bluuebunny/crossref_metadata_2025_split huggingface dataset:
On-surface synthesis of a nitrogen-embedded buckybowl with inverse Stone–Thrower–Wales topology
Authors: Mishra Shantanu , Krzeszewski Maciej , Pignedoli Carlo A. , Ruffieux Pascal , Fasel Roman , Gryko Daniel T. 
Published: April 2018

AbstractCurved π-conjugated polycyclic aromatic hydrocarbons, buckybowls, constitute an important class of materials with wide applications in materials science. Heteroatom doping of buckybowls is a viable route to tune their intrinsic physicochemical properties. However, synthesis of heteroatom-doped buckybowls is a challenging task. We report on a combined in-solution and on-surface synthetic strategy toward the fabrication of a buckybowl containing two fused nitrogen-doped pentagonal rings. We employ ultra-high-resolution scanning tunneling microscopy and spectroscopy, in combination with density functional theory calculations to characterize the final compound. The buckybowl contains a unique combination of non-hexagonal rings at its core, identified as the inverse Stone–Thrower–Wales topology, resulting in a distinctive bowl-opening-down conformation of the buckybowl on the surface. Our controlled design of non-alternant, heteroatom-doped polycyclic aromatic frameworks with established bottom-up fabrication techniques opens new opportunities in the synthesis of carbon nanostructures with the perspective of engineering properties of graphene-based devices.
Quasi-cyclic multi-edge LDPC codes for long-distance quantum cryptography
Authors: Milicevic Mario , Feng Chen , Zhang Lei M. , Gulak P. Glenn 
Published: April 2018

AbstractThe speed at which two remote parties can exchange secret keys in continuous-variable quantum key distribution (CV-QKD) is currently limited by the computational complexity of key reconciliation. Multi-dimensional reconciliation using multi-edge low-density parity-check (LDPC) codes with low code rates and long block lengths has been shown to improve error-correction performance and extend the maximum reconciliation distance. We introduce a quasi-cyclic code construction for multi-edge codes that is highly suitable for hardware-accelerated decoding on a graphics processing unit (GPU). When combined with an 8-dimensional reconciliation scheme, our LDPC decoder achieves an information throughput of 7.16 Kbit/s on a single NVIDIA GeForce GTX 1080 GPU, at a maximum distance of 142 km with a secret key rate of 6.64 × 10−8 bits/pulse for a rate 0.02 code with block length of 106 bits. The LDPC codes presented in this work can be used to extend the previous maximum CV-QKD distance of 100 km to 142 km, while delivering up to 3.50× higher information throughput over the tight upper bound on secret key rate for a lossy channel.
High-density lipoprotein suppresses tumor necrosis factor alpha production by mycobacteria-infected human macrophages
Authors: Inoue Manabu , Niki Mamiko , Ozeki Yuriko , Nagi Sachiyo , Chadeka Evans Asena , Yamaguchi Takehiro , Osada-Oka Mayuko , Ono Kenji , Oda Tetsuya , Mwende Faith , Kaneko Yukihiro , Matsumoto Makoto , Kaneko Satoshi , Ichinose Yoshio , Njenga Sammy M. , Hamano Shinjiro , Matsumoto Sohkichi 
Published: April 2018

AbstractImmune responses to parasitic pathogens are affected by the host physiological condition. High-density lipoprotein (HDL) and low-density lipoprotein (LDL) are transporters of lipids between the liver and peripheral tissues, and modulate pro-inflammatory immune responses. Pathogenic mycobacteria are parasitic intracellular bacteria that can survive within macrophages for a long period. Macrophage function is thus key for host defense against mycobacteria. These basic facts suggest possible effects of HDL and LDL on mycobacterial diseases, which have not been elucidated so far. In this study, we found that HDL and not LDL enhanced mycobacterial infections in human macrophages. Nevertheless, we observed that HDL remarkably suppressed production of tumor necrosis factor alpha (TNF-α) upon mycobacterial infections. TNF-α is a critical host-protective cytokine against mycobacterial diseases. We proved that toll-like receptor (TLR)-2 is responsible for TNF-α production by human macrophages infected with mycobacteria. Subsequent analysis showed that HDL downregulates TLR2 expression and suppresses its intracellular signaling pathways. This report demonstrates for the first time the substantial action of HDL in mycobacterial infections to human macrophages.
Disequilibrium of fire-prone forests sets the stage for a rapid decline in conifer dominance during the 21st century
Authors: Serra-Diaz Josep M. , Maxwell Charles , Lucash Melissa S. , Scheller Robert M. , Laflower Danelle M. , Miller Adam D. , Tepley Alan J. , Epstein Howard E. , Anderson-Teixeira Kristina J. , Thompson Jonathan R. 
Published: April 2018

