bluuebunny/crossref_metadata_2025_split huggingface dataset:
AHSI: the Hyperspectral Imager on China’s GaoFen-5 Satellite
Authors: Liu Yin-Nian , Sun De-Xin , Hu Xiao-Ning , Liu Shu-Feng , Cao Kai-Qin 
Published: July 2020

Abstract
The Advanced Hyperspectral Imager (AHSI) is a visible/short-wave infrared hyperspectral imager on China’s GaoFen-5 satellite, which was launched on May 9th, 2018. The AHSI is the first spaceborne hyperspectral sensor that utilizes both the convex grating spectrophotometry and an improved three concentric-mirror (Offner) configuration. It has 60 km swath width, 30 m spatial resolution, 5-10 nm spectral resolution, and 330 spectral bands. Instrument performance was evaluated and validated through well-designed experiments on orbit. Results show that the performance of AHSI has met or exceeded predictions. The AHSI has outstanding capability of detecting and identifying different ground objects and in ecological environment monitoring and natural resource exploration.
Application of inpainting technique for reconstruction of partially detected curvilient features derived from the process of extraction of cartographic features
Authors: Figueira A , Da Silva E 
Published: July 2020

Abstract
Extraction processes of cartographic features from digital images have been of great importance in the area of Cartography, however, the results obtained by these techniques usually have partially detected features, culminating in loss of quality of the extraction process. Thus, this work shows how to improve the quality of the extraction process, by employing an inpainting based technique proposed by Deng L-J et al. The use of this algorithm may contribute greatly to increasing quality of the process of extraction of curvilinear cartographic features partially detected in digital images and can be used in the area of cartography, supporting processes to update cartographic products.
Multi-temporal SAR and optical change detection with COSMO-SkyMed and Copernicus Sentinels for digital recording of cultural heritage at risk
Authors: Tapete D , Cigna F 
Published: July 2020

Abstract
In the context of the current discussion about Copernicus services for cultural heritage integrating imagery from the Sentinels with those from contributing missions, such as the Italian Space Agency (ASI)’s X-band SAR constellation COSMO-SkyMed, we explore benefits and limitations of a multi-technique and multi-platform approach of change detection for heritage conservation. We prove the concept in selected heritage sites across the globe, with regard to: (i) anthropogenic disturbance, and (ii) urban sprawl. In Nasca, Peru, a systematic COSMO-SkyMed StripMap time series at 3-m resolution allowed precise identification of the extent of damage caused by a truck that accidentally crossed over three linear geoglyphs in early 2018, that Sentinel-2 could barely capture at 10-m. On the other hand, in Cyrenaica, Libya, Sentinel-2 proved effective to screen wider regions and undertake comparative condition assessment of sites impacted by unregulated urbanization across the landscape.
Impact of tree breeding on managing forest genetic resources: a review with a particular reference to Acacias and Eucalyptus grown in Indonesia
Authors: Nirsatmanto A 
Published: July 2020

Abstract
Declining genetic resource for some species is evident due to biotic and abiotic pressures which are aggravated by inappropriate management of conservation and utilization. Although breeding is one of good practices for increasing the utilization of genetic resources, inadequate breeding strategy could be the source of the diminishing genetic resources.Acacias and Eucalyptus are among the species experiencing good progress in genetic improvement due to its fast growth and high value wood for industries. Besides improving productivity, breeding program should be continued to overcome the increasing threats of pest, disease, and climate change. However, there appeared to be some problems with the developing advanced generation breeding, particularly those related to small genetic diversity as an impact of the decreased genetic resources and the improper breeding activities. Therefore, ensuring the sustainable benefits of germplasm for future uses, managing genetic resources and breeding practices should be properly linked.This paper reviews the impact of current adopted breeding strategy of Acacias and Eucalyptus on the declining genetic resources. It also discusses some possible ways to improve breeding strategy while maintaining genetic resources for the targeted species.
Predicting the potential distribution of Taxussumatrana using Maximum Entropy Model
Authors: Saputra M H , Sunandar A D 
Published: July 2020

