bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract PR09: A systematic approach to create patient-derived models of rare tumors
Authors: Tseng Yuen-Yi , Keskula Paula , Deasy Rebecca , Hong Andrew , Chatterji Priya , Vazquez Francisca , Bass Adam , Van Hare Barbara , Sandak David , Ligon Keith , Boehm Jesse 
Published: June 2020

Abstract
Precision cancer medicine is based on the ability to predict the dependencies of a given tumor from its molecular makeup. Despite successes in multiple common cancers, such prediction remains challenging for the majority of rare and understudied tumors, given the absence of laboratory model systems in which to discover and/or validate therapeutic hypotheses. Here, we describe our efforts to address this challenge systematically with the ultimate goal of making it possible to learn how to predict ex vivo growth requirements for cancer samples based on technical, clinical, and genomic properties of the starting tumor material. Over the last 5 years, we have processed nearly 2,000 tumor biospecimens and created over 375 genomically confirmed patient-derived cell lines, organoids, and neurosphere cultures, with &gt;10% of these representing rare cancers. To make this possible, we have implemented three key workflows including (1) direct-to-patient sample sourcing, (2) a tissue cryopreservation and genomic credentialing system to ensure quality prior to model creation, and (3) a systematic empirical approach to screening rich media and variations on organoid technologies ex vivo (HYBRID). We have begun performing genome-wide CRISPR viability screens in these cultures as part of our larger activities to generate a systematic laboratory-based functional map of cancer dependencies (a “Cancer Dependency Map”). The novel organoid, spheroid, and cell line models created as part of this effort are being made publicly available to the scientific community. Looking ahead, as the barriers to culturing rare tumors are overcome, we expect that preclinical functional genomics data will be useful for difficult-to-treat tumors without existing molecularly guided standard-of-care regimens.
This abstract is also being presented as Poster A06.
Citation Format: Yuen-Yi Tseng, Paula Keskula, Rebecca Deasy, Andrew Hong, Priya Chatterji, Francisca Vazquez, Adam Bass, Barbara Van Hare, David Sandak, Keith Ligon, Jesse Boehm. A systematic approach to create patient-derived models of rare tumors [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR09.
Abstract PR10: A versatile ES cell-based melanoma mouse modeling platform
Authors: Karreth Florian A. 
Published: June 2020

Abstract
The cumbersome and time-consuming process of generating new mouse strains and multiallelic experimental animals often hinders the use of genetically engineered mouse models (GEMM) in cancer research. Here, we describe the development and validation of an embryonic stem cell (ESC)-GEMM platform for rapid modeling of melanoma in mice. The platform incorporates twelve clinically relevant genotypes composed of combinations of four driver alleles (LSL-BrafV600E, LSL-NrasQ61R, PtenFlox, Cdkn2aFlox) and regulatory alleles to spatiotemporally control the perturbation of genes of interest. The ESCs produce high-contribution chimeras, which recapitulate the melanoma phenotypes of conventionally bred mice. Using the ESC-GEMM platform to modulate Pten expression in melanocytes in vivo, we highlighted the utility and advantages of gene depletion by CRISPR-Cas9, RNAi, or conditional knockout for melanoma modeling. Moreover, complementary genetic methods demonstrated the impact of Pten restoration on the prevention and maintenance of Pten-deficient melanomas. Finally, we showed that chimera-derived melanoma cell lines retain regulatory allele competency and are a powerful resource to complement ESC-GEMM chimera experiments in vitro and in syngeneic grafts in vivo. Thus, when combined with sophisticated genetic tools, the ESC-GEMM platform enables rapid, high-throughput, and versatile studies aimed at addressing outstanding questions in melanoma biology.
This abstract is also being presented as Poster B45.
Citation Format: Florian A. Karreth. A versatile ES cell-based melanoma mouse modeling platform [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR10.
Abstract PR14: A multiscale map of recurrently mutated systems in cancer
Authors: Zheng Fan , Ono Keiichiro , Silva Erica , Swaney Danielle , Kim Minkyu , Shangguan Julia , Pratt Dexter , Nan Xiaolin , Krogan Nevan , Ideker Trey 
Published: June 2020

