bluuebunny/crossref_metadata_2025_split huggingface dataset:
Slightly Degenerate Categories and ℤ-Modular Data
Authors: Lacabanne Abel 
Published: April 2019

AbstractGiven a slightly degenerate braided pivotal fusion category $\mathscr{C}$, we explain how it naturally gives rise to a $\mathbb{Z}$-modular data. We do not restrict to spherical categories and work with pivotal categories. Finally, we give an interpretation in this framework of the Bonnafé–Rouquier categorification of the $\mathbb{Z}$-modular datum associated to nontrivial family of the cyclic complex reflection group.
Access of patients with breast and lung cancer to chemotherapy treatment in public and private hospitals in the city of Buenos Aires
Authors: Recondo Gonzalo , Cosacow César , Cutuli Hernán Javier , Cermignani Luciano , Straminsky Samanta , Naveira Martin , Pitzzu Martin , De Ronato Gabriela , Nacuzzi Gabriela , Taetti Gonzalo , Corsico Santiago , Berrueta Mabel , Colucci Giuliana , Gibbons Luz , Gutierrez Laura , García-Elorrio Ezequiel 
Published: April 2019

Abstract

Objectives
Describe the time elapsed from the diagnosis to treatment with chemotherapy for patients with breast and lung cancer at public and private hospitals in Buenos Aires.

Design
Retrospective cohort study.

Setting
Three public and three private academic hospitals in Buenos Aires.

Participants
Patients with breast (n = 168) or lung cancer (n = 100) diagnosis treated with chemotherapy.

Main outcomes measures
Clinical and sociodemographic data were collected in a stratified sample. We used the Kaplan–Meier estimator to analyse the time elapsed and the log rank test to compare both groups

Results
For breast cancer patients, median time elapsed between diagnosis and treatment with chemotherapy was 76 days (95% CI: 64–86) in public and 60 days (95% CI: 52–65) in private hospitals (P = 0.0001). For adjuvant and neoadjuvant treatments, median time was 130 (95% CI: 109–159) versus 64 (95% CI: 56–73) days (P &lt; 0.0001) and 57 days (95% CI: 49–75) versus 26 (95% CI: 16–41) days, respectively (P = 0.0002). There were no significant differences in the time from first consultation to diagnosis. In patients with lung cancer, median time from diagnosis to treatment was 71 days (95% CI: 60–83) in public hospitals and 31 days (95% CI: 24–39) in private hospitals (P = 0.0002). In the metastatic setting, median time to treatment was 63 days (95% CI: 45–83) in public and 33 (95% CI: 26–44) days in private hospitals (P = 0.005).

Conclusions
There are significant disparity in the access to treatment with chemotherapy for patients in Buenos Aires, Argentina.
Cellular development in muscle differs between Angus steers from low and high muscle score selection lines1
Authors: Greenwood Paul L , O’Rourke Brendon A , Brunner Joe , Johns William H , Arthur Paul F , Cafe Linda M 
Published: April 2019

