bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating microRNA trafficking and regulation: computational principles and practice
Authors: Cui Juan , Shu Jiang 
Published: June 2019

Abstract
Rapid advances in genomics discovery tools and a growing realization of microRNA’s implication in intercellular communication have led to a proliferation of studies of circulating microRNA sorting and regulation across cells and different species. Although sometimes, reaching controversial scientific discoveries and conclusions, these studies have yielded new insights in the functional roles of circulating microRNA and a plethora of analytical methods and tools. Here, we consider this body of work in light of key computational principles underpinning discovery of circulating microRNAs in terms of their sorting and targeting, with the goal of providing practical guidance for applications that is focused on the design and analysis of circulating microRNAs and their context-dependent regulation. We survey a broad range of informatics methods and tools that are available to the researcher, discuss their key features, applications and various unsolved problems and close this review with prospects and broader implication of this field.
Evolution of reproductive traits and selfing syndrome in the sub-endemic Mediterranean genus Centaurium Hill (Gentianaceae)
Authors: Jiménez-Lobato Vania , Escudero Marcial , Díaz Lifante Zoila , Andrés Camacho Cristina , de Castro Alejandra , Mansion Guilhem , Zeltner Louis , Arroyo Juan 
Published: June 2019

AbstractIn flowering plants, the shift from outcrossing to selfing is associated with a set of correlated changes in morphological and reproductive features known as the ‘selfing syndrome’. Species of the sub-endemic Mediterranean genus Centaurium Hill (Gentianaceae) exhibit a wide array of flower traits related to pollination biology and different ploidy levels. We explored if the evolutionary transitions of seven flower traits and life cycle, typically associated with the selfing syndrome, are related to polyploidy, diversification patterns, divergence times and the geological and climatic history of the Mediterranean Basin. Using 26 species of Centaurium we reconstructed a phylogenetic tree, inferred the ancestral states of the selected traits, estimated their phylogenetic signal and tested the correlative evolution among them. We found a significant increase in diversification rates during the Quaternary. Anther length, flower size, herkogamy and polyploidy undergo rapid state transitions without phylogenetic signal that could be the result of adaptation for selfing. Changes in character states do not show evidence of correlative evolution among them, as would be predicted during the evolution of selfing syndrome. The evolution of reproductive traits in Centaurium has probably relied on a more diverse array of drivers than just reproductive assurance or polyploidy events.
MicroRNA-301a promotes pancreatic cancer invasion and metastasis through the JAK/STAT3 signaling pathway by targeting SOCS5
Authors: Hu Hui , Zhang Qin , Chen Weiqun , Wu Tangwei , Liu Shuiyi , Li Xiaoyi , Luo Bo , Zhang Tianzhu , Yan Ge , Lu Hongda , Lu Zhongxin 
Published: June 2019

AbstractPancreatic cancer is one of the most lethal digestive malignant tumors. We had previously found that microRNA-301a (miR-301a) is a oncogenic microRNA whose recognized conduce to nuclear factor-kappa B (NF-κB) activation in pancreatic cancer, yet the underlying mechanisms of miR-301a in promoting pancreatic cancer invasion and migration is obscure. In this work we found that high expression of miR-301a in human pancreatic cancer patients is related to poor survival. Overexpression of miR-301a enhances pancreatic cancer cell invasion, angiogenesis and migration, whereas inhibition of miR-301a suppresses pancreatic cancer cell invasion and reduces orthotopic pancreatic tumor growth and metastasis. Furthermore, suppressor of cytokine signaling 5 (SOCS5) is identified as a target gene of miR-301a. We found that miR-301a suppressed the expression of SOCS5 leads to janus kinase/signal transducer and activator of transcription 3 (JAK/STAT3) activation and is related to poor overall survival of pancreatic cancer patients. Taken together, our data show for the first time that the feedback loop between miR-301a and JAK/STAT3 pathway may play a significant role in pancreatic cancer invasion and metastasis. Targeting the loop may prove beneficial to prevent metastasis and provide a more effective therapeutic strategy for pancreatic cancer.
Quality Evaluation of Andrographis paniculata Capsules Based on Rapid and Accurate LC–ESI–MS/MS Assay of Three Diterpenoids
Authors: Fu Shujun , Du Lemei , Yuan Yuan , He Xin 
Published: June 2019