Abstract
Interpreting cancer genomes requires a broad understanding of the composition and organization of cellular processes under selective pressure for mutations. Here, we integrate systematic screens for protein interaction with tumor genetic analysis to elucidate a multiscale hierarchical map of 378 protein systems recurrently altered in one or more cancer types. Diverse gene mutations converge on commonly mutated systems, from small protein complexes in specific tumor types to large molecular assemblies and organelles disrupted in most cancers. Unexpected findings include collagen structural alterations with significant prognostic value; mutations impacting the desmosome in 65% melanomas; complexes related to splicing and DNA repair; and an expanded actomyosin cluster involving PIK3CA. The map implicates 556 cancer genes, many well supported by functional assays, including canonical genes implicated in new tissues (e.g., BRCA1/2 mutations in bladder cancer). This work explains mutational heterogeneity as a collection of convergence points across scales of cell biology.
This abstract is also being presented as Poster B52.
Citation Format: Fan Zheng, Keiichiro Ono, Erica Silva, Danielle Swaney, Minkyu Kim, Julia Shangguan, Dexter Pratt, Xiaolin Nan, Nevan Krogan, Trey Ideker. A multiscale map of recurrently mutated systems in cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR14.
Long Range Endocrine Delivery of Circulating miR-210 to Endothelium Promotes Pulmonary Hypertension
Authors: Zhao Jingsi , Florentin Jonathan , Tai Yi-Yin , Torrino Stéphanie , Ohayon Lee , Brzoska Tomasz , Tang Ying , Yang Jimin , Negi Vinny , Woodcock Chen-Shan Chen , Risbano Michael G. , Nouraie Seyed Mehdi , Sundd Prithu , Bertero Thomas , Dutta Partha , Chan Stephen Y. 
Published: June 2020

Rationale:
Unproven theories abound regarding the long-range uptake and endocrine activity of extracellular blood-borne microRNAs into tissue. In pulmonary hypertension (PH), microRNA-210 (miR-210) in pulmonary endothelial cells promotes disease, but its activity as an extracellular molecule is incompletely defined.

Objective:
We investigated whether chronic and endogenous endocrine delivery of extracellular miR-210 to pulmonary vascular endothelial cells promotes PH.

Methods and Results:

Using
miR-210
replete (wild-type [WT]) and knockout mice, we tracked blood-borne miR-210 using bone marrow transplantation and parabiosis (conjoining of circulatory systems). With bone marrow transplantation, circulating miR-210 was derived predominantly from bone marrow. Via parabiosis during chronic hypoxia to induce miR-210 production and PH, miR-210 was undetectable in knockout-knockout mice pairs. However, in plasma and lung endothelium, but not smooth muscle or adventitia, miR-210 was observed in knockout mice of WT-knockout pairs. This was accompanied by downregulation of miR-210 targets ISCU (iron-sulfur assembly proteins)1/2 and COX10 (cytochrome c oxidase assembly protein-10), indicating endothelial import of functional miR-210. Via hemodynamic and histological indices, knockout-knockout pairs were protected from PH, whereas knockout mice in WT-knockout pairs developed PH. In particular, pulmonary vascular engraftment of miR-210–positive interstitial lung macrophages was observed in knockout mice of WT-knockout pairs. To address whether engrafted miR-210–positive myeloid or lymphoid cells contribute to paracrine miR-210 delivery, we studied miR-210 knockout mice parabiosed with miR-210 WT;
Cx3cr1
knockout mice (deficient in myeloid recruitment) or miR-210 WT;
Rag1
knockout mice (deficient in lymphocytes). In both pairs, miR-210 knockout mice still displayed miR-210 delivery and PH, thus demonstrating a pathogenic endocrine delivery of extracellular miR-210.

