bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling pKas of unfolded proteins to probe structural models of unfolded state
Authors: Tajielyato Nayere , Alexov Emil 
Published: June 2019

Modeling unfolded states of proteins has implications for protein folding and stability. Since in unfolded state proteins adopt multiple conformations, any experimentally measured quantity is ensemble averaged, therefore the computed quantity should be ensemble averaged as well. Here, we investigate the possibility that one can model an unfolded state ensemble with the coil model approach, algorithm such as “flexible-meccano” [Ozenne V et al., Flexible-meccano: A tool for the generation of explicit ensemle descriptions of intrinsically disordered proteins and their associated experimental observables, Bioinformatics 28:1463–1470, 2012], developed to generate structures for intrinsically disordered proteins. We probe such a possibility by using generated structures to calculate pKas of titratable groups and compare with experimental data. It is demonstrated that even with a small number of representative structures of unfolded state, the average calculated pKas are in very good agreement with experimentally measured pKas. Also, predictions are made for titratable groups for which there is no experimental data available. This suggests that the coil model approach is suitable for generating 3D structures of unfolded state of proteins. To make the approach suitable for large-scale modeling, which requires limited number of structures, we ranked the structures according to their solvent accessible surface area (SASA). It is shown that in the majority of cases, the top structures with smallest SASA are enough to represent unfolded state.
Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma
Authors: Amin-Mansour Ali , George Suzanne , Sioletic Stefano , Carter Scott L. , Rosenberg Mara , Taylor-Weiner Amaro , Stewart Chip , Chevalier Aaron , Seepo Sara , Tracy Adam , Getz Gad , Hornick Jason L. , Nucci Marisa R. , Quade Bradley , Demetri George D. , Raut Chandrajit P. , Garraway Levi A. , Van Allen Eliezer M. , Wagner Andrew J. 
Published: June 2019

Abstract

Purpose:
Leiomyosarcoma and liposarcoma are common subtypes of soft tissue sarcoma (STS). Patients with metastatic leiomyosarcoma or dedifferentiated liposarcoma (DDLPS) typically have worse outcomes compared with localized leiomyosarcoma or well-differentiated liposarcoma (WDLPS). A better understanding of genetic changes between primary/metastatic leiomyosarcoma and between WDLPS/DDLPS may provide insight into their genetic evolution.

Experimental Design:
We interrogated whole-exome sequencing (WES) from “trios” of normal tissue, primary tumor, and metastatic tumor from individual patients with leiomyosarcoma (n = 9), and trios of normal tissue, well-differentiated tumor, and dedifferentiated tumor from individual patients with liposarcoma (n = 19). Specifically, we performed mutational, copy number, and tumor evolution analyses on these cohorts and compared patterns among leiomyosarcoma and liposarcoma trios.

Results:
Leiomyosarcoma cases harbored shared drivers through a typical parent/child relationship where the metastatic tumor was derived from the primary tumor. In contrast, while all liposarcoma cases shared the characteristic focal chromosome 12 amplicon, most paired liposarcoma cases did not share additional mutations, suggesting a divergent evolutionary pattern from a common precursor. No highly recurrent genomic alterations from WES were identified that could be implicated as driving the progression of disease in either sarcoma subtype.

Conclusions:
From a genomic perspective, leiomyosarcoma metastases contain genetic alterations that are also found in primary tumors. WDLPS and DDLPS, however, appear to divergently evolve from a common precursor harboring 12q amplification, rather than as a transformation to a higher-grade tumor. Further efforts to identify specific drivers of these distinct evolutionary patterns may inform future translational and clinical research in STS.
Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers
Authors: Parkhurst Maria R. , Robbins Paul F. , Tran Eric , Prickett Todd D. , Gartner Jared J. , Jia Li , Ivey Gabriel , Li Yong F. , El-Gamil Mona , Lalani Almin , Crystal Jessica S. , Sachs Abraham , Groh Eric , Ray Satyajit , Ngo Lien T. , Kivitz Scott , Pasetto Anna , Yossef Rami , Lowery Frank J. , Goff Stephanie L. , Lo Winifred , Cafri Gal , Deniger Drew C. , Malekzadeh Parisa , Ahmadzadeh Mojgan , Wunderlich John R. , Somerville Robert P.T. , Rosenberg Steven A. 
Published: June 2019

