bluuebunny/crossref_metadata_2025_split huggingface dataset:
Derivation of induced pluripotent stem cells in Japanese macaque (Macaca fuscata)
Authors: Nakai Risako , Ohnuki Mari , Kuroki Kota , Ito Haruka , Hirai Hirohisa , Kitajima Ryunosuke , Fujimoto Toko , Nakagawa Masato , Enard Wolfgang , Imamura Masanori 
Published: August 2018

AbstractNon-human primates are our closest relatives and are of special interest for ecological, evolutionary and biomedical research. The Japanese macaque (Macaca fuscata) has contributed to the progress of primatology and neurosciences over 60 years. Despite this importance, the molecular and cellular basis of the Japanese macaque remains unexplored since useful cellular tools are lacking. Here we generated induced pluripotent stem cells (iPSCs) from skin fibroblasts of the Japanese macaque with Sendai virus or plasmid vectors. The Japanese macaque iPSCs (jm-iPSCs) were established under feeder-free culture conditions, but feeder cells turned out to be essential for their maintenance. The jm-iPSCs formed human iPSC-like flat colonies which were positive for pluripotent antigens including alkaline phosphatase, SSEA4, and TRA-1-81. They also expressed endogenous OCT3/4, SOX2, L-MYC, and KLF4 and other pluripotent marker genes. The potential to differentiate into all three germ layers and neural stem cells was confirmed by embryoid body and neurosphere formation, respectively. The jm-iPSCs will provide a robust in vitro tool for investigating the underlying mechanisms of development and physiology studies with the Japanese macaque.
Changes in the gut microbiota composition during pregnancy in patients with gestational diabetes mellitus (GDM)
Authors: Ferrocino Ilario , Ponzo Valentina , Gambino Roberto , Zarovska Adriana , Leone Filomena , Monzeglio Clara , Goitre Ilaria , Rosato Rosalba , Romano Angelo , Grassi Giorgio , Broglio Fabio , Cassader Maurizio , Cocolin Luca , Bo Simona 
Published: August 2018

AbstractGestational diabetes mellitus (GDM), a common pregnancy complication, is associated with an increased risk of maternal/perinatal outcomes. We performed a prospective observational explorative study in 41 GDM patients to evaluate their microbiota changes during pregnancy and the associations between the gut microbiota and variations in nutrient intakes, anthropometric and laboratory variables. GDM patients routinely received nutritional recommendations according to guidelines. The fecal microbiota (by 16S amplicon-based sequencing), was assessed at enrolment (24–28 weeks) and at 38 weeks of gestational age. At the study end, the microbiota α-diversity significantly increased (P < 0.001), with increase of Firmicutes and reduction of Bacteroidetes and Actinobacteria. Patients who were adherent to the dietary recommendations showed a better metabolic and inflammatory pattern at the study-end and a significant decrease in Bacteroides. In multiple regression models, Faecalibacterium was significantly associated with fasting glucose; Collinsella (directly) and Blautia (inversely) with insulin, and with Homeostasis-Model Assessment Insulin-Resistance, while Sutterella with C-reactive protein levels. Consistent with this latter association, the predicted metagenomes showed a correlation between those taxa and inferred KEGG genes associated with lipopolysaccharide biosynthesis. A higher bacterial richness and strong correlations between pro-inflammatory taxa and metabolic/inflammatory variables were detected in GDM patients across pregnancy. Collectively these findings suggest that the development of strategies to modulate the gut microbiota might be a potentially useful tool to impact on maternal metabolic health.
Stimulation of carbon nanomaterials on syntrophic oxidation of butyrate in sediment enrichments and a defined coculture
Authors: Zhang Wei , Zhang Jianchao , Lu Yahai 
Published: August 2018