Abstract
Andrographis paniculata is an important traditional Chinese herbal material widely used for treatment of fever and diarrhea. The three diterpenoids [andrographolide (AP), dehydroandrographolide (DP) and neoandrographolide (NP)] in A. paniculata were characterized as the key active components for its extractive and related medicinal preparations. A rapid and accurate quantitative analysis of these three diterpenoids in A. paniculata capsules was accomplished by means of a valid and reliable high-performance liquid chromatography with tandem mass spectrometric (HPLC–MS/MS) analytical method. An optimized gradient elution method, which under the mobile phase consisting of methanol and water, was established successfully. An XDB C18 column (3.5 μm, 2.1 mm × 50 mm) was successfully applied to separate these three diterpenoids at the flow rate of 0.55 mL/min. A triple quadrupole mass spectrometer with multiple reaction monitoring (MRM) mode using an electrospray ionization source was served for analytical detection. The linearity, specificity, accuracy, recovery, precision, stability and repeatability were demonstrated to fully confirm the validity of this study. Good linear regression relationships for the three analytes were obtained over the range of 0.50–1000 ng/mL. Intra-day and inter-day precisions were evaluated with relative standard deviation < 7.62%, and the extraction recovery varied from 93.8% to 102.0%. The rapid and accurate HPLC–MS/MS analytical method was developed for the quality evaluation of A. paniculata capsules successfully. The content of AP, DP and NP obtained were 3.90–4.08, 4.77–5.04, 4.32–4.48 mg/g in A. paniculata capsules, respectively. Moreover, it is expected that this analytical technique can be applied to detect three effective components rapidly and accurately in other different medicinal preparations of A. paniculata as a method for their quality control.
Multimodality imaging in the diagnosis, risk stratification, and management of patients with dilated cardiomyopathies: an expert consensus document from the European Association of Cardiovascular Imaging
Authors: Donal Erwan , Delgado Victoria , Bucciarelli-Ducci Chiara , Galli Elena , Haugaa Kristina H , Charron Philippe , Voigt Jens-Uwe , Cardim Nuno , Masci P G , Galderisi Maurizio , Gaemperli Oliver , Gimelli Alessia , Pinto Yigal M , Lancellotti Patrizio , Habib Gilbert , Elliott Perry , Edvardsen Thor , Cosyns Bernard , Popescu Bogdan A ,   2016–18 EACVI Scientific Documents Committee, Gerber Bernhard , Muraru Denisa , Flachskampf Frank , Plein Sven , Neglia Danilo , Cameli Matteo , Weytjens Caroline 
Published: June 2019

Abstract
Dilated cardiomyopathy (DCM) is defined by the presence of left ventricular or biventricular dilatation and systolic dysfunction in the absence of abnormal loading conditions or coronary artery disease sufficient to explain these changes. This is a heterogeneous disease frequently having a genetic background. Imaging is important for the diagnosis, the prognostic assessment and for guiding therapy. A multimodality imaging approach provides a comprehensive evaluation of all the issues related to this disease. The present document aims to provide recommendations for the use of multimodality imaging according to the clinical question. Selection of one or another imaging technique should be based on the clinical condition and context. Techniques are presented with the aim to underscore what is ‘clinically relevant’ and what are the tools that ‘can be used’. There remain some gaps in evidence on the impact of multimodality imaging on the management and the treatment of DCM patients where ongoing research is important.
“From Victimhood to Warriors”: Super-researchers’ Insights Into Alzheimer’s Disease Clinical Trial Participation Motivations
Authors: Bardach Shoshana H , Parsons Kelly , Gibson Allison , Jicha Gregory A 
Published: June 2019

Abstract

Background and Objectives
Recruitment and retention of research participant serve as a significant challenge in the search for ways to slow or prevent Alzheimer’s disease. While barriers to participation are well documented, less is known about motivations for Alzheimer’s disease clinical research participation. The purpose of this study was to explore what motivates individuals—who ultimately develop an ongoing connection to research and frequently participate—to engage and stay involved in Alzheimer’s disease research.