Abstract

Taxussumatrana as the medicinal plant is noted as endangered species. As a potential medicinal plant, conservation act is important. This study aims to identify the environmental variablesthat contributes to T. sumatrana distribution and predict the potential areas for T.sumatrana conservation area. The Maximum Entropy (Maxent) was applied to model the species distribution. The presence of T. sumatrana was collected from 77 locations across the Sumatra. Climate and biophysical variables were used to determine the potential distribution of species. The results showed that a minimum temperature of coldest months has the highest permutation importanceby 66.3% while the highest contribution variable was altitude by 48.1%. Soil type has an important value that is not presented in other variables. Potential regions for T. sumatrana distribution were: North Sumatra (Karo, Dairi, Toba Samosir, and Simalungun District), West Sumatra (Agam, Tanah Datar, SawahLunto and Solok District), Jambi (Bungo, Merangin and Kerinci District), Bengkulu (Bengkulu Utara), and South Sumatra (Lahat District). The potential environmental condition for T. sumatranais 1,500m above sea level and upper, minimum temperature of the coldest month below 100C with precipitation in the driest month between 50-70 mm/month. The species is potentially found in Humid Andosol and Vitric Andosol soil types.
Advance technology of tropical tree seed handling in Indonesia for high quality seed and seedling productions
Authors: Syamsuwida D , Nurhasybi  , Sudrajat DJ 
Published: July 2020

Abstract
Seed, as a primary input, plays a vital role for establishment of forest plantation and for any afforestation program. In the recent years, forest and land rehabilitation and community forestry become a great emphasis for Indonesian national forestry programs that make the requirement of seed has multiplied manifold. Seed has become a valuable commodity and thus needs a prudent planning and sophisticated innovated equipment to support procurement of high-quality seeds and seedlings. In the last few years, research and development in seed science and technology have made significant progress. Basic problems faced in tree seed procurement in the tropic are seed characters of recalcitrant and intermediate which well known for drastically deteriorating in seed viability and vigor, sensitive to drying process and low storability. Applied technology for improving seed and seedling quality can be conducted by invigoration methods including physical invigoration (hydro-priming, osmo-priming, matri- conditioning, gamma-ray irradiation) and physiological invigoration (hormone priming, micronutrient, bio-priming, ultra-fine bubble). Seed storage technique has been developing for preparation of planting program and in-situ conservation through seedling storage and cryopreservation. In seed distribution scheme, seed and seedling certifications were developed by compiling the seed testing and seed quality standard of Indonesian Nasional Standard.
OCSANA+: optimal control and simulation of signaling networks from network analysis
Authors: Marazzi Lauren , Gainer-Dewar Andrew , Vera-Licona Paola 
Published: July 2020

Abstract

Summary
OCSANA+ is a Cytoscape app for identifying nodes to drive the system toward a desired long-term behavior, prioritizing combinations of interventions in large-scale complex networks, and estimating the effects of node perturbations in signaling networks, all based on the analysis of the network’s structure. OCSANA+ includes an update to optimal combinations of interventions from network analysis software tool with cutting-edge and rigorously tested algorithms, together with recently developed structure-based control algorithms for non-linear systems and an algorithm for estimating signal flow. All these algorithms are based on the network’s topology. OCSANA+ is implemented as a Cytoscape app to enable a user interface for running analyses and visualizing results.

Availability and implementation
OCSANA+ app and its tutorial can be downloaded from the Cytoscape App Store or https://veraliconaresearchgroup.github.io/OCSANA-Plus/. The source code and computations are available in https://github.com/VeraLiconaResearchGroup/OCSANA-Plus_SourceCode.

Supplementary information
Supplementary data are available at Bioinformatics online.
Single-cell RNA sequencing reveals the cellular heterogeneity of aneurysmal infrarenal abdominal aorta
Authors: Zhao Guizhen , Lu Haocheng , Chang Ziyi , Zhao Yang , Zhu Tianqing , Chang Lin , Guo Yanhong , Garcia-Barrio Minerva T , Chen Y Eugene , Zhang Jifeng 
Published: July 2020

