bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reactive Magnetron Sputter Deposition of Copper on TiO2 Support for Photoreduction of CO2 to CH4
Authors: Jantarasorn Nantiya , Mekasuwandumrong Okorn , Kelly Peter , Praserthdam Piyasan 
Published: June 2019

Abstract
In this work, nanocrystalline Cu/TiO2 catalysts have been synthesized by using pulsed direct current (DC) reactive magnetron sputtering of Cu targets in an Ar atmosphere onto P25-TiO2 support. The oscillating bowl was used to make the uniform coating on the substrate. The Cu doping content was varied by adjusting the coating time. The thus-obtained catalysts were characterized by using the X-ray diffraction (XRD), UV-Vis spectroscopy, scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDX). The photocatalytic activities of all catalysts were studied via the photocatalytic reduction of CO2 and H2O to CH4 under UV irradiation, and compared with the pure TiO2 support and conventional-impregnation-made Cu/TiO2. The results showed that the photocatalytic performance of sputtering-made Cu/TiO2 catalyst was much better than the pure TiO2 support. Therefore, reactive magnetron sputtering was a promising technique for deposition of metal onto the support and use as the catalytic process.
Our Town, the MacDowell Colony, and the Art of Civic Mediation
Authors: Roberts Kathryn S 
Published: June 2019

Abstract
Thornton Wilder’s Our Town (1938) has found unusual currency of late. In 2011, the play lent its name to a major funding program launched by the National Endowment for the Arts; in 2017, it appeared in the center of a popular podcast and was revived by a British theater company in the wake of a terrorist attack. These productions recognize what terms like middlebrow obscure: Our Town is a civic mediator, a performance that installs art at the center of community life and community at the center of art. Taking inspiration from Antoine Hennion’s sociology of music, this essay ventures into the archive to trace an unfamiliar origin story for Our Town, involving a turn-of-the-century writers’ colony, a Progressive-Era historical pageant, and Wilder’s self-understanding as both confirmed bachelor and “community man.” Through the trajectory of a single play, civic mediation emerges as a pervasive strategy and ethos of American cultural practice, connecting diverse media through time and space.
Plant speciation in the age of climate change
Authors: Levin Donald A 
Published: June 2019

AbstractBackgroundSpecies diversity is likely to undergo a sharp decline in the next century. Perhaps as many as 33 % of all plant species may expire as a result of climate change. All parts of the globe will be impacted, and all groups of organisms will be affected. Hundreds of species throughout the world have already experienced local extinctionPerspectivesWhile thousands of species may become extinct in the next century and beyond, species formation will still occur. I consider which modes of plant species formation are likely to prevail in the next 500 years. I argue that speciation primarily will involve mechanisms that produce reproductively isolated lineages within less (often much less) than 100 generations. I will not especially consider the human element in promoting species formation, because it will continue and because the conclusions presented here are unaffected by it. The impact of climate change may be much more severe and widespread.ConclusionsThe most common modes of speciation likely to be operative in the next 500 years ostensibly will be auto- and allopolyploidy. Polyploid species or the antecedents thereof can arise within two generations. Moreover, polyploids often have broader ecological tolerances, and are likely to be more invasive than are their diploid relatives. Polyploid species may themselves spawn additional higher level polyploids either through crosses with diploid species or between pre-existing polyploids. The percentage of polyploid species is likely to exceed 50 % within the next 500 years vs. 35 % today. The stabilized hybrid derivatives (homoploid hybrid speciation) could emerge within a hundred generations after species contact, as could speciation involving chromosomal rearrangements (and perhaps number), but the number of such events is likely to be low. Speciation involving lineage splitting will be infrequent because the formation of substantive pre- and post-zygotic barriers typically takes many thousands of years.
A beginner’s guide for FMDV quasispecies analysis: sub-consensus variant detection and haplotype reconstruction using next-generation sequencing
Authors: Cacciabue Marco , Currá Anabella , Carrillo Elisa , König Guido , Gismondi María Inés 
Published: June 2019

