bluuebunny/crossref_metadata_2025_split huggingface dataset:
PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA interaction prediction
Authors: Kang Qiang , Meng Jun , Cui Jun , Luan Yushi , Chen Ming 
Published: January 2020

Abstract

Motivation
The studies have indicated that not only microRNAs (miRNAs) or long non-coding RNAs (lncRNAs) play important roles in biological activities, but also their interactions affect the biological process. A growing number of studies focus on the miRNA–lncRNA interactions, while few of them are proposed for plant. The prediction of interactions is significant for understanding the mechanism of interaction between miRNA and lncRNA in plant.

Results
This article proposes a new method for fulfilling plant miRNA–lncRNA interaction prediction (PmliPred). The deep learning model and shallow machine learning model are trained using raw sequence and manually extracted features, respectively. Then they are hybridized based on fuzzy decision for prediction. PmliPred shows better performance and generalization ability compared with the existing methods. Several new miRNA–lncRNA interactions in Solanum lycopersicum are successfully identified using quantitative real time–polymerase chain reaction from the candidates predicted by PmliPred, which further verifies its effectiveness.

Availability and implementation
The source code of PmliPred is freely available at http://bis.zju.edu.cn/PmliPred/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Renal amyloidosis: validation of a proposed histological scoring system in an independent cohort
Authors: Hoelbeek Joris J , Kers Jesper , Steenbergen Eric J , Roelofs Joris J T H , Florquin Sandrine 
Published: January 2020

Abstract

Background
In systemic amyloidosis, the kidney is frequently affected and renal involvement has a major impact on survival. Renal involvement is clinically characterized by decreased estimated glomerular filtration rate (eGFR) and proteinuria. The two most common renal amyloidosis types are light chain-related amyloidosis (AL) and serum amyloid A (AA) amyloidosis. Standardized histopathological scoring of amyloid deposits is crucial to assess disease progression. Therefore, we aimed to validate the proposed scoring system from Rubinstein et al. (Novel pathologic scoring tools predict end-stage kidney disease in light chain (AL) amyloidosis. Amyloid 2017; 24: 205–211) in an independent patient cohort.

Methods
We attempt to reproduce the scoring system, consisting of an amyloid score (AS) and a composite scarring injury score (CSIS), in a multicentre AL and AA case series. Additionally, we analysed all renal amyloidosis kidney biopsies performed in the Netherlands between 1993 and 2012.

Results
Similar to the original study, AS and CSIS correlated to eGFR (r = −0.45, P = 0.0061 and r = −0.60, P &lt; 0.0001, respectively) but not to proteinuria at diagnosis. Furthermore, AS, but not CSIS, was associated with renal outcome. The scoring system was not reproducible in AA patients. The median incidence rate for renal amyloidosis in the Netherlands was 2.3 per million population per year, and increased during the study period.

Conclusions
In our AL case series and the original study, AS and CSIS were correlated to eGFR but not to proteinuria, and AS correlated with renal outcome. Overall, we regard this scoring system as competent for standardized histopathological assessment of amyloid deposits burden and thereby disease advancement in renal biopsies.
Treatment of coronary microvascular dysfunction
Authors: Bairey Merz C Noel , Pepine Carl J , Shimokawa Hiroki , Berry Colin 
Published: January 2020

