bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprotection rates of vaccine-preventable diseases among newly arrived Eritrean asylum seekers in Switzerland: a cross-sectional study
Authors: Staehelin Cornelia , Chernet Afona , Sydow Véronique , Piso Rein J , Suter-Riniker Franziska , Funez Sabine , Nickel Beatrice , Paris Daniel H , Labhardt Niklaus D 
Published: May 2019

Abstract

Background
According to 2016 World Health Organization and United Nations Children’s Fund country estimates, Eritrea has overall high vaccination coverage with immunization rates for three doses of diphtheria/tetanus/pertussis and polio vaccine of 95%, for two doses measles vaccine of 85% and for three doses hepatitis B vaccine of 85%. If confirmed, this could imply that routine basic vaccination of newly arrived Eritreans could be safely omitted.

Methods
We used stored serum samples from two cross-sectional studies that screened newly arrived Eritrean refugees for infectious diseases. Consenting refugees aged 16 years and older who registered in one of three neighbouring cantons in northwestern Switzerland were enrolled between January 2016 and December 2017. Antibody titers against the following vaccine-preventable diseases were measured (applied thresholds for seroprotection in brackets): diphtheria (>0.1 IU/ml), tetanus (>0.1 IU/ml), measles (>150 mIU/ml), rubella (only for women, >11 IU/ml), varicella (>50 mIU/ml), hepatitis B [hepatitis B surface antigen (HBsAg) Index >0.9, Hepatitis B core antibody (anti-HBc) Index >0.9 and antibodies to HBsAg (anti-HBs) >10 IE/L]. Differences between sex and age groups (≤25 and >25 years) were measured by Fisher’s exact test.

Results
We analysed samples of 133 study participants (20 women, 15%) with a median age of 25 years (range 16–61). Rates of seropositivity were as follows for women/men, respectively: diphtheria 57.9%/74.8% (difference non-significant), tetanus 94.8%/41.1% (P < 0.001), measles 73.7%/76.6% (non-significant), rubella in women 78.9%, varicella 89.5%/95.3% (non-significant), anti-HBc 15.8%/26.2% (non-significant) and anti-HBs 15.8%/17.8% (non-significant).

Conclusion
Seroprevalence for vaccine-preventable infections did not meet levels required to confer herd immunity in any of the human-to-human transmissible diseases that were studied. In general, the strategy proposed by the Federal Office of Public Health to offer basic immunization to all newly arrived refugees, including newly arriving Eritrean refugees, is justified.
Article 5—Mediation
Authors: Gusy Martin F , Hosking James M 
Published: May 2019

Abstract
This chapter explores Article 5 on mediation of the 2014 ICDR Rules. Mediation is a very effective alternative dispute-resolution process, in which the mediator assists the parties to settle their disputes by a process of discussion and narrowing differences. The mediator does not have the power to render binding decisions, rather the parties aim to reach agreement amongst themselves with the mediator’s assistance. Under Article 5, the ICDR may invite the parties to mediate or the parties may agree to mediate in accordance with the ICDR’s International Mediation Rules at any time while the arbitration proceedings are pending. The mediation shall in principle proceed in parallel with arbitration to avoid any delay. Ultimately, the 2014 ICDR Rules reflect a desire to encourage the parties to consider the benefits of mediation, particularly early in the dispute resolution process, without forcing them to mediate.
Article 7—Joinder
Authors: Gusy Martin F , Hosking James M 
Published: May 2019

Abstract
This chapter discusses Article 7 on joinder of the 2014 ICDR Rules. Article 7 allows a party to a pending arbitration to join an additional party by submitting a Notice of Arbitration against the additional party to the Administrator and at the same time to the additional party and all other parties. It further sets forth the conditions and formal requirements for adding an additional party to the pending arbitration. Ultimately, Article 7 deals with multi-party and multi-contract transaction disputes where not all concerned parties are part of the pending arbitral proceedings, but a full and efficient resolution of the entire dispute would benefit from the participation of all parties in one proceeding. Additionally, a joinder mitigates the risk of inconsistent decisions.
Article 10—Notices
Authors: Gusy Martin F , Hosking James M 
Published: May 2019