Abstract
Deep sequencing of viral genomes is a powerful tool to study RNA virus complexity. However, the analysis of next-generation sequencing data might be challenging for researchers who have never approached the study of viral quasispecies by this methodology. In this work we present a suitable and affordable guide to explore the sub-consensus variability and to reconstruct viral quasispecies from Illumina sequencing data. The guide includes a complete analysis pipeline along with user-friendly descriptions of software and file formats. In addition, we assessed the feasibility of the workflow proposed by analyzing a set of foot-and-mouth disease viruses (FMDV) with different degrees of variability. This guide introduces the analysis of quasispecies of FMDV and other viruses through this kind of approach.
Increasing the efficiency and accuracy of the ABACUS protein sequence design method
Authors: Xiong Peng , Hu Xiuhong , Huang Bin , Zhang Jiahai , Chen Quan , Liu Haiyan 
Published: June 2019

Abstract

Motivation
The ABACUS (a backbone-based amino acid usage survey) method uses unique statistical energy functions to carry out protein sequence design. Although some of its results have been experimentally verified, its accuracy remains improvable because several important components of the method have not been specifically optimized for sequence design or in contexts of other parts of the method. The computational efficiency also needs to be improved to support interactive online applications or the consideration of a large number of alternative backbone structures.

Results
We derived a model to measure solvent accessibility with larger mutual information with residue types than previous models, optimized a set of rotamers which can approximate the sidechain atomic positions more accurately, and devised an empirical function to treat inter-atomic packing with parameters fitted to native structures and optimized in consistence with the rotamer set. Energy calculations have been accelerated by interpolation between pre-determined representative points in high-dimensional structural feature spaces. Sidechain repacking tests showed that ABACUS2 can accurately reproduce the conformation of native sidechains. In sequence design tests, the native residue type recovery rate reached 37.7%, exceeding the value of 32.7% for ABACUS1. Applying ABACUS2 to designed sequences on three native backbones produced proteins shown to be well-folded by experiments.

Availability and implementation
The ABACUS2 sequence design server can be visited at http://biocomp.ustc.edu.cn/servers/abacus-design.php.

Supplementary information
Supplementary data are available at Bioinformatics online.
HUNER: improving biomedical NER with pretraining
Authors: Weber Leon , Münchmeyer Jannes , Rocktäschel Tim , Habibi Maryam , Leser Ulf 
Published: June 2019

AbstractMotivationSeveral recent studies showed that the application of deep neural networks advanced the state-of-the-art in named entity recognition (NER), including biomedical NER. However, the impact on performance and the robustness of improvements crucially depends on the availability of sufficiently large training corpora, which is a problem in the biomedical domain with its often rather small gold standard corpora.ResultsWe evaluate different methods for alleviating the data sparsity problem by pretraining a deep neural network (LSTM-CRF), followed by a rather short fine-tuning phase focusing on a particular corpus. Experiments were performed using 34 different corpora covering five different biomedical entity types, yielding an average increase in F1-score of ∼2 pp compared to learning without pretraining. We experimented both with supervised and semi-supervised pretraining, leading to interesting insights into the precision/recall trade-off. Based on our results, we created the stand-alone NER tool HUNER incorporating fully trained models for five entity types. On the independent CRAFT corpus, which was not used for creating HUNER, it outperforms the state-of-the-art tools GNormPlus and tmChem by 5–13 pp on the entity types chemicals, species and genes.Availability and implementationHUNER is freely available at https://hu-ner.github.io. HUNER comes in containers, making it easy to install and use, and it can be applied off-the-shelf to arbitrary texts. We also provide an integrated tool for obtaining and converting all 34 corpora used in our evaluation, including fixed training, development and test splits to enable fair comparisons in the future.Supplementary informationSupplementary data are available at Bioinformatics online.
Sunken Worlds: The Past and Future of Human-Made Reefs in Marine Conservation
Authors: Tickell Sofia Castelló y , Sáenz-Arroyo Andrea , Milner-Gulland E J 
Published: June 2019

AbstractStructures submerged in the sea by humans over millennia provide hard and longstanding evidence of anthropogenic influence in the marine environment. Many of these human-made reefs (HMRs) may provide opportunities for conservation despite having been created for different purposes such as fishing or tourism. In the middle of controversy around the costs and benefits of HMRs, a broad analysis of biodiversity and social values is necessary to assess conservation potential. This requires reframing HMRs as social–ecological systems, moving beyond comparisons with natural coral or rocky reefs to consider their roles as ecosystems in their own right; creating frameworks to track their type, number, size, units, location, characteristics, origins, social uses, and associated biodiversity locally and worldwide; and applying systematic assessment of conservation benefits in relation to stated conservation intentions. This integrative approach can catalyze learning, identify conservation opportunities, and inform positive management of HMRs into the future.
Child Protection With Muslim Communities: Considerations For Non-Muslim-Based Orthodoxies/Paradigms in Child Welfare and Social Work
Authors: O’Leary Patrick , Abdalla Mohamad , Hutchinson Aisha , Squire Jason , Young Amy 
Published: June 2019

