bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of gut microbiota in shaping the relapse-remitting and chronic-progressive forms of multiple sclerosis in mouse models
Authors: Gandy K. Alexa Orr , Zhang Jiajia , Nagarkatti Prakash , Nagarkatti Mitzi 
Published: May 2019

AbstractUsing a mouse model of multiple sclerosis (MS), experimental autoimmune encephalitis (EAE), we evaluated the role of gut microbiota in modulating chronic-progressive (CP) versus relapse-remitting (RR) forms of the disease. We hypothesized that clinical courses of EAE may be shaped by differential gut microbiota. Metagenomic sequencing of prokaryotic 16S rRNA present in feces from naïve mice and those exhibiting CP-EAE or RR-EAE revealed significantly diverse microbial populations. Microbiota composition was considerably different between naïve strains of mice, suggesting microbial components present in homeostatic conditions may prime mice for divergent courses of disease. Additionally, there were differentially abundant bacteria in CP and RR forms of EAE, indicating a potential role for gut microbiota in shaping tolerant or remittance-favoring, and pathogenic or pro-inflammatory-promoting conditions. Furthermore, immunization to induce EAE led to significant alterations in gut microbiota, some were shared between disease courses and others were course-specific, supporting a role for gut microbial composition in EAE pathogenesis. Moreover, using Linear Discriminant Analysis (LDA) coupled with effect size measurement (LEfSe) to analyze microbial content, biomarkers of each naïve and disease states were identified. Our findings demonstrate for the first time that gut microbiota may determine the susceptibility to CP or RR forms of EAE.
DNA Length-dependent Division of a Giant Vesicle-based Model Protocell
Authors: Matsuo Muneyuki , Kan Yumi , Kurihara Kensuke , Jimbo Takehiro , Imai Masayuki , Toyota Taro , Hirata Yuiko , Suzuki Kentaro , Sugawara Tadashi 
Published: May 2019

AbstractDNA is an essential carrier of sequence-based genetic information for all life today. However, the chemical and physical properties of DNA may also affect the structure and dynamics of a vesicle-based model protocell in which it is encapsulated. To test these effects, we constructed a polyethylene glycol-grafted giant vesicle system capable of undergoing growth and division. The system incorporates a specific interaction between DNA and lipophilic catalysts as well as components of PCR. We found that vesicle division depends on the length of the encapsulated DNA, and the self-assembly of an internal supramolecular catalyst possibly leads to the direct causal relationship between DNA length and the capacity of the vesicle to self-reproduce. These results may help elucidate how nucleic acids could have functioned in the division of prebiotic protocells.
Musashi binding elements in Zika and related Flavivirus 3′UTRs: A comparative study in silico
Authors: Schneider Adriano de Bernardi , Wolfinger Michael T. 
Published: May 2019

AbstractZika virus (ZIKV) belongs to a class of neurotropic viruses that have the ability to cause congenital infection, which can result in microcephaly or fetal demise. Recently, the RNA-binding protein Musashi-1 (Msi1), which mediates the maintenance and self-renewal of stem cells and acts as a translational regulator, has been associated with promoting ZIKV replication, neurotropism, and pathology. Msi1 predominantly binds to single-stranded motifs in the 3′ untranslated region (UTR) of RNA that contain a UAG trinucleotide in their core. We systematically analyzed the properties of Musashi binding elements (MBEs) in the 3′UTR of flaviviruses with a thermodynamic model for RNA folding. Our results indicate that MBEs in ZIKV 3′UTRs occur predominantly in unpaired, single-stranded structural context, thus corroborating experimental observations by a biophysical model of RNA structure formation. Statistical analysis and comparison with related viruses show that ZIKV MBEs are maximally accessible among mosquito-borne flaviviruses. Our study addresses the broader question of whether other emerging arboviruses can cause similar neurotropic effects through the same mechanism in the developing fetus by establishing a link between the biophysical properties of viral RNA and teratogenicity. Moreover, our thermodynamic model can explain recent experimental findings and predict the Msi1-related neurotropic potential of other viruses.
A Fully-Flexible Solution-Processed Autonomous Glucose Indicator
Authors: Yuen Jonathan D. , Baingane Ankit , Hasan Qumrul , Shriver-Lake Lisa C. , Walper Scott A. , Zabetakis Daniel , Breger Joyce C. , Stenger David A. , Slaughter Gymama 
Published: May 2019

