bluuebunny/crossref_metadata_2025_split huggingface dataset:
GRANDMA observations of advanced LIGO’s and advanced Virgo’s third observational campaign
Authors: Antier S , Agayeva S , Almualla M , Awiphan S , Baransky A , Barynova K , Beradze S , Blažek M , Boër M , Burkhonov O , Christensen N , Coleiro A , Corre D , Coughlin M W , Crisp H , Dietrich T , Ducoin J-G , Duverne P-A , Marchal-Duval G , Gendre B , Gokuldass P , Eggenstein H B , Eymar L , Hello P , Howell E J , Ismailov N , Kann D A , Karpov S , Klotz A , Kochiashvili N , Lachaud C , Leroy N , Lin W L , Li W X , Mašek M , Mo J , Menard R , Morris D , Noysena K , Orange N B , Prouza M , Rattanamala R , Sadibekova T , Saint-Gelais D , Serrau M , Simon A , Stachie C , Thöne C C , Tillayev Y , Turpin D , Postigo A de Ugarte , Vasylenko V , Vidadi Z , Was M , Wang X F , Zhang J J , Zhang T M , Zhang X H 
Published: June 2020

ABSTRACT
GRANDMA (Global Rapid Advanced Network Devoted to the Multi-messenger Addicts) is a network of 25 telescopes of different sizes, including both photometric and spectroscopic facilities. The network aims to coordinate follow-up observations of gravitational-wave (GW) candidate alerts, especially those with large localization uncertainties, to reduce the delay between the initial detection and the optical confirmation. In this paper, we detail GRANDMA’s observational performance during Advanced LIGO/Advanced Virgo Observing Run 3 (O3), focusing on the second part of O3; this includes summary statistics pertaining to coverage and possible astrophysical origin of the candidates. To do so, we quantify our observation efficiency in terms of delay between GW candidate trigger time, observations, and the total coverage. Using an optimized and robust coordination system, GRANDMA followed-up about 90 per cent of the GW candidate alerts, that is 49 out of 56 candidates. This led to coverage of over 9000 deg2 during O3. The delay between the GW candidate trigger and the first observation was below 1.5 h for 50 per cent of the alerts. We did not detect any electromagnetic counterparts to the GW candidates during O3, likely due to the very large localization areas (on average thousands of degrees squares) and relatively large distance of the candidates (above 200 Mpc for 60 per cent of binary neutron star, BNS candidates). We derive constraints on potential kilonova properties for two potential BNS coalescences (GW190425 and S200213t), assuming that the events’ locations were imaged.
Inhomogeneous He ii reionization in hydrodynamic simulations
Authors: Upton Sanderbeck Phoebe , Bird Simeon 
Published: June 2020

ABSTRACT
The reionization of the second electron of helium shapes the physical state of intergalactic gas at redshifts between 2 ≲ z ≲ 5. Because performing full in situ radiative transfer in hydrodynamic simulations is computationally expensive for large volumes, the physics of He ii reionization is often approximated by a uniform ultraviolet background model that does not capture the spatial inhomogeneity of reionization. We have devised a model that implements the effects of He ii reionization using semi-analytic calculations of the thermal state of intergalactic gas – a way to bypass a full radiative transfer simulation while still realizing the physics of He ii reionization that affects observables such as the Lyman α forest. Here, we present a publicly available code that flexibly models inhomogeneous He ii reionization in simulations at a negligible computational cost. Because many of the parameters of He ii reionization are uncertain, our model is customizable from a set of free parameters. We show results from this code in mp-gadget, where this model is implemented. We demonstrate the resulting temperature evolution and temperature–density relation of intergalactic gas – consistent with recent measurements and previous radiative transfer simulations. We show that the impact of He ii reionization gives rise to subtle signatures in the 1D statistics of the Lyman α forest at the level of several percent, in agreement with previous findings. The flexible nature of these simulations is ideal for studies of He ii reionization and future observations of the He ii Lyman α forest.
Using quasar X-ray and UV flux measurements to constrain cosmological model parameters
Authors: Khadka Narayan , Ratra Bharat 
Published: June 2020

