bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey for variable young stars with small telescopes: II – mapping a protoplanetary disc with stable structures at 0.15 au
Authors: Evitts Jack J , Froebrich Dirk , Scholz Aleks , Eislöffel Jochen , Campbell-White Justyn , Furnell Will , Stecklum Bringfried , Urtly Thomas , Pickard Roger , Wiersema Klaas , Dubovský Pavol A , Kudzej Igor , Naves Ramon , Morales Aimar Mario , Castillo García Rafael , Vanmunster Tonny , Schwendeman Erik , Soldán Alfaro Francisco C , Johnstone Stephen , Gonzalez Farfán Rafael , Killestein Thomas , DelgadoCasal Jesús , García de la Cuesta Faustino , Roberts Dean , Kolb Ulrich , Montoro Luís , Licchelli Domenico , Escartin Perez Alex , Perelló Perez Carlos , Deldem Marc , Futcher Stephen R L , Nelson Tim , Dvorak Shawn , Moździerski Dawid , Quinn Nick , Kotysz Krzysztof , Kowalska Katarzyna , Mikołajczyk Przemysław , Fleming George , Phillips Mark , Vale Tony , Dubois Franky , Logie Ludwig , Rau Steve , Vanaverbeke Siegfried , Merrikin Barry , Fernández Mañanes Esteban , Erdelyi Emery , Gonzalez Carballo Juan-Luis , Limon Martinez Fernando , Long Timothy P , San Segundo Delgado Adolfo , Salto González Josép Luis , Tremosa Espasa Luis , Piehler Georg , Crumpton James , Billington Samuel J , D’Arcy Emma , Makin Sally V , Dover Lord 
Published: January 2020

ABSTRACT
The HOYS citizen science project conducts long-term, multifilter, high-cadence monitoring of large YSO samples with a wide variety of professional and amateur telescopes. We present the analysis of the light curve of V1490 Cyg in the Pelican Nebula. We show that colour terms in the diverse photometric data can be calibrated out to achieve a median photometric accuracy of 0.02 mag in broad-band filters, allowing detailed investigations into a variety of variability amplitudes over time-scales from hours to several years. Using Gaia DR2, we estimate the distance to the Pelican Nebula to be 870 $^{+70}_{-55}$ pc. V1490 Cyg is a quasi-periodic dipper with a period of 31.447 ± 0.011 d. The obscuring dust has homogeneous properties, and grains larger than those typical in the ISM. Larger variability on short time-scales is observed in U and Rc−H α, with U amplitudes reaching 3 mag on time-scales of hours, indicating that the source is accreting. The H α equivalent width and NIR/MIR colours place V1490 Cyg between CTTS/WTTS and transition disc objects. The material responsible for the dipping is located in a warped inner disc, about 0.15 au from the star. This mass reservoir can be filled and emptied on time-scales shorter than the period at a rate of up to 10−10 M⊙ yr−1, consistent with low levels of accretion in other T Tauri stars. Most likely, the warp at this separation from the star is induced by a protoplanet in the inner accretion disc. However, we cannot fully rule out the possibility of an AA Tau-like warp, or occultations by the Hill sphere around a forming planet.
Limits on the electromagnetic counterpart to S190814bv
Authors: Watson A M , Butler N R , Lee W H , Becerra R L , Pereyra M , Angeles F , Farah A , Figueroa L , Gónzalez-Buitrago D , Quirós F , Ruíz-Díaz-Soto J , Tejada de Vargas C , Tinoco S J , Wolfram T 
Published: January 2020

ABSTRACTWe derive limits on any electromagnetic counterpart to the compact binary merger S190814bv, whose parameters are consistent with the merger of a black hole and a neutron star. We present observations with the new wide-field optical imager DDOTI and also consider Swift/BAT observations reported by Palmer et al. We show that Swift/BAT would have detected a counterpart with similar properties to a typical on-axis short GRB at the 98 per cent confidence level, whereas our DDOTI observations only rule out such a counterpart at the 27 per cent confidence level. Neither has sufficient sensitivity to rule out an off-axis counterpart like GW 170817. We compare the efficiency of Swift/BAT and DDOTI for future observations, and show that DDOTI is likely to be about twice as efficient as Swift/BAT for off-axis events up to about 100 Mpc.
Simulating star clusters across cosmic time – II. Escape fraction of ionizing photons from molecular clouds
Authors: He Chong-Chong , Ricotti Massimo , Geen Sam 
Published: January 2020