Abstract

Immunotherapies can mediate regression of human tumors with high mutation rates, but responses are rarely observed in patients with common epithelial cancers. This raises the question of whether patients with these common cancers harbor T lymphocytes that recognize mutant proteins expressed by autologous tumors that may represent ideal targets for immunotherapy. Using high-throughput immunologic screening of mutant gene products identified via whole-exome sequencing, we identified neoantigen-reactive tumor-infiltrating lymphocytes (TIL) from 62 of 75 (83%) patients with common gastrointestinal cancers. In total, 124 neoantigen-reactive TIL populations were identified, and all but one of the neoantigenic determinants were unique. The results of in vitro T-cell recognition assays demonstrated that 1.6% of the gene products encoded by somatic nonsynonymous mutations were immunogenic. These findings demonstrate that the majority of common epithelial cancers elicit immune recognition and open possibilities for cell-based immunotherapies for patients bearing these cancers.

Significance:
TILs cultured from 62 of 75 (83%) patients with gastrointestinal cancers recognized neoantigens encoded by 1.6% of somatic mutations expressed by autologous tumor cells, and 99% of the neoantigenic determinants appeared to be unique and not shared between patients.
This article is highlighted in the In This Issue feature, p. 983
Une Théorie de la Justice peut-elle être Réaliste ?
Authors: Spector Céline 
Published: June 2019

In lieu of an abstract, here is a brief excerpt of the content:
"Si la philosophie politique aspire à la justice, s’interdit-elle de penser l’histoire, les individus en chair et en os ? En bâtissant des châteaux en Espagne, n’a-t-elle pas peuplé la théorie politique d’artefacts imaginaires ou de « zombies raisonnables » ? Le mythe rationaliste en philosophie politique semble être le comble de l’aveuglement théorique. La théorie politique devient ipso facto aveugle à la violence – violence réelle des rapports sociaux, violence des rapports de genre, violence des guerres et des crimes de masse. La philosophie semble sourde à l’agonisme de la scène politique, incapable de prendre la mesure des situations réelles d’oppression et d’aliénation."
Les Grands Arguments d’Aristote et Descartes
Authors: Bimbenet Étienne 
Published: June 2019

In lieu of an abstract, here is a brief excerpt of the content:
"La question anthropologique est aujourd’hui une question nouvellement débattue, dans le cadre de ce qu’il est convenu d’appeler « l’anthropologie philosophique ». Deux raisons au moins peuvent expliquer un tel phénomène. Elles tiennent chacune à notre « image de l’homme » – à l’inéluctable effacement de cette image, ou plus exactement de ses contours. Comme on sait, il devient chaque jour plus malaisé de savoir où commence notre humanité, lorsqu’on confronte celle-ci aux différents précurseurs que lui découvrent depuis plus d’un demi-siècle et l’éthologie animale, et la primatologie. L’animal est devenu partie prenante de la vie humaine, une présence obsédante, un compagnon qui nous presse de questions et qui défie les frontières de notre humanité aussi bien par sa position de victime que par la proximité nouvelle que lui confère la science. Il est, comme le chat de Derrida, celui qui sinon accuse du moins interroge et met en question1. C’est comme si nous avions des comptes à lui rendre, sur ce que nous sommes et avons fait de lui ; et cette tâche regarde au premier chef la philosophie."
La Fragrance et le Musique, ou l’Invention d’un Art « Sonolfactif »
Authors: Jaquet Chantal 
Published: June 2019

In lieu of an abstract, here is a brief excerpt of the content:
"Souvent, l’art des parfums emprunte ses images, voire ses concepts à la musique pour exprimer sa temporalité évanescente et invisible. La création de parfums se présente comme une composition rythmée de notes olfactives : notes de tête, plus légères et volatiles, à la manière de croches aromatiques, comme les agrumes ou les menthes ; notes de cœur, florales et épicées, de plus longue durée ; notes de fond, plus lourdes et persistantes, comme un refrain musqué ou boisé. Faute d’un vocabulaire olfactif riche et développé, la description des fragrances puise elle aussi ses expressions dans un registre musical et s’appuie sur des analogies et des correspondances poétiques nourries par le symbolisme de Baudelaire. L’auteur des Fleurs du mal n’hésite pas à parler de parfums « doux comme les hautbois1 » et à mêler les « parfums des verts tamariniers » au chant des mariniers. » Dans La chevelure, son esprit qui se baigne dans cette forêt aromatique répond à ceux qui « voguent sur la musique »."
Sulla’s Phthiriasis and the Republican Body Politic
Authors: Walters Brian 
Published: June 2019