AbstractWe present the first demonstration of a fully-flexible, self-powered glucose indicator system that synergizes two flexible electronic technologies: a flexible self-powering unit in the form of a biofuel cell, with a flexible electronic device - a circuit-board decal fabricated with biocompatible microbial nanocellulose. Our proof-of-concept device, comprising an enzymatic glucose fuel cell, glucose sensor and a LED indicator, does not require additional electronic equipment for detection or verification; and the entire structure collapses into a microns-thin, self-adhering, single-centimeter-square decal, weighing less than 40 mg. The flexible glucose indicator system continuously operates a light emitting diode (LED) through a capacitive charge/discharge cycle, which is directly correlated to the glucose concentration. Our indicator was shown to operate at high sensitivity within a linear glucose concentration range of 1 mM–45 mM glucose continuously, achieving a 1.8 VDC output from a flexible indicator system that deliver sufficient power to drive an LED circuit. Importantly, the results presented provide a basis upon which further development of indicator systems with biocompatible diffusing polymers to act as buffering diffusion barriers, thereby allowing them to be potentially useful for low-cost, direct-line-of-sight applications in medicine, husbandry, agriculture, and the food and beverage industries.
Selection of reference genes for qPCR normalization in buffalobur (Solanum rostratum Dunal)
Authors: Zhao Dandan , Wang Xu , Chen Jingchao , Huang Zhaofeng , Huo Heqiang , Jiang Cuilan , Huang Hongjuan , Zhang Chaoxian , Wei Shouhui 
Published: May 2019

AbstractBuffalobur (Solanum rostratumDunal), which belongs to the Solanaceae family, is a worldwide noxious invasive weed and is listed as one of the top 10 alien invasive species in China. It is harmful to humans and livestock because the entire plant is covered with spines containing toxins. Many studies have analysed the gene expression in this weed species under different stress conditions using quantitative real-time PCR (qPCR). However, until now, there has been no report on suitable reference genes in buffalobur. Herein, 14 candidate reference genes were selected and evaluated for their expression stability in buffalobur in different tissues, at different developmental stages, and in response to several stress conditions using the geNorm, NormFinder, BestKeeper and RefFinder statistical algorithms. The results showed thatEF1α,ACTandSANDare suitable reference genes across all samples tested. We recommend the normalization of target gene expression under different experimental conditions using these three genes together. Validation of selected reference genes was achieved by assessing the relative expression levels ofP5CSandGI. This work identified the appropriate reference genes for transcript normalization in buffalobur, which will be helpful in future genetic studies of this invasive weed.
Whole-genome sequencing reveals nosocomial Clostridioides difficile transmission and a previously unsuspected epidemic scenario
Authors: García-Fernández Sergio , Frentrup Martinique , Steglich Matthias , Gonzaga Aitor , Cobo Marta , López-Fresneña Nieves , Cobo Javier , Morosini María-Isabel , Cantón Rafael , del Campo Rosa , Nübel Ulrich 
Published: May 2019

AbstractTo trace the routes and frequencies of transmission of Clostridioides difficile in a tertiary-care hospital in Madrid (Spain), we sequenced the genomes from all C. difficile isolates collected over 36 months (2014–2016) that were indistinguishable from any other isolate by PCR ribotyping. From a total of 589 C. difficile infection cases, we cultivated and PCR-ribotyped 367 C. difficile isolates (62%), of which 265 were genome-sequenced. Based on close relatedness of successively collected isolates (≤2 SNPs difference in their genomes), whole-genome sequencing revealed a total of 17 independent, putative transmission clusters, caused by various C. difficile strains and each containing 2 to 18 cases, none of which had been detected previously by standard epidemiological surveillance. Proportions of linked isolates varied widely among PCR ribotypes, from 3% (1/36) for ribotype 014/020 to 60% (12/20) for ribotype 027, suggesting differential aptitudes for nosocomial spread. Remarkably, only a minority (17%) of transmission recipients had direct ward contact to their presumed donors and specific C. difficile genome types frequently went undetectable for several months before re-emerging later, suggesting reservoirs for the pathogen outside of symptomatic patients. Taken together, our analysis based on genome sequencing suggested considerable within-hospital epidemic spread of C. difficile, even though epidemiological data initially had been inconspicuous.
Increased risk of asthma in patients with rheumatoid arthritis: A longitudinal follow-up study using a national sample cohort
Authors: Kim So Young , Min Chanyang , Oh Dong Jun , Choi Hyo Geun 
Published: May 2019

