bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of a large H i ring around the quiescent galaxy AGC 203001
Authors: Bait Omkar , Kurapati Sushma , Duc Pierre-Alain , Cuillandre Jean-Charles , Wadadekar Yogesh , Kamphuis Peter , Barway Sudhanshu 
Published: October 2019

Abstract
Here we report the discovery with the Giant Metrewave Radio Telescope of an extremely large (∼115 kpc in diameter) H i ring, located around a massive quenched galaxy, AGC 203001, but off-centered, with respect to it. This ring does not have any bright extended optical counterpart unlike several other known ring galaxies. Our deep g, r, and i optical imaging of the H i ring, using the MegaCam instrument on the Canada-France-Hawaii Telescope, shows however several regions with faint optical emission at a surface brightness level of ∼28 mag/arcsec2. Such an extended H i structure is very rare with only one other case known so far – the Leo ring. Conventionally, off-centered rings have been explained by a collision with an “intruder” galaxy leading to expanding density waves of gas and stars in the form of a ring. However, in such a scenario the impact also leads to large amounts of star formation in the ring which is not observed in the ring presented in this paper. We discuss possible scenarios for the formation of such H i dominated rings.
More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment
Authors: Liu Yichen , Weyrich Laura S , Llamas Bastien 
Published: October 2019

AbstractWhether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
EPD in 2020: enhanced data visualization and extension to ncRNA promoters
Authors: Meylan Patrick , Dreos René , Ambrosini Giovanna , Groux Romain , Bucher Philipp 
Published: October 2019

Abstract
The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome browser, queried or analyzed via web interfaces, or exported in standard formats (FASTA, BED, CSV) for subsequent analysis with other tools. Recent work has focused on the improvement of the EPD promoter viewers, which use the UCSC Genome Browser as visualization platform. Thousands of high-resolution tracks for CAGE, ChIP-seq and similar data have been generated and organized into public track hubs. Customized, reproducible promoter views, combining EPD-supplied tracks with native UCSC Genome Browser tracks, can be accessed from the organism summary pages or from individual promoter entries. Moreover, thanks to recent improvements and stabilization of ncRNA gene catalogs, we were able to release promoter collections for certain classes of ncRNAs from human and mouse. Furthermore, we developed automatic computational protocols to assign orphan TSS peaks to downstream genes based on paired-end (RAMPAGE) TSS mapping data, which enabled us to add nearly 9000 new entries to the human promoter collection. Since our last article in this journal, EPD was extended to five more model organisms: rhesus monkey, rat, dog, chicken and Plasmodium falciparum.
Follow the (ISSUE) Leader? The Leader-Led Nexus Revisited
Authors: Bodet Marc André , Dufresne Yannick , Bouchard Joanie , Gélineau François 
Published: October 2019

AbstractPublic opinion scholars have long debated the relationship between policy preferences, electoral candidates, and voters. While some argue that voters’ positions on the issues of the day affect the positions candidates take, others argue that relationship runs the other way. Gabriel Lenz’s 2012 book on the leader-led nexus provides an original design and provocative conclusions in a comparative context, though some have criticized the author’s findings (see, for instance, Matthews 2017). This article makes use of a multiwave voting advice application (VAA) panel dataset collected in the Canadian province of Quebec to test the generalizability of some of Lenz’s fundamental conclusions. Our results show that the influence of leaders on voters may be less important—or even reversed—where issues at stake are easy for voters to understand. The results offer evidence of issue priming and partisan influence; as well, the effect of leader influence on voters’ issue positions can vary by age group.
BLOCKS WITH NORMAL ABELIAN DEFECT AND ABELIAN p′ INERTIAL QUOTIENT
Authors: Benson David , Kessar Radha , Linckelmann Markus 
Published: October 2019

Abstract
Let $k$ be an algebraically closed field of characteristic $p$, and let ${\mathcal{O}}$ be either $k$ or its ring of Witt vectors $W(k)$. Let $G$ be a finite group and $B$ a block of ${\mathcal{O}} G$ with normal abelian defect group and abelian $p^{\prime}$ inertial quotient $L$. We show that $B$ is isomorphic to its second Frobenius twist. This is motivated by the fact that bounding Frobenius numbers is one of the key steps towards Donovan’s conjecture. For ${\mathcal{O}}=k$, we give an explicit description of the basic algebra of $B$ as a quiver with relations. It is a quantized version of the group algebra of the semidirect product $P\rtimes L$.
When Investor Incentives and Consumer Interests Diverge: Private Equity in Higher Education
Authors: Eaton Charlie , Howell Sabrina T , Yannelis Constantine 
Published: October 2019

