bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observational constraints of a new unified dark fluid and the H0 tension
Authors: Yang Weiqiang , Pan Supriya , Paliathanasis Andronikos , Ghosh Subir , Wu Yabo 
Published: October 2019

ABSTRACT
Unified cosmological models have received a lot of attention in astrophysics community for explaining both the dark matter and dark energy evolution. The Chaplygin cosmologies, a well-known name in this group have been investigated matched with observations from different sources. Obviously, Chaplygin cosmologies have to obey restrictions in order to be consistent with the observational data. As a consequence, alternative unified models, differing from Chaplygin model, are of special interest. In the present work, we consider a specific example of such a unified cosmological model, that is quantified by only a single parameter μ, that can be considered as a minimal extension of the Λ-cold dark matter cosmology. We investigate its observational boundaries together with an analysis of the universe at large scale. Our study shows that at early time the model behaves like a dust, and as time evolves, it mimics a dark energy fluid depicting a clear transition from the early decelerating phase to the late cosmic accelerating phase. Finally, the model approaches the cosmological constant boundary in an asymptotic manner. We remark that for the present unified model, the estimations of H0 are slightly higher than its local estimation and thus alleviating the H0 tension.
Two-index model for characterizing site-specific night sky brightness patterns
Authors: Kocifaj Miroslav , Bará Salvador 
Published: October 2019

ABSTRACTThe determination of the all-sky radiance distribution produced by artificial light sources is a computationally demanding task that generally requires intensive calculations. In this paper, we develop an analytical formulation that provides the all-sky radiance distribution produced by an artificial light source as an explicit and analytical function of the observation direction, depending on two single parameters that characterize the overall effects of the atmosphere. One of these parameters is related to the effective attenuation of the light beams, whereas the other accounts for the overall asymmetry of the combined scattering processes in molecules and aerosols. Using this formulation, a wide range of all-sky radiance distributions can be efficiently and accurately calculated in a short time. This substantial reduction in the number of required parameters, in comparison with other approaches that are currently used, is expected to facilitate the development of new applications in the field of light pollution research.
Spatially resolved signature of quenching in star-forming galaxies
Authors: Quai Salvatore , Pozzetti Lucia , Moresco Michele , Citro Annalisa , Cimatti Andrea , Brinchmann Jarle , Gunawardhana Madusha L P , Paalvast Mieke 
Published: October 2019

ABSTRACT
Understanding when, how, and where star formation ceased (quenching) within galaxies is still a critical subject in galaxy evolution studies. Taking advantage of the new methodology developed by Quai et al. to select recently quenched galaxies, we explored the spatial information provided by the IFU data to get critical insights on this process. In particular, we analyse 10 SDSS-IV MaNGA galaxies that show regions with low [O iii]/H α compatible with a recent quenching of the star formation. We compare the properties of these 10 galaxies with those of a control sample of 8 MaNGA galaxies with ongoing star formation in the same stellar mass, redshift, and gas-phase metallicity range. The quenching regions found are located between 0.5 and 1.1 effective radii from the centre. This result is supported by the analysis of the average radial profile of the ionization parameter, which reaches a minimum at the same radii, while the one of the star-forming sample shows an almost flat trend. These quenching regions occupy a total area between ∼ 15 and 45 per cent of our galaxies. Moreover, the average radial profile of the star formation rate surface density of our sample is lower and flatter than that of the control sample, at any radii, suggesting a systematic suppression of the star formation in the inner part of our galaxies. Finally, the radial profiles of gas-phase metallicity of the two samples have a similar slope and normalization. Our results cannot be ascribed to a difference in the intrinsic properties of the analysed galaxies, suggesting a quenching scenario more complicated than a simple inside-out quenching.
Additional Layer of Regulation via Convergent Gene Orientation in Yeasts
Authors: Gilet Jules , Conte Romain , Torchet Claire , Benard Lionel , Lafontaine Ingrid 
Published: October 2019

