bluuebunny/crossref_metadata_2025_split huggingface dataset:
The dynamical Roche lobe in hierarchical triples
Authors: Di Stefano Rosanne 
Published: October 2019

ABSTRACT
The Roche lobe formalism describes mass transfer from one star to another. We develop an extension to hierarchical triples, considering the case in which a star donates mass to a companion which is itself a binary. The L1 point moves as the inner binary rotates, and the Roche lobe pulsates with the period of the inner binary. Signatures of mass transfer may therefore be imprinted with the orbital period of the inner binary. For some system parameters, the pulsing Roche lobe can drive mass transfer at high rates. Systems undergoing this type of mass transfer include those with inner binaries consisting of compact objects that will eventually merge, as well as progenitors of Type Ia supernovae.
Laboratory study on the fullerene–PAH-derived cluster cations in the gas phase
Authors: Zhen Junfeng , Zhang Weiwei , Yang Yuanyuan , Zhu Qingfeng 
Published: October 2019

ABSTRACT
It is possible that fullerene–polycyclic aromatic hydrocarbon (PAH) clusters or associations of fullerenes with PAHs contain a large fraction of interstellar fullerenes in the interstellar medium. Herein, we report the formation and photofragmentation behaviour of fullerene–PAH derivatives, fullerene/9-vinylanthracene (C16H12) and fullerene/9-methylanthracene (C15H12) cluster cations. Experiments are carried out using a quadrupole ion trap in combination with time-of-flight mass spectrometry in the gas phase. The results show that fullerene (C60)/9-vinylanthracene (e.g. [(C16H12)3C60]+), fullerene (C56 and C58)/9-vinylanthracene (e.g. [(C16H12)4C56]+ and [(C16H12)4C58]+), fullerene (C60)/9-methylanthracene (e.g. [(C15H12)3C60]+), and fullerene (C56 and C58)/9-methylanthracene (e.g. [(C15H12)4C56]+ and [(C15H12)4C58]+) cluster cations, i.e. large fullerene-derived molecules, are formed in the gas phase through the ion–molecule reaction pathway. With irradiation, all fullerene–PAH-derived cluster cations lose their monomolecular groups without other fragmentation channels (e.g. dehydrogenation). The structure of newly formed fullerene–PAH-derived cluster cations and the bond energy for these adduction formation pathways are investigated with theoretical calculations.
The obtained results provide a general molecular growth route towards large fullerene–PAH derivatives (e.g. large fullerene-derived molecules) with functional PAHs in a bottom-up formation process and insights into the effect of functional groups (e.g. vinyl, –C2H3, and methyl, –CH3) on their formation and photoevolution behaviours. In addition, the fullerene–PAH-derived clusters (from 83 to 170 atoms in total, or ∼2 nm in size) offer a good model of carbon dust grains, and the relevance to the nanometre-sized carbon dust grain in space is briefly discussed.
The dust mass function from z ∼0 to z ∼2.5
Authors: Pozzi F , Calura F , Zamorani G , Delvecchio I , Gruppioni C , Santini P 
Published: October 2019

ABSTRACT
We derive for the first time the dust mass function (DMF) in a wide redshift range, from z ∼ 0.2 up to z ∼ 2.5. In order to trace the dust emission, we start from a far-IR (160-μm) Herschel selected catalogue in the COSMOS field. We estimate the dust masses by fitting the far-IR data (λrest$\,\, \buildrel\gt \over \sim \,\,$50 μm) with a modified black body function and we present a detailed analysis to take into account the incompleteness in dust masses from a far-IR perspective. By parametrizing the observed DMF with a Schechter function in the redshift range 0.1 &lt; z ≤ 0.25, where we are able to sample faint dust masses, we measure a steep slope (α ∼1.48), as found by the majority of works in the Local Universe. We detect a strong dust mass evolution, with $M_{\rm d}^{\star }$ at z ∼ 2.5 almost 1 dex larger than in the local Universe, combined with a decrease in their number density. Integrating our DMFs, we estimate the dust mass density (DMD), finding a broad peak at z ∼ 1, with a decrease by a factor of ∼ 3 towards z ∼ 0 and z ∼ 2.5. In general, the trend found for the DMD mostly agrees with the derivation of Driver et al., another DMD determination based also on far-IR detections, and with other measures based on indirect tracers.
Young stars raining through the galactic halo: the nature and orbit of price-whelan 1
Authors: Bellazzini Michele , Ibata Rodrigo A , Martin Nicolas , Malhan Khyati , Marasco Antonino , Famaey Benoit 
Published: October 2019