Abstract
Contemporary data indicate that patients with signs and symptoms of ischaemia and non-obstructive coronary artery disease (INOCA) often have coronary microvascular dysfunction (CMD) with elevated risk for adverse outcomes. Coronary endothelial (constriction with acetylcholine) and/or microvascular (limited coronary flow reserve with adenosine) dysfunction are well-documented, and extensive non-obstructive atherosclerosis is often present. Despite these data, patients with INOCA currently remain under-treated, in part, because existing management guidelines do not address this large, mostly female population due to the absence of evidence-based data. Relatively small sample-sized, short-term pilot studies of symptomatic mostly women, with INOCA, using intense medical therapies targeting endothelial, microvascular, and/or atherosclerosis mechanisms suggest symptom, ischaemia, and coronary vascular functional improvement, however, randomized, controlled outcome trials testing treatment strategies have not been completed. We review evidence regarding CMD pharmacotherapy. Potent statins in combination with angiotensin-converting enzyme inhibitor (ACE-I) or receptor blockers if intolerant, at maximally tolerated doses appear to improve angina, stress testing, myocardial perfusion, coronary endothelial function, and microvascular function. The Coronary Microvascular Angina trial supports invasive diagnostic testing with stratified therapy as an approach to improve symptoms and quality of life. The WARRIOR trial is testing intense medical therapy of high-intensity statin, maximally tolerated ACE-I plus aspirin on longer-term outcomes to provide evidence for guidelines. Novel treatments and those under development appear promising as the basis for future trial planning.
The geographical diversification in varanid lizards: the role of mainland versus island in driving species evolution
Authors: Zhu Xia-Ming , Du Yu , Qu Yan-Fu , Li Hong , Gao Jian-Fang , Lin Chi-Xian , Ji Xiang , Lin Long-Hui 
Published: January 2020

Abstract
Monitor lizards (Varanidae) inhabit both the mainland and islands of all geological types and have diversified into an exceptionally wide range of body sizes, thus providing an ideal model for examining the role of mainland versus island in driving species evolution. Here we use phylogenetic comparative methods to examine whether a link exists between body size-driven diversification and body size-frequency distributions in varanid lizards and to test the hypothesis that island lizards differ from mainland species in evolutionary processes, body size, and life-history traits (offspring number and size). We predict that: 1) since body size drives rapid diversification in groups, a link exists between body size-driven diversification and body size-frequency distributions; 2) because of various environments on island, island species will have higher speciation, extinction, and dispersal rates, compared with mainland species; 3) as a response to stronger intraspecific competition, island species will maximize individual ability associated with body size to outcompete closely-related species, and island species will produce smaller clutches of larger eggs to increase offspring quality. Our results confirm that the joint effect of differential macroevolutionary rates shapes the species richness pattern of varanid lizards. There is a link between body size-driven diversification and body size-frequency distributions, and the speciation rate is maximized at medium body sizes. Island species will have higher speciation, equal extinction, and higher dispersal rates compared with mainland species. Smaller clutch size and larger hatchling in the island than in mainland species indicate that offspring quality is more valuable than offspring quantity for island varanids.
CancerLivER: a database of liver cancer gene expression resources and biomarkers
Authors: Kaur Harpreet , Bhalla Sherry , Kaur Dilraj , Raghava Gajendra PS 
Published: January 2020

Abstract
Liver cancer is the fourth major lethal malignancy worldwide. To understand the development and progression of liver cancer, biomedical research generated a tremendous amount of transcriptomics and disease-specific biomarker data. However, dispersed information poses pragmatic hurdles to delineate the significant markers for the disease. Hence, a dedicated resource for liver cancer is required that integrates scattered multiple formatted datasets and information regarding disease-specific biomarkers. Liver Cancer Expression Resource (CancerLivER) is a database that maintains gene expression datasets of liver cancer along with the putative biomarkers defined for the same in the literature. It manages 115 datasets that include gene-expression profiles of 9611 samples. Each of incorporated datasets was manually curated to remove any artefact; subsequently, a standard and uniform pipeline according to the specific technique is employed for their processing. Additionally, it contains comprehensive information on 594 liver cancer biomarkers which include mainly 315 gene biomarkers or signatures and 178 protein- and 46 miRNA-based biomarkers. To explore the full potential of data on liver cancer, a web-based interactive platform was developed to perform search, browsing and analyses. Analysis tools were also integrated to explore and visualize the expression patterns of desired genes among different types of samples based on individual gene, GO ontology and pathways. Furthermore, a dataset matrix download facility was provided to facilitate the users for their extensive analysis to elucidate more robust disease-specific signatures. Eventually, CancerLivER is a comprehensive resource which is highly useful for the scientific community working in the field of liver cancer.Availability: CancerLivER can be accessed on the web at https://webs.iiitd.edu.in/raghava/cancerliver.
Effect of functional lateral shift of the mandible on hyaluronic acid metabolism related to lubrication of temporomandibular joint in growing rats
Authors: Guo Xiyuan , Watari Ippei , Ikeda Yuhei , Yang Wu , Ono Takashi 
Published: January 2020

