bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between X-ray and optical absorbers in active galactic nuclei
Authors: Jaffarian Gunnar W , Gaskell C Martin 
Published: January 2020

ABSTRACT
We present a large compilation of reddening estimates from broad-line Balmer decrements for active galactic nuclei (AGNs) with measured X-ray column densities. The median reddening is E(B − V) ≈ 0.77 ± 0.10 for type-1 to type-1.9 AGNs with reported column densities. This is notably higher than the median reddening of AGNs from the SDSS. We attribute this to the selection bias of the SDSS towards blue AGNs. For other AGNs, we find evidence of a publication bias against reporting low column densities. We find a significant correlation between NH and E(B − V) but with a large scatter of ±1 dex. On average, the X-ray columns are consistent with those predicted from E(B − V) for a solar neighbourhood dust-to-gas ratio. We argue that the large scatter of column densities and reddenings can be explained by X-ray column density variability. For AGNs with detectable broad-line regions (BLRs) that have undergone significant changes of Seyfert type (‘changing-look’ AGNs), we do not find any statistically significant differences in NH or E(B − V) compared to standard type-1 to type-1.9 AGNs. There is no evidence for any type-1 AGNs being Compton thick. We also analyse type-2 AGNs and find no significant correlation between NH and narrow-line region reddening. We find no evidence for a previously claimed anticorrelation. The median column density of LINERs is 22.68 ± 0.75 compared to a column density of 22.90 ± 0.28 for type-2 AGNs. We find the majority of low column density type-2 AGNs are LINERs, but NH is probably underestimated because of scattered light.
Effects of opacity temperature dependence on radiatively accelerated clouds
Authors: Dyda Sergei , Proga Daniel , Reynolds Christopher S 
Published: January 2020

ABSTRACT
We study how different opacity–temperature scalings affect the dynamical evolution of irradiated gas clouds using time-dependent radiation-hydrodynamics simulations. When clouds are optically thick, the bright side heats up and expands, accelerating the cloud via the rocket effect. Clouds that become more optically thick as they heat accelerate $\sim\! 35{{\ \rm per\ cent}}$ faster than clouds that become optically thin. An enhancement of $\sim\! 85{{\ \rm per\ cent}}$ in the acceleration can be achieved by having a broken power-law opacity profile, which allows the evaporating gas driving the cloud to become optically thin and not attenuate the driving radiation flux. We find that up to $\sim\! 2{{\ \rm per\ cent}}$ of incident radiation is re-emitted by accelerating clouds, which we estimate as the contribution of a single accelerating cloud to an emission or absorption line. Re-emission is suppressed by ‘bumps’ in the opacity–temperature relation since these decrease the opacity of the hot, evaporating gas, primarily responsible for the reradiation. If clouds are optically thin, they heat nearly uniformly, expand and form shocks. This triggers the Richtmyer–Meshkov instability, leading to cloud disruption and dissipation on thermal time-scales. Our work shows that, for some parameters, the rocket effect due to radiation-ablated matter leaving the back of the cloud is important for cloud acceleration. We suggest that this rocket effect can be at work in active galactic nuclei outflows.
RNU6-1 in circulating exosomes differentiates GBM from non-neoplastic brain lesions and PCNSL but not from brain metastases
Authors: Puigdelloses Montserrat , González-Huárriz Marisol , García-Moure Marc , Martínez-Vélez Naiara , Esparragosa Vázquez Inés , Bruna Jordi , Zandio Beatriz , Agirre Amaia , Marigil Miguel , Petrirena Gregorio , Nuñez-Córdoba Jorge M , Tejada-Solís Sonia , Díez-Valle Ricardo , Gállego-Culleré Jaime , Martínez-Vila Eduardo , Patiño-García Ana , Alonso Marta M , Gállego Pérez-Larraya Jaime 
Published: January 2020

Abstract

Background
Glioblastoma (GBM) is the most common malignant primary brain tumor in adults. Circulating biomarkers may assist in the processes of differential diagnosis and response assessment. GBM cells release extracellular vesicles containing a subset of proteins and nucleic acids. We previously demonstrated that exosomes isolated from the serum of GBM patients had an increased expression of RNU6-1 compared to healthy subjects. In this exploratory study, we investigated the role of this small noncoding RNA as a diagnostic biomarker for GBM versus other brain lesions with some potential radiological similarities.