AbstractThis study assessed cellular characteristics of longissimus lumborum (LL) and semitendinosus (ST) muscles in steers genetically selected for low (Low) or high (High) muscling using live muscle scoring, and High steers with 1 copy of the loss-of-function 821 del11 MSTN allele (HighHet). We hypothesized High and HighHet have altered muscle cellular characteristics and mechanisms influencing muscling compared with Low steers. Angus steers 25 mo old comprising 14 High, 19 Low, and 11 HighHet were backgrounded to 20 mo of age, grain finished for 150 d, and then slaughtered. Body and carcass weights did not differ due to muscling line (P = 0.46). Weight of LL was 16% greater (P = 0.004) and total protein in LL was 18% greater (P = 0.012) in HighHet than Low steers. ST weight in HighHet was 10% and 13% greater than in High and Low steers (P = 0.007), respectively, and of total ST protein 12% and 17% greater in HighHet than High or Low (P = 0.002). Cross-sectional area (CSA) of LL was greater in HighHet than in High and greater in High than in Low (85.0 vs. 77.0 vs. 70.4 cm2, P < 0.001). Apparent number of myofibers and myofibers per unit CSA did not differ between the muscling lines in LL (P = 0.14) or ST (P = 0.47). Myofiber CSA was greater in the ST of Low than of High and HighHet for type 1 (36% and 31% respectively, P = 0.005) and 2A (22% and 25%, P < 0.001). HighHet steers had greater area of glycolytic (type 2X) relative to more oxidative myofiber types within LL (P = 0.02; 11% and 43% more than High and Low, respectively) and ST (P < 0.001; 27% and 75%). Concentration of RNA in LL was 13% and 10% greater (P = 0.005) in High than in Low and HighHet, respectively, and total amount of RNA in LL was 22% greater in High and 20% greater in HighHet than in Low (P < 0.001). The LL of High steers had less protein to RNA (P = 0.03; 57.4 vs. 65.6) and more RNA to DNA (P = 0.007; 9.03 vs. 7.83) than Low. HighHet steers had 11% more DNA in ST than High (P = 0.04) and 19% more RNA in ST than Low (P = 0.012). The shift towards glycolytic myofibers was consistent with loadings in a principal component that explained 39% of the variation in LL and 38% in ST. Overall, these findings show that selection for increased muscling using live cattle muscle scoring, and 1 copy of the 821 del11 MSTN allele, results in more glycolytic muscle. They also suggest that increased muscling of the High compared with Low steers may be associated with increased translational capacity in the LL.
Effect of whole foods and dietary patterns on markers of subclinical inflammation in weight-stable overweight and obese adults: a systematic review
Authors: Cowan Stephanie F , Leeming Emily R , Sinclair Andrew , Dordevic Aimee L , Truby Helen , Gibson Simone J 
Published: April 2019

Abstract

Context
Reduction of subclinical inflammation is a potential target for chronic disease management. Adiposity is a known modifier of meta-inflammation; however, the influence of dietary factors is less clear.

Objective
This review examines evidence from human trials evaluating effects of whole foods or dietary patterns on circulating inflammatory markers in weight-stable overweight and obese adults. It is the first review to investigate effects of diet on inflammation, independent of changes in adiposity.

Data Sources
The Ovid MEDLINE, EMBASE, CINAHL, and Cochrane databases were searched.

Data Extraction
Data extraction was conducted using the Cochrane Collaboration Handbook for Systematic Reviews of Interventions.

Data Analysis
Study quality was evaluated using the Cochrane Collaboration Risk of Bias Assessment tool. Thirty-three studies were included assessing effects of 17 foods and dietary patterns on 39 inflammatory markers.

Conclusions
Overall, foods and dietary patterns were not found to have significant effects on inflammatory markers in weight-stable individuals. Inconsistencies among studies were largely due to methodological limitations. Future research should invest in longer intervention periods and standardization of inflammatory marker panels paired with novel technologies, while ensuring anthropometric measures are monitored and adequately controls are used.

Systematic Review Registration
Prospero registration number CRD42017067765.
Bernard Lonergan
Authors: Byrne Patrick 
Published: April 2019

As with many thinkers of his generation, the Canadian philosopher and theologian Bernard Joseph Francis Xavier Lonergan, SJ (b. 1904–d. 1984), sought to overcome the limitations of the traditions of thought that he inherited. Although a Catholic theologian by profession, he found it necessary to also think through major issues posed by modern philosophy, science, modern mathematics, the historical condition of humanity, economics, ethics, art, and education. He became best known for his theory of knowledge in the decades immediately following the publication of his masterwork, Insight: A Study of Human Understanding (1957). However, the discovery of his numerous unpublished writings following his death in 1984 required a major rethinking of his project. In light of those discoveries, his work on the theory of knowledge has come to be understood as one contribution to his broader effort to find an adequate way to think about and respond authentically to the human condition as historical. As he once put it, “All my work has been introducing history into Catholic theology.” He was dissatisfied with the static metaphysical context of the scholastic philosophy he was taught as a young man, as well as with the historicism that was adopted by many thinkers of the 19th and early 20th centuries. He refined his ideas in numerous unpublished essays, written both before and after the publication of Insight, that addressed the questions of historical process, knowledge, method, and responsibility. He has long been mistakenly categorized as a “transcendental Thomist,” and therefore rejected as a subjectivist and antirealist by many Thomist authors and teachers. It is certainly true that Lonergan was deeply indebted to the thought of Thomas Aquinas, but his studies found in Aquinas a theory of knowledge and a kind of realism that was, and still is, at odds with other prevailing Thomist interpretations. Prior to his two studies of Aquinas, he was already deeply influenced by his readings of Plato, John Henry Newman, Hegel, and Marx. These thinkers prepared him to find in Aquinas ideas that earlier scholars had overlooked—ideas that he would develop into his own unique treatments of knowledge, science, the natural world, history, truth, goodness, and God. He taught at the University of Toronto (Regis College), the Gregorian University (Rome), Harvard University, and Boston College.
Jean Genet
Authors: Hanrahan Mairéad 
Published: April 2019