AbstractIt remains elusive if direct interspecies electron transfer (DIET) occurs in canonical syntrophy involving short-chain fatty acids oxidation. In the present study, we determined the effects of carbon nanomaterials on syntrophic oxidation of butyrate in two lake sediment enrichments and a defined coculture comprisingSyntrophomonas wolfeiandMethanococcus Maripaludis. After four continuous transfers of enrichment cultivation,Syntrophomonasdominated the bacterial populations in enrichments, and the dominated methanogens comprisedMethanosarcinaandMethanospirillumin one enrichment (from Weiming Lake) andMethanoregulaandMethanospirillumin another (from Erhai Lake). Butyrate oxidation and CH4production was significantly accelerated by carbon nanotubes (CNTs) in both enrichments. Replacement of CNTs by magnetite caused similar stimulating effect. For the defined coculture, two carbon nanomaterials, CNTs and reduced graphene oxide (rGO), were tested, both showed consistently stimulating effects on butyrate oxidation. Addition of kaolinite, an electric nonconductive clay mineral, however, revealed no effect. The test onM.maripaludisin pure culture showed no effect by rGO and a negative effect by CNTs (especially at a high concentration). Fluorescencein situhybridization (FISH) and scanning electron microscopy (SEM) revealed that microbial cells were interwoven by CNTs forming cell-CNT mixture aggregates, and in case of rGO, cells were attached to surface or wrapped-up by rGO thin sheets. Collectively, our data suggest that the presence of conductive nanomaterials likely induces DIET in syntrophic butyrate oxidation.
Large-Scale Encapsulation of Magnetic Iron Oxide Nanoparticles via Syngas Photo-Initiated Chemical Vapor Deposition
Authors: Farhanian Donya , De Crescenzo Gregory , Tavares Jason R. 
Published: August 2018

AbstractPhoto-initiated chemical vapor deposition (PICVD) has been adapted for use in a jet-assisted fluidized bed configuration, allowing for the encapsulation of magnetic iron oxide nanoparticles on a larger scale than ever reported (5 g). This new methodology leads to a functional coating with a thickness of 1.4–10 nm, confirmed by HRTEM and TGA. XPS and TOF-SIMS characterization confirm that the coating is composed of both aliphatic and polymerized carbon chains, with incorporated organometallic bonds and oxygen-containing moieties. UV-Vis absorbance spectra show that the coating improved dispersion in non-polar solvents, such as n-dodecane. This process represents a first step towards the large-scale, solvent-free post-synthesis processing of nanoparticles to impart a functional coating.
The divergence and dispersal of early perissodactyls as evidenced by early Eocene equids from Asia
Authors: Bai Bin , Wang Yuan-Qing , Meng Jin 
Published: August 2018

AbstractThe earliest perissodactyls are represented by some basal equoid fossils from Euramerica near the Paleocene/Eocene boundary. Unequivocal early equoids have yet to be reported from the early Eocene of Asia, although other groups of early perissodactyls were indeed present in Asia. Here we report the earliest Eocene Asian equid,Erihippus tingaegen. et sp. nov., based on partial specimens initially assigned to the ceratomorphOrientolophus hengdongensis, from the Hengyang Basin of Hunan Province, China. The specimens previously assigned to ‘Propachynolophus’hengyangensisfrom the same Lingcha fauna are split and now reassigned as an ancylopodProtomoropus?hengyangensisand a brontothereDanjiangia lambdodonsp. nov. The nearly simultaneous appearance of equids, ceratomorphs, ancylopods, and brontotheres in the Hengyang Basin suggests that the four main groups of perissodactyls diverged as early as, or no later than, the beginning of the Eocene (about 56 Ma), and displayed different dispersal scenarios during the early Eocene.
Coupled Cu and Mn charge and orbital orders in YBa2Cu3O7/Nd0.65(Ca1-ySry)0.35MnO3 multilayers
Authors: Perret E. , Monney C. , Johnston S. , Khmaladze J. , Lyzwa F. , Gaina R. , Dantz M. , Pelliciari J. , Piamonteze C. , Mallett B. P. P. , Minola M. , Keimer B. , Schmitt T. , Bernhard C. 
Published: August 2018

AbstractThe observation of a charge density wave in the underdoped cuprate high Tc superconductors (Cu-CDW) raised a debate about its relationship with superconductivity. In bulk YBa2Cu3O7−δ the Cu-CDW is incipient and mainly pinned by defects. Nevertheless, a large magnetic field can induce a true long-range Cu-CDW order as it suppresses superconductivity. An enhanced Cu-CDW order was also observed in YBa2Cu3O7/La2/3Ca1/3MnO3 multilayers. Here, we show that the magnitude of the Cu-CDW in YBa2Cu3O7−δ / Nd0.65(Ca1-ySry)0.35MnO3 multilayers can be varied by adjusting the strength of the manganite charge and orbital order via the Sr content (tolerance factor). Furthermore, we resolve the reconstruction of the crystal field levels of the interfacial Cu ions that are also affected by the manganite charge and orbital order. This tuneable interfacial coupling and Cu-CDW in YBa2Cu3O7−δ can be used for studying the relationship between the Cu-CDW and superconductivity and, possibly, for inducing new intertwined quantum states.
Solar flares and Kelvin-Helmholtz instabilities: A parameter survey
Authors: Ruan W. , Xia C. , Keppens R. 
Published: August 2018