ABSTRACT
We present radial velocities for five member stars of the recently discovered young (age ≃ 100−150 Myr) stellar system Price-Whelan 1 (PW 1), which is located far away in the Galactic Halo (D≃ 29 kpc, Z≃ 15 kpc), and that is probably associated with the leading arm (LA) of the Magellanic Stream. We measure the systemic radial velocity of PW 1, Vr = 275 ± 10 km s−1, significantly larger than the velocity of the LA gas in the same direction. We re-discuss the main properties and the origin of this system in the light of these new observations, computing the orbit of the system and comparing its velocity with that of the H i in its surroundings. We show that the bulk of the gas at the velocity of the stars is more than 10 deg (5 kpc) away from PW 1 and the velocity difference between the gas and the stars becomes larger as gas closer to the stars is considered. We discuss the possibilities that (1) the parent gas cloud was dissolved by the interaction with the Galactic gas, and (2) that the parent cloud is the high-velocity cloud (HVC) 287.5+22.5 + 240, lagging behind the stellar system by ≃ 25 km s−1 and ≃10 deg ≃ 5 kpc. This HVC, which is part of the LA, has metallicity similar to PW 1, displays a strong magnetic field that should help to stabilize the cloud against ram pressure, and shows traces of molecular hydrogen. We also show that the system is constituted of three distinct pieces that do not differ only by position in the sky but also by stellar content.
An optimised STAPUT method for the purification of mouse spermatocyte and spermatid populations
Authors: Dunleavy Jessica E M , O’Connor Anne E , O’Bryan Moira K 
Published: October 2019

AbstractThe purification of individual male germ cell populations is integral for the molecular and biochemical characterisation of specific spermatogenic phases. Although a number of more contemporary techniques have been developed, velocity sedimentation using the STAPUT method remains as a gold standard for this purpose. The gentle nature of the technique, wherein germ cell subpopulations are separated by sedimentation at unit gravity, results in the isolation of viable and high-purity cells. We provide an updated and simplified step-by-step version of the STAPUT protocol for the purification of mouse male germ cells. As per the original method, the protocol described herein allows for the purification of mouse spermatocyte and round spermatids, however it also allows for successful purification of elongating, and elongated spermatid populations, and is optimised for the preservation of cellular ultrastructure. This method yields sufficient numbers of high-purity cells from one adult mouse for RNA or protein extraction or for immunolocalisation studies.
Genus for biomolecules
Authors: Rubach Paweł , Zajac Sebastian , Jastrzebski Borys , Sulkowska Joanna I , Sułkowski Piotr 
Published: October 2019

Abstract
The ‘Genus for biomolecules’ database (http://genus.fuw.edu.pl) collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule, this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all and RNA structures deposited in the Protein Data Bank (PDB). This database presents also various statistics and extensive information about the biological function of the analyzed biomolecules. The database is regularly self-updating, once new structures are deposited in the PDB. Moreover, users can analyze their own structures.
Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures
Authors: Chen Feng , Bai Min , Cao Xiaowen , Zhao Yue , Xue Jing , Zhao Yongxi 
Published: October 2019