AbstractConvergent gene pairs can produce transcripts with complementary sequences. We had shown that mRNA duplexes form in vivo in Saccharomyces cerevisiae via interactions of mRNA overlapping 3′-ends and can lead to posttranscriptional regulatory events. Here we show that mRNA duplex formation is restricted to convergent genes separated by short intergenic distance, independently of their 3′-untranslated region (UTR) length. We disclose an enrichment in genes involved in biological processes related to stress among these convergent genes. They are markedly conserved in convergent orientation in budding yeasts, meaning that this mode of posttranscriptional regulation could be shared in these organisms, conferring an additional level for modulating stress response. We thus investigated the mechanistic advantages potentially conferred by 3′-UTR mRNA interactions. Analysis of genome-wide transcriptome data revealed that Pat1 and Lsm1 factors, having 3′-UTR binding preference and participating to the remodeling of messenger ribonucleoprotein particles, bind differently these messenger-interacting mRNAs forming duplexes in comparison to mRNAs that do not interact (solo mRNAs). Functionally, messenger-interacting mRNAs show limited translational repression upon stress. We thus propose that mRNA duplex formation modulates the regulation of mRNA expression by limiting their access to translational repressors. Our results thus show that posttranscriptional regulation is an additional factor that determines the order of coding genes.
Along the Indian Ocean Coast: Genomic Variation in Mozambique Provides New Insights into the Bantu Expansion
Authors: Semo Armando , Gayà-Vidal Magdalena , Fortes-Lima Cesar , Alard Bérénice , Oliveira Sandra , Almeida João , Prista António , Damasceno Albertino , Fehn Anne-Maria , Schlebusch Carina , Rocha Jorge 
Published: October 2019

Abstract
The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory routes they followed during various phases of the expansion remain poorly understood. Here, we analyze the genetic profiles of southwestern and southeastern Bantu-speaking peoples located at the edges of the Bantu expansion by generating genome-wide data for 200 individuals from 12 Mozambican and 3 Angolan populations using ∼1.9 million autosomal single nucleotide polymorphisms. Incorporating a wide range of available genetic data, our analyses confirm previous results favoring a “late split” between West and East Bantu speakers, following a joint passage through the rainforest. In addition, we find that Bantu speakers from eastern Africa display genetic substructure, with Mozambican populations forming a gradient of relatedness along a North–South cline stretching from the coastal border between Kenya and Tanzania to South Africa. This gradient is further associated with a southward increase in genetic homogeneity, and involved minimum admixture with resident populations. Together, our results provide the first genetic evidence in support of a rapid North–South dispersal of Bantu peoples along the Indian Ocean Coast, as inferred from the distribution and antiquity of Early Iron Age assemblages associated with the Kwale archaeological tradition.
Thermal cycling of DNA devices via associative strand displacement
Authors: Hahn Jaeseung , Shih William M 
Published: October 2019

Abstract
DNA-based devices often operate through a series of toehold-mediated strand-displacement reactions. To achieve cycling, fluidic mixing can be used to introduce ‘recovery’ strands to reset the system. However, such mixing can be cumbersome, non-robust, and wasteful of materials. Here we demonstrate mixing-free thermal cycling of DNA devices that operate through associative strand-displacement cascades. These cascades are favored at low temperatures due to the primacy of a net increase in base pairing, whereas rebinding of ‘recovery’ strands is favored at higher temperatures due to the primacy of a net release of strands. The temperature responses of the devices could be modulated by adjustment of design parameters such as the net increase of base pairs and the concentrations of strands. Degradation of function was not observable even after 500 thermal cycles. We experimentally demonstrated simple digital-logic circuits that evaluate at 35°C and reset after transient heating to 65°C. Thus associative strand displacement enables robust thermal cycling of DNA-based devices in a closed system.
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts
Authors: Monteiro Pedro T , Oliveira Jorge , Pais Pedro , Antunes Miguel , Palma Margarida , Cavalheiro Mafalda , Galocha Mónica , Godinho Cláudia P , Martins Luís C , Bourbon Nuno , Mota Marta N , Ribeiro Ricardo A , Viana Romeu , Sá-Correia Isabel , Teixeira Miguel C 
Published: October 2019

