bluuebunny/crossref_metadata_2025_split huggingface dataset:
PS15cey and PS17cke: prospective candidates from the Pan-STARRS Search for kilonovae
Authors: McBrien O R , Smartt S J , Huber M E , Rest A , Chambers K C , Barbieri C , Bulla M , Jha S , Gromadzki M , Srivastav S , Smith K W , Young D R , McLaughlin S , Inserra C , Nicholl M , Fraser M , Maguire K , Chen T-W , Wevers T , Anderson J P , Müller-Bravo T E , Olivares E. F , Kankare E , Gal-Yam A , Waters C 
Published: November 2020

ABSTRACT
Time domain astronomy was revolutionized with the discovery of the first kilonova, AT2017gfo, in August 2017, which was associated with the gravitational wave signal GW170817. Since this event, numerous wide-field surveys have been optimizing search strategies to maximize their efficiency of detecting these fast and faint transients. With the Panoramic Survey Telescope and Rapid Response System (Pan-STARRS), we have been conducting a volume-limited survey for intrinsically faint and fast-fading events to a distance of D ≃ 200 Mpc. Two promising candidates have been identified from this archival search, with sparse data – PS15cey and PS17cke. Here, we present more detailed analysis and discussion of their nature. We observe that PS15cey was a luminous, fast-declining transient at 320 Mpc. Models of BH–NS mergers with a very stiff equation of state could possibly reproduce the luminosity and decline but the physical parameters are extreme. A more likely scenario is that this was an AT2018kzr-like merger event. PS17cke was a faint and fast-declining event at 15 Mpc. We explore several explosion scenarios of this transient including models of it as a NS–NS and BH–NS merger, the outburst of a massive luminous star, and compare it against other known fast-fading transients. Although there is uncertainty in the explosion scenario due to difficulty in measuring the explosion epoch, we find PS17cke to be a plausible kilonova candidate from the model comparisons.
Locating the gamma-ray emission region in the brightestFermi-LAT flat-spectrum radio quasars
Authors: Acharyya Atreya , Chadwick Paula M , Brown Anthony M 
Published: November 2020

ABSTRACTWe present a temporal and spectral analysis of the gamma-ray flux from nine of the brightest flat-spectrum radio quasars (FSRQs) detected with the Fermi Large Area Telescope during its first 8 yr of operation, with the aim of constraining the location of the emission region. Using the increased photon statistics obtained from the two brightest flares of each source, we find evidence of sub-hour variability from B2 1520+31, PKS 1502+106, and PKS 1424−41, with the remaining sources showing variability on time-scales of a few hours. These indicate gamma-ray emission from extremely compact regions in the jet, potentially compatible with emission from within the broad-line region (BLR). The flare spectra show evidence of a spectral cut-off in 7 of the 18 flares studied, further supporting the argument for BLR emission in these sources. An investigation into the energy dependence of cooling time-scales finds evidence for both BLR origin and emission from within the molecular torus (MT). However, Monte Carlo simulations show that the very high energy (Eγ ≥ 20 GeV) emission from all sources except 3C 279, 3C 454.3, and 4C 21.35 is incompatible with a BLR origin. The combined findings of all the approaches used suggest that the gamma-ray emission in the brightest FSRQs originates in multiple compact emission regions throughout the jet, within both the BLR and the MT.
Quark-Novae in the outskirts of galaxies: an explanation of the fast radio burst phenomenon
Authors: Ouyed Rachid , Leahy Denis , Koning Nico 
Published: November 2020

ABSTRACT
We show that old isolated neutron stars in groups and clusters of galaxies experiencing a Quark-Nova phase (QN: an explosive transition to a quark star) may be the source of fast radio bursts (FRBs). Each of the millions of fragments of the ultrarelativistic QN ejecta provides a collisionless plasma for which the ambient medium (galactic/halo, the intragroup/intracluster medium) acts as a relativistic plasma beam. The Buneman and the Weibel instabilities, successively induced by the beam in the fragment, generate particle bunching and observed coherent emission at GHz frequency with a corresponding fluence in the Jy ms range. The duration, frequency drift, and the rate are in agreement with observed properties of FRBs. Repeats (on time-scales of minutes to months) are due to seeing multiple fragments each beaming at a different direction and coming in at different times. Single (non-repeating) FRBs occur when only emission from the primary fragment is within the detector’s sensitivity. Key properties of FRB 121102 (its years of activity) and of FRB 180916.J0158+65 (its ∼16 d period) are recovered. The spatial and temporal coincidence between SGR 1935+2154 and FRB 200428 finds an explanation in our model. We give testable predictions.
Parameter study for the burst mode of accretion in massive star formation
Authors: Meyer D M-A , Vorobyov E I , Elbakyan V G , Eislöffel J , Sobolev A M , Stöhr M 
Published: November 2020