SummaryBackgroundHyaluronic acid (HA) is a major molecular component of the articular cartilage of the temporomandibular joint (TMJ) influencing joint lubrication. Functional lateral shift of the mandible (FLSM) can lead to malocclusion. This study investigated the effects of FLSM on HA metabolism and lubrication of the TMJ in growing rats.MethodsThirty 5-week-old male Wistar rats were divided into shift, recovery, and control groups. Rats in the shift and recovery groups were fitted with guiding plates to produce a 2-mm FLSM which were removed from the rats in the recovery group 14 days later. Animals were sacrificed at 14 and 28 days after the appliances were attached. Immunohistochemistry of HA-binding protein (HABP), hyaluronan synthase (HAS), and hyaluronoglucosaminidases (HYALs) was examined.ResultsThe thickness of HABP-positively stained areas in the lateral regions in the bilateral condyle was reduced during the experimental period in the shift group compared with that in the control group. The proportion of HAS2-stained areas was bilaterally decreased in different regions of condylar cartilage during the experimental period in the shift group. The reduction of the HYAL2-stained area proportion in the condylar cartilage was more significant than that of HYAL1 at 14 days after appliance attachment in the shift group. HAS2 staining was not recovered in the recovery group.LimitationsThis research was based on animal experiments with a limited experimental period.ConclusionFLSM altered lubrication related HA metabolism in the articular cartilage of the TMJ in growing rats.
3D mapping for the identification of the fossa ovalis in left atrial ablation procedures: a pilot study of a first step towards an electroanatomic-guided transseptal puncture
Authors: Eichenlaub Martin , Weber Reinhold , Minners Jan , Allgeier Hans-Jürgen , Jadidi Amir , Müller-Edenborn Björn , Neumann Franz-Josef , Arentz Thomas , Lehrmann Heiko 
Published: January 2020

Abstract

Aims
Transseptal puncture (TP) for left atrial (LA) catheter ablation procedures is routinely performed under fluoroscopic guidance. To decrease radiation exposure and increase safety alternative techniques are desirable. The aim of this study was to assess whether right atrial (RA) electroanatomic 3D mapping can reliably identify the fossa ovalis (FO) in preparation of TP.

Methods and results
Between May 2019 and August 2019, electroanatomic RA mapping was performed before TP in 61 patients with paroxysmal or persistent atrial fibrillation. Three electroanatomic methods for FO identification, mapping catheter-induced FO protrusion, electroanatomic-guided analysis, and voltage mapping, were evaluated and compared with transoesophageal echocardiography (TOE). Mapping catheter-induced FO protrusion was feasible in 60 patients (98%) with a mean displacement of 6.8 ± 2.5 mm, confirmed by TOE, and proofed to be the most valuable and easiest marker for FO identification. Electroanatomic-guided analysis localized the FO midpoint consistently in the lower half (43 ± 7%) and posterior (18.2 ± 4.4 mm) to a line between coronary sinus and vena cava superior. Analysis of RA voltage maps during sinus rhythm (n = 40, low-voltage cut-off value 1.0 and 1.5 mV) allowed secure FO recognition in 33% and 18%, only. A step-by-step approach, combining FO protrusion (first step) with anatomy criteria in case of protrusion failure (second step) would have allowed for the correct localization of a TP site within the FO in all patients.

Conclusion
Right atrial electroanatomic 3D mapping prior to TP proofed to be a simple tool for FO identification and may potentially be of use in the safe and radiation-free performance of TP prior to LA ablation procedures.
Left atrial volume and function assessed by cardiac magnetic resonance imaging are markers of subclinical atrial fibrillation as detected by continuous monitoring
Authors: Bertelsen Litten , Diederichsen Søren Zöga , Haugan Ketil Jørgen , Brandes Axel , Graff Claus , Krieger Derk , Kronborg Christian , Køber Lars , Højberg Søren , Vejlstrup Niels , Svendsen Jesper Hastrup 
Published: January 2020

Abstract

Aims
We aimed to investigate whether left atrial (LA) markers from cardiovascular magnetic resonance (CMR) were able to predict atrial fibrillation (AF) in elderly patients with risk factors for stroke.