Jean Genet (b. 19 December 1910–d. 15 April 1986) was a 20th-century French poet, novelist, playwright, film director, essayist, and political activist. His work is renowned for its literary experimentation and poetic intensity and for its unequivocal opposition to the norms of bourgeois culture. Genet’s profile was singularly unconventional for a man of letters. His trajectory was far from traditional: abandoned by his mother when seven months old, he was placed in a foster family until his adolescence. He spent much of his teenage years in a reform school, Mettray, before joining the army only to desert soon afterward. Repeatedly convicted over the following decade for petty theft, he began to write in prison at the age of thirty. His use of highly poetic language in conjunction with an extremely explicit, unapologetic treatment of themes such as homosexuality and criminality won him recognition as a major literary figure in a remarkably short space of time. Within ten years, he had published a collection of poems as well as five dense prose texts and two plays, directed a film, and staged a ballet. Moreover, the prestigious publishing house Gallimard had commissioned his “Completed Works” in an unprecedented gesture for a living author, let alone one only forty years old. Genet then published very little over the next five years, before producing three plays in quick succession. Following the suicide of his lover in 1964, Genet claimed that he would write no more and he tore up his manuscripts; although the archives show that he continued to work on a number of projects, he would publish no further major work during his lifetime. He turned to political activism, culminating in 1970 when he accepted an invitation to tour the United States in support of the Black Panthers, and he spent six months with the Palestinian fedayeen in Jordan. By chance, he was one of the first people to enter the camps of Sabra and Shatila after the massacres in 1982; the experience appears to have been decisive in motivating him to return to writing. Although he had been diagnosed with throat cancer in 1979, he spent his final years working on a text about the Palestinian revolution. He died while correcting the proofs of this book, which was published posthumously one month later. He is buried in Larache, Morocco.
Jurij Lotman
Authors: Lorusso Anna Maria 
Published: April 2019

Jurij (or Yuri) Lotman (b. 1922–d. 1993) was a Russian semiotician and cofounder of the Tartu-Moscow school of semiotics. A Russian philologist by education, his interests ranged from aesthetics to literary and cultural history; from narrative theory to intellectual history; from cinema to mythology. At the core of his theory is a holistic approach to culture as a system whose main feature is the modeling property. Culture is a structural mechanism that generates structurality through a primary modeling system (the verbal language) and secondary modeling systems (art, literature, religion, mythology, etc.). Clearly inspired in the 1970s by the emergence of structuralism in Moscow, over the years he gave an increasingly dynamic interpretation of “structure,” focusing on the evolution of systems and continuous hybridizations of languages. The idea of dialogue as a condition for cultural evolution is a personal echo of Bakhtin’s theory, which assumes an absolute centrality in Lotman. Cultural evolution comes from the relationship with the Other and the exchange with spaces different from our own. In this frame, the idea of border is also pivotal: cultural identities need to define their own borders, but it is precisely on the borders—lines of separation—that we find the maximum exchange. These ideas form the basis of the theory of semiosphere, a successful neologism that, echoing the biosphere of Vernadskij, points out the holistic, functional, and self-organized quality of cultural systems. In his last works (published posthumously in 2009 and 2013), Lotman’s interest in history and temporal layers of cultures is increasingly in the foreground. He focuses on the predictability or otherwise of historical situations, putting the category of explosion at the center of his reflection, as a moment of unexpected acceleration of the historical-cultural dynamism and the creativity of systems. During the 1970s, Lotman’s works and those of other Soviet semioticians were widely read and proved influential, especially in the field of Slavic studies. In the 1980s, they become influential in American and West European academia. Among the scholars who used Lotman’s concepts are the philosopher Paul Ricoeur, the New Historicist Stephen Greenblatt, the semiotician Umberto Eco, the reception theorist Wolfgang Iser, and the feminist critic Julia Kristeva. From 2000s onward, Lotman’s legacy has been pivotal in the field of semiotics, and relevant also to the field of cultural and media studies.
BONNER CYLINDER SET FOR NEUTRON SPECTROSCOPY AT HIGH ENERGY ACCELERATORS
Authors: Sokolov Alexey , Kozlova Ekaterina , Radon Torsten 
Published: April 2019