ABSTRACT
It is now a widely held view that, in their formation and early evolution, stars build up mass in bursts. The burst mode of star formation scenario proposes that the stars grow in mass via episodic accretion of fragments migrating from their gravitationally unstable circumstellar discs, and it naturally explains the existence of observed pre-main-sequence bursts from high-mass protostars. We present a parameter study of hydrodynamical models of massive young stellar objects (MYSOs) that explores the initial masses of the collapsing clouds (Mc = 60–$200\, \rm M_{\odot }$) and ratio of rotational-to-gravitational energies (β = 0.005–0.33). An increase in Mc and/or β produces protostellar accretion discs that are more prone to develop gravitational instability and to experience bursts. We find that all MYSOs have bursts even if their pre-stellar core is such that β ≤ 0.01. Within our assumptions, the lack of stable discs is therefore a major difference between low- and high-mass star formation mechanisms. All our disc masses and disc-to-star mass ratios Md/M⋆ &gt; 1 scale as a power law with the stellar mass. Our results confirm that massive protostars accrete about $40\, -\, 60{{\ \rm per\ cent}}$ of their mass in the burst mode. The distribution of time periods between two consecutive bursts is bimodal: there is a short duration ($\sim 1\, -\, 10~\rm yr$) peak corresponding to the short, faintest bursts and a long-duration peak (at $\sim 10^{3}\, -\, 10^{4} \rm yr$) corresponding to the long, FU-Orionis-type bursts appearing in later disc evolution, i.e. around $30\, \rm kyr$ after disc formation. We discuss this bimodality in the context of the structure of massive protostellar jets as potential signatures of accretion burst history.
Diversification of Fungal Chitinases and Their Functional Differentiation in Histoplasma capsulatum
Authors: Goughenour Kristie D , Whalin Janice , Slot Jason C , Rappleye Chad A 
Published: November 2020

Abstract
Chitinases enzymatically hydrolyze chitin, a highly abundant and utilized polymer of N-acetyl-glucosamine. Fungi are a rich source of chitinases; however, the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C) as chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin-binding domains (including the LysM domain) do not define specific clades, but instead are found more broadly across clades of chitinases. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus, Histoplasma capsulatum: six A clade, one B clade, and one formerly classified C clade chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression of CTS3 in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. These results suggest chitinase activity is variable even within subclades and that predictions of functionality require more sophisticated models.
Divergent molecular profile of PIK3CA gene in arsenic-associated bladder carcinoma
Authors: Basu Mukta , Chakraborty Balarko , Ghosh Sabnam , Samadder Sudip , Dutta Sankhadeep , Roy Anup , Pal Dilip Kumar , Ghosh Amlan , Panda Chinmay Kumar 
Published: November 2020