AbstractThe impacts of climatic changes on forests may appear gradually on time scales of years to centuries due to the long generation times of trees. Consequently, current forest extent may not reflect current climatic patterns. In contrast with these lagged responses, abrupt transitions in forests under climate change may occur in environments where alternative vegetation states are influenced by disturbances, such as fire. The Klamath forest landscape (northern California and southwest Oregon, USA) is currently dominated by high biomass, biodiverse temperate coniferous forests, but climate change could disrupt the mechanisms promoting forest stability (e.g. growth, regeneration and fire tolerance). Using a landscape simulation model, we estimate that about one-third of the Klamath forest landscape (500,000 ha) could transition from conifer-dominated forest to shrub/hardwood chaparral, triggered by increased fire activity coupled with lower post-fire conifer establishment. Such shifts were widespread under the warmer climate change scenarios (RCP 8.5) but were surprisingly prevalent under the climate of 1949–2010, reflecting the joint influences of recent warming trends and the legacy of fire suppression that may have enhanced conifer dominance. Our results demonstrate that major forest ecosystem shifts should be expected when climate change disrupts key stabilizing feedbacks that maintain the dominance of long-lived, slowly regenerating trees.
Evolution of Metastable Defects and Its Effect on the Electronic Properties of MoS2 Films
Authors: Precner M. , Polaković T. , Qiao Qiao , Trainer D. J. , Putilov A. V. , Di Giorgio C. , Cone I. , Zhu Y. , Xi X. X. , Iavarone M. , Karapetrov G. 
Published: April 2018

AbstractWe report on structural and electronic properties of defects in chemical vapor-deposited monolayer and few-layer MoS2 films. Scanning tunneling microscopy, Kelvin probe force microscopy, and transmission electron microscopy were used to obtain high resolution images and quantitative measurements of the local density of states, work function and nature of defects in MoS2 films. We track the evolution of defects that are formed under heating and electron beam irradiation. We observe formation of metastable domains with different work function values after annealing the material in ultra-high vacuum to moderate temperatures. We attribute these metastable values of the work function to evolution of crystal defects forming during the annealing. The experiments show that sulfur vacancies formed after exposure to elevated temperatures diffuse, coalesce, and migrate bringing the system from a metastable to equilibrium ground state. The process could be thermally or e-beam activated with estimated energy barrier for sulfur vacancy migration of 0.6 eV in single unit cell MoS2. Even at equilibrium conditions, the work function and local density of states values are strongly affected near grain boundaries and edges. The results provide initial estimates of the thermal budgets available for reliable fabrication of MoS2-based integrated electronics and indicate the importance of defect control and layer passivation.
Appetitive and reactive aggression are differentially associated with the STin2 genetic variant in the serotonin transporter gene
Authors: Hemmings Sian Megan Joanna , Xulu Khethelo , Sommer Jessica , Hinsberger Martina , Malan-Muller Stefanie , Tromp Gerard , Elbert Thomas , Weierstall Roland , Seedat Soraya 
Published: April 2018

AbstractAppetitive aggression is a sub-category of instrumental aggression, characterised by the primary intrinsic enjoyment of aggressive activity. Aggression is heritable, and serotonergic and monoaminergic neurotransmitter systems have been found to contribute to the underlying molecular mechanisms. The aim of this study was to investigate the role that genetic variants in the serotonin transporter (SLC6A4) and monoamine oxidase A (MAOA) genes play in the aetiology of appetitive aggression in South African Xhosa males (n = 290).SLC6A45-HTTLPR, rs25531, and STin2 variants, as well asMAOA-uVNTR were investigated for their association with levels of appetitive aggression using Poisson regression analysis. The STin2 VNTR12 allele was found to be associated with increased levels of appetitive aggression (p = 0.003), but with decreased levels of reactive aggression (p = 7 × 10−5). This study is the first to investigate genetic underpinnings of appetitive aggression in a South African population, with preliminary evidence suggesting thatSCL6A4STin2 variants play a role in its aetiology, and may also be important in differentiating between appetitive and reactive aggression. Although the results require replication, they shed some preliminary light on the molecular dichotomy that may underlie the two forms of aggression.
Gaining new insights into nanoporous gold by mining and analysis of published images
Authors: McCue Ian , Stuckner Joshua , Murayama Mitsu , Demkowicz Michael J. 
Published: April 2018