Abstract
Spatially resolved visualization of RNA processing and structures is important for better studying single-cell RNA function and landscape. However, currently available RNA imaging methods are limited to sequence analysis, and not capable of identifying RNA processing events and structures. Here, we developed click-encoded rolling FISH (ClickerFISH) for visualizing RNA polyadenylation and structures in single cells. In ClickerFISH, RNA 3′ polyadenylation tails, single-stranded and duplex regions are chemically labeled with different clickable DNA barcodes. These barcodes then initiate DNA rolling amplification, generating repetitive templates for FISH to image their subcellular distributions. Combined with single-molecule FISH, the proposed strategy can also obtain quantitative information of RNA of interest. Finally, we found that RNA poly(A) tailing and higher-order structures are spatially organized in a cell type-specific style with cell-to-cell heterogeneity. We also explored their spatiotemporal patterns during cell cycle stages, and revealed the highly dynamic organization especially in S phase. This method will help clarify the spatiotemporal architecture of RNA polyadenylation and structures.
Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition
Authors: Hirata Akira , Okada Keisuke , Yoshii Kazuaki , Shiraishi Hiroyuki , Saijo Shinya , Yonezawa Kento , Shimizu Nobutaka , Hori Hiroyuki 
Published: October 2019

Abstract
The complex between Trm7 and Trm734 (Trm7–Trm734) from Saccharomyces cerevisiae catalyzes 2′-O-methylation at position 34 in tRNA. We report biochemical and structural studies of the Trm7–Trm734 complex. Purified recombinant Trm7–Trm734 preferentially methylates tRNAPhe transcript variants possessing two of three factors (Cm32, m1G37 and pyrimidine34). Therefore, tRNAPhe, tRNATrp and tRNALeu are specifically methylated by Trm7–Trm734. We have solved the crystal structures of the apo and S-adenosyl-L-methionine bound forms of Trm7–Trm734. Small angle X-ray scattering reveals that Trm7–Trm734 exists as a hetero-dimer in solution. Trm7 possesses a Rossmann-fold catalytic domain, while Trm734 consists of three WD40 β-propeller domains (termed BPA, BPB and BPC). BPA and BPC form a unique V-shaped cleft, which docks to Trm7. The C-terminal region of Trm7 is required for binding to Trm734. The D-arm of substrate tRNA is required for methylation by Trm7–Trm734. If the D-arm in tRNAPhe is docked onto the positively charged area of BPB in Trm734, the anticodon-loop is located near the catalytic pocket of Trm7. This model suggests that Trm734 is required for correct positioning of tRNA for methylation. Additionally, a point-mutation in Trm7, which is observed in FTSJ1 (human Trm7 ortholog) of nosyndromic X-linked intellectual disability patients, decreases the methylation activity.
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies
Authors: Beck Tim , Shorter Tom , Brookes Anthony J 
Published: October 2019

Abstract
The GWAS Central resource provides a toolkit for integrative access and visualization of a uniquely extensive collection of genome-wide association study data, while ensuring safe open access to prevent research participant identification. GWAS Central is the world's most comprehensive openly accessible repository of summary-level GWAS association information, providing over 70 million P-values for over 3800 studies investigating over 1400 unique phenotypes. The database content comprises direct submissions received from GWAS authors and consortia, in addition to actively gathered data sets from various public sources. GWAS data are discoverable from the perspective of genetic markers, genes, genome regions or phenotypes, via graphical visualizations and detailed downloadable data reports. Tested genetic markers and relevant genomic features can be visually interrogated across up to sixteen multiple association data sets in a single view using the integrated genome browser. The semantic standardization of phenotype descriptions with Medical Subject Headings and the Human Phenotype Ontology allows the precise identification of genetic variants associated with diseases, phenotypes and traits of interest. Harmonization of the phenotype descriptions used across several GWAS-related resources has extended the phenotype search capabilities to enable cross-database study discovery using a range of ontologies. GWAS Central is updated regularly and available at https://www.gwascentral.org.
Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns
Authors: Emperle Max , Adam Sabrina , Kunert Stefan , Dukatz Michael , Baude Annika , Plass Christoph , Rathert Philipp , Bashtrykov Pavel , Jeltsch Albert 
Published: October 2019