AbstractThe care and protection of children are a concern that crosses ethnic, religious and national boundaries. How communities act on these concerns are informed by cultural and religious understandings of childhood and protection. Islam has specific teachings that relate to the care and guardianship of children and are interpreted in diverse ways across the Muslim world. Islamic teachings on child-care mostly overlap with Western understandings of child protection, but there can be some contested positions. This creates complexities for social workers intervening in Muslim communities where the basis of their intervention is primarily informed by a non-Muslim paradigm or occurs in secular legal contexts. The purpose of this article is to address at a broad level the issue of how overarching concepts of child protection and Islam influence social work practice with Muslim communities. It addresses a gap in practical applications of the synergy of Islamic thinking with core social work practice in the field of child protection. For effective practice, it is argued that social work practitioners need to consider common ground in Islamic thinking on child protection rather than rely on Western frameworks. This requires further research to build evidence-based practice with Muslim families.
Genetic consequences of long-term isolation for the last French population of Eryngium viviparum (Apiaceae)
Authors: Rascle Pauline , Flaven Elodie , Bioret Frédéric , Magnanon Sylvie , Glemarec Erwan , Gallet Sébastien , Imbert Eric 
Published: June 2019

AbstractEryngium viviparum (Apiaceae) is an endangered endemic plant of the Atlantic region of Europe, growing in seasonally flooded sites, and is characterized by a highly disjunct distribution. It occurs in just a few sites in the north-western part of the Iberian Peninsula and in a single locality in France. To improve the conservation status of E. viviparum in France, a conservation programme has been implemented to reintroduce the species. Before considering such an operation, genetic studies were conducted to determine the genetic status of the last French population and to identify the genetic source that should be considered for the best reintroduction strategy. Using microsatellite markers, we documented the genetic structure of the last French population and compared its genetic diversity with that of ten Iberian populations, which cover the three geographical regions where the species occurs. As expected, the French population of E. viviparum shows low genetic diversity due to a bottleneck and geographical isolation. The evolutionary potential appears low, with no private alleles in this population. Furthermore, this population is highly differentiated from the Iberian populations in terms of genetic variation and ecological niche. These results bring new questions regarding the conservation of E. viviparum in France, especially for management and reintroduction aimed at favouring genetic diversity and avoiding extinction.
GABAergic cell transplants in the anterior cingulate cortex reduce neuropathic pain aversiveness
Authors: Juarez-Salinas Dina L , Braz Joao M , Etlin Alexander , Gee Steven , Sohal Vikaas , Basbaum Allan I 
Published: June 2019

AbstractDysfunction of inhibitory circuits in the rostral anterior cingulate cortex underlies the affective (aversive), but not the sensory-discriminative features (hypersensitivity) of the pain experience. To restore inhibitory controls, we transplanted inhibitory interneuron progenitor cells into the rostral anterior cingulate cortex in a chemotherapy-induced neuropathic pain model. The transplants integrated, exerted a GABA-A mediated inhibition of host pyramidal cells and blocked gabapentin preference (i.e. relieved ongoing pain) in a conditioned place preference paradigm. Surprisingly, pain aversiveness persisted when the transplants populated both the rostral and posterior anterior cingulate cortex. We conclude that selective and long lasting inhibition of the rostral anterior cingulate cortex, in the mouse, has a profound pain relieving effect against nerve injury-induced neuropathic pain. However, the interplay between the rostral and posterior anterior cingulate cortices must be considered when examining circuits that influence ongoing pain and pain aversiveness.
Sex differences in the genetic predictors of Alzheimer’s pathology
Authors: Dumitrescu Logan , Barnes Lisa L , Thambisetty Madhav , Beecham Gary , Kunkle Brian , Bush William S , Gifford Katherine A , Chibnik Lori B , Mukherjee Shubhabrata , De Jager Philip L , Kukull Walter , Crane Paul K , Resnick Susan M , Keene C Dirk , Montine Thomas J , Schellenberg Gerard D , Deming Yuetiva , Chao Michael J , Huentelman Matt , Martin Eden R , Hamilton-Nelson Kara , Shaw Leslie M , Trojanowski John Q , Peskind Elaine R , Cruchaga Carlos , Pericak-Vance Margaret A , Goate Alison M , Cox Nancy J , Haines Jonathan L , Zetterberg Henrik , Blennow Kaj , Larson Eric B , Johnson Sterling C , Albert Marilyn ,   for the Alzheimer’s Disease Genetics Consortium and the Alzheimer’s Disease Neuroimaging Initiative, Bennett David A , Schneider Julie A , Jefferson Angela L , Hohman Timothy J 
Published: June 2019