Conclusions:
Endogenous blood-borne transport of miR-210 into pulmonary vascular endothelial cells promotes PH, offering fundamental insight into the systemic physiology of microRNA activity. These results also describe a platform for RNA-mediated crosstalk in PH, providing an impetus for developing blood-based miR-210 technologies for diagnosis and therapy in this disease.
Staging Touba: The Performance of Piety
Authors: Kingsbury Kate 
Published: June 2020

Abstract
Touba, in Senegal, is the equivalent to Mecca for Sufi Mouride Muslims, who embark on an annual pilgrimage called Le Grand Magal to celebrate the founder of their faith, Cheikh Amadou Bamba. When devotees describe their sacred city they frequently compare Touba to heaven, juxtaposing it to the materiality and chaos of other Senegalese cities, as though it was distinct from these lieux. Yet Touba shares many similarities in terms of its economic importance with other metropolises. Mourides despite presenting themselves as a united religious community, have differences of opinion and even praxis. This paper explores the imagination of Touba and the Mouride order by Mourides, positing that the sacred sites of Touba comprise a stage for the performance of piety and the generation of a particular Mouride ontology through which they see Touba, their order and the world.
Heeding the Law beyond the Law: Transgendering Alterity and the Hypernomian Perimeter of the Ethical
Authors: Wolfson Elliot R. 
Published: June 2020

Abstract
This essay will examine the viability of a kabbalistic ethics from the vantage point of what I have identified in previously published studies as the hypernomian foundation of the nomos, the grounding of the law in the ground that exceeds the law of the ground. Contrary to Scholem, who put the emphasis on an antinomian impulse that is in conflict with the tenets of the tradition, I argue that the hallmark of religious nihilism is the promulgation of the belief that impiety is the gesture of supreme piety. In the ensuing analysis, I will explore the subject of hypernomianism by a close analysis of what may be called in Derridean terms the law beyond the law, which he identified further as the nonjuridical ideal of justice, the gift of forgiveness, the aspect of pure mercy in relation to which it is no longer viable to distinguish guilt and innocence.
Against Metaphysical Structuralism
Authors: Busse Ralf 
Published: June 2020

Abstract
Inductive Metaphysics (IM) combines an anti-aprioristic emphasis on an empirical and scientific basis for metaphysics with an insistence on a specifically philosophical abductive theory-building. Since the latter specifically philosophical work is not empirical itself, it may in a liberal sense be called apriori. This paper highlights this apriori dimension within IM by a case study on Structuralism, the view that fundamental reality consists of a network of relations (and properties), which a number of philosophers consider to be suggested by modern physics. Focussing on Dasgupta’s algebraic Generalism, the author argues that Structuralism suffers from a severe entailment problem, because the relations-spanning apparatus must stand for metaphysically fundamental forms. Schaffer’s contention that there are no entailment problems is rejected. Advocates of IM are well advised to take seriously their own insistence on metaphysical abduction and not to one-sidedly emphasise the empirical input: the elaboration of exact metaphysical theories and the apriori evaluation of their inherent tenability is a constituent of IM no less important than the consideration of scientific input. More traditional ways of metaphysical reasoning inevitably survive as an essential dimension within IM.
Tetractys
Authors: Izdebska Anna 
Published: June 2020

Abstract
Tetractys was a Greek technical term, specific to the Pythagorean tradition, that the late antique neoplatonist philosophers considered to be the central notion of Pythagorean metaphysics. As the Greek philosophical heritage started to be translated into Arabic, this term also made its way into the new language, resulting in a number of different translations. This paper explores the ways in which the term tetractys was expressed in Arabic and then explained to the medieval islamicate readers. By comparing the ways in which specific authors and intellectual circles coped with a technical term that no longer assumed the philosophical significance it had had in Late Antiquity, I show the vagaries of the Greco-Arabic translation movement. The changing renderings and understandings of this term offers a great opportunity to understand the different factors that influenced the course of translating the Greek heritage into the Arabic world.
Visual Comparator: An Interactive Tool for Dynamic Spatiotemporal Comparative Visualizations
Authors: Cherukuru Nihanth W. , Scheitlin Tim 
Published: June 2020