Abstract
This chapter looks at Article 10 of the ICDR Rules. Both the arbitral tribunal and the parties to an arbitration must communicate in an effective and pre-agreed manner to ensure the smooth conduct of arbitral proceedings. Article 10(1) addresses the practicalities regarding notification of all communications between the parties. Notably, it addresses the variety of forms of modern communication, paying particular attention to forms of electronic communication. Likewise, Article 10(1) is drafted in sufficiently broad terminology that permits the parties and the tribunal to communicate in a variety of ways. Meanwhile, Article 10(2) provides the framework for calculating periods of time and time limits under the Rules. By specifically defining when notice periods begin to run, and anticipating holiday and other interruptions, Article 10(2) pre-empts possible dilatory tactics and sets the parties’ expectations for prompt notification, service of documents, and other communications that are essential to the timely and effective functioning of an arbitration.
Article 18—Language of Arbitration
Authors: Gusy Martin F , Hosking James M 
Published: May 2019

Abstract
This chapter focuses on Article 18 of the ICDR Rules, which provides for the language of arbitration. Article 18 recognizes as binding the parties’ agreement—in the arbitration clause or otherwise—on a particular language in which the arbitration shall be conducted. However, where the parties have not specified the language of the arbitration, Article 18 provides that the language of the documents that contain the arbitration agreement is determinative of the language of the proceedings. Article 18 also permits the arbitrators to determine the language of the arbitration, recognizing that it may be appropriate, in some cases, to conduct the arbitration in more than one language. For example, it is not uncommon to require the parties to make submissions in one language, but to allow them to produce documents or witness statements in other languages without having to provide a translation.
Article 24—Interim Measures
Authors: Gusy Martin F , Hosking James M 
Published: May 2019

Abstract
This chapter discusses Article 24 of the ICDR Rules, which empowers the tribunal to order any interim or conservatory measures it deems necessary, including—but not limited to—injunctive relief and measures necessary for the protection of property. The measures may be intended to preserve evidence for use in the case, prevent property from being interfered with, or, more generally, to preserve the status quo pending determination of the dispute. In addition to empowering the tribunal to take such measures, Article 24(3) also states that a request to a judicial authority for interim measures is not inconsistent with the arbitration agreement. As the newly introduced Article 24(5) makes clear, Article 24 should not be confused with Article 6, which provides for ‘emergency measures of protection’ to be granted by an ‘emergency arbitrator’ where the tribunal has not yet been appointed.
Article 35—Fees and Expenses of Arbitral Tribunal
Authors: Gusy Martin F , Hosking James M 
Published: May 2019

Abstract
This chapter looks at Article 35 of the ICDR Rules, which concerns compensation of the arbitral tribunal. Under the ICDR Rules, the case Administrator at the ICDR takes the lead in ensuring that fee rates are agreed between all tribunal members and the parties. Those fees are almost always based on the arbitrators’ previously advised hourly rates, although the Administrator may intervene to modify rates to avoid any significant disparity. Similarly, although not formally required under the rules, throughout the arbitration and in the final costs of arbitration, the Administrator reviews the reasonableness of the arbitrators’ fees and expenses. In contrast to the equivalent provision in the AAA Commercial Rules, section R-55, the ICDR Rules envisage a more hands-on role to be played by the institution.
Article E-1—Scope of Expedited Procedures
Authors: Gusy Martin F , Hosking James M 
Published: May 2019

