bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weaning Stress Perturbs Gut Microbiome and Its Metabolic Profile in Piglets
Authors: Li Yuan , Guo Yong , Wen Zhengshun , Jiang Xuemei , Ma Xin , Han Xinyan 
Published: December 2018

AbstractWeaned piglets are vulnerable to nutritional, physiological, and psychological stressors, leading to abrupt taxonomic and functional shifts in the intestinal microbiome. In this study, an integrated approach combination of 16S rDNA gene sequencing and the mass spectrometry-based metabolomics techniques was used to investigate the effects of weaning stress on intestinal microbial composition and its metabolic profiles of piglets. Three litters of suckling piglets with same parity were chosen. The samples of colonic contents were collected from each selected piglets (weaned day, 3 days after weaned) for microbial and metabolomics analysis. The results showed that Lachnospiraceae, Negativicutes, Selenomonadales, Campylobacterales and other 15 species increased after weaning, while Porphyromonadaceace, Alloprevotella, Barnesiella and Oscillibacter decreased. Based on the function profiles prediction and metabolomic analysis, five key metabolic pathways including Phenylalanine metabolism, Citrate cycle (TCA cycle), Glycolysis or Gluconeogenesis, Propanoate metabolism, Nicotinate and nicotinamide metabolism might be the relevant pathways involved in weaning stress-induced gut microbiota dysbiosis. Taken together, these results indicated that weaning stress not only changed microbial composition and function but altered the microbial metabolic profiles in the intestine, which might provide a new insight in alleviating weaning stress and facilitating disease prevention during the period of weaning in piglets.
Double trouble? Gag in conjunction with double insert in HIV protease contributes to reduced DRV susceptibility
Authors: Williams Alison , Basson Adriaan , Achilonu Ikechukwu , Dirr Heini W. , Morris Lynn , Sayed Yasien 
Published: December 2018

AbstractHIV protease is essential for processing the Gag polyprotein to produce infectious virions and is a major target in antiretroviral therapy. We have identified an unusual HIV-1 subtype C variant that contains insertions of leucine and asparagine (L38↑N↑L) in the hinge region of protease at position 38. This was isolated from a protease inhibitor naïve infant. Isothermal titration calorimetry showed that 10% less of L38↑N↑L protease was in the active conformation as compared with a reference strain. L38↑N↑L protease displayed a ±50% reduction in KM and kcat. The catalytic efficiency (kcat/KM) of L38↑N↑L protease was not significantly different from that of wild type although there was a 42% reduction in specific activity for the variant. An in vitro phenotypic assay showed the L38↑N↑L protease to be susceptible to lopinavir (LPV), atazanavir (ATV) and darunavir in the context of an unrelated Gag. However, in the presence of the related Gag, L38↑N↑L showed reduced susceptibility to darunavir while remaining susceptible to LPV and ATV. Furthermore, a reduction in viral replication capacity (RC) was observed in combination with the related Gag. The reduced susceptibility to darunavir and decrease in RC may be due to PTAPP duplication in the related Gag. The present study shows the importance of considering the Gag region when looking at drug susceptibility of HIV-1 protease variants.
The Mycoplasma pneumoniae HapE alters the cytokine profile and growth of human bronchial epithelial cells
Authors: Li Shaoli , Xue Guanhua , Zhao Hanqing , Feng Yanling , Yan Chao , Cui Jinghua , Sun Hongmei 
Published: December 2018

Abstract
Mycoplasma pneumoniae is one of the most common pathogenic causes of community-acquired pneumonia. Hydrogen sulfide, alanine, and pyruvate producing enzyme (HapE) is a recently discovered M. pneumoniae virulence factor that can produce H2S to promote erythrocyte lysis. However, other cytotoxic effects of HapE have not been explored. The present study examined the effects of this enzyme on normal human bronchial epithelial (NHBE) cells, in an attempt to identify additional mechanisms of M. pneumoniae pathogenesis. Recombinant HapE was purified for use in downstream assays. MTT and colony formation assays were conducted to determine the effects of HapE on cell viability and growth, while flow cytometry was used to examine changes in cell proliferation and cell cycle function. ELISA was performed to examine changes in the cytokine profile of HapE-treated cells. HapE treatment arrested NHBE cells in S phase and inhibited cell proliferation in a concentration-dependent manner. The anti-inflammatory factors interleukin (IL)-4 and IL-6 were significantly enhanced following HapE treatment. Increased secretion of pro-inflammatory factors was not observed. The effects of HapE on the respiratory epithelium may have an impact on the efficiency of host immune surveillance and pathogen elimination, and contribute to the pathogenesis of M. pneumoniae.
Polarised structures in the radio lobes of B2 0258+35
Authors: Adebahr B. , Brienza M. , Morganti R. 
Published: December 2018