ABSTRACT
We calculate the hydrogen- and helium-ionizing radiation escaping star-forming molecular clouds, as a function of the star cluster mass and compactness, using a set of high-resolution radiation-magnetohydrodynamic simulations of star formation in self-gravitating, turbulent molecular clouds. In these simulations, presented in He et al., the formation of individual massive stars is well resolved, and their UV radiation feedback and lifetime on the main sequence are modelled self-consistently. We find that the escape fraction of ionizing radiation from molecular clouds, $\langle f_{\rm esc}^{\scriptscriptstyle \rm MC}\rangle$ , decreases with increasing mass of the star cluster and with decreasing compactness. Molecular clouds with densities typically found in the local Universe have negligible $\langle f_{\rm esc}^{\scriptscriptstyle \rm MC}\rangle$ , ranging between $0.5{{\ \rm per\ cent}}$ and $5{{\ \rm per\ cent}}$. 10 times denser molecular clouds have $\langle f_{\rm esc}^{\scriptscriptstyle \rm MC}\rangle$ $\approx 10{{\ \rm per\ cent}}{-}20{{\ \rm per\ cent}}$, while 100× denser clouds, which produce globular cluster progenitors, have $\langle f_{\rm esc}^{\scriptscriptstyle \rm MC}\rangle$ $\approx 20{{\ \rm per\ cent}}{-}60{{\ \rm per\ cent}}$. We find that $\langle f_{\rm esc}^{\scriptscriptstyle \rm MC}\rangle$ increases with decreasing gas metallicity, even when ignoring dust extinction, due to stronger radiation feedback. However, the total number of escaping ionizing photons decreases with decreasing metallicity because the star formation efficiency is reduced. We conclude that the sources of reionization at z &gt; 6 must have been very compact star clusters forming in molecular clouds about 100× denser than in today’s Universe, which lead to a significant production of old globular clusters progenitors.
Dynamic changes in cis-regulatory occupancy by Six1 and its cooperative interactions with distinct cofactors drive lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium
Authors: Li Jun , Zhang Ting , Ramakrishnan Aarthi , Fritzsch Bernd , Xu Jinshu , Wong Elaine Y M , Loh Yong-Hwee Eddie , Ding Jianqiang , Shen Li , Xu Pin-Xian 
Published: January 2020

AbstractThe transcription factor Six1 is essential for induction of sensory cell fate and formation of auditory sensory epithelium, but how it activates gene expression programs to generate distinct cell-types remains unknown. Here, we perform genome-wide characterization of Six1 binding at different stages of auditory sensory epithelium development and find that Six1-binding to cis-regulatory elements changes dramatically at cell-state transitions. Intriguingly, Six1 pre-occupies enhancers of cell-type-specific regulators and effectors before their expression. We demonstrate in-vivo cell-type-specific activity of Six1-bound novel enhancers of Pbx1, Fgf8, Dusp6, Vangl2, the hair-cell master regulator Atoh1 and a cascade of Atoh1’s downstream factors, including Pou4f3 and Gfi1. A subset of Six1-bound sites carry consensus-sequences for its downstream factors, including Atoh1, Gfi1, Pou4f3, Gata3 and Pbx1, all of which physically interact with Six1. Motif analysis identifies RFX/X-box as one of the most significantly enriched motifs in Six1-bound sites, and we demonstrate that Six1-RFX proteins cooperatively regulate gene expression through binding to SIX:RFX-motifs. Six1 targets a wide range of hair-bundle regulators and late Six1 deletion disrupts hair-bundle polarity. This study provides a mechanistic understanding of how Six1 cooperates with distinct cofactors in feedforward loops to control lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium.
Exo1 phosphorylation inhibits exonuclease activity and prevents fork collapse in rad53 mutants independently of the 14-3-3 proteins
Authors: Morafraile Esther C , Bugallo Alberto , Carreira Raquel , Fernández María , Martín-Castellanos Cristina , Blanco Miguel G , Segurado Mónica 
Published: January 2020