Methods and results
At baseline, 203 participants with stroke risk factors but without history of AF underwent advanced CMR and received an implantable loop recorder. During a median of 40 (37–42) months of continuous monitoring, incident AF was detected in 79 patients (39%). With regards to CMR markers, a steep increase in incidence rate of AF was seen with LA maximum volume (LAmax) above 55 mL/m2, LA minimum volume (LAmin) above 30 mL/m2, LA total emptying fraction (LA TEF) below 45%, LA active emptying fraction (LA AEF) below 37%, LA strain S below 25%, LA strain A below 17%, and LA strain rate A above −1.7 s−1. After multivariate adjustment, the above-mentioned CMR markers remained associated with AF incidence: hazard ratio (95% confidence interval) 1.25 (1.06–1.48) and 1.51 (1.22–1.87) per 10 mL/m2 increase of LAmax and LAmin, respectively, 1.49 (1.26–1.76) and 1.46 CI (1.25–1.71) per 5% decrease in LA TEF and LA AEF, respectively, 1.23 (1.05–1.44) and 1.56 (1.18–2.06) per 5% decrease in LA strain S and A, respectively, and 2.06 (1.31–3.23) per s−1 increase in LA strain rate A. In prediction analyses, LA functional indices increased area under the receiver operating characteristic curve significantly.

Conclusion
The risk of AF, including asymptomatic AF, increases significantly with increasing LA volumes and worsening LA function.
Unintended Consequences of Opioid Regulations in Older Adults with Multiple Chronic Conditions
Authors: Ritchie Christine S , Garrett Sarah B , Thompson Nicole , Miaskowski Christine 
Published: January 2020

Abstract

Background and Objectives
The opioid epidemic has led to substantive regulatory and policy changes. Little is known about how these changes have impacted older adults, especially those with chronic pain and multiple chronic conditions (MCC). We sought to understand the experiences of older adults with chronic pain and MCC in the context of the opioid epidemic and policy responses to it.

Research Design and Methods
Purposive sampling of older adults in a West Coast metropolitan area. Semistructured in-depth interviews lasting 45–120 min were digitally recorded and transcribed. Responses were analyzed using the constant comparative method. Participants were 25 adults aged 65 years and greater with three or more self-reported medical conditions and pain lasting for more than 6 months.

Results
Respondents’ accounts revealed numerous unintended consequences of the opioid epidemic and its policy responses. We identified four main themes: changes to the patient–clinician relationship; lack of patient agency and access in pain management; patient ambivalence and anxiety about existing opioid treatment/use; and patient concerns about future use.

Discussion and Implications
Older adults have high rates of chronic pain and MCC that may reduce their pain management options. The opioid epidemic and policies addressing it have the potential to negatively affect patient–clinician relationships and patients’ pain self-management. Clinicians may be able to mitigate these unintended consequences by actively conveying respect to the patient, empowering patients in their pain self-management activities, and proactively addressing worries and fears patients may own related to their current and future pain management regimens.
Three-station interferometry and tomography: coda versus direct waves
Authors: Zhang Shane , Feng Lili , Ritzwoller Michael H 
Published: January 2020

SUMMARYTraditional two-station ambient noise interferometry estimates the Green’s function between a pair of synchronously deployed seismic stations. Three-station interferometry considers records observed three stations at a time, where two of the stations are considered receiver–stations and the third is a source–station. Cross-correlations between records at the source–station with each of the receiver–stations are correlated or convolved again to estimate the Green’s function between the receiver–stations, which may be deployed asynchronously. We use data from the EarthScope USArray in the western United States to compare Rayleigh wave dispersion obtained from two-station and three-station interferometry. Three three-station interferometric methods are distinguished by the data segment utilized (coda-wave or direct-wave) and whether the source–stations are constrained to lie in stationary phase zones approximately inline with the receiver–stations. The primary finding is that the three-station direct wave methods perform considerably better than the three-station coda-wave method and two-station ambient noise interferometry for obtaining surface wave dispersion measurements in terms of signal-to-noise ratio, bandwidth, and the number of measurements obtained, but possess small biases relative to two-station interferometry. We present a ray-theoretic correction method that largely removes the bias below 40 s period and reduces it at longer periods. Three-station direct-wave interferometry provides substantial value for imaging the crust and uppermost mantle, and its ability to bridge asynchronously deployed stations may impact the design of seismic networks in the future.
Seismic characterization of a clay-block rupture in Harmalière landslide, French Western Alps
Authors: Fiolleau S , Jongmans D , Bièvre G , Chambon G , Baillet L , Vial B 
Published: January 2020