Research Design and Methods
Individuals who had participated in multiple Alzheimer’s disease-related clinical trials, or their study partners, were interviewed about their decisions to engage and remain in research.

Findings
Interviews were completed with 33 individuals, 28 research participants, and 5 study partners. All interviews were audio-recorded and transcribed verbatim for analysis. Respondents indicated learning about research opportunities through the media, community events, doctors, and other research participants. While many were initially motivated by a family history or knowing someone with Alzheimer’s disease, others had no personal exposure. Individuals in prevention studies were generally proactive and viewed research as a constructive way to address memory concerns. While several individuals acknowledged personal benefits of research participation, most indicated an understanding of the importance of research and being motivated to help others in the future, frequently referencing a sense of social responsibility or moral obligation to help. Positive relationships with personnel at the site encouraged continued involvement.

Discussion and Implications
These findings suggest that efforts to identify research participants should highlight the value of research and help illuminate how participation may contribute to well-being of future generations.
PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning
Authors: Fang Zhencheng , Tan Jie , Wu Shufang , Li Mo , Xu Congmin , Xie Zhongjie , Zhu Huaiqiu 
Published: June 2019

Abstract

Background
Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods that can simultaneously identify phages and plasmids in metagenomic data, and the existing tools identifying either phages or plasmids have not yet presented satisfactory performance.

Findings
We present PPR-Meta, a 3-class classifier that allows simultaneous identification of both phage and plasmid fragments from metagenomic assemblies. PPR-Meta consists of several modules for predicting sequences of different lengths. Using deep learning, a novel network architecture, referred to as the Bi-path Convolutional Neural Network, is designed to improve the performance for short fragments. PPR-Meta demonstrates much better performance than currently available similar tools individually for phage or plasmid identification, while testing on both artificial contigs and real metagenomic data. PPR-Meta is freely available via http://cqb.pku.edu.cn/ZhuLab/PPR_Meta or https://github.com/zhenchengfang/PPR-Meta.

Conclusions
To the best of our knowledge, PPR-Meta is the first tool that can simultaneously identify phage and plasmid fragments efficiently and reliably. The software is optimized and can be easily run on a local PC by non-computer professionals. We developed PPR-Meta to promote the research on mobile genetic elements and horizontal gene transfer.
Impacts of a shift to a warm-water regime in the Gulf of California on jumbo squid (Dosidicus gigas)
Authors: Frawley Timothy H , Briscoe Dana K , Daniel Patrick C , Britten Gregory L , Crowder Larry B , Robinson Carlos J , Gilly William F 
Published: June 2019

AbstractInterannual oceanic oscillations, climate change, and extreme events present a significant and complex challenge to management of pelagic fisheries. In recent years, anomalous oceanographic and atmospheric conditions have been reported across the northeast Pacific, yet research results concerning the biophysical mechanisms impacting specific organisms, populations, and fishery systems remain scarce. Here we discuss trends within the Gulf of California’s jumbo squid fishery in the context of relevant climate drivers, ecological dynamics, and mesoscale oceanographic processes. Following the 2009–2010 El Niño event, the jig-based fishery collapsed as squid adopted the small size-at-maturity phenotype characteristic of this species in the equatorial portion of its range. Analysis of regional sea surface temperatures and heights indicates a pronounced shift in the oceanographic trajectory of the system between the 2009–2010 and 2015–2016 El Niño events, whereas in situ hydrographic sampling reveals coincident changes in subsurface temperature and salinity. With persistently tropical oceanic conditions present across critical portions of their pelagic habitat, jumbo squid have lost access to previously productive coastal foraging zones, which in turn has limited opportunities for fishery recovery. Given the importance of jumbo squid to the region’s pelagic marine foodwebs, the long-term persistence of such phenomena could have significant implications for local fisheries, economies, and livelihoods.
Antibody Titers Reactive With Rickettsia rickettsii in Blood Donors and Implications for Surveillance of Spotted Fever Rickettsiosis in the United States
Authors: Straily Anne , Stuck Shawna , Singleton Joseph , Brennan Skyler , Marcum Stephanie , Condit Marah , Lee Christopher , Kato Cecilia , Tonnetti Laura , Stramer Susan L , Paddock Christopher D 
Published: June 2019