AbstractThe aim of this study was to evaluate the risk of asthma in rheumatoid arthritis patients using matched control group for socioeconomic factors and past medical history. Adults >20 years old were collected from the Korean Health Insurance Review and Assessment Service - National Sample Cohort (HIRA-NSC) from 2002 through 2013. A total of 6,695 individuals with rheumatoid arthritis were matched for age, sex, income, region of residence, hypertension, diabetes, and dyslipidemia with 26,780 individuals included in a control group. In both the rheumatoid arthritis and control groups, subjects’ history of asthma was evaluated. Asthma (J45 and J46) and rheumatoid arthritis (M05 and M06) were included based on the International Classification of Disease-10 (ICD-10) codes and medication history. The crude and adjusted (depression and Charlson Comorbidity Index) hazard ratios (HRs) and 95% confidence intervals (CI) of asthma for rheumatoid arthritis patients were analyzed using a stratified Cox proportional hazard model. Subgroup analyses were conducted according to age and sex, number of treatment histories, and medication histories. Approximately 16.4% (1,095/6,695) of rheumatoid arthritis group and 13.0% (3,469/26,780) of the control group had asthma (P < 0.001). The rheumatoid arthritis group demonstrated a higher adjusted HR for asthma than the control group (adjusted HR = 1.23, 95% CI = 1.15–1.32, P < 0.001). This result was consistent in all subgroups. Rheumatoid arthritis was related to an increase risk of asthma.
Using liner surface modes in acoustic ducts to make obstacles reflectionless
Authors: Farooqui Maaz , Aurégan Yves , Pagneux Vincent 
Published: May 2019

AbstractAcoustic cloaking for the suppression of backscattering inside ducts is proposed in the audible range where plane waves are curved around the object using the surface modes of the liner. It is numerically shown that a slowly varying resonant liner (e.g. based on an array of tubes) creates a zone of silence in which an object of arbitrary shape can be acoustically hidden for a wide range of frequencies. And then, a resonant liner has deflecting properties without reflection of the wavefront, which are close to an ideal invisibility cloak. This kind of cloaking is effective in a wide frequency band and the cloaking band is a function of the impedance and height of the obstacle relative to the conduit. For smooth shaped obstacles, there is an ability of the object to help hide itself, which increases the cloaking frequency band (self-cloaking). Dispersion effects lead to slow sounds and distortion of the wave phase.
Characterizing hydrogen-fuelled pulsating combustion on thermodynamic properties of a combustor
Authors: Zhao Dan , Guan Yiheng , Reinecke Arne 
Published: May 2019

AbstractUnlike hydrocarbon fuel, hydrogen is ‘green’ and attracting more and more attentions in energy and propulsion sectors due to the zero emission of CO and CO2. By applying numerical simulations, we explore the physics of how a hydrogen-burnt flame can sustain pulsating combustion and its impact on the thermodynamic properties of a standing-wave combustor. We also explain how implementing a heat exchanger can mitigate such pulsating combustion. The dynamic interactions of the unsteady flow-flame-acoustics-heater are examined by varying the mass flow rate ṁH2 and the heating bands’ surface temperature TH. The frequency and amplitude of the pulsating combustion are shown to depend strongly on ṁH2. In addition, varying TH is shown to lead to not only the molar fraction of the combustion species being changed but also the flame-sustained pulsating oscillations being mitigated somehow. Finally, nonlinearity is observed and identified in the unsteady flow velocity and the two heat sources.
Fusion Imaging in the Guidance of Thermal Ablations
Authors: Rossi Duccio , Nicosia Luca , Bonomo Guido , Della Vigna Paolo , Maiettini Daniele , Orsi Franco , Mauri Giovanni 
Published: May 2019