AbstractThe S phase checkpoint is crucial to maintain genome stability under conditions that threaten DNA replication. One of its critical functions is to prevent Exo1-dependent fork degradation, and Exo1 is phosphorylated in response to different genotoxic agents. Exo1 seemed to be regulated by several post-translational modifications in the presence of replicative stress, but the specific contribution of checkpoint-dependent phosphorylation to Exo1 control and fork stability is not clear. We show here that Exo1 phosphorylation is Dun1-independent and Rad53-dependent in response to DNA damage or dNTP depletion, and in both situations Exo1 is similarly phosphorylated at multiple sites. To investigate the correlation between Exo1 phosphorylation and fork stability, we have generated phospho-mimic exo1 alleles that rescue fork collapse in rad53 mutants as efficiently as exo1-nuclease dead mutants or the absence of Exo1, arguing that Rad53-dependent phosphorylation is the mayor requirement to preserve fork stability. We have also shown that this rescue is Bmh1–2 independent, arguing that the 14-3-3 proteins are dispensable for fork stabilization, at least when Exo1 is downregulated. Importantly, our results indicated that phosphorylation specifically inhibits the 5' to 3'exo-nuclease activity, suggesting that this activity of Exo1 and not the flap-endonuclease, is the enzymatic activity responsible of the collapse of stalled replication forks in checkpoint mutants.
Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom
Authors: Wallace Edward W J , Maufrais Corinne , Sales-Lee Jade , Tuck Laura R , de Oliveira Luciana , Feuerbach Frank , Moyrand Frédérique , Natarajan Prashanthi , Madhani Hiten D , Janbon Guilhem 
Published: January 2020

AbstractEukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5′ and 3′ ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.
The landscape of chimeric RNAs in non-diseased tissues and cells
Authors: Singh Sandeep , Qin Fujun , Kumar Shailesh , Elfman Justin , Lin Emily , Pham Lam-Phong , Yang Amy , Li Hui 
Published: January 2020

Abstract
Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.
Double negative T cells, a potential biomarker for systemic lupus erythematosus
Authors: Alexander Jessy J , Jacob Alexander , Chang Anthony , Quigg Richard J , Jarvis James N 
Published: January 2020

AbstractSystemic lupus erythematosus (SLE) is an autoimmune disease that is a challenge to diagnose and treat. There is an urgent need for biomarkers to help define organ involvement, and more effective therapies. A unique population of T cells, the CD3+CD4−CD8− (DNeg) cells, is significantly increased in lupus patients. Twenty-seven cases (53%) of pediatric SLE patients had elevated DNeg cells in their peripheral blood, which correlated with kidney function (R2 = 0.54). Significant infiltration of DNeg cells was observed in both adult and pediatric lupus kidneys by immunofluorescence. For the first time, this study provides direct evidence that DNeg cells facilitate kidney injury in preclinical 8-week-old MRL/lpr lupus mice. In lupus mice, the increase in DNeg cells tracked with worsening disease and correlated with kidney function (R2 = 0.85). Our results show that DNeg cells per se can cause kidney dysfunction, increase in number with increase in disease pathology, and could serve as a potential biomarker.
Countercyclical Bank Equity Issuance
Authors: Baron Matthew 
Published: January 2020

