bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the thermal Sunyaev–Zel’dovich effect and excess millimetre emission in quasar environments
Authors: Hall Kirsten R , Zakamska Nadia L , Addison Graeme E , Battaglia Nicholas , Crichton Devin , Devlin Mark , Dunkley Joanna , Gralla Megan , Hill J Colin , Hilton Matt , Hubmayr Johannes , Hughes John P , Huffenberger Kevin M , Kosowsky Arthur , Marriage Tobias A , Maurin Loïc , Moodley Kavilan , Niemack Michael D , Page Lyman A , Partridge Bruce , Dünner Planella Rolando , Schillaci Alessandro , Sifón Cristóbal , Staggs Suzanne T , Wollack Edward J , Xu Zhilei 
Published: October 2019

ABSTRACT
In this paper, we probe the hot, post-shock gas component of quasar-driven winds through the thermal Sunyaev–Zel’dovich (tSZ) effect. Combining data sets from the Atacama Cosmology Telescope, the Herschel Space Observatory, and the Very Large Array, we measure average spectral energy distributions of 109 829 optically selected, radio quiet quasars from 1.4 to 3000 GHz in six redshift bins between 0.3 &lt; z &lt; 3.5. We model the emission components in the radio and far-infrared, plus a spectral distortion from the tSZ effect. At z &gt; 1.91, we measure the tSZ effect at 3.8σ significance with an amplitude corresponding to a total thermal energy of 3.1 × 1060 erg. If this energy is due to virialized gas, then our measurement implies quasar host halo masses are ∼6 × 1012 h−1 M⊙. Alternatively, if the host dark matter halo masses are ∼2 × 1012 h−1 M⊙ as some measurements suggest, then we measure a &gt;90 per cent excess in the thermal energy over that expected due to virialization. If the measured SZ effect is primarily due to hot bubbles from quasar-driven winds, we find that $(5^{+1.2}_{-1.3}$) per cent of the quasar bolometric luminosity couples to the intergalactic medium over a fiducial quasar lifetime of 100 Myr. An additional source of tSZ may be correlated structure, and further work is required to separate the contributions. At z ≤ 1.91, we detect emission at 95 and 148 GHz that is in excess of thermal dust and optically thin synchrotron emission. We investigate potential sources of this excess emission, finding that CO line emission and an additional optically thick synchrotron component are the most viable candidates.
A black box for dark sector physics: predicting dark matter annihilation feedback with conditional GANs
Authors: List Florian , Bhat Ishaan , Lewis Geraint F 
Published: October 2019

Abstract
Traditionally, incorporating additional physics into existing cosmological simulations requires re-running the cosmological simulation code, which can be computationally expensive. We show that conditional Generative Adversarial Networks (cGANs) can be harnessed to predict how changing the underlying physics alters the simulation results. To illustrate this, we train a cGAN to learn the impact of dark matter annihilation feedback (DMAF) on the gas density distribution. The predicted gas density slices are visually difficult to distinguish from their real brethren and the peak counts differ by less than 10 per cent for all test samples (the average deviation is <3 per cent). Finally, we invert the problem and show that cGANs are capable of endowing smooth density distributions with realistic substructure. The cGAN does however have difficulty generating new knots as well as creating/eliminating bubble-like structures. We conclude that trained cGANs can be an effective approach to provide mock samples of cosmological simulations incorporating DMAF physics from existing samples of standard cosmological simulations of the evolution of cosmic structure.
Evolution of supernovae-driven superbubbles with conduction and cooling
Authors: El-Badry Kareem , Ostriker Eve C , Kim Chang-Goo , Quataert Eliot , Weisz Daniel R 
Published: October 2019