AbstractIt has long been suspected that Roman moralizing and the slander of political enemies lay behind the story of Sulla’s horrific death by vermin. This study traces the evocative logic of Sulla’s affliction to a constellation of Roman attitudes about corruption, self-mastery, and the body politic. It also argues that Sulla’s own rhetoric about the health of the state played a formative role in shaping narratives about his gruesome end.
Cognitive Innovation, Cumulative Cultural Evolution, and Enculturation
Authors: Fabry Regina E. 
Published: June 2019

Abstract
Cognitive innovation has shaped and transformed our cognitive capacities throughout history. Until recently, cognitive innovation has not received much attention by empirical and conceptual research in the cognitive sciences. This paper is a first attempt to help close this gap. It will be argued that cognitive innovation is best understood in connection with cumulative cultural evolution and enculturation. Cumulative cultural evolution plays a vital role for the inter-generational transmission of the products of cognitive innovation. Furthermore, there are at least two important functions of enculturation for cognitive innovation. First, enculturation is responsible for the ontogenetic acquisition of cognitive practices governing the interaction with innovative products. Second, successful processes of enculturation provide opportunities for subsequent innovative processes. The trans-generational trajectory of calculation from mathematical symbol systems to the first digital computers will serve as a paradigm example of the delicate interplay of cognitive innovation, cumulative cultural evolution, and enculturation.
The (possible) Cognitive Naturalness of Witchcraft Beliefs: An Exploration of the Existing Literature
Authors: Parren Nora 
Published: June 2019

Abstract
Cross-culturally, misfortune is often attributed to witchcraft despite the high human and social costs of these beliefs. The evolved cognitive features that are often used to explain religion more broadly, in combination with threat perception and coalitional psychology, may help explain why these particular supernatural beliefs are so prevalent. Witches are minimally counter intuitive, agentic, and build upon intuitive understandings of ritual efficacy. Witchcraft beliefs may gain traction in threatening contexts and because they are threatening themselves, while simultaneously activating coalitional reasoning systems that make rejection of the idea costly. This article draws possible connections between these cognitive and environmental features with an eye toward future empirical examination.
Observations on crustacean zooplankton in two connected north Patagonian lakes (Calafquén-Pellaifa, 39°S, Chile)
Authors: De los Ríos Patricio , Farias-Avendaño Jorge , Suazo Maria J. 
Published: June 2019

Abstract
The northern Patagonian lakes (38-41°S), are characterized by their location in catchment basins that have been markedly altered through human intervention. In those basins, the original native, perennial forest has been replaced by towns, villages and agricultural zones. The present study was done in two interconnected north Patagonian lakes (the lakes Calafquén and Pellaifa), where the species composition of the crustacean zooplankton community was compared, using a biodiversity index and size-structure null models. The results denoted the presence of marked differences between both sites, Calafquén lake being inhabited by less species and in general showing lower abundances of individuals in comparison to Pellaifa lake. The results of size-structure null models revealed the absence of interspecific competition for both sites. The obtained results would agree with similar observations for other northern Patagonian lakes in Argentina and Chile.
“I Don’t Love My Baby?!”
Authors: Røseth Idun , Bongaardt Rob 
Published: June 2019

Abstract
Many new mothers question the nature of their motherly love after birth. This affectionate relationship towards the infant is commonly called bonding in everyday speech, clinical practice and research. Bonding may not sufficiently describe the mother’s emotional response to the infant and does not capture the ambivalence and struggle to develop maternal affection of many women. This study aims to explore the phenomenon of disturbed maternal affection through the clinical case of one mother who experienced severe and prolonged disturbances. Two in-depth interviews led to a descriptive phenomenological analysis. The mother developed depressive symptoms from not feeling enough for her child, not the opposite, as is often hypothesized. We describe and discuss crucial constituents of her experience, such as ambivalence, remoteness, boredom, guilt, and the looming repetition of parenting patterns, and a solution resulting from therapy-enhanced reflection on motherhood vis-à-vis early life patterns, sociocultural expectations and existential predicaments.
Is the Filioque an Obstacle to a Pneumatologically Robust Christology?
Authors: Kieser Ty 
Published: June 2019