Context. Hard X-ray (HXR) sources are frequently observed near the top of solar flare loops, which are also bright in soft X-ray (SXR) and extreme ultraviolet (EUV) wavebands. We revisit a recent scenario proposed by Fang et al. (2016) to trigger loop-top turbulence in flaring loops, which can help explain variations seen in SXR and EUV brightenings and potentially impact and induce HXR emission. It is conjectured that evaporation flows from flare-impacted chromospheric footpoints interact with each other near the loop top and produce turbulence via the Kelvin–Helmholtz instability (KHI).
Aims. By performing a rigorous parameter survey, in which we vary the duration, total amount, and asymmetry of the energy deposition at both footpoints, we assess the relevance of the KHI in triggering and sustaining loop-top turbulence. We synthesize SXR and EUV emission and discuss the possibility of HXR emission through bremsstrahlung or inverse Compton processes, which scatter SXR photons to HXR photons via the inverse Compton mechanism.
Methods. We performed 2.5D numerical simulations in which the magnetohydrodynamic model incorporates a realistic photosphere to coronal stratification, parametrized heating, radiative losses, and field-aligned anisotropic thermal conduction. We focus on the trigger of the KHI and the resulting turbulence, as well as identify various oscillatory patterns that appear in the evolutions.
Results. We find that a M2.2-class related amount of energy should be deposited in less than four minutes to trigger a KHI interaction. Slower deposition, or lesser energy (< 0.33 × 1029 ergs) rather leads to mere loop-top compression sites bounded by shocks, without KHI development. Asymmetry in the footpoint deposition determines whether the KHI turbulent zone gets produced away from the apex, and asymmetric cases can show a slow-mode mediated, periodic displacement of the turbulent zone. Our reference simulation further demonstrates a clear 25 s periodicity in the declining phase of the SXR light curve, wherein compressional effects dominate.
Conclusions. When turbulence is produced in the loop apex, an index of −5/3 can be found in the spectra of velocity and magnetic field fluctuations. Typical values for M-class flares routinely show KHI development. The synthesized SXR light curve shows a clear periodic signal related to the sloshing motion of the vortex pattern created by the KHI.
Survival following Multimodality Treatment Including Surgery for Stage IA–IIIB Small-Cell Lung Cancer
Authors: Weckler Barbara Christine , Baldes Natalie , Schirren Joachim 
Published: August 2018

Background Prognosis in limited disease small-cell lung cancer (SCLC) after concurrent chemoradiotherapy is poor. While some studies show better survival after multimodality treatment including surgery, other trials failed to prove a surgery-related survival benefit. Therefore, this study investigated survival in stage IA–IIIB SCLC following surgery combined with chemotherapy and/or thoracic radiotherapy.
Methods We retrospectively reviewed all stage IA–IIIB SCLC patients without supraclavicular lymph node involvement at a single institution between January 1999 and August 2016 after multimodality treatment with curative intent. This comprised surgery consisting of primary tumor resection and systematic lymph node dissection combined with chemotherapy, chemoradiotherapy, or thoracic radiotherapy. Survival was determined using the Kaplan–Meier method, and differences were compared using log-rank tests. The risk of locoregional relapse was calculated.
Results A total of 47 patients (29 men, 18 women; mean age: 62 years) were included. Thirty-day mortality was 0%. Overall median survival was 56 months, and 2-, 3-, 5-, and 10-year survival rates were 69, 54, 46, and 30%, respectively. The only significant prognostic factor (p = 0.006) was R0 resection (n = 40) increasing median survival to 64 versus 17 months in case of technical inoperability (n = 5). The risk of locoregional relapse was 2.5% (n = 1) after R0 resection.
Conclusions Multimodality treatment including surgery was safe and led to considerable survival. R0 resection was the only factor extending survival. It could be achieved in most patients and was associated with a low risk of locoregional relapse. Prospective randomized controlled studies are needed to define best practice in stage IA–IIIB SCLC.
Understanding how China is championing climate change mitigation
Authors: Engels Anita 
Published: August 2018