AbstractAimsThe artery contains numerous cell types which contribute to multiple vascular diseases. However, the heterogeneity and cellular responses of these vascular cells during abdominal aortic aneurysm (AAA) progression have not been well characterized.Methods and resultsSingle-cell RNA sequencing was performed on the infrarenal abdominal aortas (IAAs) from C57BL/6J mice at Days 7 and 14 post-sham or peri-adventitial elastase-induced AAA. Unbiased clustering analysis of the transcriptional profiles from &gt;4500 aortic cells identified 17 clusters representing nine-cell lineages, encompassing vascular smooth muscle cells (VSMCs), fibroblasts, endothelial cells, immune cells (macrophages, T cells, B cells, and dendritic cells), and two types of rare cells, including neural cells and erythrocyte cells. Seurat clustering analysis identified four smooth muscle cell (SMC) subpopulations and five monocyte/macrophage subpopulations, with distinct transcriptional profiles. During AAA progression, three major SMC subpopulations were proportionally decreased, whereas the small subpopulation was increased, accompanied with down-regulation of SMC contractile markers and up-regulation of pro-inflammatory genes. Another AAA-associated cellular response is immune cell expansion, particularly monocytes/macrophages. Elastase exposure induced significant expansion and activation of aortic resident macrophages, blood-derived monocytes and inflammatory macrophages. We also identified increased blood-derived reparative macrophages expressing anti-inflammatory cytokines suggesting that resolution of inflammation and vascular repair also persist during AAA progression.ConclusionOur data identify AAA disease-relevant transcriptional signatures of vascular cells in the IAA. Furthermore, we characterize the heterogeneity and cellular responses of VSMCs and monocytes/macrophages during AAA progression, which provide insights into their function and the regulation of AAA onset and progression.
Many Zeros of Many Characters of GL(n,q)
Authors: Gallagher Patrick X , Larsen Michael J , Miller Alexander R 
Published: July 2020

Abstract
For $G=\textrm{GL}(n,q)$, the proportion $P_{n,q}$ of pairs $(\chi ,g)$ in $\textrm{Irr}(G)\times G$ with $\chi (g)\neq 0$ satisfies $P_{n,q}\to 0$ as $n\to \infty $.
Imaging with surface-related multiples to overcome large acquisition gaps
Authors: Nath Aparajita , Verschuur Dirk J 
Published: July 2020

Abstract
To get the best result for seismic imaging using primary reflections, data with densely-spaced sources and receivers are ideally preferred. However, dense acquisition can sometimes be hindered by various obstacles, like platforms or complex topography. Such areas with large data gaps may deter exploration or monitoring, as conventional imaging strategies would either provide poor seismic images or turn out to be very expensive. Surface-related multiples travel along different paths compared to primaries, illuminating a wider subsurface area and hence making them valuable in case of data with large gaps. We propose different strategies of using surface-related multiples to get around the problem of imaging in the case of a large data gap. Conventional least-squares imaging methods that incorporate surface-related multiples do so by re-injecting the measured wavefield in the forward-modelling process, which makes it still sensitive to missing data. We introduce a ‘non-linear’ inversion approach in which the surface multiples are modelled from the original source field. This makes the method less dependent on the receiver geometry, therefore, effectively exploiting the information from surface multiples in cases of limited illumination. However, such an approach is sensitive to the knowledge of the source properties. Therefore, we propose a ‘hybrid’ method that combines the non-linear imaging method with the conventional ‘linear’ multiple imaging method, which further improves our imaging result. We test the methods on numerical as well as field data. The results indicate substantial removal of artefacts in the image derived from linear imaging methods due to incomplete data, by exploiting the surface multiples to a maximum extent.
Molecular Correlates of Long Survival in IDH-Wildtype Glioblastoma Cohorts
Authors: Galbraith Kristyn , Kumar Ashwani , Abdullah Kalil G , Walker Jamie M , Adams Steven H , Prior Timothy , Dimentberg Ryan , Henderson Fraser C , Mirchia Kanish , Sathe Adwait Amod , Viapiano Mariano S , Chin Lawrence S , Corona Robert J , Hatanpaa Kimmo J , Snuderl Matija , Xing Chao , Brem Steven , Richardson Timothy E 
Published: July 2020