AbstractThis article provides examples of pneumatologically robust Reformed Christologies that are founded upon the doctrine of the filioque, as counter-evidence against the charge that the filioque prohibits the possibility of a ‘Spirit Christology.’ In order to provide this evidence, four Reformed theologians from four centuries (Calvin, Owen, Edwards, and Bavinck) are surveyed, particularly as they articulate the doctrine of the filioque and its significance for the role of the Holy Spirit in their Christologies. The article concludes that, rather than constituting an obstacle to a pneumatologically robust Christology, the filioque can positively contribute to a genuine Spirit Christology.
The Ancient Greek sentence left periphery
Authors: Beschi Fulvio 
Published: June 2019

Abstract
The pattern (Setting – Topic –) Focus. NB: The Verb always follows, which was proposed by H. Dik in order to describe AG’s left periphery, raises some issues. In particular, it presents a number of exceptions, which scholars (Matić and others) have variously attempted to resolve. In the present contribution, based on case studies drawn from Homer, the following pattern for the Homeric left periphery is proposed: (Setting – Topic – Focus). NB: Unmarked elements follow. This is not dramatically different from Dik’s pattern; rather, it is an extension of it.
Protecting the Holy Race and Holy Space: Judith’s Reenactment of the Slaughter of Shechem
Authors: Thiessen Matthew 
Published: June 2019

Abstract
The book of Judith employs the narrative of Genesis 34 in order to depict Judith’s actions as an imitation of the violent slaughter of the Shechemites. Through his skillful retelling of the story in her prayer (Judith 9) and then his repeated allusions to this story throughout the narrative, the author portrays Judith’s trust in God to protect both her body and her nation’s temple from the impurity, profanation, and disgrace of foreign aggression. Her deceitful words and actions are based on her belief that God would strengthen her hand, just as he had previously strengthened the hand of Simeon, to bring down vengeance upon Israel’s adversaries.
Isocrates’s phronesis and the Early Jesuits
Authors: Kainulainen Jaska 
Published: June 2019

Abstract
The following article studies the connections between Isocrates’s idea of phronesis (pragmatic wisdom) and the early-modern Jesuit notions of rhetoric and prudence. The article develops previous research on Cicero’s influence on early Jesuits by emphasizing Isocrates’s importance in the history of rhetoric and civic philosophy. Cicero himself was influenced by Isocrates and, more to the point, Isocrates’s writings were widely read and taught by early-modern Jesuits. The article demonstrates that Isocrates and early Jesuits had much in common with regard to their views on rhetoric and pragmatic wisdom. In so doing, the article contributes to our understanding of the early Jesuits’ views on rhetoric, ethics and civic life. Generally speaking, the article points towards compatibility between civic and Christian values and explores the reception of Isocrates and Greco-Roman ideas in early-modern Europe.
Personality Traits of Church Planters and Other Church Leaders in Europe (II)
Authors: Foppen Annemarie , Paas Stefan , Saane Joke van 
Published: June 2019

Abstract
In search of a renewal of their mission in the secularized West, an increasing number of (Protestant) churches have embarked on the creation of new faith communities with a strong missionary purpose. This entrepreneurial approach of mission raises a number of questions, among which the issue of leadership is paramount. Currently, however, very little reliable empirical research has been done among faith entrepreneurs, or ‘church planters’, in Europe. In this article the personality dimensions of 215 church planters are compared with 307 ‘regular’ church leaders (pastors), based on the so-called ‘Big Five’ personality test. Independent samples t-tests showed that church planters are significantly more extravert, open to new experiences, and conscientious than ‘regular’ pastors, and significantly less neurotic, while scores on agreeableness are more or less similar. These results are discussed with a view to existing literature on church planting and entrepreneurship in the West.
Lexical Gleanings from Bašākard
Authors: Boyajian-Sureniants Vahe , Voskanian Vardan 
Published: June 2019

AbstractThe paper presents some comparative notes on a number of lexical items recorded during a field expedition to Bašākard and its neighbouring areas. The whole related vocabulary in the dialects of the region, denoting kidney, lizard, hedgehog, frog, and date-palm are thoroughly discussed. The history of the study of Baškardī with the relevant literature is also provided.
Islamism in the South Caucasus
Authors: Ter-Abrahamian Hrant 
Published: June 2019

