavior of spectators such that they perceive themselves to be immersed.
Speculative Futures
Authors: Ritter Julia M. 
Published: November 2020

AbstractChapter 6 expands upon fundamental arguments put forth in the preceding chapters to further assert the importance of centering choreography within the discourse that surrounds the field of immersive theater studies. In addition, this chapter looks forward, speculating on the potential contributions of dance to the changing landscape of immersive performance, as strategies used to create participatory performance and experiential entertainment are increasingly adopted within commercial business sectors. The book concludes with a defense of dance as a broad field of study, and a call to properly acknowledge its contributions to the development of new cultural forms, including the innovation of immersive performance.
Introduction
Authors: Hájková Anna 
Published: November 2020

Abstract
The introduction outlines the objectives of the book and contextualizes it in terms of existing Holocaust studies scholarship in general and Theresienstadt in particular. It offers a brief chronology of the ghetto and explains why it was a ghetto and not a concentration camp. It also relates the work to issues pertinent to modern Jewish history, the history of everyday life, and research on ethnicity and Central Europe. Specifically, it shows how ethnicity became the central category of difference in the prisoner society, one directly linked to stratification. This introduction also lays out the central claim of the book that social interaction continues under extreme circumstances and brings Holocaust and Jewish history into the wider context of modern history. It also discusses forms of prisoners’ agency in the everyday of the ghetto.
The Overorganized Ghetto
Authors: Hájková Anna 
Published: November 2020

Abstract
This chapter examines the administration of the ghetto, the most complex and largest Jewish self-administration per capita in German-occupied Europe. It also offers background on the German and Austrian SS, who controlled but did not administer the ghetto. The Theresienstadt bureaucracy developed its own politics, wherein the ethnicity of functionaries carried as much weight as belonging to one of the often competing departments of the self-administration. The chapter explores the agency of the Jewish functionaries vis-à-vis the SS, and how they interacted with and were perceived by ordinary prisoners. In doing so it contributes to the debate on Jewish Councils. It also discusses the role of Leo Baeck and shows that he was a skillful, occasionally cunning functionary. Finally, the chapter discusses the Jewish informers, their motivation, and their contributions to the German running of the ghetto.
A Society Based on Inequality
Authors: Hájková Anna 
Published: November 2020

Abstract
This chapter looks at the formation and hierarchy of the prisoner society. It explores the differentiation of prisoner society by ethnicity, time of arrival, age, and social capital. It shows how people got used to life in Theresienstadt, what it meant to be “well off” and “poor,” and how inmates made sense of their lives. Prisoners employed an “ethnic gaze” that made sense of others through perceived ethnic and biological differences, with Jewishness not functioning as a connecting factor but rather as an ethnic demarcator. The Terezín prisoners employed a binary vision that differentiated between Czech and “foreign” prisoners. The periodic arrival of new inmates and the emergence of a master narrative of Theresienstadt meant that the veterans—young Czech Jews—became the social elite. The chapter also explores the role of gender, sexuality, and queer desire in the workings of the victim society.
The Age of Pearl Barley
Authors: Hájková Anna 
Published: November 2020

Abstract
This chapter presents a hidden history of how food and hunger shaped the politics of everyday life in Terezín. It offers a social and cultural history of food, eating, and hunger, and of how food defined social structures and kinship. The German authorities consigned Jews to Terezín and restricted the supply of food. Shortages led to maldistribution, caused by the food categories introduced by the Jewish self-administration and corruption, which vastly increased rates of hunger and death. Maldistribution was a consequence of inmate society. The social hierarchy in Theresienstadt resulted in stark differences in access to food, with younger prisoners enjoying relatively good access while the underfed elderly population was deprived and had an extremely high mortality rate. Mass starvation in Theresienstadt was caused more by maldistribution than by lack of food.
Medicine and Illness
Authors: Hájková Anna 
Published: November 2020