AbstractOver the period 1980–2012, large U.S. commercial banks raise and retain less equity during credit expansions, which amplifies their leverage. The decrease in equity issuance is large relative to subsequent banking losses. I consider a variety of explanations for why banks resist raising equity and find evidence consistent with the diminishment of creditor market discipline due to government guarantees. I test this explanation by analyzing the removal of government guarantees to German Landesbank creditors and find that creditor market discipline and equity issuance increase. These findings help explain why banks resist raising equity, making financial distress more likely.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.
Multidimensional tracking of phenotypes and organ involvement in a complete nationwide systemic sclerosis cohort
Authors: Fretheim Håvard , Halse Anne-Kristine , Seip Marit , Bitter Helle , Wallenius Marianne , Garen Torhild , Salberg Anne , Brunborg Cathrine , Midtvedt Øyvind , Molberg Øyvind , Hoffmann-Vold Anna-Maria 
Published: January 2020

Abstract

Objective
SSc is a severe, heterogeneous multi-organ disease where population-based estimates on phenotypic spectrum, overall disease burden and societal impact are largely missing. Here the objective was to provide the first-ever complete national-level data on phenotype and major organ afflictions in SSc.

Methods
A stepwise strategy was applied to find and characterize every SSc patient resident in Norway from 2000 to 2012. First we identified every case in the country registered with an International Classification of Diseases, Tenth Revision code for SSc (M34). Next we manually reviewed all cases coded as M34 to determine whether they met the 1980 ACR and/or 2013 ACR/EULAR classification criteria for SSc and could be included in the Norwegian SSc cohort (Nor-SSc). Finally, all disease features from SSc onset to study end were reviewed.

Results
The Nor-SSc cohort included 815 SSc patients. The mean age at diagnosis was 53 years, with 84% females and 77% limited cutaneous SSc. The estimated incidence increased from 4 per million in 2000 to 13 per million in 2012. We identified high cumulative frequencies of internal organ involvement, coexistence of multiple organ afflictions across disease subsets and autoantibody status and stable frequencies of pulmonary arterial hypertension across haemodynamic definitions, but indications of referral-related differences in pulmonary hypertension detection rates across the study area.

Conclusion
This nationwide cohort study provides new, unbiased evidence for a high disease burden in SSc patients of Caucasian descent and indicates the existence of hurdles preventing equality of assessment across the SSc population.
Neural activity in human ventromedial prefrontal cortex reflecting the intention to save reward
Authors: Zangemeister Leopold , Grabenhorst Fabian , Schultz Wolfram 
Published: January 2020

Abstract
Saving behavior usually requires individuals to perform several consecutive choices before collecting the final reward. The overt behavior is preceded by an intention to perform an appropriate choice sequence. We studied saving sequences for which each participant rated the intention numerically as willingness to save. Each sequence resulted in a specific reward amount and thus had a particular value for the participant, which we assessed with a Becker-DeGroot-Marschak auction-like mechanism. Using functional MRI, we found that blood-oxygen-level-dependent signals in human ventromedial prefrontal cortex (vmPFC) correlated with the participant’s stated intention before each choice sequence. An adjacent vmPFC region showed graded activation that reflected the value of the sequence. These results demonstrate an involvement of vmPFC in intentional processes preceding sequential economic choices.
Trust arbitration: 99 problems and 99 solutions
Authors: Clover Alcolea Lucas 
Published: January 2020

Abstract
Although in recent years there has been considerable interest in arbitrating internal trust disputes with a large body of literature produced on the subject, as well as statutory reform to permit it in several jurisdictions, it remains the fact that trust arbitration is still relatively uncommon. This is likely due to the complex problems of cross-border testamentary, trust, arbitration and human rights law. However, the aim of this article is to demonstrate that these difficulties are often exaggerated and can be solved with proper drafting and a little creativity.
The effect of varicocele on semen quality in boars exposed to heat stress1
Authors: Gruhot Tasha R , Rempel Lea A , White Brett R , Mote Benny E 
Published: January 2020