AbstractOne way of expediting materials development is to decrease the need for new experiments by making greater use of published literature. Here, we use data mining and automated image analysis to gather new insights on nanoporous gold (NPG) without conducting additional experiments or simulations. NPG is a three-dimensional porous network that has found applications in catalysis, sensing, and actuation. We assemble and analyze published images from among thousands of publications on NPG. These images allow us to infer a quantitative description of NPG coarsening as a function of time and temperature, including the coarsening exponent and activation energy. They also demonstrate that relative density and ligament size in NPG are not correlated, indicating that these microstructure features are independently tunable. Our investigation leads us to propose improved reporting guidelines that will enhance the utility of future publications in the field of dealloyed materials.
Annexin A5 reduces infarct size and improves cardiac function after myocardial ischemia-reperfusion injury by suppression of the cardiac inflammatory response
Authors: de Jong Rob C. M. , Pluijmert Niek J. , de Vries Margreet R. , Pettersson Knut , Atsma Douwe E. , Jukema J. Wouter , Quax Paul H. A. 
Published: April 2018

AbstractAnnexin A5 (AnxA5) is known to have anti-inflammatory and anti-apoptotic properties. Inflammation and apoptosis are key processes in post-ischemic cardiac remodeling. In this study, we investigated the effect of AnxA5 on left ventricular (LV) function and remodeling three weeks after myocardial ischemia-reperfusion (MI-R) injury in hypercholesterolemic ApoE*3-Leiden mice. Using a mouse model for MI-R injury, we demonstrate AnxA5 treatment resulted in a 27% reduction of contrast-enhanced MRI assessed infarct size (IS). End-diastolic and end-systolic volumes were decreased by 22% and 38%, respectively. LV ejection fraction was increased by 29% in the AnxA5 group compared to vehicle. Following AnxA5 treatment LV fibrous content after three weeks was reduced by 42%, which was accompanied by an increase in LV wall thickness of the infarcted area by 17%. Two days and three weeks after MI-R injury the number of cardiac macrophages was significantly reduced in both the infarct area and border zones following AnxA5 treatment compared to vehicle treatment. Finally, we found that AnxA5 stimulation leads to a reduction of IL-6 production in bone-marrow derived macrophages in vitro. AnxA5 treatment attenuates the post-ischemic inflammatory response and ameliorates LV remodeling which improves cardiac function three weeks after MI-R injury in hypercholesterolemic ApoE*3-Leiden mice.
Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community
Authors: Kadnikov Vitaly V. , Mardanov Andrey V. , Ivasenko Denis A. , Antsiferov Dmitry V. , Beletsky Alexey V. , Karnachuk Olga V. , Ravin Nikolay V. 
Published: April 2018

AbstractThermal ecosystems associated with underground coal combustion sites are rare and less studied than geothermal features. Here we analysed microbial communities of near-surface ground layer and bituminous substance in an open quarry heated by subsurface coal fire by metagenomic DNA sequencing. Taxonomic classification revealed dominance of only a few groups of Firmicutes. Near-complete genomes of three most abundant species, ‘Candidatus Carbobacillus altaicus’ AL32, Brockia lithotrophica AL31, and Hydrogenibacillus schlegelii AL33, were assembled. According to the genomic data, Ca. Carbobacillus altaicus AL32 is an aerobic heterotroph, while B. lithotrophica AL31 is a chemolithotrophic anaerobe assimilating CO2 via the Calvin cycle. H. schlegelii AL33 is an aerobe capable of both growth on organic compounds and carrying out CO2 fixation via the Calvin cycle. Phylogenetic analysis of the large subunit of RuBisCO of B. lithotrophica AL31 and H. schlegelii AL33 showed that it belongs to the type 1-E. All three Firmicutes species can gain energy from aerobic or anaerobic oxidation of molecular hydrogen, produced as a result of underground coal combustion along with other coal gases. We propose that thermophilic Firmicutes, whose spores can spread from their original geothermal habitats over long distances, are the first colonizers of this recently formed thermal ecosystem.
Impact of HIV and Type 2 diabetes on Gut Microbiota Diversity, Tryptophan Catabolism and Endothelial Dysfunction
Authors: Hoel Hedda , Hove-Skovsgaard Malene , Hov Johannes R. , Gaardbo Julie Christine , Holm Kristian , Kummen Martin , Rudi Knut , Nwosu Felix , Valeur Jørgen , Gelpi Marco , Seljeflot Ingebjørg , Ueland Per Magne , Gerstoft Jan , Ullum Henrik , Aukrust Pål , Nielsen Susanne Dam , Trøseid Marius 
Published: April 2018