AbstractImage-guided thermal ablations are having an increasingly widespread effect on the treatment of several different abdominal conditions, and particularly on the treatment of liver and kidney tumors. In other conditions, such as in the case of pancreatic cancers, image-guided thermal ablations are still under investigation, but some studies showed promising results. Regardless the target organ to be treated, imaging represents one of the most important aspects for a safe and effective application of these techniques. To improve the image guidance in thermal ablations, some systems have been developed to fuse together two or more imaging modalities, providing the operator a real-time visualization of different information during the treatment. In the present review, the principles of fusion imaging will be described, and the principal application in the abdomen will be illustrated.
Effects and Interferences of Emicizumab, a Humanised Bispecific Antibody Mimicking Activated Factor VIII Cofactor Function, on Coagulation Assays
Authors: Adamkewicz Joanne I. , Chen David C. , Paz-Priel Ido 
Published: May 2019

AbstractEmicizumab bridges activated factor IX (FIX) and FX to restore the tenase function mediated by activated FVIII (FVIIIa), which is deficient in people with haemophilia A (PwHA). Unlike FVIII, emicizumab does not require activation to function; thus, in coagulation assays, the behavior of emicizumab may differ from that of FVIII. The objective of this study was to assess the effect of emicizumab on coagulation assays, including potential interference behavior that may produce inaccurate or misleading results. A variety of clotting-based, amidolytic/chromogenic, latex particle-enhanced turbidometric, and enzyme-linked immunosorbent methods were investigated. As expected based on its pharmacologic mechanism of action, emicizumab exhibited strong activity on the activated partial thromboplastin time (aPTT), which resulted in interference with several aPTT-based assays, most importantly the one-stage FVIII activity assay; these assays are not recommended for PwHA receiving emicizumab therapy. Pharmacodynamic activity of emicizumab, as measured by FVIII chromogenic assays, was species-dependent due to the binding specificity of the drug antibody. Outside of FVIII assays, emicizumab did not interfere with assays based on immunologic or chromogenic principles, nor with clotting assays based on nonintrinsic pathway activators, thus offering alternative choices where aPTT-based assays might otherwise be used. The observed interferences are in line with the unique mechanism of action of emicizumab. Potential interferences should be taken into account in the selection of coagulation assays and interpretation of coagulation assay test results for PwHA receiving emicizumab therapy.
Effect Estimates in Randomized Trials and Observational Studies: Comparing Apples With Apples
Authors: Lodi Sara , Phillips Andrew , Lundgren Jens , Logan Roger , Sharma Shweta , Cole Stephen R , Babiker Abdel , Law Matthew , Chu Haitao , Byrne Dana , Horban Andrzej , Sterne Jonathan A C , Porter Kholoud , Sabin Caroline , Costagliola Dominique , Abgrall Sophie , Gill John , Touloumi Giota , Pacheco Antonio G , van Sighem Ard , Reiss Peter , Bucher Heiner C , Montoliu Giménez Alexandra , Jarrin Inmaculada , Wittkop Linda , Meyer Laurence , Perez-Hoyos Santiago , Justice Amy , Neaton James D , Hernán Miguel A ,   INSIGHT START Study Group and the HIV-CAUSAL Collaboration
Published: May 2019

AbstractEffect estimates from randomized trials and observational studies might not be directly comparable because of differences in study design, other than randomization, and in data analysis. We propose a 3-step procedure to facilitate meaningful comparisons of effect estimates from randomized trials and observational studies: 1) harmonization of the study protocols (eligibility criteria, treatment strategies, outcome, start and end of follow-up, causal contrast) so that the studies target the same causal effect, 2) harmonization of the data analysis to estimate the causal effect, and 3) sensitivity analyses to investigate the impact of discrepancies that could not be accounted for in the harmonization process. To illustrate our approach, we compared estimates of the effect of immediate with deferred initiation of antiretroviral therapy in individuals positive for the human immunodeficiency virus from the Strategic Timing of Antiretroviral Therapy (START) randomized trial and the observational HIV-CAUSAL Collaboration.
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells
Authors: Lu Alex X , Zarin Taraneh , Hsu Ian S , Moses Alan M 
Published: May 2019

Abstract

Summary
We introduce YeastSpotter, a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines.