Abstract
Semen quality has a dramatic impact on reproductive efficiency in the swine industry, influencing both conception rate and litter size. The objective of this study was to assess whether the presence of varicocele hinders semen quality in both thermoneutral and heat stress (HS) conditions. At approximately 6 mo of age, ultrasonography was used to measure left and right pampiniform plexus area in order to detect varicocele in maternal line boars at the University of Nebraska–Lincoln. Between 10 and 12 mo of age, semen was collected from each boar (n = 28) twice weekly. Boars were collected under thermoneutral conditions, were then heat stressed for 7 d to exacerbate any semen quality issues, and semen was collected post-HS for 6 wk. Sperm characteristics were determined by computer-assisted semen analysis. The presence of varicocele had a significant effect on sperm concentration (P = 0.04) and trended toward significance for mean sperm head area (P = 0.06) throughout the duration of the study. An interaction existed between varicocele and collection time point at weeks 2–5 post-HS for distal droplet percentage, suggesting that boars with varicocele were possibly more susceptible to heat-stress-induced semen quality issues than boars without varicocele. Moreover, semen quality was reduced in boars with versus without varicocele under both thermoneutral and HS conditions. Therefore, detection of varicocele by ultrasound could represent a potential marker of fertility in young boars or as a component trait in selection indices for fertility.
Evaluation of dietary trace mineral supplementation in young horses challenged with intra-articular lipopolysaccharide1
Authors: Millican Allison A , Leatherwood Jessica L , Coverdale Josie A , Arnold Carolyn E , Bradbery Amanda N , Larson Connie K , Lamprecht Emily D , White Sarah H , Paulk Chad B , Welsh Thomas H , Wickersham Tryon A 
Published: January 2020

Abstract
Sixteen weanling Quarter Horses (255 ± 22 kg) were utilized in a 56-d trial to evaluate the effects of trace mineral (TM) source on intra-articular inflammation following a single acute inflammatory insult. Horses were stratified by age, sex, and BW and then randomly assigned to dietary treatment: concentrate formulated with Zn, Mn, Cu, and Co as inorganic sources (CON; n = 8) or complexed TMs (CTM; n = 8). Added TM were formulated at iso-levels across treatments and intakes met or exceeded NRC requirements. Horses were offered 1.75% BW (as-fed) of treatment concentrate and 0.75% BW (as-fed) coastal Bermudagrass hay. Growth measurements were collected on days 0, 28, and 56, and plasma was collected biweekly for determination of Mn, Cu, Zn, and Co concentrations. On day 42, carpal joints were randomly assigned to receive injections of 0.5 ng lipopolysaccharide (LPS) or sterile lactated Ringer’s solution (LRS; contralateral control). Synovial fluid was collected at preinjection hours (PIH) 0, and 6, 12, 24, 168, and 336 h post-injection and analyzed for TM concentration, prostaglandin E2 (PGE2), carboxypeptide of type II collagen (CPII), collagenase cleavage neopeptide (C2C), and aggrecan chondroitin sulfate 846 epitope (CS846). Data were analyzed using the MIXED procedure of SAS. Results showed a TM source × LPS × h effect for synovial fluid Co, Cu, and Se (P &lt; 0.05); concentrations of TM peaked at hour 6 and decreased to preinjection values by hour 168 in both CON and CTM–LPS knees. A delayed peak was observed at hour 12 for CTM–LRS. Peak synovial fluid Cu and Se concentrations were higher in LPS knees, and Co was highest in CTM–LPS. A TM source × h interaction was observed for Zn (P &lt; 0.05); concentrations peaked at hour 6 in CON vs. hour 12 for CTM. An LPS × h interaction was observed for Mn (P &lt; 0.01); synovial concentration peaked at hour 6 in LPS knees compared with hour 24 in LRS. Synovial PGE2, C2C, CPII, and CS846 concentrations were greater with LPS (P ≤ 0.01), and C2C was greater (P &lt; 0.01) in CTM compared with CON. Concentrations of CPII and PGE2 were unaffected by diet. A TM source × h × LPS interaction was observed for CS846 (P = 0.02). Concentrations of CS846 in CTM peaked at 12 h, whereas CON peaked at a lower concentration at 24 h (P &lt; 0.05). Data indicate sufficient intake of a complexed TM source may support cartilage metabolism through increased aggrecan synthesis and type II collagen breakdown following an intra-articular LPS challenge in growing horses.