SUMMARYIn late June 2016, the Harmalière clayey landslide (located 30 km south of the city of Grenoble, French Alps) was dramatically reactivated at the headscarp after a 35-yr-long period of continuous but limited activity. The total involved volume, which moved as sliding blocks of various sizes, was estimated to be about 2 × 10 6 m3. Two seismometers were installed at the rear of the main headscarp in August 2016, on both sides of a developing fracture delineating a block with a volume of a few hundred cubic metres. For 4 months, they continuously recorded seismic ambient vibrations and microearthquakes until the block broke. Five seismic parameters were derived from the monitoring: the cumulative number of microearthquakes (CNe), the seismic energy (SE), the block resonance frequency (fB), the relative variation in Rayleigh wave velocity (dV/V) deduced from noise cross-correlations between the two sensors and the associated correlation coefficient (CC). All parameters showed a significant precursory signal before the rupture, but at very different times, which indicates the complexity of the rupture mechanism in this clay material.
Wartime paradigms and the future of western military power
Authors: Schmitt Olivier 
Published: January 2020

Abstract
From the perception of the imminence of threats at the political level to the seizing of initiative through proper timing at the tactical level, temporality is directly related to war and warfare. Yet, despite some analyses of the importance of time at the political/grand strategic level (usually by scholars) and at the tactical level (usually by military professionals) there is surprisingly little discussion of the impact of time on the preparation and the conduct of warfare. This article introduces the concept of ‘wartime paradigm’ as a heuristic device to understand the relationship between the perception of time and the conduct of warfare, and argues that after the Cold War, a specific ‘wartime paradigm’ combining an optimization for speed and an understanding of war as risk management has guided western warfare, from force structure to the conduct of actual operations. It shows how the changing character of warfare directly challenges this wartime paradigm and why, if western forces want to prevail in future conflicts, the establishment of a new wartime paradigm guiding technological improvements and operational concepts is critical.
The juche H-bomb? North Korea, nuclear weapons and regime-state survival
Authors: Howell Edward 
Published: January 2020

Abstract
Existing scholarship on North Korea's nuclear programme remains overwhelmingly centred around questions of containment or engagement with the North Korean regime-state, amid international calls for denuclearization. Yet, scholarship has rarely interrogated the precise value of nuclear weapons to the regime-state. This article develops a new theoretical framework of nuclear ideology to explore the puzzle of the survival of North Korea. This framework aims to show how the North Korean nuclear programme is deeply entrenched within the state ideology of juche, as one device for continued regime-state survival. Through interviews with elite North Korean defectors and textual analysis of North Korean and international sources, I show that North Korea's nuclear ideology has been constructed according to different frames of meaning, targeting referent actors of international ‘enemy’ powers and domestic audiences. This article concludes that nuclear ideology functions primarily as a tool to arouse domestic legitimacy for the North Korean regime-state, by targeting elite actors within the highly stratified domestic population. From an international perspective, perception of North Korea's survival remains tied largely to the regime-state's physical possession of nuclear weapons. This article has extremely timely theoretical and policy implications given the current ‘dialogue’ between US and North Korean leaders. First, it opens up fruitful avenues of inquiry surrounding questions of the legitimacy of rogue states within international relations. Secondly, this article calls for a more robust understanding of the domestic-level politics of North Korea, in order to understand the regime-state's foreign policy decisions vis-à-vis its nuclear programme.