Context. The contribution of active galactic nuclei to the magnetisation of the Universe can be constrained by knowing their duty cycles, jet and magnetic field morphologies, and the physical processes dominating their interaction with the surrounding environment.
Aims. The magnetic field morphology and strength of radio lobes of AGN has an influence on the mechanisms for the propagation of cosmic rays into intergalactic space. Using the source B2 0258+35 we want to investigate the interaction of its radio lobes with the surrounding environment and examine the underlying physical effects.
Methods. Published H I and radio continuum data at λ21 cm were combined with newly reduced archival Westerbork Radio Synthesis Telescope polarisation data at the same wavelength to investigate the polarised emission in the radio lobes of B2 0258+35. We assumed energy equipartition between the cosmic rays and the magnetic field to calculate their pressure and investigate the physical processes leading to the detected emission.
Results. We detected a unique S-shaped diffuse polarised structure. The lobes have a pressure of p = 1.95 ± 0.4 × 10−14 dyn cm−2. The calculated total magnetic field strengths are low (Beq = 1.21 ± 0.12 μG). We observe depolarisation in the northern lobe, which might originate from the H I-disc in the foreground. In addition we see an anti-correlation between the pressure and the fractional polarisation along the S-shaped structure. Therefore we consider magnetic draping and magnetic field compression as possible effects that might have created the observed S-shape.
Conclusions. Our results suggest that magnetic draping can be effectively used to explain the observed polarised structures. This is likely due to the combination of a relatively low magnetic field strength, enabling super-Alfvénic motion of the rising lobes (with MA = 2.47 − 3.50), and the coherency of the surrounding magnetic field. Moreover, the draped layer tends to suppress any mixing of the material between the radio lobes and the surrounding environment, but can enhance the mixing and re-acceleration efficiencies inside the lobes, providing an explanation for the average flat spectral index observed in the lobes.
Prediabetes is Characterized by Higher FGF23 Levels and Higher Prevalence of Vitamin D Deficiency Compared to Normal Glucose Tolerance Subjects
Authors: Gateva Antoaneta , Assyov Yavor , Tsakova Adelina , Kamenov Zdravko 
Published: December 2018

AbstractIn the last years there is an increasing interest towards the bone as an endocrine organ and the role of bone and calcium-phosphate metabolism markers in a range of metabolic disturbances. The aim of the present study is to assess the changes of calcium phosphate metabolism markers in patients with prediabetes compared to normogycemic controls and their link to glucose disturbances and cardiovascular risk factors. In this study, 80 patients with mean age 50.4±10.6 years were included, divided into 2 age- and BMI-matched groups – group 1 with obesity without glycemic disturbances (n=41) and group 2 with obesity and prediabetes (n=39). Oral glucose tolerance test (OGTT) with measurement of immunoreactive insulin was performed in all participants and levels of PTH, 25(OH)D, FGF23, and Klotho were measured. We found significantly higher levels of FGF23 in patients with prediabetes compared to normal glucose tolerance subjects (10.4±10.7 vs. 5.8±7.3 pg/ml; p=0.03). FGF23 showed a weak positive correlation to fasting blood glucose (r=0.224; p=0.048) but not to blood glucose on the first and second hour of oral glucose tolerance test or insulin levels. There was extremely high prevalence of vitamin D deficiency in both groups. Lower levels of 25(OH)D were observed in prediabetes group, although without statistical significance (p=0.57). Patients with prediabetes have higher FGF23 levels and higher prevalence of vitamin D deficiency compared to normal glucose tolerance subjects. Elevated FGF23 levels seem to be correlated more to elevated fasting blood glucose levels than to insulin resistance state of the patients.
Self-organized shape dynamics of active surfaces
Authors: Mietke Alexander , Jülicher Frank , Sbalzarini Ivo F. 
Published: December 2018