Availability and implementation
YeastSpotter is available at http://yeastspotter.csb.utoronto.ca/. Code is available at https://github.com/alexxijielu/yeast_segmentation.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Prevalence and Characterization of Axial Spondyloarthritis Among Veterans with Inflammatory Bowel Disease
Authors: Salem Mark , Malaty Hoda , Criner Karla , Caplan Liron , Hou Jason 
Published: May 2019

Abstract

Background
Axial spondyloarthritis (axSpA) includes ankylosing spondylitis and inflammatory spinal disease. We validated an algorithm to identify patients with axSpA and examine the prevalence of axSpA in inflammatory bowel disease (IBD) patients.

Methods
Diagnostic code algorithms to identify patients with axSpA were compared using a sample of randomly selected patients for chart review and used to estimate prevalence in a national cohort of IBD patients.

Results
Using the best performing algorithm for axSpA among IBD patients [&gt;3 codes and &gt;90 days between encounters (positive predictive value = 0.813, negative predictive value = 0.742)], 1545 cases of axSpA were identified among 77,824 IBD patients, a prevalence of 1.99%. Fifty-five percent of patients were diagnosed with IBD before axSpA, 24% were diagnosed concurrently, and 21% of patients were diagnosed with axSpA before IBD.
Abnormal aortic flow profiles persist after aortic valve replacement in the majority of patients with aortic valve disease: how model-based personalized therapy planning could improve results. A pilot study approach
Authors: Nordmeyer Sarah , Hellmeier Florian , Yevtushenko Pavel , Kelm Marcus , Lee Chong-Bin , Lehmann Daniel , Kropf Siegfried , Berger Felix , Falk Volkmar , Knosalla Christoph , Kuehne Titus , Goubergrits Leonid 
Published: May 2019

Abstract

OBJECTIVES
Complex blood flow profiles in the aorta are known to contribute to vessel dilatation. We studied flow profiles in the aorta in patients with aortic valve disease before and after surgical aortic valve replacement (AVR).

METHODS
Thirty-four patients with aortic valve disease underwent 4-dimensional velocity-encoded magnetic resonance imaging before and after AVR (biological valve = 27, mechanical valve = 7). Seven healthy volunteers served as controls. Eccentricity (ES) and complex flow scores (CFS) were determined from the degree of helicity, vorticity and eccentricity of flow profiles in the aorta. Model-based therapy planning was used in 4 cases to improve in silico postoperative flow profiles by personalized adjustment of size, rotation and angulation of the valve as well as aorta diameter.

RESULTS
Patients with aortic valve disease showed more complex flow than controls [median ES 2.5 (interquartile range (IQR) 2.3–2.7) vs 1.0 (IQR 1.0–1.0), P &lt; 0.001, median CFS 4.7 (IQR 4.3–4.8) vs 1.0 (IQR 1.0–2.0), P &lt; 0.001]. After surgery, flow complexity in the total patient cohort was reduced, but remained significantly higher compared to controls [median ES 2.3 (IQR 1.9–2.3) vs 1.0 (IQR 1.0–1.0), P &lt; 0.001, median CFS 3.8 (IQR 3.0–4.3) vs 1.0 (IQR 1.0–2.0), P &lt; 0.001]. In patients after mechanical AVR, flow complexity fell substantially and showed no difference from controls [median ES 1.0 (IQR 1.0–2.3) vs 1.0 (IQR 1.0–1.0), P = 0.46, median CFS 1.0 (IQR 1.0–3.3) vs 1.0 (IQR 1.0–2.0), P = 0.71]. In all 4 selected cases (biological, n = 2; mechanical, n = 2), model-based therapy planning reduced in silico complexity of flow profiles compared to the existing post-surgical findings [median ES 1.7 (IQR 1.4–1.7) vs 2.3 (IQR 2.3–2.3); CFS 1.7 (IQR 1.4–2.5) vs 3.8 (IQR 3.3–4.3)].

CONCLUSIONS
Abnormal flow profiles in the aorta more frequently persist after surgical AVR. Model-based therapy planning might have the potential to optimize treatment for best possible individual outcome.

Clinical trial registration number
clinicaltrials.gov NCT03172338, 1 June 2017, retrospectively registered; NCT02591940, 30 October 2015, retrospectively registered.