Abstract
The activation of PIK3CA in bladder carcinoma (BlCa) with its recurrent mutations in exon 9 and 20 were well reported. But the association of arsenic on the activation of the pathway is not well elucidated. Therefore, we aimed to analyse the effect of arsenic on the genetic (copy number variation/mutation) and expression profiles of PIK3CA in primary BlCa samples. Infrequent amplification (16%) of the PIK3CA locus was observed, with higher frequency among the arsenic-high (AsH) than arsenic-low (AsL) samples. Frequent (54%) tumour-specific mutations in exon 9 and 20 of PIK3CA were observed in the BlCa samples with prevalent (47%) C&gt;T transition mutations. Exon 9 and 20 harboured 48% and 73% of the total mutations, respectively, with 37% in E542K/E545K and 25% of the mutation in H1047Y/R. Though mutation frequency in AsH and AsL was found to be comparable, we observed some arsenic-specific mutation at c.1633G&gt;A, c.1634A&gt;C (E545K) and c.2985C&gt;T and c.3130G&gt;T mutations, as well as prevalent transverse mutations of A&gt;C and G&gt;T in AsH group. Furthermore, 73% of the BlCa samples showed overexpression (mRNA/protein) of PIK3CA with genetic alterations (amplification/mutation), significantly (P = 0.01) higher in AsH group. However, 36% of the samples showed overexpressed PIK3CA, independent of mutation or amplification, signifying a transcriptional upregulation of PIK3CA gene. Therefore, the expression status of NFκB, a transcription factor of PIK3CA, was assessed and found to be significantly correlated with the overexpression of PIK3CA (mRNA/protein) in AsH group. Similarly, the expression pattern of pAKT1 (Thr 308) was also found to be significantly correlated with PIK3CA overexpression. Finally, AsH patients with the overexpression of PIK3CA or NFκB had the worst overall survival, signifying a strong impact of arsenic on this pathway and outcome of the patients. Thus, our study showed that the arsenic-associated differential molecular profile of PIK3CA/AKT1/NFkB in BlCa has an important role in the molecular pathogenesis of the disease.
Open Targets Platform: supporting systematic drug–target identification and prioritisation
Authors: Ochoa David , Hercules Andrew , Carmona Miguel , Suveges Daniel , Gonzalez-Uriarte Asier , Malangone Cinzia , Miranda Alfredo , Fumis Luca , Carvalho-Silva Denise , Spitzer Michaela , Baker Jarrod , Ferrer Javier , Raies Arwa , Razuvayevskaya Olesya , Faulconbridge Adam , Petsalaki Eirini , Mutowo Prudence , Machlitt-Northen Sandra , Peat Gareth , McAuley Elaine , Ong Chuang Kee , Mountjoy Edward , Ghoussaini Maya , Pierleoni Andrea , Papa Eliseo , Pignatelli Miguel , Koscielny Gautier , Karim Mohd , Schwartzentruber Jeremy , Hulcoop David G , Dunham Ian , McDonagh Ellen M 
Published: November 2020

Abstract
The Open Targets Platform (https://www.targetvalidation.org/) provides users with a queryable knowledgebase and user interface to aid systematic target identification and prioritisation for drug discovery based upon underlying evidence. It is publicly available and the underlying code is open source. Since our last update two years ago, we have had 10 releases to maintain and continuously improve evidence for target–disease relationships from 20 different data sources. In addition, we have integrated new evidence from key datasets, including prioritised targets identified from genome-wide CRISPR knockout screens in 300 cancer models (Project Score), and GWAS/UK BioBank statistical genetic analysis evidence from the Open Targets Genetics Portal. We have evolved our evidence scoring framework to improve target identification. To aid the prioritisation of targets and inform on the potential impact of modulating a given target, we have added evaluation of post-marketing adverse drug reactions and new curated information on target tractability and safety. We have also developed the user interface and backend technologies to improve performance and usability. In this article, we describe the latest enhancements to the Platform, to address the fundamental challenge that developing effective and safe drugs is difficult and expensive.
cola: an R/Bioconductor package for consensus partitioning through a general framework
Authors: Gu Zuguang , Schlesner Matthias , Hübschmann Daniel 
Published: November 2020

AbstractClassification of high-throughput genomic data is a powerful method to assign samples to subgroups with specific molecular profiles. Consensus partitioning is the most widely applied approach to reveal subgroups by summarizing a consensus classification from a list of individual classifications generated by repeatedly executing clustering on random subsets of the data. It is able to evaluate the stability of the classification. We implemented a new R/Bioconductor package, cola, that provides a general framework for consensus partitioning. With cola, various parameters and methods can be user-defined and easily integrated into different steps of an analysis, e.g., feature selection, sample classification or defining signatures. cola provides a new method named ATC (ability to correlate to other rows) to extract features and recommends spherical k-means clustering (skmeans) for subgroup classification. We show that ATC and skmeans have better performance than other commonly used methods by a comprehensive benchmark on public datasets. We also benchmark key parameters in the consensus partitioning procedure, which helps users to select optimal parameter values. Moreover, cola provides rich functionalities to apply multiple partitioning methods in parallel and directly compare their results, as well as rich visualizations. cola can automate the complete analysis and generates a comprehensive HTML report.
Prevalence and Risk Factors for Mycobacterium tuberculosis Infection Among Adolescents in Rural South Africa
Authors: Mzembe Themba , Lessells Richard , Karat Aaron S , Randera-Rees Safiyya , Edwards Anita , Khan Palwasha , Tomita Andrew , Tanser Frank , Baisley Kathy , Grant Alison D 
Published: November 2020