AbstractBackgroundSince 2000, the reported prevalence of tick-borne spotted fever rickettsiosis has increased considerably. We compared the level of antibody reactivity among healthy blood donors from 2 widely separated regions of the United States and evaluated the impact of antibody prevalence on public health surveillance in one of these regions.MethodsDonor serum samples were evaluated by indirect immunofluorescence antibody assay to identify immunoglobulin G (IgG) antibodies reactive with Rickettsia rickettsii. The Georgia Department of Public Health (GDPH) analyzed characteristics of cases from 2016 surveillance data to evaluate the utility of laboratory surveillance for case assessment.ResultsOf the Georgia donors (n = 1493), 11.1% demonstrated antibody titers reactive with R. rickettsii at titers ≥64, whereas 6.3% of donors from Oregon and Washington (n = 1511) were seropositive. Most seropositive donors had a titer of 64; only 3.1% (n = 93) of all donors had titers ≥128. During 2016, GDPH interviewed 243 seropositive case patients; only 28% (n = 69) met inclusion criteria in the national case definition for spotted fever rickettsiosis.ConclusionsThese findings suggest that a single IgG antibody titer is an unreliable measure of diagnosis and could inaccurately affect surveillance estimates that define magnitude and clinical characteristics of Rocky Mountain spotted fever and other spotted fever rickettsioses.
Contamination of Cockroaches (Insecta: Blattaria) by Medically Important Bacteriae: A Systematic Review and Meta-analysis
Authors: Nasirian Hassan 
Published: June 2019

Abstract
Cockroaches have the potential to disseminate bacteria in their environments and therefore a systematic review and meta-analysis was conducted to assess the state-of-the-art of our knowledge regarding bacterial contaminants of cockroaches. At least 78 bacterial species and 42 genera from 24 families and 11 orders of bacteria were reported to have contaminated cockroaches. At least 61, 42, 12, 13, 7, and 16 bacterial species have contaminated Blattella germanica (L.) (Blattaria: Ectobiidae), Periplaneta americana (L.) (Blattaria: Blattidae), Blatta orientalis (L.) (Blattaria: Blattidae), Diploptera punctata (Eschscholtz) (Blattaria: Blaberidae), Periplaneta fuliginosa (Serville) (Blattaria: Blattidae), and Supella longipalpa (F.) (Blattaria: Ectobiidae), respectively. Blattella germanica is the most commonly contaminated cockroach species, with the widest bacterial species diversity that threatens human health, followed by P. americana. Cockroach bacterial contaminants may result in the dissemination of opportunistic or pathogenic infections, particularly nosocomial and foodborne infections. One-way analysis of variance (ANOVA) revealed significant differences between bacterial contaminant species of cockroaches, species of cockroaches with bacterial contaminants, cockroach body part surfaces from the point of view bacterial contaminants and countries of cockroach infested with bacterial contaminants (P < 0.05). This statistical analysis indicates that the bacterial contaminants of the external cockroach body parts are potentially more harmful than from internal surfaces, and secondly, the bacterial contaminants of cockroaches in hospital environments are potentially more harmful than from other human environments. The survey indicated that the bacterial contaminant species of cockroaches appear to be mostly multiple drug resistant. The challenges of cockroaches as being potential vectors of pathogenic or opportunistic agents of human infections are discussed.
Use of Letermovir for Salvage Therapy for Resistant Cytomegalovirus in a Pediatric Hematopoietic Stem Cell Transplant Recipient
Authors: Kilgore Jacob T , Becken Bradford , Varga Matthew G , Parikh Suhag , Prasad Vinod , Lugo Debra , Chang Yeh-Chung 
Published: June 2019

Abstract
We present here the first published use of letermovir for the treatment of resistant cytomegalovirus (CMV) in a pediatric patient. A 14-year-old girl underwent a double unrelated umbilical cord blood transplantation to treat her sickle cell disease (hemoglobin SS) and developed ganciclovir-resistant CMV DNAemia with end-organ involvement that was treated successfully with a combination of foscarnet and letermovir. After she was transitioned to letermovir monotherapy for secondary prophylaxis, she developed recurrent DNAemia with laboratory-confirmed ganciclovir, foscarnet, and letermovir resistance.
3D GIS and ‘The Royaltie Of Sight’: Recreating ‘Prospects’ and ‘Perspectives’ within an English designed landscape c. 1550–1660
Authors: Stewart Elizabeth 
Published: June 2019