Abstract
At particle accelerators, the knowledge of neutron spectra is important for radiation protection to improve the accuracy of dose measurements, for activation and radiation damage studies. Classical Bonner sphere spectrometer is a common reliable tool for this kind of measurements. Here we present a new set of cylinders with TLD cards as a sensitive element to be used for neutron spectroscopy in a wide energy range for continuous and ultra-short pulse radiation. A simple layout, relatively small dimensions and weight, as well as implementation of common materials providing low construction costs make the set useful for spectroscopic purposes. The unfolding results for various simulated radiation scenarios are also presented.
Interaction between DNA damage response, translation and apoptosome determines cancer susceptibility to TOP2 poisons
Authors: Awah Chidiebere U , Chen Li , Bansal Mukesh , Mahajan Aayushi , Winter Jan , Lad Meeki , Warnke Louisa , Gonzalez-Buendia Edgar , Park Cheol , Daniel Zhang , Feldstein Eric , Yu Dou , Zannikou Markella , Balyasnikova Irina V. , Martuscello Regina , Konerman Silvana , Győrffy Balázs , Burdett Kirsten B , Scholtens Denise M , Stupp Roger , Ahmed Atique , Hsu Patrick , Sonabend Adam 
Published: April 2019

AbstractTopoisomerase II poisons are one of the most common class of chemotherapeutics used in cancer. We show that glioblastoma (GBM), the most malignant of all primary brain tumors in adults is responsive to TOP2 poisons. To identify genes that confer susceptibility to this drug in gliomas, we performed a genome-scale CRISPR knockout screen with etoposide. Genes involved in protein synthesis and DNA damage were implicated in etoposide susceptibility. To define potential biomarkers for TOP2 poisons, CRISPR hits were overlapped with genes whose expression correlates with susceptibility to this drug across glioma cell lines, revealing ribosomal protein subunit RPS11, 16, 18 as putative biomarkers for response to TOP2 poisons. Loss of RPS11 impaired the induction of pro-apoptotic gene APAF1 following etoposide treatment, and led to resistance to this drug and doxorubicin. The expression of these ribosomal subunits was also associated with susceptibility to TOP2 poisons across cell lines from multiple cancers.Graphical Abstract
A Bayesian Monte Carlo approach for predicting the spread of infectious diseases
Authors: Stojanović Olivera , Leugering Johannes , Pipa Gordon , Ghozzi Stéphane , Ullrich Alexander 
Published: April 2019

AbstractIn this paper, a simple yet interpretable, probabilistic model is proposed for the prediction of reported case counts of infectious diseases. A spatio-temporal kernel is derived from training data to capture the typical interaction effects of reported infections across time and space, which provides insight into the dynamics of the spread of infectious diseases. Testing the model on a one-week-ahead prediction task for campylobacteriosis and rotavirus infections across Germany, as well as Lyme borreliosis across the federal state of Bavaria, shows that the proposed model performs on-par with the state-of-the-arthhh4model. However, it provides a full posterior distribution over parameters in addition to model predictions, which aides in the assessment of the model. The employed Bayesian Monte Carlo regression framework is easily extensible and allows for incorporating prior domain knowledge, which makes it suitable for use on limited, yet complex datasets as often encountered in epidemiology.Author summaryWhy was this study done?Statistical modeling is invaluable to public-health policy as it helps understand and anticipate the dynamics of the spread of infectious diseases. The available training data is often limited and reported with a low spatial and temporal resolution. This poses a challenge and makes it particularly important to incorporate domain knowledge and prior assumptions to guide the modeling process.In order to evaluate the trustworthiness and reliability of a model’s predictions, it is crucial to be able to interpret the model and quantify the model uncertainty.To address this, we develop an interpretable model that uses Bayesian inference (rather than commonly used maximum likelihood estimation) and provides a probability distribution over inferred parameters.What did the researchers do and find?We develop and test a single probabilistic model that learns to predict the number of weekly case counts for three different diseases (campylobacteriosis, rotaviral enteritis and Lyme borreliosis) at the county level one week ahead of time.We employ a Bayesian Monte Carlo regression approach that provides an estimate of the full probability distribution over inferred parameters as well as model predictions.The model learns an interpretable spatio-temporal kernel that captures typical interactions between infection cases of the tested diseases.The predictive performance of our model compares favorably with a contemporary reference model for all diseases tested.What do these findings mean?Interpretable predictive models can be applied to surveillance data to gain insights into the dynamics of infectious diseases.Probabilistic modeling approaches provide a suitable framework for many challenges of working with epidemiological data.
CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length
Authors: Clarkson Christopher T. , Deeks Emma A. , Samarista Ralph , Mamayusupova Hulkar , Zhurkin Victor B. , Teif Vladimir B. 
Published: April 2019