Abstract
The YEASTRACT+ information system (http://YEASTRACT-PLUS.org/) is a wide-scope tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in yeasts of biotechnological or human health relevance. YEASTRACT+ is a new portal that integrates the previously existing YEASTRACT (http://www.yeastract.com/) and PathoYeastract (http://pathoyeastract.org/) databases and introduces the NCYeastract (Non-Conventional Yeastract) database (http://ncyeastract.org/), focused on the so-called non-conventional yeasts. The information in the YEASTRACT database, focused on Saccharomyces cerevisiae, was updated. PathoYeastract was extended to include two additional pathogenic yeast species: Candida parapsilosis and Candida tropicalis. Furthermore, the NCYeastract database was created, including five biotechnologically relevant yeast species: Zygosaccharomyces baillii, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica and Komagataella phaffii. The YEASTRACT+ portal gathers 289 706 unique documented regulatory associations between transcription factors (TF) and target genes and 420 DNA binding sites, considering 247 TFs from 10 yeast species. YEASTRACT+ continues to make available tools for the prediction of the TFs involved in the regulation of gene/genomic expression. In this release, these tools were upgraded to enable predictions based on orthologous regulatory associations described for other yeast species, including two new tools for cross-species transcription regulation comparison, based on multi-species promoter and TF regulatory network analyses.
The MetaCyc database of metabolic pathways and enzymes - a 2019 update
Authors: Caspi Ron , Billington Richard , Keseler Ingrid M , Kothari Anamika , Krummenacker Markus , Midford Peter E , Ong Wai Kit , Paley Suzanne , Subhraveti Pallavi , Karp Peter D 
Published: October 2019

Abstract
MetaCyc (MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains 2749 pathways derived from more than 60 000 publications, making it the largest curated collection of metabolic pathways. The data in MetaCyc are evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. MetaCyc is also used as a knowledge base for generating thousands of organism-specific Pathway/Genome Databases (PGDBs), which are available in BioCyc.org and other genomic portals. This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1. Some of the topics that received intensive curation during this period include cobamides biosynthesis, sterol metabolism, fatty acid biosynthesis, lipid metabolism, carotenoid metabolism, protein glycosylation, antibiotics and cytotoxins biosynthesis, siderophore biosynthesis, bioluminescence, vitamin K metabolism, brominated compound metabolism, plant secondary metabolism and human metabolism. Other additions include modifications to the GlycanBuilder software that enable displaying glycans using symbolic representation, improved graphics and fonts for web displays, improvements in the PathoLogic component of Pathway Tools, and the optional addition of regulatory information to pathway diagrams.
Exogenous pyruvate represses histone gene expression and inhibits cancer cell proliferation via the NAMPT–NAD+–SIRT1 pathway
Authors: Ma Rui , Wu Yinsheng , Zhai Yansheng , Hu Bicheng , Ma Wei , Yang Wenqiang , Yu Qi , Chen Zhen , Workman Jerry L , Yu Xilan , Li Shanshan 
Published: October 2019

AbstractPyruvate is a glycolytic metabolite used for energy production and macromolecule biosynthesis. However, little is known about its functions in tumorigenesis. Here, we report that exogenous pyruvate inhibits the proliferation of different types of cancer cells. This inhibitory effect of pyruvate on cell growth is primarily attributed to its function as a signal molecule to repress histone gene expression, which leads to less compact chromatin and misregulation of genome-wide gene expression. Pyruvate represses histone gene expression by inducing the expression of NAD+ biosynthesis enzyme, nicotinamide phosphoribosyltransferase (NAMPT) via myocyte enhancer factor 2C (MEF2C), which then increases NAD+ levels and activates the histone deacetylase activity of SIRT1. Chromatin immunoprecipitation analysis indicates that pyruvate enhances SIRT1 binding at histone gene promoters where it reduces histone acetylation. Although pyruvate delays cell entry into S phase, pyruvate represses histone gene expression independent of cell cycle progression. Moreover, we find that administration of pyruvate reduces histone expression and retards tumor growth in xenograft mice without significant side effects. Using tissues from cervical and lung cancer patients, we find intracellular pyruvate concentrations inversely correlate with histone protein levels. Together, we uncover a previously unknown function of pyruvate in regulating histone gene expression and cancer cell proliferation.
Convolutional neural network model to predict causal risk factors that share complex regulatory features
Authors: Lee Taeyeop , Sung Min Kyung , Lee Seulkee , Yang Woojin , Oh Jaeho , Kim Jeong Yeon , Hwang Seongwon , Ban Hyo-Jeong , Choi Jung Kyoon 
Published: October 2019