ABSTRACT
Risaliti and Lusso have compiled X-ray and UV flux measurements of 1598 quasars (QSOs) in the redshift range 0.036 ≤ z ≤ 5.1003, part of which, z ∼ 2.4 − 5.1, is largely cosmologically unprobed. In this paper we use these QSO measurements, alone and in conjunction with baryon acoustic oscillation (BAO) and Hubble parameter [H(z)] measurements, to constrain cosmological parameters in six different cosmological models, each with two different Hubble constant priors. In most of these models, given the larger uncertainties, the QSO cosmological parameter constraints are mostly consistent with those from the BAO + H(z) data. A somewhat significant exception is the non-relativistic matter density parameter Ωm0 where QSO data favour Ωm0 ∼ 0.5 − 0.6 in most models. As a result, in joint analyses of QSO data with H(z) + BAO data the 1D Ωm0 distributions shift slightly towards larger values. A joint analysis of the QSO + BAO + H(z) data is consistent with the current standard model, spatially-flat ΛCDM, but mildly favours closed spatial hypersurfaces and dynamical dark energy. Since the higher Ωm0 values favoured by QSO data appear to be associated with the z ∼ 2 − 5 part of these data, and conflict somewhat with strong indications for Ωm0 ∼ 0.3 from most z &lt; 2.5 data as well as from the cosmic microwave background anisotropy data at z ∼ 1100, in most models, the larger QSO data Ωm0 is possibly more indicative of an issue with the z ∼ 2 − 5 QSO data than of an inadequacy of the standard flat ΛCDM model.
Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition
Authors: Thuy-Boun Alexander S , Thomas Justin M , Grajo Herra L , Palumbo Cody M , Park SeHee , Nguyen Luan T , Fisher Andrew J , Beal Peter A 
Published: June 2020

Abstract
Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.
DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses
Authors: Yu Hao , Li Jiayi , Liu Guang , Zhao Gong , Wang Yuli , Hu Wenyue , Deng Zixin , Wu Geng , Gan Jianhua , Zhao Yi-Lei , He Xinyi 
Published: June 2020

Abstract
The sulfur atom of phosphorothioated DNA (PT-DNA) is coordinated by a surface cavity in the conserved sulfur-binding domain (SBD) of type IV restriction enzymes. However, some SBDs cannot recognize the sulfur atom in some sequence contexts. To illustrate the structural determinants for sequence specificity, we resolved the structure of SBDSpr, from endonuclease SprMcrA, in complex with DNA of GPSGCC, GPSATC and GPSAAC contexts. Structural and computational analyses explained why it binds the above PT-DNAs with an affinity in a decreasing order. The structural analysis of SBDSpr–GPSGCC and SBDSco–GPSGCC, the latter only recognizes DNA of GPSGCC, revealed that a positively charged loop above the sulfur-coordination cavity electrostatically interacts with the neighboring DNA phosphate linkage. The structural analysis indicated that the DNA–protein hydrogen bonding pattern and weak non-bonded interaction played important roles in sequence specificity of SBD protein. Exchanges of the positively-charged amino acid residues with the negatively-charged residues in the loop would enable SBDSco to extend recognization for more PT-DNA sequences, implying that type IV endonucleases can be engineered to recognize PT-DNA in novel target sequences.
Bypass of DNA interstrand crosslinks by a Rev1–DNA polymerase ζ complex
Authors: Bezalel-Buch Rachel , Cheun Young K , Roy Upasana , Schärer Orlando D , Burgers Peter M 
Published: June 2020