AbstractWe study how private equity buyouts create value in higher education, a sector with opaque product quality and intense government subsidy. With novel data on 88 private equity deals involving 994 schools, we show that buyouts lead to higher tuition and per-student debt. Exploiting loan limit increases, we find that private equity-owned schools better capture government aid. After buyouts, we observe lower education inputs, graduation rates, loan repayment rates, and earnings among graduates. Neither school selection nor student body changes fully explain the results. The results indicate that in a subsidized industry, maximizing value may not improve consumer outcomes.Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Multicentric reticulohistiocytosis: the Mayo Clinic experience (1980–2017)
Authors: Sanchez-Alvarez Catalina , Sandhu Avneek Singh , Crowson Cynthia S , Wetter David A , McKenzie Gavin A , Lehman Julia S , Makol Ashima 
Published: October 2019

Abstract

Objectives
Multicentric reticulohistiocytosis (MRH), a rare histiocytic disease that can mimic other rheumatic conditions, may be associated with cancer and other autoimmune disorders. To better understand the disorder and its other associations, we aimed to evaluate clinical correlates and outcomes of all patients with MRH seen at Mayo Clinic, Rochester between 1980 and 2017.

Methods
A retrospective medical record review was conducted to identify all patients with MRH between 1 January 1980 and 30 April 2017.

Results
We identified 24 patients with biopsy-proven MRH (58% female, 75% Caucasian, median age at diagnosis 52 years, median follow-up of 2.3 years). All patients had cutaneous and articular involvement; 23 (96%) patients had papulonodular skin lesions (87% periungual and dorsal hand) and seven (30%) mucosal nodules; and 22 (92%) patients had arthralgias, 21 (88%) joint effusions and 13 (54%) synovitis. Most frequently used therapies included corticosteroids, cyclophosphamide, methotrexate and bisphosphonates. Biologics were used in four patients. Nine patients had symptomatic resolution at 1 year and 12 partial improvement. Radiological findings included erosive changes in three (60%) patients and arthritis mutilans in two patients (40%). Twenty-nine per cent of patients had a concomitant autoimmune disease and 25% malignancy including melanoma, endometrial, peritoneal and lung carcinoma. The 5-year survival rate was 85% (95% CI: 74, 100%).

Conclusion
To our knowledge, this is the largest single-centre series of patients with MRH highlighting the rarity of the condition and an unmet need for treatment options that can allow sustained disease remission. It also highlights the need for a high vigilance for malignancy and autoimmune diseases.
Synaesthetic colour associations for Japanese Kanji characters: from the perspective of grapheme learning
Authors: Asano Michiko , Takahashi So-ichiro , Tsushiro Takuya , Yokosawa Kazuhiko 
Published: October 2019

One of the fundamental questions about grapheme–colour synaesthesia is how specific associations between the graphemes and colours are formed. We addressed this question by focusing on the determinants of synaesthetic colours for Japanese Kanji characters (logographic characters) using a psycholinguistic approach. Study 1 explored the influence meaning has on synaesthetic colours for Kanji characters representing abstract meanings by examining synaesthetic colours for antonym pairs (i.e. characters with meanings opposed to each other) in Japanese synaesthetes. Results showed that semantic relations influenced the grapheme–colour associations for characters representing abstract meanings in the early stages of learning abstract Kanji, while the influence was reduced in the grapheme–colour associations for those learned later. Study 2 examined the effect that learning new sounds or meanings of graphemes has on synaesthetic colours for those graphemes. Japanese synaesthetes were taught new sounds or new meanings for familiar Kanji characters. Results indicated that acquiring new information for graphemes slightly but significantly reduced the test–retest grapheme–colour association consistency, suggesting that synaesthetic colours can be modulated to reflect the synaesthete's latest knowledge about graphemes. Implications of these findings are discussed from the perspective of the relationship between synaesthesia and grapheme learning.
This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Distinct colours in the ‘synaesthetic colour palette’
Authors: Rouw Romke , Root Nicholas B. 
Published: October 2019

In grapheme-colour synaesthesia, particular linguistic elements evoke particular colour sensations. Interestingly, when asked, non-synaesthetes can also associate colours to letters, and previous studies show that specific letter-to-colour associations have similar biases to those of synaesthetes. However, it is an open question whether the colours reported by synaesthetes and non-synaesthetes differoverall: is there a ‘synaesthetic colour palette’? In this study, we visualize the overall distribution in colour space of colour concurrents in grapheme-colour synaesthetes, and colour associations in non-synaesthetic controls. We confirm the existence of a synaesthetic colour palette: colour concurrents in synaesthetes are different from colour associations in non-synaesthetes. We quantify three factors that distinguish the colour palette of synaesthetes and non-synaesthetes: synaesthetes have an increased over-representation of ‘pure’ (unmixed) hues, an increased presence of ‘warm’ (yellow, orange, brown) colours, and an increased presence of achromatic (grey, white, black) colours. Furthermore, we demonstrate that differences in the synaesthetic colour palette can be used to train a machine learning algorithm to reliably classify single subjects as synaesthetes versus non-synaesthetes without using test–retest consistency data. As far as we know, this is the first time an individual could be ‘diagnosed’ as a synaesthete, based only on his or her colours evoked by letters.This article is part of a discussion meeting issue ‘Bridging senses: novel insights from synaesthesia’.
Seroprevalence of Varicella Zoster virus in China: an age-stratifed systematic review and meta-analysis
Authors: Wang Li , Sun Fu , Liu Siyang , Zhang Hongyi , Lu Bo , Shao Xiaoli , Zhang Minxin , Li Zhengwei 
Published: October 2019