Abstract
This chapter discusses the provision for expedited procedures in the 2014 ICDR Rules. Prior to 2014, the AAA provided expedited procedures for some domestic cases and parties could agree to expedited rules, but there were no express provisions for expedited resolution of an international dispute. The introduction of the ICDR’s International Expedited Procedures (Expedited Procedures), and analogous provisions in other institutional rules, are a response to user demand for quicker and cheaper options in international arbitration. As such, the ICDR’s Expedited Procedures—like those at other institutions—have a number of features specifically aimed at controlling time and costs. These include shorter time periods for appointment of the arbitrator, filing of written submissions, holding a hearing, and rendering the award. With respect to costs, the ICDR has not introduced a separate fee schedule for arbitrations under the Expedited Procedures.
Time-dependent spectral modelling of Markarian 421 during a violent outburst in 2010
Authors: Banerjee B , Joshi M , Majumdar P , Williamson K E , Jorstad S G , Marscher A P 
Published: May 2019

Abstract
We present the results of extensive modelling of the spectral energy distributions (SEDs) of the closest blazar (z = 0.031) Markarian 421 (Mrk 421) during a giant outburst in 2010 February. The source underwent rapid flux variations in both X-rays and very high energy (VHE) gamma rays as it evolved from a low-flux state on 2010 February 13–15 to a high-flux state on 2010 February 17. During this period, the source exhibited significant spectral hardening from X-rays to VHE gamma rays while exhibiting a ‘harder when brighter’ behaviour in these energy bands. We reproduce the broad-band SED using a time-dependent multizone leptonic jet model with radiation feedback. We find that an injection of the leptonic particle population with a single power-law energy distribution at shock fronts followed by energy losses in an inhomogeneous emission region is suitable for explaining the evolution of Mrk 421 from low- to high-flux state in 2010 February. The spectral states are successfully reproduced by a combination of a few key physical parameters, such as the maximum and minimum cut-offs and power-law slope of the electron injection energies, magnetic field strength, and bulk Lorentz factor of the emission region. The simulated light curves and spectral evolution of Mrk 421 during this period imply an almost linear correlation between X-ray flux at 1–10 keV energies and VHE gamma-ray flux above 200 GeV, as has been previously exhibited by this source. Through this study, a general trend that has emerged for the role of physical parameters is that, as the flare evolves from a low- to a high-flux state, higher bulk kinetic energy is injected into the system with a harder particle population and a lower magnetic field strength.
Outflows, inflows, and young stars in the inner 200 pc of the Seyfert galaxy NGC 2110
Authors: Diniz Marlon R , Riffel Rogemar A , Storchi-Bergmann Thaisa , Riffel Rogério 
Published: May 2019

ABSTRACT
We present a 2D mapping of stellar population age components, emission-line fluxes, gas excitation, and kinematics within the inner ∼200 pc of the Seyfert 2 galaxy NGC 2110. We used the Gemini North Integral Field Spectrograph (NIFS) in the J and K bands at a spatial resolution of ∼22  pc. The unresolved nuclear continuum is originated in combined contributions of young stellar population (SP; age ≤ 100  Myr), a featureless AGN continuum and hot dust emission. The young-intermediate SP (100 &lt; age ≤ 700 Myr) is distributed in a ring-shaped structure at ≈140  pc from the nucleus, which is roughly coincident with the lowest values of the stellar velocity dispersion. In the inner ≈115  pc the old SP (age &gt; 2 Gyr) is dominant. The [Fe ii] $\lambda \, 1.2570\, \mu$m emission-line flux distribution is correlated with the radio emission and its kinematics comprise two components, one from gas rotating in the galaxy plane and another from gas in outflow within a bicone-oriented along north–south. These outflows seem to originate in the interaction of the radio jet with the ambient gas producing shocks that are the main excitation mechanism of the [Fe ii] emission. We estimate: (1) an ionized gas mass outflow rate of ∼0.5  M⊙ yr−1 at ∼70 pc from the nucleus; and (2) a kinetic power for the outflow of only 0.05 per cent of the AGN bolometric luminosity implying weak feedback effect on the galaxy.
Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein–protein interactions
Authors: Roy Ankit A , Dhawanjewar Abhilesh S , Sharma Parichit , Singh Gulzar , Madhusudhan M S 
Published: May 2019