AbstractDNA polymerase ζ (Pol ζ) and Rev1 are essential for the repair of DNA interstrand crosslink (ICL) damage. We have used yeast DNA polymerases η, ζ and Rev1 to study translesion synthesis (TLS) past a nitrogen mustard-based interstrand crosslink (ICL) with an 8-atom linker between the crosslinked bases. The Rev1–Pol ζ complex was most efficient in complete bypass synthesis, by 2–3 fold, compared to Pol ζ alone or Pol η. Rev1 protein, but not its catalytic activity, was required for efficient TLS. A dCMP residue was faithfully inserted across the ICL-G by Pol η, Pol ζ, and Rev1–Pol ζ. Rev1–Pol ζ, and particularly Pol ζ alone showed a tendency to stall before the ICL, whereas Pol η stalled just after insertion across the ICL. The stalling of Pol η directly past the ICL is attributed to its autoinhibitory activity, caused by elongation of the short ICL-unhooked oligonucleotide (a six-mer in our study) by Pol η providing a barrier to further elongation of the correct primer. No stalling by Rev1–Pol ζ directly past the ICL was observed, suggesting that the proposed function of Pol ζ as an extender DNA polymerase is also required for ICL repair.
Hydroxychloroquine and azithromycin tolerance in haemodialysis patients during COVID-19 infection
Authors: Giaime Philippe , Guenoun Maxime , Pedinielli Nathalie , Narbonne Hervé , Bergounioux Jean-Philippe , Solas Caroline , Guilhaumou Romain , Sampol Jérôme , Ollier Jacques , Sichez Hélène , Serveaux Marianne , Brunner Flora , Bataille Stanislas 
Published: June 2020

Abstract

Background
Haemodialysis patients are at risk of developing severe forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: coronavirus disease 2019 (COVID-19). In March 2020, hydroxychloroquine (HCQ) and azithromycin (AZI) were proposed as potential treatments of COVID-19, but with warnings concerning their possible toxicity. No data are available regarding the toxicity of this treatment in haemodialysis patients.

Methods
We report the use of HCQ and AZI in a cohort of COVID-19 haemodialysis patients with focus on safety concerns.

Results
Twenty-one patients received 200 mg HCQ thrice daily during 10 days, and AZI 500 mg on Day 1, and 250 mg on the four following days. HCQ plasma concentrations were within the recommended range (0.1–1.0 µg/mL) in all patients except one, in which maximum concentration was 1.1 µg/mL. HCQ concentration raised until the third day and remained stable thereafter. No cardiac event occurred in spite of progressive lengthening of corrected QT interval (QTc) during the treatment. One patient experienced a long QTc syndrome (QTc &gt;500 ms) without any arrhythmia episode, although HCQ concentration was in the target range. Five (23.8%) patients experienced hypoglycaemia, a well-known HCQ side-effect. SARS-CoV-2 RNA remained detectable in nasopharyngeal swabs for a long time in haemodialysis patients (mean time 21 days).

Conclusions
HCQ and AZI are safe in haemodialysis patients at these doses but can lead to long QTc syndrome and hypoglycaemia. HCQ concentrations were not correlated with side effects. We recommend monitoring of the QTc length throughout treatment, as well as glycaemia. SARS-CoV-2 could persist for longer in haemodialysis patients than in the general population.
Missing diversity in brain tumor trials
Authors: Taha Birra , Winston Graham , Tosi Umberto , Hartley Benjamin , Hoffman Caitlin , Dahmane Nadia , Mason Christopher E , Greenfield Jeffrey P 
Published: June 2020

Abstract

Background
Clinical trials for brain tumors represent a significant opportunity for both patients and providers to understand and combat a disease with substantial morbidity. The aim of this study was to quantify and map ethnic and racial representation in brain tumor trials and examine the potential gaps in trial recruitment. We also show that these representation gaps persist even in large multicultural cities like New York City.

Methods
We analyzed brain tumor clinical trials registered on www.clinicaltrials.gov between July 1, 2005 and completed on or before November 11, 2017. We used a combination of PubMed/MEDLINE and Google Scholar to find associated publications and obtained trial information as well as patient demographic information (when available) including race or ancestry.

Results
Out of 471 trials, 27% had no published results. Only 28.4% of trials with results reported race or ethnicity of trial participants, with no observed upward trend by year. Whites were significantly overrepresented in trials for metastatic brain tumors (P &lt; .001) and high-grade trials (P &lt; .001). Blacks/African Americans (AAs), Hispanics, and Asians were significantly underrepresented (P &lt; .001) in high-grade trials, while only Blacks/AAs were underrepresented in trials for metastatic brain tumors (P &lt; .001). Representation gaps were not observed in pediatric trials. Despite being a multicultural hub, New York City displayed similar gaps in trial representation.