Methods
We analyzed the expression of RNU6-1 in circulating exosomes of GBM patients (n = 18), healthy controls (n = 30), and patients with subacute stroke (n = 30), acute/subacute hemorrhage (n = 30), acute demyelinating lesions (n = 18), brain metastases (n = 21), and primary central nervous system lymphoma (PCNSL; n = 12) using digital droplet PCR.

Results
Expression of RNU6-1 was significantly higher in GBM patients than in healthy controls (P = .002). RNU6-1 levels were also significantly higher in exosomes from GBM patients than from patients with non-neoplastic lesions (stroke [P = .05], hemorrhage [P = .01], demyelinating lesions [P = .019]) and PCNSL (P = .004). In contrast, no significant differences were found between patients with GBM and brain metastases (P = .573). Receiver operator characteristic curve analyses supported the role of this biomarker in differentiating GBM from subacute stroke, acute/subacute hemorrhage, acute demyelinating lesions, and PCNSL (P &lt; .05), but again not from brain metastases (P = .575).

Conclusions
Our data suggest that the expression of RNU6-1 in circulating exosomes could be useful for the differentiation of GBM from non-neoplastic brain lesions and PCNSL, but not from brain metastases.
The state as owner—China’s experience
Authors: Milhaupt Curtis J 
Published: January 2020

AbstractThis essay explores China’s experience with state ownership of business enterprise. After a short historical survey of the rise, fall, and re-emergence of the state-owned enterprise (SOE) as a form of business organization, the essay examines the creation, ownership structure, and role of SOEs under Chinese state capitalism. It further discusses the government’s ongoing efforts to reform its SOEs. These efforts are illuminating because they highlight the serious tension inherent in the party-state’s dual goals of maintaining SOEs as a tool for advancing non-financial social and industrial policy objectives, and addressing the corporate governance challenges of these enterprises. The essay concludes by examining implications from the preceding analysis—for China’s domestic economy, for policy-makers outside China, and for the corporate form itself.
Asset Price Bubbles and Systemic Risk
Authors: Brunnermeier Markus , Rother Simon , Schnabel Isabel 
Published: January 2020

AbstractWe analyze the relationship between asset price bubbles and systemic risk, using bank-level data covering almost 30 years. Banks’ systemic risk already rises during a bubble’s buildup and even more so during its bust. The increase in risk strongly differs across banks and by bubble. It depends on bank characteristics (especially bank size) and bubble characteristics and can become very large: in a median real estate bust, systemic risk increases by almost 70% of the median for banks with unfavorable characteristics. These results emphasize the importance of bank-level factors in the buildup of financial fragility during bubble episodes.Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
Authors: Jiang Xiaodong , Edwards Scott V , Liu Liang 
Published: January 2020

AbstractA statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically congruent gene trees suggest that a poor fit of substitution models, rejected by 44% of loci, and concatenation models, rejected by 38% of loci, is widespread. Logistic regression shows that the proportions of GC content and informative sites are both negatively correlated with the fit of substitution models across loci. Moreover, a substantial violation of the concatenation assumption of congruent gene trees is consistently observed across six major groups (birds, mammals, fish, insects, reptiles, and others, including other invertebrates). In contrast, among those loci adequately described by a given substitution model, the proportion of loci rejecting the MSC model is 11%, significantly lower than those rejecting the substitution and concatenation models. Although conducted on reduced data sets due to computational constraints, Bayesian model validation and comparison both strongly favor the MSC over concatenation across all data sets; the concatenation assumption of congruent gene trees rarely holds for phylogenomic data sets with more than 10 loci. Thus, for large phylogenomic data sets, model comparisons are expected to consistently and more strongly favor the coalescent model over the concatenation model. We also found that loci rejecting the MSC have little effect on species tree estimation. Our study reveals the value of model validation and comparison in phylogenomic data analysis, as well as the need for further improvements of multilocus models and computational tools for phylogenetic inference. [Bayes factor; Bayesian model validation; coalescent prior; congruent gene trees; independent prior; Metazoa; posterior predictive simulation.]
Translating Workforce Development Policy Interventions for Community Health Workers: Application of a Policy Research Continuum
Authors: Fulmer Erika B. , Barbero Colleen , Gilchrist Siobhan , Shantharam Sharada S. , Bhuiya Aunima R. , Taylor Lauren N. , Jones Christopher D. 
Published: January 2020