Abstract
Major progress in disease genetics has been made through genome-wide association studies (GWASs). One of the key tasks for post-GWAS analyses is to identify causal noncoding variants with regulatory function. Here, on the basis of &gt;2000 functional features, we developed a convolutional neural network framework for combinatorial, nonlinear modeling of complex patterns shared by risk variants scattered among multiple associated loci. When applied for major psychiatric disorders and autoimmune diseases, neural and immune features, respectively, exhibited high explanatory power while reflecting the pathophysiology of the relevant disease. The predicted causal variants were concentrated in active regulatory regions of relevant cell types and tended to be in physical contact with transcription factors while residing in evolutionarily conserved regions and resulting in expression changes of genes related to the given disease. We demonstrate some examples of novel candidate causal variants and associated genes. Our method is expected to contribute to the identification and functional interpretation of potential causal noncoding variants in post-GWAS analyses.
CancerGeneNet: linking driver genes to cancer hallmarks
Authors: Iannuccelli Marta , Micarelli Elisa , Surdo Prisca Lo , Palma Alessandro , Perfetto Livia , Rozzo Ilaria , Castagnoli Luisa , Licata Luana , Cesareni Gianni 
Published: October 2019

Abstract
CancerGeneNet (https://signor.uniroma2.it/CancerGeneNet/) is a resource that links genes that are frequently mutated in cancers to cancer phenotypes. The resource takes advantage of a curation effort aimed at embedding a large fraction of the gene products that are found altered in cancer cells into a network of causal protein relationships. Graph algorithms, in turn, allow to infer likely paths of causal interactions linking cancer associated genes to cancer phenotypes thus offering a rational framework for the design of strategies to revert disease phenotypes. CancerGeneNet bridges two interaction layers by connecting proteins whose activities are affected by cancer drivers to proteins that impact on the ‘hallmarks of cancer’. In addition, CancerGeneNet annotates curated pathways that are relevant to rationalize the pathological consequences of cancer driver mutations in selected common cancers and ‘MiniPathways’ illustrating regulatory circuits that are frequently altered in different cancers.
snoDB: an interactive database of human snoRNA sequences, abundance and interactions
Authors: Bouchard-Bourelle Philia , Desjardins-Henri Clément , Mathurin-St-Pierre Darren , Deschamps-Francoeur Gabrielle , Fafard-Couture Étienne , Garant Jean-Michel , Elela Sherif Abou , Scott Michelle S 
Published: October 2019

AbstractSmall nucleolar RNAs (snoRNAs) are an abundant type of non-coding RNA with conserved functions in all known eukaryotes. Classified into two main families, the box C/D and H/ACA snoRNAs, they enact their most well characterized role of guiding site specific modifications in ribosomal RNA, through the formation of specific ribonucleoprotein complexes, with fundamental implications in ribosome biogenesis. However, it is becoming increasingly clear that the landscape of snoRNA cellular functionality is much broader than it once seemed with novel members, non-uniform expression patterns, new and diverse targets as well as several emerging non-canonical functions ranging from the modulation of alternative splicing to the regulation of chromatin architecture. In order to facilitate the further characterization of human snoRNAs in a holistic manner, we introduce an online interactive database tool: snoDB. Its purpose is to consolidate information on human snoRNAs from different sources such as sequence databases, target information, both canonical and non-canonical from the literature and from high-throughput RNA–RNA interaction datasets, as well as high-throughput sequencing data that can be visualized interactively.
Fluctuations in plasma potassium in patients on dialysis
Authors: Kovesdy Csaba P 
Published: October 2019