Conclusions
Despite increasing representation in the American population, minorities are underrepresented in brain tumor trials. In addition, despite numerous legal requirements and ethical mandates, published results including race-based information are remarkably absent from 70% of brain tumor trials.
Olaudah Equiano
Authors: Wagner Bryan , Kjellin-Elder Parker 
Published: June 2020

Olaudah Equiano, or Gustavus Vassa, as he was known during his lifetime (b. 1745?–d. 1797), was a writer and polemicist of extraordinary abilities. His Interesting Narrative informs readers that he was born into a ruling-class Igbo family in 1745 and was kidnapped at the age of eleven. He tells readers that he was then sold to Europeans on the Gold Coast and made to endure the dreaded transatlantic Middle Passage to Virginia. After this time, he was sold to Michael Henry Pascal, an officer in the British Royal Navy, who, against Equiano’s will, named him Gustavus Vassa, a name that Equiano used throughout the rest of his life. Traveling with Pascal to England, Equiano was officially baptized, he tells us, in 1759. After his baptism, Pascal recruited Equiano for the Seven Years’ War. Equiano mistakenly assumed that Pascal would free him at the end of the conflict. Instead, Pascal sold him into West Indian slavery. From there, Equiano worked to save enough money and purchase his own manumission in 1766. With his new freedom, Equiano sailed the world, gaining the rank of able seaman, as he traveled across the Atlantic and even to the North Pole. After that harrowing journey, Equiano experienced a spiritual conversion to Methodism in 1774, and grew publicly involved with the antislavery debate, through letters, speeches, and his own Interesting Narrative. He married a white Englishwoman, Susanna Cullen, in 1792, and had two daughters, only one of whom survived to inherit the estate that Equiano left for her when he died on 31 March 1797. Biographer Vincent Carretta suggests that aspects of Equiano’s life story, including his African nativity, may be fabricated, as Equiano’s baptismal record lists him as “a Black born in Carolina 12 years old,” a possibility supported by one ship’s muster logs. Following on Carretta’s research, critics continue to debate important questions about genre, evidence, imagination, authenticity, testimony, and authorship.
Museum Education
Authors: Hein George E. , McCray Kimberly H. 
Published: June 2020

Education has been associated with museums from their earliest days, back to the famous Hellenic Mouseion of Alexandria, a resource for scholars. The modern Western public museum’s origin is usually attributed to the 18th-century Enlightenment, when public institutions began to replace religious powers, guilds, and nobility in providing public services. By the mid-18th century the term museum referred to any kind of collection that was open to the public in theory, although admission was often restricted to upper-class visitors or scholars. Education frequently remained a minor activity compared to collection, preservation, research, and exhibition. Early efforts to reach broader audiences include Charles Willson Peale’s American Museum, which opened around 1800, and the British Victoria and Albert Museum, which opened in the mid-19th century. Museum education as an organized activity carried out by dedicated, trained staff did not arise until the 20th century and has come to prominence with its own professional associations, journals, and degree-granting academic programs only since World War II. Responsibilities of museum educators have shifted dramatically, going from mainly direct instruction to school pupils or lectures for adult visitors, to providing means for all visitors to interpret and make meaning of their museum experience. More recently, museums have reached out increasingly to communities to engage underserved populations and remain relevant at a time of dramatic social upheaval. These developments, described by some as a paradigm shift, have been influenced by increased recognition of 20th-century educational theories, criticism of traditional classification of objects, and increased recognition of the significance of people from different cultures as museum visitors. The results of museum visitor research (visitor studies), a field originally begun in the United States in the 1920s and heavily influenced by behaviorist educational theory, has also expanded over the past four decades to provide a larger range of methods to understand learning in and from museums. In the first two decades of the 21st century, museum educators have increasingly emphasized community engagement and broad accessibility to welcome an ever-wider range of visitors. Museum education has also expanded to include emotional responses, health, and well-being as desired outcomes of museum experiences. Advances in technology, especially the ability to greatly extend the possibility for visitors to rapidly gain information, interact with exhibitions, and share information or experiences, are also expanding our understanding of learning in museums and providing tools for museum educators to improve visitor experiences.
Decreased All-Cause and Liver-Related Mortality Risk in HIV/Hepatitis B Virus Coinfection Coinciding With the Introduction of Tenofovir-Containing Combination Antiretroviral Therapy
Authors: van Welzen Berend J , Smit Colette , Boyd Anders , Lieveld Faydra I , Mudrikova Tania , Reiss Peter , Brouwer Annemarie E , Hoepelman Andy I M , Arends Joop E 
Published: June 2020

Abstract

Background
The development of efficacious combination antiretroviral therapy (cART) has led to a dramatic decrease in mortality in HIV-positive patients. Specific data on the impact in HIV/hepatitis B virus (HBV)–coinfected patients are lacking. In this study, all-cause and cause-specific mortality risks stratified per era of diagnosis are investigated.