AbstractThis comment deals with the question of how current political regimes could effectively contribute to the mitigation of climate change—and why this might happen. Against the backdrop of the US government’s announcement to withdraw from the Paris agreement, the rise of populist governments across the globe, and the slow progress of energy transformation projects in pluralistic countries, this paper focuses on China’s potential role in climate change mitigation. Since 2008, the Chinese government has switched to a proactive stance on climate governance and low-carbon development. Due to significant improvements in CO2 efficiency and a clear slow-down in the rise of its annual total CO2 emissions, China is increasingly perceived as a new low-carbon champion and appears to be in a position to take over global climate mitigation leadership. This comment examines the drivers behind current low-carbon developments in China and tests the assumption that China’s state-led non-participatory authoritarianism will effectively offer a solution to the global climate problem. Any switch to low-carbon development rests on complex societal preconditions and requirements. This paper discusses the reasons why the likelihood that the Chinese authoritarian regime will be effective over the long-term in lowering greenhouse gas emissions is uncertain at best—because of internal contestations, low public and private-business participation, and countervailing strategies to secure China’s global market positions. Understanding the foundations and nature of China’s climate change mitigation championship has important implications for fostering low-carbon developments in all political regimes.
Directionally biased sidestepping of Kip3/kinesin-8 is regulated by ATP waiting time and motor–microtubule interaction strength
Authors: Mitra Aniruddha , Ruhnow Felix , Girardo Salvatore , Diez Stefan 
Published: August 2018

Significance
Microtubules consist of parallel protofilament lanes for motor-based intracellular transport. While most motors translocate along individual protofilaments, members of the kinesin-8 family have been reported to sidestep. However, the mechanism of sidestepping is currently not understood. Here, we track the 3D motion of single kinesin-8 motors on freely suspended microtubules. We find that individual motors sidestep with a bias to the left, the probability of which is increased with the time taken per forward step. We relate this behavior to a bifurcation in the step cycle of kinesin-8. Experiments on a kinesin-1 with an elongated neck linker suggest that sidestepping is intrinsic to all processive kinesins possessing long neck linkers, potentially helping them to circumnavigate obstacles on the microtubule.
Characterisation of secondary phases in Ni-base superalloy Rene 65
Authors: Wojcik Tomasz , Rath Markus , Kozeschnik Ernst 
Published: August 2018

The Ni-base superalloy Rene 65 is a newly introduced cast and wrought alloy, used for turbine disc applications in aero-engines. The fine-grained and γ′-strengthened alloy was developed to increase service temperatures up to over 700°C and therefore, enhance the efficiency of aerospace turbines. In this work, the phases occurring in the as-received material as well as after continuous cooling experiments are characterised by transmission electron microscopy (TEM). In the as-received material, a tri-modal γ′ size distribution is found, ranging from a few nanometres up to approx. 5 µm. In addition, borides are found preferentially at grain boundaries with a size of approx. 1 µm. For different cooling rates, a change in morphology and size distribution of γ′ precipitates is found. This is part of a thematic issue on Nanoscale Materials Characterisation and Modeling by Advances Microscopy Methods - EUROMAT.
PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples
Authors: Andrusch Andreas , Dabrowski Piotr W , Klenner Jeanette , Tausch Simon H , Kohl Claudia , Osman Abdalla A , Renard Bernhard Y , Nitsche Andreas 
Published: August 2018

Abstract

Motivation
Next generation sequencing (NGS) has provided researchers with a powerful tool to characterize metagenomic and clinical samples in research and diagnostic settings. NGS allows an open view into samples useful for pathogen detection in an unbiased fashion and without prior hypothesis about possible causative agents. However, NGS datasets for pathogen detection come with different obstacles, such as a very unfavorable ratio of pathogen to host reads. Alongside often appearing false positives and irrelevant organisms, such as contaminants, tools are often challenged by samples with low pathogen loads and might not report organisms present below a certain threshold. Furthermore, some metagenomic profiling tools are only focused on one particular set of pathogens, for example bacteria.