Abstract
Illness was a defining experience for Holocaust victims, yet their medical history is missing. This chapter studies the medical staff, patients, and diseases in the Theresienstadt ghetto. In examining medical care in extremis, it studies how the Central European Jewish doctors succeeded in providing comparably excellent healthcare and good medications for the inmates. However, the medical staff applied triage, separating “important” from “irrelevant,” that is elderly, patients. The chapter examines the mentality, experience, and gendered power mechanisms that characterized the medical staff; the agency of the doctors; and the hierarchies they assigned to patients. Finally, in exploring how the prisoner physicians made sense of Theresienstadt as a part of their medical careers, the chapter shows what kind of historical protagonists doctors are.
Hatred
Authors: Brogaard Berit 
Published: November 2020

Abstract
The book explores how personal hatred can foster domestic violence and emotional abuse; how hate-proneness is a main contributor to the aggressive tendencies of borderlines, narcissists, psychopaths, and hatemongers; how seemingly ordinary people embark on some of history’s worst hate crimes; and how cohesive groups can develop extremist viewpoints that motivate hate crimes, mass shootings, and genocide. The book’s first part explores hate in personal relationships, looking for an answer to the question of why our personal relationships can survive hate and resentment but not disrespect or contempt. It shows that where contempt creates an irreparable power imbalance, hate is tied to fear, which our brains may reinterpret as thrill, attraction, and arousal. But this can also make hate a dangerous emotion that convinces people to hang on to abusive relationships. When tied to vengeance and the dark triad of personality, hate is not only dangerous but also dehumanizing. Vengeance and the dark personalities are not essential to hate, however. Without them, hate can have more admirable ends. The book’s second part explores the polarizing forces that can bias cohesive groups of like-minded individuals and contribute to what is effectively a hate crisis. Drawing on history, politics, legal theory, philosophy, and psychology, it shows how cultural myths about femininity, ethnic groups, and the land of opportunity perpetuate misogyny, racism, white supremacy, and anti-Semitism. But politicians and policymakers have it in their power to address the hate crisis through legislation that preserves the original incentive behind our constitutional rights.
A Century of Saints
Authors: Calvillo Jonathan E. 
Published: November 2020

Abstract
This chapter chronicles the emergence of Santa Ana’s distinct Latinx majority religious ecology. The diversity of Latinx religious communities significantly shapes Santa Ana as an ethnic space. The author delineates how the religious ecology navigated today by Santaneros is tied to histories of local religious institutions and to patterns of racialized, ethnic exclusion. Ethnic identities that residents have had to contend with today are rooted in patterns of negotiations and struggles that Mexican-identified individuals have long contended with. Religion, the author argues, has often been used by whites in the construction of exclusionary boundary markers against Latinxs. Likewise, religious differences among co-ethnics have been salient points of in-group distinction. Nevertheless, Latinx majority religious communities have provided Mexican immigrants in Santa Ana with opportunities to exercise agency and leadership.
After Arminius
Authors: H. McCall Thomas , D. Stanglin Keith 
Published: November 2020

Abstract“Arminianism” was the subject of important theological controversies in the seventeenth and eighteenth centuries, and it maintains an important position within Protestant thought. What became known as “Arminian” theology was held by people across a swath of geographical and ecclesial positions; it developed in European, British, and American contexts, and it engaged with a wide range of intellectual challenges. While standing together in their common rejection of several key planks of Reformed theology, proponents of Arminianism took various positions on other matters. Some were broadly committed to catholic and creedal theology; others were more open to theological revision. Some were concerned primarily with practical concerns; others were engaged in system building as they sought to articulate and defend an overarching vision of God and the world. The story of this development is both complex and important for a proper understanding of the history of Protestant theology. However, this historical development of Arminian theology is not well known. In this book, Thomas H. McCall and Keith D. Stanglin offer a historical introduction to Arminian theology as it developed in modern thought, providing an account that is based upon important primary sources and recent secondary research that will be helpful to scholars of ecclesial history and modern thought as well as comprehensible and relevant for students.
Arminianism
Authors: McCall Thomas H. , Stanglin Keith D. 
Published: November 2020

AbstractChapter 1 discusses the purpose of the book as an introduction to the historical development of Arminian theology. It then offers a preliminary description and definition of Arminianism. The late medieval and early modern background of Arminianism is summarized. This background includes a brief overview of the most well-known aspects of Arminius’s thought. The chapter concludes with an outline of the contents of the subsequent chapters.