Significance
Morphogenesis, the emergence of shape and form in biological systems, is a process that is fundamentally mechanochemical: Shape changes of material are driven by active mechanical forces that are generated by chemical processes, which in turn can be affected by the deformations and flows that occur. We provide a framework that integrates these interactions between the geometry of deforming materials and active processes in them by introducing the shape dynamics of self-organized active surfaces. We show that the tight coupling between surface mechanics and active processes gives rise to the spontaneous formation of nontrivial shapes, shape oscillations, and directed peristaltic motion. Our simple yet general description lays the foundation to explore the regulatory role of shape in morphogenetic processes.
In vitro and in vivo cancer cell apoptosis triggered by competitive binding of Cinchona alkaloids to the RING domain of TRAF6
Authors: Qi Yonghao , Zhao Xuan , Chen Jiaying , Pradipta Ambara R , Wei Jing , Ruan Haihua , Zhou Lijun , Hsung Richard P , Tanaka Katsunori 
Published: December 2018

ABSTRACT
TRAF6 is highly expressed in many tumors and plays an important role in the immune system. The aim of this study is to confirm anti-tumor activities of all naturally occurring Cinchona alkaloids that have been screened using computational docking program, and to validate the accuracy and specificity of the RING domain of TRAF6 as a potential anti-tumor target, and to explore their effect on the immune system. Results reported herein would demonstrate that Cinchona alkaloids could induce apoptosis in HeLa cells, inhibit the ubiquitination and phosphorylation of both AKT and TAK1, and up-regulate the ratio of Bax/Bcl-2. In addition, these compounds could induce apoptosis in vivo, and increase the secretion of TNF-α, IFN-γ, and IgG, while not significantly impacting the ratio of CD4+T/CD8+T. These investigations suggest that the RING domain of TRAF6 could serve as a de novo biological target for therapeutic treatment in cancers.
Fugitive Slave, Fugitive Novelist: The Narrative of James Williams (1838)
Authors: Santamarina Xiomara 
Published: December 2018

AbstractThis essay argues for reading a discredited slave narrative—the Narrative of James Williams (1838)—as an early black novel. Reading this narrative as a founding black novel à la Robinson Crusoe complicates the genealogy and theoretical parameters of literary criticism about early US black fiction. Such a reading revises accounts about the emergence of the third-person fictive voice inaugurated by Frederick Douglass and William Wells Brown in the 1850s. It also offers a new understanding of the antislavery movement’s quest for authenticity. More importantly, reading NJW as novelistic fiction illustrates how a fugitive slave might narrativize muddied textual politics and effectively challenge the reparative vision with which we theorize the genres and politics of early African American literary texts.
Curse: building expression atlases and co-expression networks from public RNA-Seq data
Authors: Vaneechoutte Dries , Vandepoele Klaas 
Published: December 2018

Abstract

Summary
Public RNA-Sequencing (RNA-Seq) datasets are a valuable resource for transcriptome analyses, but their accessibility is hindered by the imperfect quality and presentation of their metadata and by the complexity of processing raw sequencing data. The Curse suite was created to alleviate these problems. It consists of an online curation tool named Curse to efficiently build compendia of experiments hosted on the Sequence Read Archive, and a lightweight pipeline named Prose to download and process the RNA-Seq data into expression atlases and co-expression networks. Curse networks showed improved linking of functionally related genes compared to the state-of-the-art.

Availability and implementation
Curse, Prose and their manuals are available at http://bioinformatics.psb.ugent.be/webtools/Curse/. Prose was implemented in Java.

Supplementary information
Supplementary data are available at Bioinformatics online.
miR-338-5p inhibits cell proliferation, colony formation, migration and cisplatin resistance in esophageal squamous cancer cells by targeting FERMT2
Authors: Lin Wen-Chun , Chen Li-Han , Hsieh Yao-Chin , Yang Pei-Wen , Lai Liang-Chuan , Chuang Eric Y , Lee Jang-Ming , Tsai Mong-Hsun 
Published: December 2018