AbstractVisualizations enable us to detect patterns, time-evolving features, and trends in complex datasets that might not be obvious by looking at the raw data. The visual exploration process often requires comparisons between multiple visualizations, either from the same dataset or a different one, to identify relationships and patterns. This visualization process, referred to as comparative visualization, is valuable for analyzing multivariate, multispectral, or multidimensional data. The existing tools that facilitate visual comparisons do this by three means: juxtaposition (placing visuals side by side), superposition (overlaying visuals), and explicit encoding (visualizing a derived quantity corresponding to the relationship being studied). While superposition is ideal for static, geospatial datasets, where spatialization is a key component of the data, the spatiotemporal nature of Earth science datasets presents a challenge with comparative visualizations. Visual Comparator is an interactive, cross-platform (desktops, kiosks, and web), open-source application, developed to address this shortcoming. The application is used to superimpose and compare up to three synchronized, animated visualizations, and a transition between the visualizations is provided through a slider-based interface. This form of visualization has the advantage of drawing the viewers’ attention to changes between the datasets, enabling comparisons of scale, and reducing the clutter caused by having multiple variables in one visual. This article provides an overview of the project, a brief review of literature pertaining to human perception research and comparative visualizations, and a guide to accessing this application.
Performance of self-reported and unsupervised antenatal pelvic floor muscle training and its effects on postpartum stress urinary incontinence among Chinese women: a cohort study
Authors: Chen Ling , Chen Xiaomin , Luo Dan , Jin Mei , Hu Yingjie , Cai Wenzhi 
Published: June 2020

Objectives We investigated performance of antenatal pelvic floor muscle training (PFMT) among Chinese pregnant women, to explore its effects on postpartum stress urinary incontinence (SUI). Methods We conducted a prospective cohort study in Shenzhen, China among 815 singleton pregnant women age ≥18 years, who were continent before pregnancy. Telephone follow-up was conducted at 6 weeks postpartum. Logistic univariable and multivariable regression analyses were used to estimate effects of antenatal PFMT (frequency and duration) on SUI postpartum among subgroups defined by SUI during pregnancy. The interactions of antenatal PFMT and PFMT duration on SUI postpartum were tested. Results Among 798 women included in the analysis, 127 (15.91%) had SUI at 6 weeks postpartum. Only 157 (19.67%) women performed antenatal PFMT, none under supervision. After adjusting potential confounders, neither frequency (odds ratio (OR) = 1.08, 95% confidence interval (CI) 0.89–1.32) nor duration (OR = 1.03, 95% CI 0.87–1.23) of antenatal PFMT was a significant factor in postpartum SUI. No interactions of antenatal PFMT and PFMT duration on SUI postpartum were found in any participants or subgroups. Conclusion No effect of self-reported, unsupervised, self-initiated antenatal PFMT on SUI 6 weeks postpartum was found. Low doses and no supervision may have contributed to the negative results.
Can We Reduce Deception in Elite Field Experiments? Evidence from a Field Experiment with State Legislative Offices
Authors: Landgrave Michelangelo 
Published: June 2020

AbstractThe use of deception is common in elite correspondence audit studies. Elite audit studies are a type of field experiment used by researchers to test for discrimination against vulnerable populations seeking to access government resources. These studies have provided invaluable insights, but they have done so at the cost of using deception. They have relied on identity, activity, and motivation deception. In addition, they request unnecessary work. Is there a less deceptive alternative? In this article, I present results from a field experiment with state legislative offices that minimize the use of deception. Consistent with elite correspondence audit studies, I find evidence of discrimination against Hispanics among state legislative offices. In addition, I find that discrimination is mitigated when subjects believe their behavior will be public knowledge. This suggests that discrimination can be mitigated through increased monitoring. This article advances the discussion on how to minimize the use of deception in elite field experimentation and how to mitigate discrimination against vulnerable populations.
Low folate intake and serum levels are associated with higher body mass index and abdominal fat accumulation: a case control study
Authors: Mlodzik-Czyzewska Monika A. , Malinowska Anna M. , Chmurzynska Agata 
Published: June 2020

Abstract
Background
The link between folate metabolism and obesity has recently been underlined, suggesting that folate deficiency may lead to body weight gain and adiposity. We thus wished to determine whether the inefficiency in folate metabolism caused by genetic variation in the MTHFR and DHFR genes in folate metabolism, or inadequate folate intake, is associated with obesity.