Abstract
Somatic DNMT3A mutations at R882 are frequently observed in AML patients including the very abundant R882H, but also R882C, R882P and R882S. Using deep enzymology, we show here that DNMT3A-R882H has more than 70-fold altered flanking sequence preferences when compared with wildtype DNMT3A. The R882H flanking sequence preferences mainly differ on the 3′ side of the CpG site, where they resemble DNMT3B, while 5′ flanking sequence preferences resemble wildtype DNMT3A, indicating that R882H behaves like a DNMT3A/DNMT3B chimera. Investigation of the activity and flanking sequence preferences of other mutations of R882 revealed that they cause similar effects. Bioinformatic analyses of genomic methylation patterns focusing on flanking sequence effects after expression of wildtype DNMT3A and R882H in human cells revealed that genomic methylation patterns reflect the details of the altered flanking sequence preferences of R882H. Concordantly, R882H specific hypermethylation in AML patients was strongly correlated with the R882H flanking sequence preferences. R882H specific DNA hypermethylation events in AML patients were accompanied by R882H specific mis-regulation of several genes with strong cancer connection, which are potential downstream targets of R882H. In conclusion, our data provide novel and detailed mechanistic understanding of the pathogenic mechanism of the DNMT3A R882H somatic cancer mutation.
Survival of patients treated with extended-hours haemodialysis in Europe: an analysis of the ERA-EDTA Registry
Authors: Jansz Thijs T , Noordzij Marlies , Kramer Anneke , Laruelle Eric , Couchoud Cécile , Collart Frederic , Cases Aleix , Arici Mustafa , Helve Jaako , Waldum-Grevbo Bård , Rydell Helena , Traynor Jamie P , Zoccali Carmine , Massy Ziad A , Jager Kitty J , van Jaarsveld Brigit C 
Published: October 2019

Abstract

Background
Previous US studies have indicated that haemodialysis with ≥6-h sessions [extended-hours haemodialysis (EHD)] may improve patient survival. However, patient characteristics and treatment practices vary between the USA and Europe. We therefore investigated the effect of EHD three times weekly on survival compared with conventional haemodialysis (CHD) among European patients.

Methods
We included patients who were treated with haemodialysis between 2010 and 2017 from eight countries providing data to the European Renal Association–European Dialysis and Transplant Association Registry. Haemodialysis session duration and frequency were recorded once every year or at every change of haemodialysis prescription and were categorized into three groups: CHD (three times weekly, 3.5–4 h/treatment), EHD (three times weekly, ≥6 h/treatment) or other. In the primary analyses we attributed death to the treatment at the time of death and in secondary analyses to EHD if ever initiated. We compared mortality risk for EHD to CHD with causal inference from marginal structural models, using Cox proportional hazards models weighted for the inverse probability of treatment and censoring and adjusted for potential confounders.

Results
From a total of 142 460 patients, 1338 patients were ever treated with EHD (three times, 7.1 ± 0.8 h/week) and 89 819 patients were treated exclusively with CHD (three times, 3.9 ± 0.2 h/week). Crude mortality rates were 6.0 and 13.5/100 person-years. In the primary analyses, patients treated with EHD had an adjusted hazard ratio (HR) of 0.73 [95% confidence interval (CI) 0.62–0.85] compared with patients treated with CHD. When we attributed all deaths to EHD after initiation, the HR for EHD was comparable to the primary analyses [HR 0.80 (95% CI 0.71–0.90)].