Abstract
Autopsy measures of Alzheimer’s disease neuropathology have been leveraged as endophenotypes in previous genome-wide association studies (GWAS). However, despite evidence of sex differences in Alzheimer’s disease risk, sex-stratified models have not been incorporated into previous GWAS analyses. We looked for sex-specific genetic associations with Alzheimer’s disease endophenotypes from six brain bank data repositories. The pooled dataset included 2701 males and 3275 females, the majority of whom were diagnosed with Alzheimer’s disease at autopsy (70%). Sex-stratified GWAS were performed within each dataset and then meta-analysed. Loci that reached genome-wide significance (P < 5 × 10−8) in stratified models were further assessed for sex interactions. Additional analyses were performed in independent datasets leveraging cognitive, neuroimaging and CSF endophenotypes, along with age-at-onset data. Outside of the APOE region, one locus on chromosome 7 (rs34331204) showed a sex-specific association with neurofibrillary tangles among males (P = 2.5 × 10−8) but not females (P = 0.85, sex-interaction P = 2.9 × 10−4). In follow-up analyses, rs34331204 was also associated with hippocampal volume, executive function, and age-at-onset only among males. These results implicate a novel locus that confers male-specific protection from tau pathology and highlight the value of assessing genetic associations in a sex-specific manner.
Ribavirin and Interferon Therapy for Critically Ill Patients With Middle East Respiratory Syndrome: A Multicenter Observational Study
Authors: Arabi Yaseen M , Shalhoub Sarah , Mandourah Yasser , Al-Hameed Fahad , Al-Omari Awad , Al Qasim Eman , Jose Jesna , Alraddadi Basem , Almotairi Abdullah , Al Khatib Kasim , Abdulmomen Ahmed , Qushmaq Ismael , Sindi Anees A , Mady Ahmed , Solaiman Othman , Al-Raddadi Rajaa , Maghrabi Khalid , Ragab Ahmed , Al Mekhlafi Ghaleb A , Balkhy Hanan H , Al Harthy Abdulrahman , Kharaba Ayman , Gramish Jawaher A , Al-Aithan Abdulsalam M , Al-Dawood Abdulaziz , Merson Laura , Hayden Frederick G , Fowler Robert 
Published: June 2019

Abstract

Background
The objective of this study was to evaluate the effect of ribavirin and recombinant interferon (RBV/rIFN) therapy on the outcomes of critically ill patients with Middle East respiratory syndrome (MERS), accounting for time-varying confounders.

Methods
This is a retrospective cohort study of critically ill patients with laboratory-confirmed MERS from 14 hospitals in Saudi Arabia diagnosed between September 2012 and January 2018. We evaluated the association of RBV/rIFN with 90-day mortality and MERS coronavirus (MERS-CoV) RNA clearance using marginal structural modeling to account for baseline and time-varying confounders.

Results
Of 349 MERS patients, 144 (41.3%) patients received RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a; none received rIFN-β1b). RBV/rIFN was initiated at a median of 2 days (Q1, Q3: 1, 3 days) from intensive care unit admission. Crude 90-day mortality was higher in patients with RBV/rIFN compared to no RBV/rIFN (106/144 [73.6%] vs 126/205 [61.5%]; P = .02]. After adjusting for baseline and time-varying confounders using a marginal structural model, RBV/rIFN was not associated with changes in 90-day mortality (adjusted odds ratio, 1.03 [95% confidence interval {CI}, .73–1.44]; P = .87) or with more rapid MERS-CoV RNA clearance (adjusted hazard ratio, 0.65 [95% CI, .30–1.44]; P = .29).