AbstractOur web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein–protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts emanate from the main chain or side chain. We tested the score on 174 native interactions for which 100 decoys each were constructed using ZDOCK. The native structure scored better than any of the decoys in 146 cases and was able to rank within the 95th percentile in 162 cases. This easily outperforms a competing method, CIPS. We also benchmarked our scoring scheme on 15 targets from the CAPRI dataset and found that our method had results comparable to that of CIPS. Further, our method is able to analyse higher order protein complexes without the need to explicitly identify chains as receptors or ligands. The PIZSA server is easy to use and could be used to score any input three-dimensional structure and provide a residue pair-wise break up of the results. Attractively, our server offers a platform for users to upload their own potentials and could serve as an ideal testing ground for this class of scoring schemes.
hnRNPC regulates cancer-specific alternative cleavage and polyadenylation profiles
Authors: Fischl Harry , Neve Jonathan , Wang Zhiqiao , Patel Radhika , Louey Alastair , Tian Bin , Furger Andre 
Published: May 2019

AbstractAlternative cleavage and polyadenylation (APA) can occur at more than half of all human genes, greatly enhancing the cellular repertoire of mRNA isoforms. As these isoforms can have altered stability, localisation and coding potential, deregulation of APA can disrupt gene expression and this has been linked to many diseases including cancer progression. How APA generates cancer-specific isoform profiles and what their physiological consequences are, however, is largely unclear. Here we use a subcellular fractionation approach to determine the nuclear and cytoplasmic APA profiles of successive stages of colon cancer using a cell line-based model. Using this approach, we show that during cancer progression specific APA profiles are established. We identify that overexpression of hnRNPC has a critical role in the establishment of APA profiles characteristic for metastatic colon cancer cells, by regulating poly(A) site selection in a subset of genes that have been implicated in cancer progression including MTHFD1L.
The dynamics of forming a triplex in an artificial telomere inferred by DNA mechanics
Authors: Li Ning , Wang Junli , Ma Kangkang , Liang Lin , Mi Lipei , Huang Wei , Ma Xiaofeng , Wang Zeyu , Zheng Wei , Xu Linyan , Chen Jun-Hu , Yu Zhongbo 
Published: May 2019

Abstract
A telomere carrying repetitive sequences ends with a single-stranded overhang. The G-rich overhang could fold back and bind in the major groove of its upstream duplex, forming an antiparallel triplex structure. The telomeric triplex has been proposed to function in protecting chromosome ends. However, we lack strategies to mechanically probe the dynamics of a telomeric triplex. Here, we show that the topological dynamics of a telomeric triplex involves 3′ overhang binding at the ds/ssDNA junction inferred by DNA mechanics. Assisted by click chemistry and branched polymerase chain reaction, we developed a rescue-rope-strategy for mechanically manipulating an artificial telomeric DNA with a free end. Using single-molecule magnetic tweezers, we identified a rarely forming (5%) telomeric triplex which pauses at an intermediate state upon unzipping the Watson–Crick paired duplex. Our findings revealed that a mechanically stable triplex formed in a telomeric DNA can resist a force of 20 pN for a few seconds in a physiological buffer. We also demonstrated that the rescue-rope-strategy assisted mechanical manipulation can directly rupture the interactions between the third strand and its targeting duplex in a DNA triplex. Our single-molecule rescue-rope-strategy will serve as a general tool to investigate telomere dynamics and further develop triplex-based biotechnologies.
A group II intron-encoded protein interacts with the cellular replicative machinery through the β-sliding clamp
Authors: García-Rodríguez Fernando M , Neira José L , Marcia Marco , Molina-Sánchez María D , Toro Nicolás 
Published: May 2019