AbstractExperience through sight has been recognized as a contributing factor in the shaping of historic landscapes, where humans could express themselves in response to their aesthetic and intellectual qualities. What was experienced, however, was not only dependent on the ‘prospect’, or landscape view, but also on the individual ‘perspective’ of the spectator. Three-dimensional Geographical Information Systems (3D GIS) has enabled investigations into landscape visibility within digitized historic environments and can therefore assist the analysis and understanding of this phenomenon. This article applies 3D GIS to a currently under-researched area of landscape history, English designed landscapes of the 16th and 17th centuries. From country houses and gardens to parks and working estates, these landscapes were manipulated in response to the landowners’ ‘perspectives’ towards the landscape, which subsequently determined the visibility or invisibility of features within certain ‘prospects’. This concept was dubbed ‘The Royaltie of Sight’ by Henry Wotton in 1624. By using 3D GIS to recreate a designed landscape that poses challenges which have previously hindered its analysis, the characteristics of ‘prospects’ can be ascertained using viewshed analysis and the individual ‘perspective’ of the landowner interpreted using phenomenology and reception theory. The results presented in this article demonstrate how 3D GIS has benefited studies into English designed landscapes and improved knowledge of how perception influenced landscape change.
ϵ Lupi: measuring the heartbeat of a doubly magnetic massive binary with BRITE Constellation
Authors: Pablo H , Shultz M , Fuller J , Wade G A , Paunzen E , Mathis S , Le Bouquin J-B , Pigulski A , Handler G , Alecian E , Kuschnig R , Moffat A F J , Neiner C , Popowicz A , Rucinski S , Smolec R , Weiss W , Zwintz K ,   the BinaMIcS Collaboration
Published: June 2019

ABSTRACT
ϵ Lupi A is a binary system consisting of two main-sequence early B-type stars Aa and Ab in a short period, moderately eccentric orbit. The close binary pair is the only doubly magnetic massive binary currently known. Using photometric data from the BRITE Constellation we identify a modest heartbeat variation. Combining the photometry with radial velocities of both components we determine a full orbital solution including empirical masses and radii. These results are compared with stellar evolution models as well as interferometry and the differences discussed. We also find additional photometric variability at several frequencies, finding it unlikely these frequencies can be caused by tidally excited oscillations. We do, however, determine that these signals are consistent with gravity mode pulsations typical for slowly pulsating B stars. Finally we discuss how the evolution of this system will be affected by magnetism, determining that tidal interactions will still be dominant.
Building a cluster: shocks, cavities, and cooling filaments in the group–group merger NGC 6338
Authors: O’Sullivan Ewan , Schellenberger Gerrit , Burke D J , Sun Ming , Vrtilek Jan M , David Laurence P , Sarazin Craig 
Published: June 2019

Abstract
We present deep Chandra, XMM–Newton, Giant Metrewave Radio Telescope, and Hα observations of the group–group merger NGC 6338. X-ray imaging and spectral mapping show that as well as trailing tails of cool, enriched gas, the two cool cores are embedded in an extensive region of shock-heated gas with temperatures rising to ∼5 keV. The velocity distribution of the member galaxies show that the merger is occurring primarily along the line of sight, and we estimate that the collision has produced shocks of Mach number $\mathcal {M}$ = 2.3 or greater, making this one of the most violent mergers yet observed between galaxy groups. Both cool cores host potential AGN cavities and Hα nebulae, indicating rapid radiative cooling. In the southern cool core around NGC 6338, we find that the X-ray filaments associated with the Hα nebula have low entropies (&lt;10 keV cm2) and short cooling times (∼200–300 Myr). In the northern core, we identify an Hα cloud associated with a bar of dense, cool X-ray gas offset from the dominant galaxy. We find no evidence of current jet activity in either core. We estimate the total mass of the system and find that the product of this group–group merger will likely be a galaxy cluster.