Conclusions
In this observational study, RBV/rIFN (RBV and/or rIFN-α2a, rIFN-α2b, or rIFN-β1a) therapy was commonly used in critically ill MERS patients but was not associated with reduction in 90-day mortality or in faster MERS-CoV RNA clearance.
Immunogenicity of Oral Polio Vaccine and Salk Inactive Polio Vaccine Against Xinjiang Imported Type 1 Wild Poliovirus
Authors: Yan Dongmei , Wang Dongyan , Zhu Shuangli , Zhang Yong , Li Xiaolei , Tang Haishu , Guan Jing , Xu Wenbo 
Published: June 2019

AbstractBackgroundAn outbreak of an imported Type 1 wild poliovirus from Pakistan occurred in the Xinjiang Uygur Autonomous Region of China in 2011, although the local immunity status of the oral polio vaccine (OPV) was relatively satisfied.MethodsNeutralizing antibody titers against the Xinjiang strain and Sabin 1 strain were measured in 237 sera from 3 groups of fully OPV-vaccinated persons and 1 group of infants fully vaccinated with the inactive polio vaccine (IPV). Additionally, 17 sera collected from 1 Xinjiang poliomyelitis case and his 16 contacts were also tested. Genomic sequencing was conducted the Xinjiang strain.ResultsThe antibody titers against the Xinjiang strain in each of 237 sera were significantly lower than those against the Sabin 1 strain. Notably, 40.0% of children in Group 1 were seronegative against the Xinjiang strain, which indicated that they might play an important role in wild poliovirus transmission, although their antibody titers against the Sabin 1 strain varied between 1:8 and 1:512. Meanwhile, serological results of the Xinjiang poliomyelitis case and his contacts also provided evidence that a proportion of OPV-vaccinated children had indeed been involved in the transmission chain of the Xinjiang outbreak. Genomic sequencing indicated that the Xinjiang strain was greatly distinguishable from the Sabin 1 strain in neutralizing antigenic sites.ConclusionThe lack of neutralizing antibodies against the Xinjiang strain in persons vaccinated by OPV may be associated with the transmission of Type 1 wild poliovirus in Xinjiang. Using Salk IPV along with OPV might be considered in a wild poliovirus outbreak response, especially in the countries which continued to have persistent wild poliovirus circulation.
High Levels of Circulating Cell-free DNA Are Associated With a Poor Prognosis in Patients With Severe Fever With Thrombocytopenia Syndrome
Authors: Zhang Yue , Song Rui , Shen Yi , Zhao Yongxiang , Zhao Zhenghua , Fan Tianli , Yang Xiaoyu , Wang Lin , Zhang Wei , Chen Chong , Tian Di , Wang Ying , Wen Jing , Ge Ziruo , Yu Xiaoli , Liu Li , Feng Yang , Duan Jianping , Ma Yanli , Li Xingwang , Zeng Hui , Chen Zhihai , Zhu Liuluan 
Published: June 2019

AbstractBackgroundThe extensive geographical distribution and high mortality rate of severe fever with thrombocytopenia syndrome (SFTS) have made it an important threat to public health. Neutrophil extracellular traps (NETs) can be activated by a variety of pathogens and are associated with thrombocytopenia in viral infections. We aimed to identify NET production and its predictive value for disease progression and prognosis in patients with SFTS.MethodsA prospective study was performed with a multicenter cohort of patients with SFTS (n = 112) to quantify serum NET levels. Three markers of NETs—namely, cell-free DNA (cfDNA), myeloperoxidase-DNA complexes, and lactoferrin-DNA complexes—were measured with PicoGreen double-stranded DNA assays and enzyme-linked immunosorbent assays. Receiver operating characteristic curves and multivariate regression analyses were performed to calculate the predictive value of cfDNA levels.ResultsSFTS was characterized by pronounced NET formation. The serum levels of NETs changed dynamically during disease progression, with an inverse pattern of the trends of platelet and neutrophil levels. High cfDNA levels were strongly associated with multiple pathological processes, including coagulopathy, myocardial damage, liver dysfunction, and the development of encephalopathy. A high level of cfDNA (&gt;711.7 ng/mL) at the time of the initial diagnosis predicted severe illness in patients with SFTS (odds ratio, 8.285 [95% confidence interval, 2.049–33.503]; P = .003).ConclusionsThis study has a high degree of clinical impact for identification of cfDNA as a useful predictive biomarker of clinical outcomes of SFTS.