Results
We present PAIPline, a bioinformatics pipeline specifically designed to address problems associated with detecting pathogens in diagnostic samples. PAIPline particularly focuses on userfriendliness and encapsulates all necessary steps from preprocessing to resolution of ambiguous reads and filtering up to visualization in a single tool. In contrast to existing tools, PAIPline is more specific while maintaining sensitivity. This is shown in a comparative evaluation where PAIPline was benchmarked along other well-known metagenomic profiling tools on previously published well-characterized datasets. Additionally, as part of an international cooperation project, PAIPline was applied to an outbreak sample of hemorrhagic fevers of then unknown etiology. The presented results show that PAIPline can serve as a robust, reliable, user-friendly, adaptable and generalizable stand-alone software for diagnostics from NGS samples and as a stepping stone for further downstream analyses.

Availability and implementation
PAIPline is freely available under https://gitlab.com/rki_bioinformatics/paipline.
Comparative assessment of content overlap between written documentation and verbal communication: an observational study of resident sign-outs
Authors: Abraham Joanna , Ihianle Imade , Ward Charlotte E , Arora Vineet M , Kannampallil Thomas G 
Published: August 2018

Abstract

Objective
Effective sign-outs involve verbal communication supported by written or electronic documentation. We investigated the clinical content overlap between sign-out documentation and face-to-face verbal sign-out communication.

Methods
We audio-recorded resident verbal sign-out communication and collected electronically completed (“written”) sign-out documentation on 44 sign-outs in a General Medicine service. A content analysis framework with nine sign-out elements was used to qualitatively code both written and verbal sign-out content. A content overlap framework based on the comparative analysis between written and verbal sign-out content characterized how much written content was verbally communicated. Using this framework, we computed the full, partial, and no overlap between written and verbal content.

Results
We found high a high degree of full overlap on patient identifying information [name (present in 100% of sign-outs), age (96%), and gender (87%)], past medical history [hematology (100%), renal (100%), cardiology (79%), and GI (67%)], and tasks to-do (97%); lesser degree of overlap for active problems (46%), anticipatory guidance (46%), medications/treatments (15%), pending labs/studies/procedures (7%); and no overlap for code status (&lt;1%), allergies (0%) and medical record number (0%).

Discussion and Conclusion
Three core functions of sign-outs are transfer of information, responsibility, and accountability. The overlap—highlighting what written content was communicated—characterizes how these functions manifest during sign-outs. Transfer of information varied with patient identifying information being explicitly communicated and remaining content being inconsistently communicated. Transfer of responsibility was explicit, with all pending and future tasks being communicated. Transfer of accountability was limited, with limited discussion of written contingency plans.
Pediatric Tetanus in Central Pennsylvania
Authors: Ahmed Bilaal S , Beck Michael J , Williamson Gregory , Ericson Jessica E , Kumar Parvathi 
Published: August 2018

Abstract
Approximately 20% of the nationally reported tetanus infections in children aged 0 to 14 years that occurred in the United States between 2005 and 2015 were treated at Penn State Children’s Hospital. With an electronic medical record search, we identified 5 cases of pediatric tetanus; 100% of these cases occurred in unimmunized children. Their median length of stay was 10 days, and the costs were significant.
Defeaters and Disqualifiers
Authors: Muñoz Daniel 
Published: August 2018

AbstractJustification depends on context: even if E on its own justifies H, still it might fail to justify in the context of D. This sort of effect, epistemologists think, is due to defeaters, which undermine or rebut a would-be justifier. I argue that there is another fundamental sort of contextual feature, disqualification, which doesn't involve rebuttal or undercutting, and which cannot be reduced to any notion of screening-off. A disqualifier makes some would-be justifier otiose, as direct testimony sometimes does to distal testimony, and as manifestly decisive evidence might do to gratuitous evidence on the same team. Basing a belief on disqualified evidence, moreover, is distinctively irrational. One is not necessarily irresponsible. Instead one is turning down a free upgrade to a sleeker, stabler basis for one's beliefs. Such an upgrade would prevent wastes of epistemic effort, since someone who bases her belief on a disqualified proposition E will need to remember E and rethink her belief should E ever be defeated. The upgrade might also reduce reliance on unwieldy evidence, if E is relevant only thanks to some labyrinthine argument; and if even ideal agents should doubt their ability to follow such arguments, even they should care about disqualifiers.