Context:
There is a need for knowledge translation to advance health equity in the prevention and control of cardiovascular disease and type 2 diabetes. One recommended strategy is engaging community health workers (CHWs) to have a central role in related interventions. Despite strong evidence of effectiveness for CHWs, there is limited information examining the impact of state CHW policy interventions. This article describes the application of a policy research continuum to enhance knowledge translation of CHW workforce development policy in the United States.

Methods:
During 2016-2019, a team of public health researchers and practitioners applied the policy research continuum, a multiphased systematic assessment approach that incorporates legal epidemiology to enhance knowledge translation of CHW workforce development policy interventions in the United States. The continuum consists of 5 discrete, yet interconnected, phases including early evidence assessments, policy surveillance, implementation studies, policy ratings, and impact studies.

Results:
Application of the first 3 phases of the continuum demonstrated (1) how CHW workforce development policy interventions are linked to strong evidence bases, (2) whether existing state CHW laws are evidence-informed, and (3) how different state approaches were implemented.

Discussion:
As a knowledge translation tool, the continuum enhances dissemination of timely, useful information to inform decision making and supports the effective implementation and scale-up of science-based policy interventions. When fully implemented, it assists public health practitioners in examining the utility of different policy intervention approaches, the effects of adaptation, and the linkages between policy interventions and more distal public health outcomes.
Laparoscopic Hyperthermic Intraperitoneal Perfusion Chemotherapy for Patients With Malignant Ascites Secondary to Unresectable Gastric Cancer: Retracted
Authors: Ba Ming-Chen , Long Hui , Zhang Xiang-Liang , Gong Yuan-Feng , Tang Yun-Qiang , Wu Yin-Bing , Yu Fei-Hong , Cui Shu-Zhong 
Published: January 2020

Background:
To compare the efficacy of 3 chemotherapeutic combinations for laparoscopic hyperthermic intraperitoneal perfusion chemotherapy (HIPPC) in the treatment of malignant ascites secondary to unresectable gastric cancer (GC).

Materials and Methods:
From January 2010 to December 2013, 38 GC patients were randomly divided into 3 groups and treated by laparoscopic HIPPC with 1 of the 3 following chemotherapy combinations: raltitrexed (Ra) with oxaliplatin (L-OHP), Ra with cisplatin (DDP), and Ra with mitomycin C (MMC). Perioperative complications, patients’ quality of life, and survival were recorded and compared among the 3 groups.

Results:
The intraoperative course was successful in all patients, and no perioperative death or complication related to laparoscopic HIPPC was documented. The median follow-up period was 9 months and the median survival was 7.5 months for all patients. Patients in the Ra/L-OHP group had a median survival of 8.7 months, the Ra/DDP group had a median survival of 5.6 months, and the Ra/MMC group had a median survival of 7.5 months. Patients’ median survival in the Ra/L-OHP group and Ra/MMC group is significantly longer than Ra/DDP group (P<0.05). No significant difference was found in total remission rate of ascites, increase in the Karnofsky performance scale, and incidence rate of port-site metastases among the 3 groups.