AbstractEsophageal cancer is one of the leading causes of cancer death in the male population of Eastern Asia. In addition, esophageal squamous cell carcinoma (ESCC) is the major type of esophageal cancer among the world. Owing to the poor overall 5-year survival rate, novel effective treatment strategies are needed. MicroRNAs are important gene regulators that are dysregulated in many cancer types. In our previous study, we applied next-generation sequencing to demonstrate that miR-338-5p was downregulated in the tumor tissue of patients with versus without recurrence. In this study, we further studied the roles of miR-338-5p in ESCC. The expression of endogenous miR-338-5p was at lower levels in ESCC cells compared with normal cells. Functional assays showed that miR-338-5p reduced cell proliferation, colony formation, migration and cisplatin resistance in an ESCC cell line, CE-81T. Potential target genes of miR-338-5p were identified by microarray and prediction tools, and 31 genes were selected. Among these, Fermitin family homolog 2 (FERMT2) plays an oncogenic role in ESCC, so it was chosen for further study. Luciferase assays showed the direct binding between miR-338-5p and the 3′ untranslated region of FERMT2. Silencing of FERMT2 inhibited cell proliferation, colony formation, migration and cisplatin resistance. Pathway analysis revealed that the integrin-linked protein kinase signaling pathway, in which FERMT2 participates, was significantly affected by a miR-338-5p mimic. Our results suggest that miR-338-5p may play an antioncogenic role in ESCC via repressing FERMT2.
Increase in emergency department visits related to cannabis reported using syndromic surveillance system
Authors: Noel G N , Maghoo A M , Franke F F , Viudes G V , Minodier P M 
Published: December 2018

Abstract

Background
Cannabis is illegal in France but, as in many countries, legalization is under debate. In the United States, an increase of emergency department (ED) visits related to cannabis exposure (CE) in infants and adults was reported. In France, a retrospective observational study also suggested an increase of CE in children under 6 years old. This study only included toddlers and the data sources used did not allow repeated analysis for monitoring.

Methods
Our study aimed to evaluate the trend in visits for CE in ED in patients younger than 27 years old in Southern France. A cross-sectional study using the Electronic Emergency Department Abstracts (EEDA) included in the national Syndromic Surveillance System. CE visits were defined using International Classification of Disease (ICD-10).

Results
From 2009 to 2014, 16 EDs consistently reported EEDA with <5% missing diagnosis code. Seven hundred and ninety seven patients were admitted for CE including 49 (4.1%) children under 8 years old. From 2009–11 to 2012–14, the rate of CE visits increased significantly across all age groups. The highest increase was in the 8–14 years old (+144%; 1.85–4.51, P < 0.001) and was also significant in children under 8 (0.53–1.06; P = 0.02). Among children under 8, hospitalization rate (75.5% vs. 16.8%; P < 0.001) and intensive care unit admissions (4.1% vs. 0.1%; P < 0.001) were higher compared with patients older than 8 years.

Conclusion
These trends occurred despite cannabis remaining illegal. EEDA could be useful for monitoring CE in EDs.
A right coronary artery aneurysm 16 years after surgical repair of anomalous origin of the right coronary artery from the pulmonary artery
Authors: Furutachi Akira , Furukawa Kojiro , Komatsu Aiko , Nogami Eijiro 
Published: December 2018

Abstract
Anomalous origin of the right coronary artery (RCA) from the pulmonary artery is a very rare congenital heart disease, and several reports have described long-term events after surgery. We report the case of a 46-year-old woman who underwent reimplantation of the RCA for anomalous origin of the right coronary artery from the pulmonary artery 16 years ago. An RCA aneurysm gradually developed and dilated over time, and we resected the aneurysm and also grafted the right gastroepiploic artery graft to the distal RCA. Careful long-term follow-up is required to avoid overlooking such a rare but life-threatening complication after surgical repair of anomalous origin of the right coronary artery from the pulmonary artery.
Psychosocial support during displacement due to a natural disaster: relationships with distress in a lower-middle income country
Authors: Zahlawi Tatiana , Roome Amanda B , Chan Chim W , Campbell Jacqueline J , Tosiro Bev , Malanga Max , Tagaro Markleen , Obed Jimmy , Iaruel Jerry , Taleo George , Tarivonda Len , Olszowy Kathryn M , Dancause Kelsey N 
Published: December 2018

Abstract

Background
Past studies show relationships between disaster-related displacement and adverse psychosocial health outcomes. The development of psychosocial interventions following displacement is thus increasingly prioritized. However, data from low- and middle-income countries (LMICs) are lacking. In October 2017, the population of Ambae Island in Vanuatu, a lower-middle income country, was temporarily displaced due to volcanic activity. We analyzed distress among adults displaced due to the event and differences based on the psychosocial support they received.