ABSTRACT
We use spherically symmetric hydrodynamic simulations to study the dynamical evolution and internal structure of superbubbles (SBs) driven by clustered supernovae (SNe), focusing on the effects of thermal conduction and cooling in the interface between the hot bubble interior and cooled shell. Our simulations employ an effective diffusivity to account for turbulent mixing from non-linear instabilities that are not captured in 1D. The conductive heat flux into the shell is balanced by a combination of cooling in the interface and evaporation of shell gas into the bubble interior. This evaporation increases the density, and decreases the temperature, of the SB interior by more than an order of magnitude relative to simulations without conduction. However, most of the energy conducted into the interface is immediately lost to cooling, reducing the evaporative mass flux required to balance conduction. As a result, the evaporation rate is typically a factor of ∼3–30 lower than predicted by the classical similarity solution of (Weaver et al. 1977), which neglects cooling. Blast waves from the first ∼30 SNe remain supersonic in the SB interior because reduced evaporation from the interface lowers the mass they sweep up in the hot interior. Updating the Weaver solution to include cooling, we construct a new analytic model to predict the cooling rate, evaporation rate, and temporal evolution of SBs. The cooling rate, and hence the hot gas mass, momentum, and energy delivered by SBs, is set by the ambient interstellar mass density and the efficiency of non-linear mixing at the bubble–shell interface.
A black hole X-ray binary at ∼100 Hz: multiwavelength timing of MAXI J1820+070 with HiPERCAM and NICER
Authors: Paice J A , Gandhi P , Shahbaz T , Uttley P , Arzoumanian Z , Charles P A , Dhillon V S , Gendreau K C , Littlefair S P , Malzac J , Markoff S , Marsh T R , Misra R , Russell D M , Veledina A 
Published: October 2019

ABSTRACT
We report on simultaneous sub-second optical and X-ray timing observations of the low-mass X-ray binary black hole candidate MAXI J1820+070. The bright 2018 outburst rise allowed simultaneous photometry in five optical bands (ugrizs) with HiPERCAM/GTC (Optical) at frame rates over 100 Hz, together with NICER/ISS observations (X-rays). Intense (factor of 2) red flaring activity in the optical is seen over a broad range of time-scales down to ∼10 ms. Cross-correlating the bands reveals a prominent anticorrelation on time-scales of ∼seconds, and a narrow sub-second correlation at a lag of ≈ +165 ms (optical lagging X-rays). This lag increases with optical wavelength, and is approximately constant over Fourier frequencies of ∼0.3–10 Hz. These features are consistent with an origin in the inner accretion flow and jet base within ∼5000 Gravitational radii. An additional ∼+5 s lag feature may be ascribable to disc reprocessing. MAXI J1820+070 is the third black hole transient to display a clear ∼0.1 s optical lag, which may be common feature in such objects. The sub-second lag variation with wavelength is novel, and may allow constraints on internal shock jet stratification models.
Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes
Authors: Donath Alexander , Jühling Frank , Al-Arab Marwa , Bernhart Stephan H , Reinhardt Franziska , Stadler Peter F , Middendorf Martin , Bernt Matthias 
Published: October 2019

Abstract
With the rapid increase of sequenced metazoan mitochondrial genomes, a detailed manual annotation is becoming more and more infeasible. While it is easy to identify the approximate location of protein-coding genes within mitogenomes, the peculiar processing of mitochondrial transcripts, however, makes the determination of precise gene boundaries a surprisingly difficult problem. We have analyzed the properties of annotated start and stop codon positions in detail, and use the inferred patterns to devise a new method for predicting gene boundaries in de novo annotations. Our method benefits from empirically observed prevalances of start/stop codons and gene lengths, and considers the dependence of these features on variations of genetic codes. Albeit not being perfect, our new approach yields a drastic improvement in the accuracy of gene boundaries and upgrades the mitochondrial genome annotation server MITOS to an even more sophisticated tool for fully automatic annotation of metazoan mitochondrial genomes.
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases
Authors: Tørresen Ole K , Star Bastiaan , Mier Pablo , Andrade-Navarro Miguel A , Bateman Alex , Jarnot Patryk , Gruca Aleksandra , Grynberg Marcin , Kajava Andrey V , Promponas Vasilis J , Anisimova Maria , Jakobsen Kjetill S , Linke Dirk 
Published: October 2019