AbstractOBJECTIVESthe aim of this meta-analysis was pooled on the comprehensive information of the epidemiology of VZV infection and analyzed the seropositivity of VZV-IgG antibodies in different age groups in China, so as to arouse people’s attention on VZV.DESIGNSystematic reviewDATA SOURCESSources included on PubMed, the China National Knowledge Infrastructure (CNKI) database, WANFANG database and the Chinese Scientific Journals Full-Text Database (CQVIP) from 1997 to 2019.ELIGIBILITY CRITERIA(1) the Chinese and English literatures of study on varicella-zoster virus immunization epidemics in different regions of China; (2) The literature has obvious age stratification; (3) The subjects are general people; (4) VZV sero-prevalence in the population investigated by the literature research institute. Exclusion criteria: Any study that did not contain these information was excluded.DATA EXTRACTION AND SYNTHESISTwo evaluators independently retrieved documents and extracted data. Information about the study design, eligible population, age and gender distribution, inclusion and exclusion criteria were checked. When they disagreed, they could solve the problem by discussion or by soliciting opinions from third parties.RESULTSLiteratures were screened according to the inclusion criteria and 10 studies from 1997 to 2019 with a total of 11666 individuals were included. The overall VZV seroprevalence in the Chinese population was 65.80% (95% CI; 56.5% - 75.1%), and the peak prevalence was seen in the age 36-45 93.50% (95% CI; 0.917-0.953) while the VZV seroprevalence rate (82.20%, 95% CI: 0.544-1.099) was not increased in individuals of 45 and older.CONCLUSIONThe incidence of VZV increases with age, and there was no significant difference between different genders or regions. This results can provide epidemiological evidence for the prevention and treatment of VZV.Strengths and limitations of this studyA broad search strategy and systematic review methodology were used to generate this comprehensive review on advice for prevention and treatment of VZV.Every inclusion article was assessed with a risk of bias tool and/or a quality assessment tool.Because of relatively small sample size, the incomplete data, and the different research objects, there are some bias in the outcomes, which limits the ability to make discrete conclusions.There were not enough articles identified to perform a meta-analysis.
Pan-cancer single cell RNA-seq uncovers recurring programs of cellular heterogeneity
Authors: Kinker Gabriela S. , Greenwald Alissa C. , Tal Rotem , Orlova Zhanna , Cuoco Michael S. , McFarland James M. , Warren Allison , Rodman Christopher , Roth Jennifer A. , Bender Samantha A. , Kumar Bhavna , Rocco James W. , Fernandes Pedro ACM , Mader Christopher C. , Keren-Shaul Hadas , Plotnikov Alexander , Barr Haim , Tsherniak Aviad , Rozenblatt-Rosen Orit , Krizhanovsky Valery , Puram Sidharth V. , Regev Aviv , Tirosh Itay 
Published: October 2019

AbstractCultured cell lines are the workhorse of cancer research, but it is unclear to what extent they recapitulate the cellular heterogeneity observed among malignant cells in tumors, given the absence of a native tumor microenvironment. Here, we used multiplexed single cell RNA-seq to profile ~200 cancer cell lines. We uncovered expression programs that are recurrently heterogeneous within many cancer cell lines and are largely independent of observed genetic diversity. These programs of heterogeneity are associated with diverse biological processes, including cell cycle, senescence, stress and interferon responses, epithelial-to-mesenchymal transition, and protein maturation and degradation. Notably, some of these recurrent programs recapitulate those seen in human tumors, suggesting a prominent role of intrinsic plasticity in generating intra-tumoral heterogeneity. Moreover, the data allowed us to prioritize specific cell lines as model systems of cellular plasticity. We used two such models to demonstrate the dynamics, regulation and drug sensitivities associated with a cancer senescence program also observed in human tumors. Our work describes the landscape of cellular heterogeneity in diverse cancer cell lines, and identifies recurrent patterns of expression heterogeneity that are shared between tumors and specific cell lines and can thus be further explored in follow up studies.
Quantitative Visualization of Hypoxia and Proliferation Gradients Within Histological Tissue Sections
Authors: Zaidi Mark , Fu Fred , Cojocari Dan , McKee Trevor D. , Wouters Bradly G. 
Published: October 2019