Methods
Data on experiences during displacement, distress and psychosocial support were collected from 443 adults 2–3 wk after repatriation to Ambae Island. Four support categories were identified: Healthcare professional, Traditional/community, Not available and Not wanted. We analyzed differences in distress by sex and group using one-way ANOVA and generalized linear models.

Results
Mean distress scores were higher among women (1.90, SD=0.97) than men (1.64, SD=0.98) (p<0.004). In multivariate models, psychosocial support group was associated with distress among women (p=0.033), with higher scores among women who reported no available support compared with every other group. Both healthcare professional and traditional support networks were widely used.

Conclusions
Women might be particularly vulnerable to distress during disaster-related displacement in LMICs, and those who report a lack of support might be at greater risk. Both healthcare professional and traditional networks provide important sources of support that are widely used and might help to ameliorate symptoms.
An outcome model approach to transporting a randomized controlled trial results to a target population
Authors: Goldstein Benjamin A , Phelan Matthew , Pagidipati Neha J , Holman Rury R , Pencina Michael J , Stuart Elizabeth A 
Published: December 2018

AbstractObjectiveParticipants enrolled into randomized controlled trials (RCTs) often do not reflect real-world populations. Previous research in how best to transport RCT results to target populations has focused on weighting RCT data to look like the target data. Simulation work, however, has suggested that an outcome model approach may be preferable. Here, we describe such an approach using source data from the 2 × 2 factorial NAVIGATOR (Nateglinide And Valsartan in Impaired Glucose Tolerance Outcomes Research) trial, which evaluated the impact of valsartan and nateglinide on cardiovascular outcomes and new-onset diabetes in a prediabetic population.Materials and MethodsOur target data consisted of people with prediabetes serviced at the Duke University Health System. We used random survival forests to develop separate outcome models for each of the 4 treatments, estimating the 5-year risk difference for progression to diabetes, and estimated the treatment effect in our local patient populations, as well as subpopulations, and compared the results with the traditional weighting approach.ResultsOur models suggested that the treatment effect for valsartan in our patient population was the same as in the trial, whereas for nateglinide treatment effect was stronger than observed in the original trial. Our effect estimates were more efficient than the weighting approach and we effectively estimated subgroup differences.ConclusionsThe described method represents a straightforward approach to efficiently transporting an RCT result to any target population.
A Heuristic Model of School Violence and Bullying in Evolving Nested Contexts
Authors: Avi Astor Ron , Benbenishty Rami 
Published: December 2018

Abstract
This chapter presents an integrated ecological theoretical model of school violence in evolving and nested contexts. In contrast to other models that put the student in the center, this heuristic model puts the school in the center of nested contexts, such as the student body, family, community, and culture. The school is also embedded in a hierarchical organizational structure, being part of a district, county, state, and country that also affect the school. All these outside contexts overflow into the school and influence internal school violence and safety. The school’s internal context, including the school organization and climate, moderates and mediates outside influences and helps shape the students’ experiences, perceptions, emotions, and behaviors Finally, the model suggests that school violence, bullying, safety, and student outcomes are dynamic and ever evolving, reflecting changes in norms and contexts. The dynamics of the school context impact all the external ecological layers as well.
Victimization
Authors: Avi Astor Ron , Benbenishty Rami 
Published: December 2018

Abstract
This chapter examines the definitions of bullying and school violence, suggesting that the use of the term “bullying” needs to be more specific and concrete, referring to behaviors that are intended to cause social, physical, emotional, sexual, or property damage. The chapter presents a wide range of victimization types that vary widely in terms of their prevalence in schools, their nature, and the severity of their impact on victims. It presents factor analyses that examine the relationships among different types of behaviors and reveal six distinct yet interrelated categories: verbal (e.g., humiliating), physical (e.g., pushing and shoving), threats, indirect social (e.g., spreading mean rumors), sexual, and cyber. Additionally, the chapter uses latent class analysis to examine how different groups of students experience multiple types of bullying and school victimization. Four groups (classes) were identified, each with a different profile of student background characteristics.