AbstractThe widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
PhaSepDB: a database of liquid–liquid phase separation related proteins
Authors: You Kaiqiang , Huang Qi , Yu Chunyu , Shen Boyan , Sevilla Cristoffer , Shi Minglei , Hermjakob Henning , Chen Yang , Li Tingting 
Published: October 2019

Abstract
It's widely appreciated that liquid–liquid phase separation (LLPS) underlies the formation of membraneless organelles, which function to concentrate proteins and nucleic acids. In the past few decades, major efforts have been devoted to identify the phase separation associated proteins and elucidate their functions. To better utilize the knowledge dispersed in published literature, we developed PhaSepDB (http://db.phasep.pro/), a manually curated database of phase separation associated proteins. Currently, PhaSepDB includes 2914 non-redundant proteins localized in different organelles curated from published literature and database. PhaSepDB provides protein summary, publication reference and sequence features of phase separation associated proteins. The sequence features which reflect the LLPS behavior are also available for other human protein candidates. The online database provides a convenient interface for the research community to easily browse, search and download phase separation associated proteins. As a centralized resource, we believe PhaSepDB will facilitate the future study of phase separation.
MatrisomeDB: the ECM-protein knowledge database
Authors: Shao Xinhao , Taha Isra N , Clauser Karl R , Gao Yu (Tom) , Naba Alexandra 
Published: October 2019

Abstract
The extracellular matrix (ECM) is a complex and dynamic meshwork of cross-linked proteins that supports cell polarization and functions and tissue organization and homeostasis. Over the past few decades, mass-spectrometry-based proteomics has emerged as the method of choice to characterize the composition of the ECM of normal and diseased tissues. Here, we present a new release of MatrisomeDB, a searchable collection of curated proteomic data from 17 studies on the ECM of 15 different normal tissue types, six cancer types (different grades of breast cancers, colorectal cancer, melanoma, and insulinoma) and other diseases including vascular defects and lung and liver fibroses. MatrisomeDB (http://www.pepchem.org/matrisomedb) was built by retrieving raw mass spectrometry data files and reprocessing them using the same search parameters and criteria to allow for a more direct comparison between the different studies. The present release of MatrisomeDB includes 847 human and 791 mouse ECM proteoforms and over 350 000 human and 600 000 mouse ECM-derived peptide-to-spectrum matches. For each query, a hierarchically-clustered tissue distribution map, a peptide coverage map, and a list of post-translational modifications identified, are generated. MatrisomeDB is the most complete collection of ECM proteomic data to date and allows the building of a comprehensive ECM atlas.
Global analysis of protein synthesis in Flavobacterium johnsoniae reveals the use of Kozak-like sequences in diverse bacteria
Authors: Baez William D , Roy Bappaditya , McNutt Zakkary A , Shatoff Elan A , Chen Shicheng , Bundschuh Ralf , Fredrick Kurt 
Published: October 2019

AbstractIn all cells, initiation of translation is tuned by intrinsic features of the mRNA. Here, we analyze translation in Flavobacterium johnsoniae, a representative of the Bacteroidetes. Members of this phylum naturally lack Shine–Dalgarno (SD) sequences in their mRNA, and yet their ribosomes retain the conserved anti-SD sequence. Translation initiation is tuned by mRNA secondary structure and by the identities of several key nucleotides upstream of the start codon. Positive determinants include adenine at position –3, reminiscent of the Kozak sequence of Eukarya. Comparative analysis of Escherichia coli reveals use of the same Kozak-like sequence to enhance initiation, suggesting an ancient and widespread mechanism. Elimination of contacts between A-3 and the conserved β-hairpin of ribosomal protein uS7 fails to diminish the contribution of A-3 to initiation, suggesting an indirect mode of recognition. Also, we find that, in the Bacteroidetes, the trinucleotide AUG is underrepresented in the vicinity of the start codon, which presumably helps compensate for the absence of SD sequences in these organisms.
A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment
Authors: Leong Ka Wai , Yu Fangyan , Adalsteinsson Viktor A , Reed Sarah , Gydush Gregory , Ladas Ioannis , Li Jiang , Tantisira Kelan G , Makrigiorgos Gerassimos Mike 
Published: October 2019