AbstractGroup II introns are self-splicing mobile genetic retroelements. The spliced intron RNA and the intron-encoded protein (IEP) form ribonucleoprotein particles (RNPs) that recognize and invade specific DNA target sites. The IEP is a reverse transcriptase/maturase that may bear a C-terminal endonuclease domain enabling the RNP to cleave the target DNA strand to prime reverse transcription. However, some mobile introns, such as RmInt1, lack the En domain but nevertheless retrohome efficiently to transient single-stranded DNA target sites at a DNA replication fork. Their mobility is associated with host DNA replication, and they use the nascent lagging strand as a primer for reverse transcription. We searched for proteins that interact with RmInt1 RNPs and direct these RNPs to the DNA replication fork. Co-immunoprecipitation assays suggested that DnaN (the β-sliding clamp), a component of DNA polymerase III, interacts with the protein component of the RmInt1 RNP. Pulldown assays, far-western blots and biolayer interferometry supported this interaction. Peptide binding assays also identified a putative DnaN-interacting motif in the RmInt1 IEP structurally conserved in group II intron IEPs. Our results suggest that intron RNP interacts with the β-sliding clamp of the DNA replication machinery, favouring reverse splicing into the transient ssDNA at DNA replication forks.
A Drosophila cell-free system that senses DNA breaks and triggers phosphorylation signalling
Authors: Harpprecht Lisa , Baldi Sandro , Schauer Tamas , Schmidt Andreas , Bange Tanja , Robles Maria S , Kremmer Elisabeth , Imhof Axel , Becker Peter B 
Published: May 2019

AbstractPreblastoderm Drosophila embryo development is characterized by fast cycles of nuclear divisions. Extracts from these embryos can be used to reconstitute complex chromatin with high efficiency. We now discovered that this chromatin assembly system contains activities that recognize unprotected DNA ends and signal DNA damage through phosphorylation. DNA ends are initially bound by Ku and MRN complexes. Within minutes, the phosphorylation of H2A.V (homologous to γH2A.X) initiates from DNA breaks and spreads over tens of thousands DNA base pairs. The γH2A.V phosphorylation remains tightly associated with the damaged DNA and does not spread to undamaged DNA in the same reaction. This first observation of long-range γH2A.X spreading along damaged chromatin in an in vitro system provides a unique opportunity for mechanistic dissection. Upon further incubation, DNA ends are rendered single-stranded and bound by the RPA complex. Phosphoproteome analyses reveal damage-dependent phosphorylation of numerous DNA-end-associated proteins including Ku70, RPA2, CHRAC16, the exonuclease Rrp1 and the telomer capping complex. Phosphorylation of spindle assembly checkpoint components and of microtubule-associated proteins required for centrosome integrity suggests this cell-free system recapitulates processes involved in the regulated elimination of fatally damaged syncytial nuclei.
High efficiency error suppression for accurate detection of low-frequency variants
Authors: Wang Ting Ting , Abelson Sagi , Zou Jinfeng , Li Tiantian , Zhao Zhen , Dick John E , Shlush Liran I , Pugh Trevor J , Bratman Scott V 
Published: May 2019

Abstract
Detection of cancer-associated somatic mutations has broad applications for oncology and precision medicine. However, this becomes challenging when cancer-derived DNA is in low abundance, such as in impure tissue specimens or in circulating cell-free DNA. Next-generation sequencing (NGS) is particularly prone to technical artefacts that can limit the accuracy for calling low-allele-frequency mutations. State-of-the-art methods to improve detection of low-frequency mutations often employ unique molecular identifiers (UMIs) for error suppression; however, these methods are highly inefficient as they depend on redundant sequencing to assemble consensus sequences. Here, we present a novel strategy to enhance the efficiency of UMI-based error suppression by retaining single reads (singletons) that can participate in consensus assembly. This ‘Singleton Correction’ methodology outperformed other UMI-based strategies in efficiency, leading to greater sensitivity with high specificity in a cell line dilution series. Significant benefits were seen with Singleton Correction at sequencing depths ≤16 000×. We validated the utility and generalizability of this approach in a cohort of >300 individuals whose peripheral blood DNA was subjected to hybrid capture sequencing at ∼5000× depth. Singleton Correction can be incorporated into existing UMI-based error suppression workflows to boost mutation detection accuracy, thus improving the cost-effectiveness and clinical impact of NGS.