AbstractPlasma potassium concentration is maintained in a narrow range to avoid deleterious electrophysiologic consequences of both abnormally low and high levels. This is achieved by redundant physiologic mechanisms, with the kidneys playing a central role in maintaining both short-term plasma potassium stability and long-term total body potassium balance. In patients with end-stage renal disease, the lack of kidney function reduces the body’s ability to maintain normal physiologic potassium balance. Routine thrice-weekly dialysis therapy achieves long-term total body potassium mass balance, but the intermittent nature of dialytic therapy can result in wide fluctuations in plasma potassium concentration and consequently contribute to an increased risk of arrhythmogenicity. Various dialytic and nondialytic interventions can reduce the magnitude of these fluctuations, but the impact of such interventions on clinical outcomes remains unclear.
Policies for Tobacco and E-Cigarette Use: A Survey of All Higher Education Institutions and NHS Trusts in England
Authors: Blackwell Anna K M , Kosīte Daina , Marteau Theresa M , Munafò Marcus R 
Published: October 2019

Abstract

Introduction
There is an absence of evidence regarding the impact of treating tobacco smoking and vaping equivalently in workplace policies. We aimed to describe and compare smoking and vaping policies in acute nonspecialist NHS Trusts (n = 131) and Higher Education Institutions (HEIs) (n = 131) in England.

Methods
We conducted a census of smoking and vaping policies through organizational websites searches and direct requests for information. We recorded whether and where smoking and vaping were permitted.

Results
Smoking was prohibited indoors in all organizations. No NHS Trust permitted smoking freely outdoors, in contrast with 60% of HEIs. In 27% of NHS Trusts and 33% of HEIs smoking was permitted in designated areas, while in 73% of NHS Trusts and 8% of HEIs smoking was prohibited anywhere on site. Vaping was prohibited indoors in all NHS Trusts and all but one HEI, but permitted freely outdoors in 18% of NHS Trusts and 75% of HEIs. Vaping was permitted in designated outdoor spaces in 23% of NHS Trusts: 21% had areas shared with smokers; 2% had separate vaping areas. Vaping was permitted in designated outdoor areas in 18% of HEIs, all of which were shared with smokers. Vaping was prohibited anywhere on site in 54% of NHS Trusts and 6% of HEIs.

Conclusions
Policies vary considerably in whether vaping and smoking are treated equivalently. Smoking policies in most HEIs should be reviewed to include more effective tobacco control approaches. Evidence is needed on the impact of imposing shared or separate spaces on vapers and smokers.

Implications
This report provides a comprehensive review of smoking and vaping policies in two types of organization across England. It highlights key discrepancies between current public health recommendations for vaping and existing workplace policies, which often lead to smokers and vapers sharing spaces. The report identifies the need for evidence on the impact of imposing shared spaces on smokers and vapers to inform workplace policies that maximize public health benefit.
The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients
Authors: An Qin , Hu Youjin , Li Qingjiao , Chen Xufeng , Huang Jiaoti , Pellegrini Matteo , Zhou Xianghong Jasmine , Rettig Matthew , Fan Guoping 
Published: October 2019

Abstract
Circulating cell-free DNAs (cfDNAs) are fragmented DNA molecules released into the blood by cells. Previous studies have suggested that mitochondria-originated cfDNA fragments (mt-cfDNAs) in cancer patients are more fragmented than those from healthy controls. However, it is still unknown where these short mt-cfDNAs originate, and whether the length of mt-cfDNAs can be correlated with tumor burden and cancer progression. In this study, we first performed whole-genome sequencing analysis (WGS) of cfDNAs from a human tumor cell line-xenotransplantation mouse model and found that mt-cfDNAs released from transplanted tumor cells were shorter than the mouse counterpart. We next analyzed blood cfDNA samples from hepatocellular carcinoma and prostate cancer patients and found that mt-cfDNA lengths were inversely related to tumor size as well as the concentration of circulating tumor DNA. Our study suggested that monitoring the size of mt-cfDNAs in cancer patients would be a useful way to estimate tumor burden and cancer progression.