Abstract
DNA target enrichment via hybridization capture is a commonly adopted approach which remains expensive due in-part to using biotinylated-probe panels. Here we provide a novel isothermal amplification reaction to amplify rapidly existing probe panels without knowledge of the sequences involved, thereby decreasing a major portion of the overall sample preparation cost. The reaction employs two thermostable enzymes, BST-polymerase and duplex-specific nuclease DSN. DSN initiates random ‘nicks’ on double-stranded-DNA which enable BST to polymerize DNA by displacing the nicked-strand. Displaced strands re-hybridize and the process leads to an exponential chain-reaction generating biotinylated DNA fragments within minutes. When starting from single-stranded-DNA, DNA is first converted to double-stranded-DNA via terminal-deoxynucleotidyl-transferase (TdT) prior to initiation of BST–DSN reaction. Biotinylated probes generated by TdT–BST–DSN (TBD) reactions using panels of 33, 190 or 7186 DNA targets are used for hybrid-capture-based target enrichment from amplified circulating-DNA, followed by targeted re-sequencing. Polymerase-nuclease isothermal-chain-reactions generate random amplified probes with no apparent sequence dependence. One round of target-capture using TBD probes generates a modest on-target sequencing ratio, while two successive rounds of capture generate &gt;80% on-target reads with good sequencing uniformity. TBD-reactions generate enough capture-probes to increase by approximately two to three orders-of-magnitude the target-enrichment experiments possible from an initial set of probes.
Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus
Authors: de Groot Arjan , Siponen Marina I , Magerand Romaric , Eugénie Nicolas , Martin-Arevalillo Raquel , Doloy Jade , Lemaire David , Brandelet Géraldine , Parcy François , Dumas Renaud , Roche Philippe , Servant Pascale , Confalonieri Fabrice , Arnoux Pascal , Pignol David , Blanchard Laurence 
Published: October 2019

Abstract
Exposure to harmful conditions such as radiation and desiccation induce oxidative stress and DNA damage. In radiation-resistant Deinococcus bacteria, the radiation/desiccation response is controlled by two proteins: the XRE family transcriptional repressor DdrO and the COG2856 metalloprotease IrrE. The latter cleaves and inactivates DdrO. Here, we report the biochemical characterization and crystal structure of DdrO, which is the first structure of a XRE protein targeted by a COG2856 protein. DdrO is composed of two domains that fold independently and are separated by a flexible linker. The N-terminal domain corresponds to the DNA-binding domain. The C-terminal domain, containing three alpha helices arranged in a novel fold, is required for DdrO dimerization. Cleavage by IrrE occurs in the loop between the last two helices of DdrO and abolishes dimerization and DNA binding. The cleavage site is hidden in the DdrO dimer structure, indicating that IrrE cleaves DdrO monomers or that the interaction with IrrE induces a structural change rendering accessible the cleavage site. Predicted COG2856/XRE regulatory protein pairs are found in many bacteria, and available data suggest two different molecular mechanisms for stress-induced gene expression: COG2856 protein-mediated cleavage or inhibition of oligomerization without cleavage of the XRE repressor.
Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR
Authors: Ouyang Zhenlin , Zheng Fang , Chew Jared Y , Pei Yingmei , Zhou Jinhong , Wen Keqing , Han Miao , Lemieux M Joanne , Hwang Peter M , Wen Yurong 
Published: October 2019