Conclusions
EHD is associated with better survival in European patients treated with haemodialysis three times weekly.
Incidence, prognostic impact and clinical outcomes of renal impairment in patients with multiple myeloma: a population-based registry
Authors: Courant Maxime , Orazio Sebastien , Monnereau Alain , Preterre Julie , Combe Christian , Rigothier Claire 
Published: October 2019

Abstract

Background
Renal impairment (RI), a severe complication in multiple myeloma (MM), is considered as a poor prognostic factor. Patient survival has increased with the use of novel drugs and autologous stem-cell transplantation (ASCT). However, specific evolution of the incidence of RI in MM and its impact on prognosis remain unclear.

Methods
Using a population-based registry of 1038 newly diagnosed MM in Gironde, France, we evaluated the incidence trends of RI in MM patients and assessed net survival according to factors of interest using Pohar-Perme indicator and excess mortality rate regression. We also reviewed 114 cases of MM with RI to describe their clinical outcomes.

Results
In our population-based study, 24.6% of MM patients presented with RI (12.9% required haemodialysis). Median survival time was 21 months in patients with RI versus not reached at 3 years for other patients (P &lt; 0.01). Age &gt;73 years, RI, comorbidities and non-use of drugs or ASCT were associated with excess mortality risk. The effect of RI on excess mortality rates was maximum in the first 6 months after diagnosis. In the observational study, median follow-up time was 22.5 months; factors associated with renal response were haematologic response [odds ratio (OR) 6.81; P &lt; 0.01] and previous chronic kidney disease (OR 0.26; P = 0.04). Factors associated with 1-year overall survival were haematological [hazard ratio (HR) 0.13; P &lt; 0.01] and renal response (HR 0.27; P = 0.03).

Conclusions
RI represents an independent negative prognostic factor in MM in the first 6 months after diagnosis. Renal recovery and haematologic response are the strongest markers associated with patient survival.
No mere tautology: the division of labour is limited by the division of labour
Authors: Smyth Andrew , Wilson Bart J 
Published: October 2019

AbstractWe explore the intersection of growth theory and the theory of the firm with an experiment. Economic growth is possible in our experiment when agents specialize to exploit increasing returns. We find that low opportunity costs are sufficient for Marshallian internal economies, but that Marshallian external economies are slow to emerge in four probing treatment conditions. Transaction costs do not hamper external economies as we anticipated prior to collecting data. When external economies falter, it is because new ideas of more extensive specialization fail to emerge. Ideas make further divisions of the division of labour—and thus economic growth—possible. Conversely, a lack of ideas make further divisions of labour and economic growth impossible. Our data reveal how the likelihood of new ideas is inseparably tied to the existing extent of specialization.
“It Hurts as If…”: Pain-Associated Language, Visual Characterization, and Storytelling in Hmong Adults
Authors: Lor Maichou , Vang Xia , Rabago David , Brown Roger L , Backonja Miroslav 
Published: October 2019

AbstractObjectivePain is challenging to diagnose and manage in primary care, especially when patients have limited English proficiency (LEP). Little is known about whether LEP patients can provide pain information that is consistent with the process and the content that providers expect in a clinical interaction. We explore how LEP Hmong patients communicate their pain to providers in primary care settings.MethodsA qualitative study with 67 Hmong participants (63% female and x̄ age = 53.7 years) were recruited from a Midwestern state. Semistructured interviews on pain communication were conducted, audio-recorded, transcribed, and analyzed using directed content analysis.ResultsThe Hmong participants described pain using stories that generally had the same dimensions of information that providers require for pain assessment. These included references to time, causality, associated symptoms or related experiences, intensity, and consequences of pain. However, the participants expressed some pain dimensions in language that was not shared by providers: visual metaphors that were generally in reference to pain quality and fewer words for pain location, intensity, and some qualities. Participants used two strategies to decide whether they should tell their pain story: assessing the provider and determining whether their story was appreciated. The perception that providers underappreciated their stories resulted in dissatisfaction and undertreatment of pain. Ultimately, this resulted in having less frequent contact with providers or changing providers.ConclusionsFindings demonstrate a discordance in the expected process and content of the clinical interaction between LEP Hmong patients and providers, suggesting the need for culturally appropriate pain assessments in this population.