AbstractThe CCCTC-binding factor (CTCF) organises the genome in 3D through DNA loops and in 1D by setting boundaries isolating different chromatin states, but these processes are not well understood. Here we focus on the relationship between CTCF binding and the decrease of the Nucleosome Repeat Length (NRL) for ∼20 adjacent nucleosomes, affecting up to 10% of the mouse genome. We found that the chromatin boundary near CTCF is created by the nucleosome-depleted region (NDR) asymmetrically located >40 nucleotides 5’-upstream from the centre of CTCF motif. The strength of CTCF binding to DNA is correlated with the decrease of NRL near CTCF and anti-correlated with the level of asymmetry of the nucleosome array. Individual chromatin remodellers have different contributions, with Snf2h having the strongest effect on the NRL decrease near CTCF and Chd4 playing a major role in the symmetry breaking. Upon differentiation of embryonic stem cells to neural progenitor cells and embryonic fibroblasts, a subset of common CTCF sites preserved in all three cell types maintains a relatively small local NRL despite genome-wide NRL increase. The sites which lost CTCF upon differentiation are characterised by nucleosome rearrangement 3’-downstream, but the boundary defined by the NDR 5’-upstream of CTCF motif remains.
Genomic hypervariability of phage Andromeda is unique among known dsDNA viruses
Authors: Magill Damian J. , Kulakov Leonid A. , Skvortsov Timofey A. 
Published: April 2019

AbstractA new lytic bacteriophage Andromeda, specific to the economically important plant pathogenPseudomonas syringae, was isolated and characterised. It belongs to thePodoviridaefamily,Autographivirinaesubfamily and possesses a linear dsDNA genome of 40,008 bp with four localised nicks. Crucially, Andromeda’s genome has no less than 80 hypervariable sites (SNPs), which show genome wide distribution resulting in heterogenous populations of this phage reminiscent of those of RNA virus quasispecies. Andromeda has no nucleotide sequence homology to phage phiNFS, a member ofphiKMVviruses, in which a similar phenomenon was discovered. We show that Andromeda and Andromeda-related phages form a group within theAutographivirinae, designated here as the “ExophiKMVviruses”. The “ExophiKMVviruses” were revealed to share conservation of gene order with corephiKMVvirusesdespite their sequence-based relationship to SP6-related phages. Our findings suggest that genomic hypervariability might be a feature that occurs among variousAutographivirinaegroups.
GABA-A signaling maintains melanocyte stem cell quiescence in larval zebrafish
Authors: Allen James R. , Skeath James B. , Johnson Stephen L. 
Published: April 2019

AbstractAdult stem cells (ASCs) contribute to long-term homeostasis and regeneration of many adult tissues. Some ASCs proliferate continuously, others remain quiescent awaiting activation. To identify pathways that regulate ASC quiescence and tissue homeostasis, we study melanocyte stem cells (MSCs) that drive vertebrate pigmentation. In larval zebrafish, MSCs are quiescent, but can be recruited to regenerate the larval pigment pattern following melanocyte ablation. Through pharmacological experiments, we found that inhibition of GABA-A receptor function, specifically the GABA-A rho subtype, induces excessive melanocyte production in larval zebrafish. Conversely, pharmacological activation of GABA-A inhibited melanocyte regeneration. We used CRISPR to generate two mutant alleles ofgabrr1, a subtype of GABA-A. Both alleles exhibited robust melanocyte overproduction, while conditional overexpression ofgabrr1inhibited larval melanocyte regeneration. Our data suggest thatgabrr1signaling is necessary and sufficient to maintain MSC quiescence and prevent excessive pigmentation of the larval zebrafish.