AbstractThe article is dedicated to Islamism and its specific forms of manifestation in the South Caucasus (in Georgia and Azerbaijan Republic in particular). Making no attempt to a full-scale coverage of the subject, the author aims at identifying and displaying the specific targets of a complex study of Islamism, indicating its primary and secondary geographic, social and other points, as well as specifying the basic tendencies for each point thus identified. A special attention is paid to the Internet forums and blogs as more relevant sources for specifying the lines of conflict within diverse trends of Islam and Islamism in the South Caucasus.
Idols and Land Grabs, Ancient and Modern: Creation and Ecotheology in Ezekiel 6; 35:1-36:15
Authors: Briggs William 
Published: June 2019

Abstract
In light of the growing importance of creation in contemporary discussions of the theology of the Hebrew Bible as well as modern ecological concerns, this essay examines the connected passages of Ezek 6; 35:1-36:15. These texts portray Yahweh as concerned with issues of order, land and land ownership, and the pollution of the land. Human idolatry and failure to recognize that the land belongs to Yahweh leads to the pollution of the land and the violation of the creational order. Ezekiel 6; 35:1-36:15 are considered in view of the contemporary malpractices of large agricultural corporations, allowing the text of Ezekiel and the modern world to shed light on one another. In contexts both ancient and modern, Ezekiel speaks against notions of unbridled human dominion over creation and asserts that humans are deeply intertwined with the world around them, in line with Terrance Fretheim’s conception of creation theology.
Rereading the Ark Narrative: An Exilic Word of Hope and Warning
Authors: Beach Matthew D. 
Published: June 2019

Abstract
This article explains how 2 Sam 6:1-8 was redacted during the Babylonian exile in order to impart a theological message of hope and warning to the exilic community. This is demonstrated through an exploration of the similarities between 2 Sam 6:1-8 and Exod 32. The primary similarities include: (1) how Uzzah fulfills the same priestly role as Aaron; (2) how David serves as a symbolic “Moses figure” who guides the people and the ark to Jerusalem; and (3) how Yahweh broke out against Uzzah in anger, symbolic of how Yahweh allowed the Babylonian army to overthrow Jerusalem and take the people captive.
May the Reinforcement Be with You: On the Reconstruction of Scientific Episodes
Authors: Martínez-Ordaz María del Rosario , Estrada-González Luis 
Published: June 2019

Abstract
Like theories, reconstructions of episodes in the history of science can possess, or lack, certain virtues such that, when we face two or more different reconstructions of the same episode, we assume that we should choose the most “virtuous one”. However, we will argue that, with dissimilar reconstructions of the same episode, it is not always necessary to separate the “good ones” from the “wrong ones”, and that, as a matter of fact, each reconstruction could provide different but perhaps equally relevant data about the episode, about science in general, and about particular philosophical theses. In order to help us to identify these benefits, we will present a criterion that guides the search for historiographical reinforcement of philosophical theses and we will use it to evaluate three different reconstructions of the same scientific episode.
A Dutchman Views the World – Ankersmit as a Reader
Authors: Kellner Hans 
Published: June 2019

AbstractThroughout his extensive work, Frank Ankersmit presents a mode of reading that informs his philosophy of history. He has commented in passing that the visuality of his approach is a Dutch trait, and that historical works succeed when they serve as a “belvedere,” offering a panoramic view. His discussions of Erich Auerbach and Hayden White reveal his own reading protocols, which differ from those of the great readers Auerbach and White, however, in that Ankersmit does not read his texts “proximally,” as linguistic artefacts. Instead, he favors a “distal” stance from his texts in order to see the work as a whole, as a pictorial narratio. In this way, the reader-viewer may experience an aesthetic mood like the one Ankersmit feels, for example, when confronted by a Guardi painting. Further, in his discussion of Gibbon and Ovid, he shows that the myth of Narcissus, in which admiration of an image is replaced by a mere echo, reveals a danger of historical representation and the need for a metamorphic picture, blurring the contours. If we consider Ankersmit as a reader with a pictorial sense, whether “Dutch” or not, his position as a philosopher of experience will come into better focus.