AbstractHIV infection and type 2 diabetes are associated with altered gut microbiota, chronic inflammation, and increased cardiovascular risk. We aimed to investigate the combined effect of these diseases on gut microbiota composition and related metabolites, and a potential relation to endothelial dysfunction in individuals with HIV-infection only (n = 23), diabetes only (n = 16) or both conditions (n = 21), as well as controls (n = 24). Fecal microbiota was analyzed by Illumina sequencing of the 16 S rRNA gene. Markers of endothelial dysfunction (asymmetric dimethylarginine [ADMA]), tryptophan catabolism (kynurenine/tryptophan [KT]-ratio), and inflammation (neopterin) were measured by liquid chromatography-tandem mass spectrometry. The combination of HIV and type 2 diabetes was associated with reduced gut microbiota diversity, increased plasma KT-ratio and neopterin. Microbial genes related to tryptophan metabolism correlated with KT-ratio and low alpha diversity, in particular in HIV-infected with T2D. In multivariate analyses, KT-ratio associated with ADMA (β = 4.58 [95% CI 2.53–6.63], p < 0.001), whereas microbiota composition per se was not associated with endothelial dysfunction. Our results indicate that tryptophan catabolism may be related to endothelial dysfunction, with a potentially detrimental interaction between HIV and diabetes. The potential contribution of gut microbiota and the impact for cardiovascular risk should be further explored in prospective studies powered for clinical end points.
Author Correction: Formation and purification of tailored liposomes for drug delivery using a module-based micro continuous-flow system
Authors: Dimov Nikolay , Kastner Elisabeth , Hussain Maryam , Perrie Yvonne , Szita Nicolas 
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype
Authors: Bai Xiangning , Fu Shanshan , Zhang Ji , Fan Ruyue , Xu Yanmei , Sun Hui , He Xiaohua , Xu Jianguo , Xiong Yanwen 
Published: April 2018

AbstractShiga toxin (Stx) is the key virulent factor in Shiga toxin-producing Escherichia coli (STEC). To date, three Stx1 subtypes and seven Stx2 subtypes have been described in E. coli, which differed in receptor preference and toxin potency. Here, we identified a novel Stx2 subtype designated Stx2h in E. coli strains isolated from wild marmots in the Qinghai-Tibetan plateau, China. Stx2h shares 91.9% nucleic acid sequence identity and 92.9% amino acid identity to the nearest Stx2 subtype. The expression of Stx2h in type strain STEC299 was inducible by mitomycin C, and culture supernatant from STEC299 was cytotoxic to Vero cells. The Stx2h converting prophage was unique in terms of insertion site and genetic composition. Whole genome-based phylo- and patho-genomic analysis revealed STEC299 was closer to other pathotypes of E. coli than STEC, and possesses virulence factors from other pathotypes. Our finding enlarges the pool of Stx2 subtypes and highlights the extraordinary genomic plasticity of E. coli strains. As the emergence of new Shiga toxin genotypes and new Stx-producing pathotypes pose a great threat to the public health, Stx2h should be further included in E. coli molecular typing, and in epidemiological surveillance of E. coli infections.
Structures of Angptl3 and Angptl4, modulators of triglyceride levels and coronary artery disease
Authors: Biterova Ekaterina , Esmaeeli Mariam , Alanen Heli I. , Saaranen Mirva , Ruddock Lloyd W. 
Published: April 2018