Conclusions:
Laparoscopy-assisted HIPPC provide modest yet encouraging efficacy for malignant ascites secondary to disseminated GC. Our preliminary data indicate that the chemotherapeutical combination of Ra/L-OHP and Ra/MMC might be more beneficial compared with Ra/DDP in terms of patients’ survival.
Pharmacological modulation of the autophagy pathway enhances Mtb killing
Authors: Quaid Kate Mc , Keane Joseph , Kornfeld Hardy , O'Sullivan Mary , O'leary Seonadh 
Published: January 2020

Mycobacterium tuberculosis (Mtb) is the causative agent for tuberculosis which remains a serious health concern globally. The emergence of multi-drug resistant strains and the failure of BCG vaccine to control the epidemic highlight the need to achieve a better understanding of the host immune response and develop new therapies. Autophagy has been identified as an important element in both innate and adaptive immunity against tuberculosis. However Mtb employs an array of immune modulators to invade and thrive in macrophages including by inhibiting autophagosome fusion with lysosomes. Our aim is to identify novel modulators of the autophagy pathway. To do this we have screened a number of FDA approved autophagy-enhancing drugs to reverse the Mtb-induced block of autophagic flux and boost host immune responses.
Murine BMDMs expressing EGFP-LC3 were infected with H37Ra and treated with or without autophagy-enhancing drugs. The number of GFP-LC3-positive puncta per cell was quantified by high content analysis to assess autophagic induction and flux, thereby identifying compounds capable of overcoming the Mtb-induced block in autophagy. We identified three compounds, Sorafenib, Valproic Acid and Carbamazepine, which promote autophagic flux in Mtb-infected cells. Human MDMs were infected with H37Ra and treated with or without these drugs to determine their ability to promote intracellular killing of Mtb and boost the innate immune response. Our data show that Sorafenib, Valproic Acid and Carbamazepine are capable of overcoming the Mtb-induced block in autophagy and reducing bacterial burden in MDMs. This work highlights the potential for autophagy-enhancing drugs as adjunctive treatment for tuberculosis.
Antimicrobial resistance in bacteria associated with childhood pneumonia in Malawi
Authors: Moody Mitchell 
Published: January 2020

Community acquired pneumonia (CAP) is a disease caused by an infection (by bacteria, viruses or fungi) that in cases of chronic infection lead to high mortality rates particularly in children. Pneumonia is the leading cause of death in children under the age of five worldwide with over 2 million deaths reported in 2016 by the World Health Organisation. Developing countries in sub Saharan Africa such as Malawi see some of the highest rates of the disease. CAP infections are responsible for 20% of deaths of new-borns in Malawi. Antibiotic resistance in disease causing organisms is of growing concern in countries like Malawi.
We obtained bacterial isolates from blood samples taken from Malawian children, aged 18 -60 months, diagnosed with CAP. Streptococcus pneumonia is the primary pathogen in CAP but associated ESKAPE pathogens like Pseudomonas and Staphylococci spp. and Escherichia coli are of growing importance. These were the most common bacteria purified, isolated and characterised from these samples resulting in a unique culture collection. These pathogens have been screened for antimicrobial resistance with a variety of antibiotics to generate a resistance profile based on the minimal inhibitory concentrations of selected isolates using antibiotic susceptibility disks and by broth dilution method. Initial assessment shows current front-line therapies used by the Malawian ministry of health are ineffective in treating CAP.
Our research aims to fully characterise these strains at the genetic level to better understand the mechanisms behind how antibiotic resistance develops to aid in combating this growing issue in countries like Malawi.
Vorinostat (SAHA) promotes innate and adaptive immunity to Mycobacterium tuberculosis
Authors: Cox Donal , Coleman Amy , Gogan Karl , Dunne Padraic , Basdeo Sharee , Keane Joseph 
Published: January 2020