Methods
Data were analyzed from HIV/HBV-coinfected patients enrolled in the ATHENA cohort between January 1, 1998, and December 31, 2017. Risk for (cause-specific) mortality was calculated using Cox proportional hazard regression analysis, comparing patients diagnosed before 2003 with those diagnosed ≥2003. Risk factors for all-cause and liver-related mortality were also assessed using Cox proportional hazard regression analysis.

Results
A total of 1301 HIV/HBV-coinfected patients were included (14 882 person-years of follow-up). One-hundred ninety-eight patients (15%) died during follow-up. The adjusted hazard ratio (aHR) for all-cause mortality in patients diagnosed in or after 2003 was 0.50 (95% CI, 0.35–0.72) relative to patients diagnosed before 2003. Similar risk reduction was observed for liver-related (aHR, 0.29; 95% CI, 0.11–0.75) and AIDS-related mortality (aHR, 0.44; 95% CI, 0.22–0.87). Use of a tenofovir-containing regimen was independently associated with a reduced risk of all-cause and liver-related mortality. Prior exposure to didanosine/stavudine was strongly associated with liver-related mortality. Ten percent of the population used only lamivudine as treatment for HBV.

Conclusions
All-cause, liver-related, and AIDS-related mortality risk in HIV/HBV-coinfected patients has markedly decreased over the years, coinciding with the introduction of tenofovir. Tenofovir-containing regimens, in absence of major contraindications, should be strongly encouraged in this population.
Renal Impairment,C. difficileRecurrence, and the Differential Effect of Bezlotoxumab: A Post Hoc Analysis of Pooled Data From 2 Randomized Clinical Trials
Authors: Golan Yoav , DuPont Herbert L , Aldomiro Fernando , Jensen Erin H , Hanson Mary E , Dorr Mary Beth 
Published: June 2020

AbstractBackgroundRenal impairment is not a consistently cited risk factor for recurrent Clostridioides difficile infection (rCDI). We examined the association between renal impairment and rCDI and the effect of bezlotoxumab, an anti–toxin B monoclonal antibody, in reducing rCDI in participants with renal impairment.MethodsWe pooled data from 2 randomized, double-blind, placebo-controlled, multicenter, phase 3 clinical trials conducted in participants receiving bezlotoxumab or placebo infusion during oral antibacterial drug treatment for CDI. We assessed the association between renal impairment and rCDI in placebo-treated participants and evaluated the effect of bezlotoxumab vs placebo in reducing rCDI among participants with renal impairment, defined as an estimated glomerular filtration rate &lt;90 mL/min.ResultsThe proportion of placebo-treated participants experiencing rCDI within 12 weeks was higher in those with renal impairment (n = 919) vs those without renal impairment (n = 612; 36.6% and 27.7%, respectively; difference, 8.9%; 95% CI, 1.3% to 16.3%). Renal impairment was significantly associated with a higher rate of recurrence in placebo-treated participants lacking commonly recognized risk factors for rCDI (renal impairment as only risk factor, 28.8%; vs normal renal function and no risk factors, 12.5%; difference, 16.3%; 95% CI, 3.4% to 28.8%). Among all participants with renal impairment, the rate of rCDI was 19.5% among bezlotoxumab-treated vs 36.6% among placebo-treated participants (difference, –17.1%; 95% CI, –23.4% to –10.6%).ConclusionsThis post hoc analysis adds to the literature suggesting an association of renal impairment as an independent risk factor for rCDI and provides preliminary evidence that patients with renal impairment who suffer with CDI may benefit from adjunctive treatment with bezlotoxumab.