AbstractCoronary artery disease is the most common cause of death globally and is linked to a number of risk factors including serum low density lipoprotein, high density lipoprotein, triglycerides and lipoprotein(a). Recently two proteins, angiopoietin-like protein 3 and 4, have emerged from genetic studies as being factors that significantly modulate plasma triglyceride levels and coronary artery disease. The exact function and mechanism of action of both proteins remains to be elucidated, however, mutations in these proteins results in up to 34% reduction in coronary artery disease and inhibition of function results in reduced plasma triglyceride levels. Here we report the crystal structures of the fibrinogen-like domains of both proteins. These structures offer new insights into the reported loss of function mutations, the mechanisms of action of the proteins and open up the possibility for the rational design of low molecular weight inhibitors for intervention in coronary artery disease.
Postoperative Rehabilitation May Reduce the Risk of Readmission After Groin Hernia Repair
Authors: Mercier Grégoire , Spence Jessica , Ferreira Christelle , Delay Jean-Marc , Meunier Charles , Millat Bertrand , Nguyen Tri-Long , Seguret Fabienne 
Published: April 2018

AbstractThirty-day readmission after surgery has been proposed as a quality-of-care indicator. We explored the effect of postoperative rehabilitation on readmission risk after groin hernia repair. We used the French National Discharge Database to identify all index hospitalizations for groin hernia repair in 2011. Readmissions within 30 days of discharge were clinically classified in terms of their relationship to the index stay. We used logistic regression to adjust the risk of readmission for patient, procedure and hospital factors. Among 122,952 index hospitalizations for inguinal hernia repair, 3,357 (2.7%) related 30-day readmissions were recorded. Reiterated analyses indicated that readmission risk was consistently associated with patient complexity: age (per year after 60 years, OR 1.03, 95% CI 1.02–1.03, P < 0.001), hospitalization within the previous year (OR 1.56, 95% CI 1.44–1.69, P < 0.001), and increasing severity and combination of co-morbidities. Postoperative rehabilitation was identified as a protective factor (OR 0.56, 95% CI 0.46–0.69, P < 0.001). Older patients and those with greater comorbidity are at elevated risk of readmission after inguinal hernia repair. Postoperative rehabilitation may reduce this risk. Further studies are warranted to confirm the protective effect of postoperative rehabilitation.
The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces
Authors: Whon Tae Woong , Chung Won-Hyong , Lim Mi Young , Song Eun-Ji , Kim Pil Soo , Hyun Dong-Wook , Shin Na-Ri , Bae Jin-Woo , Nam Young-Do 
Published: April 2018

AbstractHigh-quality and high-throughput sequencing technologies are required for therapeutic and diagnostic analyses of human gut microbiota. Here, we evaluated the advantages and disadvantages of the various commercial sequencing platforms for studying human gut microbiota. We generated fecal bacterial sequences from 170 Korean subjects using the GS FLX+ (V1–4), Illumina MiSeq (V1–3, V3–4 and V4), and PacBio (V1–9) systems. Comparative analyses revealed that the PacBio data showed the weakest relationship with the reference whole-metagenome shotgun datasets. The PacBio system generated sequences with a significantly higher level of deletions than datasets generated by other platforms, with an abnormally high proportion of sequences assigned to the phylum Proteobacteria. Low sequencing accuracy and low coverage of terminal regions in public 16 S rRNA databases deteriorate the advantages of long read length, resulting in low taxonomic resolution in amplicon sequencing of human gut microbiota.
Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia
Authors: Siraj Amir S. , Rodriguez-Barraquer Isabel , Barker Christopher M. , Tejedor-Garavito Natalia , Harding Dennis , Lorton Christopher , Lukacevic Dejan , Oates Gene , Espana Guido , Kraemer Moritz U.G. , Manore Carrie , Johansson Michael A. , Tatem Andrew J. , Reiner Robert C. , Perkins T. Alex 
Published: April 2018

AbstractDespite a long history of mosquito-borne virus epidemics in the Americas, the impact of the Zika virus (ZIKV) epidemic of 2015–2016 was unexpected. The need for scientifically informed decision-making is driving research to understand the emergence and spread of ZIKV. To support that research, we assembled a data set of key covariates for modeling ZIKV transmission dynamics in Colombia, where ZIKV transmission was widespread and the government made incidence data publically available. On a weekly basis between January 1, 2014 and October 1, 2016 at three administrative levels, we collated spatiotemporal Zika incidence data, nine environmental variables, and demographic data into a single downloadable database. These new datasets and those we identified, processed, and assembled at comparable spatial and temporal resolutions will save future researchers considerable time and effort in performing these data processing steps, enabling them to focus instead on extracting epidemiological insights from this important data set. Similar approaches could prove useful for filling data gaps to enable epidemiological analyses of future disease emergence events.