Mycobacterium tuberculosis (Mtb) is increasingly resistant to antibiotics. Therefore, it is paramount to develop host-directed therapies (HDT) aimed at activating the host immune response to promote bacterial killing. Mtb is phagocytosed by alveolar macrophages (AM) and infiltrating monocyte-derived macrophages (MDM) in the lung which upregulate effector functions by epigenetic modifications to enable transcription. Suberanilohydroxamic acid (Vorinostat; SAHA), an FDA-approved histone deacetylase inhibitor, can modulate these changes and support immunity.
Human AM were purified from bronchoalveolar lavage. MDM were obtained from blood of healthy donors and patients with TB. Macrophages were infected with Mtb in the presence of SAHA. After 24 hours, cytokine secretion was quantified. Macrophages were washed and co-cultured with CFSE-labelled PBMC from IGRA positive donors. T-cell responses were analysed by flow cytometry and ELISA. Macrophages were lysed and colony forming units were enumerated.
SAHA increased IL-1β and decreased IL-10 in human AM and MDM infected with Mtb. Proliferating T-helper cells co-cultured with Mtb-infected, SAHA-treated AM or MDM exhibited enhanced IFN-γ and GMCSF co-production. SAHA promotes proinflammatory immune responses to Mtb infection in human AM and MDM, with a subsequent effect on T cell responses. SAHA may therefore be beneficial as a host-directed therapy or vaccine adjunct against TB.
Oligonucleotides can act as superscaffolds that enhance liquid-liquid phase separation of intracellular mixtures
Authors: Joseph Jerelle A. , Espinosa Jorge R. , Sanchez-Burgos Ignacio , Garaizar Adiran , Frenkel Daan , Collepardo-Guevara Rosana 
Published: January 2020

AbstractIntracellular liquid-liquid phase separation (LLPS) enables the formation of biomolecular condensates, which play a crucial role in the spatiotemporal organisation of biomolecules (proteins, oligonucleotides). While LLPS of biopolymers has been demonstrated in both experiments and computer simulations, the physical determinants governing phase separation of protein-oligonucleotide systems are not fully understood. Here, we introduce a minimal coarse-grained model to investigate concentration-dependent features of protein-oligonucleotide mixtures. We demonstrate that adding oligonucleotides to biomolecular condensates composed of oligonucleotide-binding scaffold proteins enhances LLPS; since oligonucleotides act as ultra-high-valency molecules (termed ‘superscaffolds’) that increase the molecular connectivity among scaffold proteins. Importantly, we find that oligonucleotides promote protein LLPS via a seeding-type mechanism; recruiting numerous protein molecules and reducing the thermodynamic and kinetic barriers for nucleation and phase separation. By probing the conformational properties of oligonucleotides within droplets, we show that these biopolymers can undergo phase separation-driven compaction, which may be entropic in nature. Finally, we provide a quantitative comparison between mixture composition, protein valency, and protein-oligonucleotide interaction strengths. We find that superscaffolds preferentially recruit higher valency proteins to condensates, and that multiphase immiscibility within condensates can be achieved by modulating the relative protein-oligonucleotide binding strengths. These results shed light on the roles of oligonucleotides in ribonu-cleoprotein granule formation, heterochromatin compaction, and internal structuring of the nucleolus and stress granules.
Luciferase Immunoprecipitation Systems immunoassay is a sensitive, rapid method to detect allergen component-specific IgE
Authors: Lin Adora A. , Perez Natalia S. , Frischmeyer-Guerrerio Pamela A. , Nutman Thomas B. 
Published: January 2020

AbstractCurrent assays to detect allergen-specific IgE have constraints related to obtaining pure, conformationally active allergen, variability in allergen extracts, sample volume required, and turnaround time. The luciferase immunoprecipitation systems (LIPS) immunoassay is a fast, sensitive assay created using recombinant antigens that requires a low specimen volume. These assays can also be easily modified to detect multiple antigens and antibody isotypes. Here, we demonstrate the use of LIPS assays as an innovative method to quantitatively measure allergen component-specific IgE in small sample volumes. Sera from healthy volunteers, helminth-infected adults, and peanut-allergic children were screened for IgE to cat using ImmunoCAP. These samples were also measured for IgE against Fel d 1 using LIPS. LIPS signal correlated to cat IgE levels withrS= 0.6204, p < 0.001. The LIPS signal: noise ratio differed significantly between cat IgE-samples and cat IgE+ samples with values > 0.5 kU/L, with the ability to differentiate cat IgE – individuals from cat IgE+ individuals with 85% sensitivity and 76% specificity. Given their rapidity, efficiency, sensitivity, and quantitation over a broad dynamic range, LIPS immunoassays can be a robust and flexible tool with potential uses in allergy research, diagnostics, and treatment.