Abstract
Staphylococcus aureus ArlRS is a key two-component regulatory system necessary for adhesion, biofilm formation, and virulence. The response regulator ArlR consists of a C-terminal DNA-binding effector domain and an N-terminal receiver domain that is phosphorylated by ArlS, the cognate transmembrane sensor histidine kinase. We demonstrate that the receiver domain of ArlR adopts the canonical α5β5 response regulator assembly, which dimerizes upon activation, using beryllium trifluoride as an aspartate phosphorylation mimic. Activated ArlR recognizes a 20-bp imperfect inverted repeat sequence in the ica operon, which is involved in intercellular adhesion polysaccharide production. Crystal structures of the inactive and activated forms reveal that activation induces a significant conformational change in the β4-α4 and β5-α5-connecting loops, in which the α4 and α5 helices constitute the homodimerization interface. Crystal structures of the DNA-binding ArlR effector domain indicate that it is able to dimerize via a non-canonical β1–β2 hairpin domain swapping, raising the possibility of a new mechanism for signal transduction from the receiver domain to effector domain. Taken together, the current study provides structural insights into the activation of ArlR and its recognition, adding to the diversity of response regulation mechanisms that may inspire novel antimicrobial strategies specifically targeting Staphylococcus.
Analysis of the structural variability of topologically associated domains as revealed by Hi-C
Authors: Sauerwald Natalie , Singhal Akshat , Kingsford Carl 
Published: October 2019

Abstract
Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside the region. A central question is the degree to which TADs are conserved or vary between conditions. We analyze 137 Hi-C samples from 9 studies under 3 measures to quantify the effects of various sources of biological and experimental variation. We observe significant variation in TAD sets between both non-replicate and replicate samples, and provide initial evidence that this variability does not come from genetic sequence differences. The effects of experimental protocol differences are also measured, demonstrating that samples can have protocol-specific structural changes, but that TADs are generally robust to lab-specific differences. This study represents a systematic quantification of key factors influencing comparisons of chromosome structure, suggesting significant variability and the potential for cell-type-specific structural features, which has previously not been systematically explored. The lack of observed influence of heredity and genetic differences on chromosome structure suggests that factors other than the genetic sequence are driving this structure, which plays an important role in human disease and cellular functioning.
Renal outcomes in adult patients with horseshoe kidney
Authors: Kang Minjung , Kim Yong Chul , Lee Hajeong , Kim Dong Ki , Oh Kook-Hwan , Joo Kwon Wook , Kim Yon Su , Chin Ho Jun , Han Seung Seok 
Published: October 2019

AbstractBackground Horseshoe kidney (HSK) is a congenital disorder that is usually asymptomatic, but that increases the risks of kidney stones and infectious disease. However, renal outcomes such as end-stage renal disease (ESRD) in patients with HSK remain unclear.MethodsIn total, 146 patients with HSK (age of ≥20 years) from two tertiary hospitals were included in this study. Control individuals who underwent medical check-ups were selected by matching for age, sex, serum creatinine level, hypertension and diabetes. The hazard ratios (HRs) for the risks of ESRD and all-cause mortality were calculated after adjustment for multiple variables.ResultsThe proportions of HSK-related complications for obstruction, kidney stones, urinary tract infection and urogenital cancer were 26, 25, 19 and 4%, respectively. During the median follow-up period of 9 years (maximum 32 years), the incidence of ESRD was 2.6/10 000 person-years. The risk of ESRD in patients with HSK was higher than in control individuals [adjusted HR = 7.6; 95% confidence interval (CI) 1.14–50.47]. All-cause mortality did not differ between the two groups (adjusted HR = 0.6; 95% CI 0.08–4.29).ConclusionsPatients with HSK are at risk of ESRD, which may be attributable to the high prevalence of complications. Accordingly, these patients should be regarded as having chronic kidney disease and require regular monitoring of both kidney function and potential complications.