Abstract

Background
We aimed to estimate the prevalence of and explore risk factors for Mycobacterium tuberculosis infection among adolescents in a high tuberculosis (TB) and human immunodeficiency virus (HIV) prevalence setting.

Methods
A cross-sectional study of adolescents (10–19 years) randomly selected from a demographic surveillance area (DSA) in rural KwaZulu-Natal, South Africa. We determined M tuberculosis infection status using the QuantiFERON-TB Gold-plus assay. We used HIV data from the DSA to estimate community-level adult HIV prevalence and random-effects logistic regression to identify risk factors for TB infection.

Results
We enrolled 1094 adolescents (548 [50.1%] female); M tuberculosis infection prevalence (weighted for nonresponse by age, sex, and urban/rural residence) was 23.0% (95% confidence interval [CI], 20.6–25.6%). Mycobacterium tuberculosis infection was associated with older age (adjusted odds ratio [aOR], 1.37; 95% CI, 1.10–1.71, for increasing age-group [12–14, 15–17, and 18–19 vs 10–11 years]), ever (vs never) having a household TB contact (aOR, 2.13; 95% CI, 1.25–3.64), and increasing community-level HIV prevalence (aOR, 1.43 and 95% CI, 1.07–1.92, for increasing HIV prevalence category [25%–34.9%, 35%–44.9%, ≥45% vs &lt;25%]).

Conclusions
Our data support prioritizing TB prevention and care activities in TB-affected households and high HIV prevalence communities.
Lecture on the Automatic Computing Engine (1947)
Authors: Turing Alan 
Published: November 2020

Abstract
On 8 December 1943 the world’s first large-scale special-purpose electronic digital computer—‘Colossus’, as it became known—went into operation at the Government Code and Cypher School (see ‘Computable Numbers: A Guide’, ‘Enigma’, and the introduction to Chapter 4). Colossus was built by Thomas H. Flowers and his team of engineers at the Post Office Research Station in Doll is Hill, London. Until relatively recently, few had any idea that electronic digital computation was used successfully during the Second World War, since those who built and worked with Colossus were prohibited by the Official Secrets Act from sharing their knowledge. Colossus contained approximately the same number of electronic valves (vacuum tubes) as von Neumann’s IAS computer, built at the Princeton Institute of Advanced Study and dedicated in 1952. The IAS computer was forerunner of the IBM 701, the company’s first mass-produced stored-programme electronic computer (1953). The first Colossus had 1,600 electronic valves and Colossus II, installed in mid-1944, 2,400, while the IAS computer had 2,600. Colossus lacked two important features of modern computers. First, it had no internally stored programmes (see ‘Computable Numbers: A Guide’). To set up Colossus for a new task, the operators had to alter the machine’s physical wiring, using plugs and switches. Second, Colossus was not a general-purpose machine, being designed for a specific cryptanalytic task (involving only logical operations and counting). Nevertheless, Flowers had established decisively and for the first time that large-scale electronic computing machinery was practicable. The implication of Flowers’s racks of electronic equipment would have been obvious to Turing. Once Turing had seen Colossus it was, Flowers said, just a matter of Turing’s waiting to see what opportunity might arise to put the idea of his universal computing machine into practice. Precisely such an opportunity fell into Turing’s lap in 1945, when John Womersley invited him to join the Mathematics Division of the National Physical Laboratory (NPL) at Teddington in London, in order to design and develop an electronic stored-programme digital computer—a concrete form of the universal Turing machine of 1936.
Coinage and Identity in the Roman Provinces
Authors: Howgego Christopher , Heuchert Volker , Burnett Andrew 
Published: November 2020