AbstractThe formation of hypoxic microenvironments within solid tumors is known to contribute to radiation resistance, chemotherapy resistance, immune suppression, increased metastasis, and an overall poor prognosis. It is therefore crucial to understand the spatial and molecular mechanisms that contribute to tumor hypoxia formation to improve the efficacy of radiation treatment, develop hypoxia-directed therapies, and increase patient survival. The objective of this study is to present a number of complementary novel methods for quantifying tumor hypoxia and proliferation, especially in relation to the location of perfused blood vessels.Multiplexed immunofluorescence staining can produce whole slide scanned image datasets that are amenable for computational pathology analysis. A standard marker analysis strategy is to take a positive pixel count approach, in which a threshold for positive stain is used to compute a positive area fraction for hypoxia. This work is a reassessment of that approach, utilizing not only cell segmentation but also distance to nearest blood vessel in order to incorporate spatial information into the analysis. We describe a reproducible pipeline for the visualization and quantitative analysis of hypoxia using a vessel distance analysis approach. This methodological pipeline can serve to further elucidate the relationship between vessel distance and microenvironment-linked markers such as hypoxia and proliferation, can help to quantify parameters relating to oxygen consumption and hypoxic tolerance in tissues, as well as potentially serve as a hypothesis generating tool for future studies testing hypoxia-linked markers.
Translation inhibition from a distance: the small RNA SgrS interferes with a ribosomal protein S1-dependent enhancer
Authors: Azam Muhammad S. , Vanderpool Carin K. 
Published: October 2019

SummaryMany bacterial small RNAs (sRNAs) efficiently inhibit translation of target mRNAs by forming a duplex that sequesters the Shine-Dalgarno (SD) sequence or start codon and prevents formation of the translation initiation complex. There are a growing number of examples of sRNA-mRNA binding interactions distant from the SD region, but how these mediate translational regulation remains unclear. Our previous work in Escherichia coli and Salmonella identified a mechanism of translational repression of manY mRNA by the sRNA SgrS through a binding interaction upstream of the manY SD. Here, we report that SgrS forms a duplex with a uridine-rich translation-enhancing element in the manY 5’ untranslated region. Notably, we show that the enhancer is ribosome-dependent and that the small ribosomal subunit protein S1 interacts with the enhancer to promote translation of manY. In collaboration with the chaperone protein Hfq, SgrS interferes with the interaction between the translation enhancer and ribosomal protein S1 to repress translation of manY mRNA. Since bacterial translation is often modulated by enhancer-like elements upstream of the SD, sRNA-mediated enhancer silencing could be a common mode of gene regulation.
Novelty and emergent patterns in sperm: morphological diversity and evolution of spermatozoa and sperm conjugation in ground beetles (Coleoptera: Carabidae)
Authors: Gomez R. Antonio , Maddison David R. 
Published: October 2019

1.AbstractThe beetle family Carabidae, with about 40,000 species, exhibits enough diversity in sperm structure and behavior to be an excellent model system for studying patterns and processes of sperm evolution. We explore their potential, documenting sperm form in 177 species of ground beetles and collecting data on 1 qualitative and 7 quantitative sperm phenotypic traits. Our sampling captures 61% of the tribal-level diversity of ground beetles. These data highlight the notable morphological diversity of sperm in ground beetles and suggest that sperm in the group have dynamic evolutionary histories with much morphological innovation and convergence. Sperm vary among species in total length from 48-3,400μm and in length and width of the sperm head. Most ground beetles make filamentous sperm with visually indistinct heads, but some or all studied members of the genusOmophron,genusTrachypachus,and tribe Dyschiriini make broad-headed sperm that show morphological differences between species. Most ground beetles package their sperm into groups of sperm, termed conjugates, and ground beetles show variation in conjugate form and in the number and arrangement of sperm in a conjugate. Most ground beetles make sperm conjugates by embedding their sperm in a non-cellular rod or spermatostyle, but some Trechitae make conjugates without a spermatostyle. The spermatostyle is remarkably variable among species and varies in length from 17-41,000μm. Several unrelated groups of ground beetles make only singleton sperm, including Nebriinae, Cicindelinae, many Trechinae, and the tribe Paussini. Given current views about ground beetle relationships, we propose preliminary hypotheses on ground beetle sperm diversification. We hypothesize that spermatostyle and conjugate traits evolve faster than sperm traits and that head width evolves more slowly than head length and sperm length. We propose that conjugation with a spermatostyle evolved early within the history of Carabidae and that it has been lost independently at least three times.Research highlightsGround beetle sperm is morphologically diverse.Most species make sperm conjugates with a spermatostyle, and there is variation in sperm, spermatostyles, and conjugates.Sperm have dynamic evolutionary histories.