Methods
A case–control study including 421 healthy participants (aged 20–40) was performed in Poznań, Poland. The cases were 213 subjects with BMI > 25 kg/m2, while the controls were 208 subjects with BMI < 25 kg/m2. Genotyping of rs70991108 (DHFR) and rs1801133 (MTHFR) was performed using TaqMan probes. Serum folate concentrations were measured using an enzyme-linked immunosorbent assay and homocysteine was assessed with high performance liquid chromatography.

Results
Subjects with overweight and obesity had 12% lower folate intake (p < 0.05) and 8.5% lower folate serum concentrations (p < 0.01) than the controls. Serum folate concentrations and folate intake were inversely associated with body fat percentage (p < 0.05) and waist circumference (p < 0.05 and p < 0.001, respectively). Serum folate concentration, though not folate intake, was negatively associated with WHR and BMI (p < 0.05, for both associations).

Conclusions
Lower folate intake and serum levels are weakly, but independently, associated with greater body weight and central adiposity in people aged 20–40. MTHFR and DHFR polymorphism seems not to have significant impact on body weight.
Coagulase-negative staphylococci (CoNS) as a significant etiological factor of laryngological infections: a review
Authors: Michalik Michał , Samet Alfred , Podbielska-Kubera Adrianna , Savini Vincenzo , Międzobrodzki Jacek , Kosecka-Strojek Maja 
Published: June 2020

AbstractThis review article shows that coagulase-negative staphylococci (CoNS) are widely responsible for laryngological diseases. General characteristics of CoNS infections are shown in the introduction, and the pathogenicity in terms of virulence determinants, biofilm formation and genetic regulation mechanisms of these bacteria is presented in the first part of the paper to better display the virulence potential of staphylococci. The PubMed search keywords were as follows: CoNS and: nares infections, nasal polyps, rhinosinusitis, necrosing sinusitis, periprosthetic joint infection, pharyngitis, osteomyelitis of skull and neck bones, tonsillitis and recurrent tonsillitis. A list of laryngological infections and those related to skull and neck bones was presented with descriptions of the following diseases: rhinosinusitis, necrotizing sinusitis, nasal polyps, nares and nasal skin infections, periprosthetic joint infections, osteomyelitis, pharyngitis, and tonsillitis. Species identification and diagnostic problems challenging for diagnosticians are presented. Concluding remarks regarding the presence of CoNS in humans and their distribution, particularly under the effect of facilitating factors, are mentioned.
Dental disorders in sows from Swedish commercial herds
Authors: Malmsten Anna , Lundeheim Nils , Dalin Anne-Marie 
Published: June 2020

AbstractKnowledge on dental disorders in commercial sows is limited although such conditions may have important animal welfare implications. In a pilot study, the dental and periodontal health of 58 sows (Landrace*Yorkshire-crosses) from 8 Swedish commercial pig herds, slaughtered at one abattoir, were investigated. The oral cavity was inspected and abnormalities were recorded on a dental chart modified for pigs. Dental abnormalities, absence of teeth, supernumerary teeth, tooth fractures, signs of caries, and malalignment were recorded. The study revealed that 19% of the sows had supernumerary teeth and 59% of the sows missed at least one tooth. Periodontitis, calculus and malalignment were observed in 33%, 45% and 17%, respectively. Tooth wear was very common both in incisors (total 83%) and in premolars/molars (total 84%). One or more tooth fractures (between 1 and 6 per sow) was found in 41%. Signs of caries was found in 9%. In order to assess oral health, three indices were used: calculus index (CI), periodontal index (PDI) and tooth wear index (TWI). Severe periodontitis, tooth wear in incisors and tooth wear in premolars/molars were found in 7%, 34% and 35%, respectively. With respect to animal welfare, the etiology and the effects of the disorders on health, stress and pain need to be investigated.