AbstractCoins were the most deliberate of all symbols of public communal identities, yet the Roman historian will look in vain for any good introduction to, or systematic treatment of, the subject. Sixteen leading international scholars have sought to address this need by producing this authoritative collection of essays, which ranges over the whole Roman world from Britain to Egypt, from 200 BC to AD 300. The subject is approached through surveys of the broad geographical and chronological structure of the evidence, through chapters which focus on ways of expressing identity, and through regional studies which place the numismatic evidence in local context.
Aspects of Identity
Authors: Williamson George 
Published: November 2020

AbstractAmodern Example May Help to Clarify some of the issues to be discussed in this chapter. Formerly one of the six republics forming the Socialist Federal Republic of Yugoslavia (SFRY), Bosnia-Hercegovina has since 1995’s Dayton Agreement been an uneasy international protectorate, divided into a Croat-Muslim Federation, and the Serbian ‘Republika Srpska’ (RS). Bosnia’s coinage speaks powerfully about the paradoxes of a state created through a bloody war of identity and ethnic cleansing. These two entities—the Federation and the RS— and three communities—Serbian, Croatian, and Bosnian Muslim—display strong and sometimes aggrieved senses of their own individual identities, and ethnic divisions can arise over the simplest of everyday differences. For example, car registration stickers until recently identified cars as registered either in the Federation or in the RS. The International Community felt compelled to design a coinage in which ethnic differences were avoided. The currency itself is a paradox—known as the ‘Convertible Mark’ (KM), it converts to another currency, the Deutschmark, which no longer exists. But it is in the choice of iconography that the Bosnian KM is most striking; these are some of the least attractive coins ever issued, more akin to subway tokens than to genuine coinage. One side of the 1 KM coin displays the stylized shield motif of Bosnia-Hercegovina, a device approved by the International Community. The other bears the denomination and the words ‘Bosne i Hercegovina’ twice, in one language, and two alphabets, though Serbs, Muslims, and Croats might deny that the Latin script of Catholic Croatia, and the Cyrillic of Orthodox Serbia represent the same language. Aside from this need for linguistic even-handedness, no other motifs are to be found. An iconographic void appears to be the only means of compromise. What does this tell us? First, any minting authority can use coins to send an ideological and iconographical message. Coinages represent both political and economic acts. Second, coinage is in no sense an unmediated or direct guide to the ethnic identities of communities; it represents deliberate political choices made by those in control and may therefore mirror social attitudes of those not in control, attempt to modify them, or ignore them outright.
The Cities and their Money
Authors: Peter Weiss 
Published: November 2020

AbstractIn their Kind Invitation to Contribute to this book the editors assigned me the topic of ‘Authority/control’. The authors of RPC devoted an intensive discussion to the subject, with many facets and displaying an extraordinary knowledge of the material. This is in many respects a difficult field, and it is obvious how wide and heterogeneous is the material, how different the presuppositions were in the various parts of the Roman empire, and with what a broad timespan one has to deal: some three centuries, in which there were many developments and several changes. Despite its gigantic bulk, the coinage affords far fewer unambiguous indications permitting a clear conception of how minting came about and was controlled than one would wish. Epigraphy, which in other cases provides an enormous fund of information, here by contrast leaves us almost entirely in the lurch. It follows that many differences of opinion exist, and in many matters, even on points of central importance, our vision is still clouded. The topic is too complex to permit a thorough discussion of all the questions before us in this narrow space. For that reason I have undertaken a limited evaluation. In what follows, I am concerned only with coins pertaining to the cities. Attention is therefore not paid, for example, to the cistophori in Asia, the coins of Alexandria in Egypt, or of Caesarea in Cappadocia, or to the provincial coinage of Syria. I shall first consider the question of Roman control, but only in the form of some basic observations and reflections. Much must here remain unresolved. My central concern will therefore be the following set of questions: How did the cities organize their monetary production? How were responsibilities apportioned, and who was directly involved? What range of possibilities was there? How in this context are we to interpret the numerous names and functional titles on the coins of many Roman cities, especially in the west, down to Julio-Claudian times, and above all, in continuity with Hellenistic practice, on very many coins from the Greek poleis in Provincia Asia?