Abstract
IDH-wildtype glioblastoma is a relatively common malignant brain tumor in adults. These patients generally have dismal prognoses, although outliers with long survival have been noted in the literature. Recently, it has been reported that many histologically lower-grade IDH-wildtype astrocytomas have a similar clinical outcome to grade IV tumors, suggesting they may represent early or undersampled glioblastomas. cIMPACT-NOW 3 guidelines now recommend upgrading IDH-wildtype astrocytomas with certain molecular criteria (EGFR amplifications, chromosome 7 gain/10 loss, and/or TERT promoter mutations), establishing the concept of a “molecular grade IV” astrocytoma. In this report, we apply these cIMPACT-NOW 3 criteria to 2 independent glioblastoma cohorts, totaling 393 public database and institutional glioblastoma cases: 89 cases without any of the cIMPACT-NOW 3 criteria (GBM-C0) and 304 cases with one or more criteria (GBM-C1-3). In the GBM-C0 groups, there was a trend toward longer recurrence-free survival (median 12–17 vs 6–10 months), significantly longer overall survival (median 32–41 vs 15–18 months), younger age at initial diagnosis, and lower overall mutation burden compared to the GBM-C1-3 cohorts. These data suggest that while histologic features may not be ideal indicators of patient survival in IDH-wildtype astrocytomas, these 3 molecular features may also be important prognostic factors in IDH-wildtype glioblastoma.
A probabilistic framework for cosmological inference of peculiar velocities
Authors: Dam Lawrence 
Published: July 2020

ABSTRACT
We present a Bayesian hierarchical framework for a principled data analysis pipeline of peculiar velocity surveys, which makes explicit the inference problem of constraining cosmological parameters from redshift-independent distance indicators. We demonstrate our method for a Fundamental Plane (FP)-based survey. The essence of our approach is to work closely with observables (e.g. angular size, surface brightness, redshift, etc.), through which we bypass the use of summary statistics by working with the probability distributions. The hierarchical approach improves upon the usual analysis in several ways. In particular, it allows a consistent analysis without having to make prior assumptions about cosmology during the calibration phase. Moreover, calibration uncertainties are correctly accounted for in parameter estimation. Results are presented for a new, fully analytic posterior marginalized over all latent variables, which we expect to allow for more principled analyses in upcoming surveys. A maximum a posteriori estimator is also given for peculiar velocities derived from FP data.
Comparing shape along growth trajectories in two marine snail ecotypes of Littorina saxatilis: a test of evolution by paedomorphosis
Authors: Gefaell J , Varela N , Rolán-Alvarez E 
Published: July 2020

ABSTRACT
Two sympatric ecotypes (‘crab’ and ‘wave’) of Littorina saxatilis are adapted to different microhabitats. It has been claimed, based on the comparison of proteomic differentiation across ontogeny, that the wave ecotype may have evolved by paedomorphosis from an ancestor more similar to the crab ecotype. Here, we test the paedomorphosis hypothesis at a morphological level by comparing crab and wave specimens from two localities using the pattern of shell shape differentiation across ontogeny. The results obtained show a pattern of shell shape differentiation similar to the one observed in previous proteomic studies, but such a pattern could be caused by different modes of evolution, and not necessarily by paedomorphosis. This study emphasizes that in addition to studying the pattern of differentiation, the direction of the evolutionary change across ontogeny has to be analysed before conclusions can be drawn on particular developmental modes of evolution.
Developing a novel meatal areolar tissue autograft for minimally invasive tympanoplasty
Authors: Chen Yen-Chi , Huang Chii-Yuan , Kuo Ying-Ju , Cheng Hsiu-Lien , Cheng Yen-Fu , Liao Wen Huei 
Published: July 2020

Background:
We developed an easy and minimally invasive method of transmeatal tympanoplasty using meatal areolar tissue (MAT) grafts to achieve less postoperative morbidity or surgical scarring. We compared the functional and anatomical results of the developed method with conventional endaural tympanoplasty with a temporalis fascia (TF) graft.

Methods:
In this retrospective cohort study, 58 patients (59 ears) with simple chronic otitis media who underwent type I tympanoplasty between January 2016 and August 2018 were included. All surgeries were performed in a tertiary referral hospital and by the same senior surgeon. The tympanic membrane (TM) was repaired with either a TF or an MAT graft.

Results:
Healing of the perforated TM and improvement in a hearing test by air-bone gap (ABG) closure were identified. Postoperative wound conditions were also evaluated. Twenty-eight ears were grafted with MAT, and 31 ears were grafted with TF. Graft success was observed in 26 patients (92.9%) in the MAT group and 28 patients (90.3%) in the TF group. Both groups showed functional improvement compared with the preoperative measurements. The postoperative pure tone audiogram (p = 0.737), ABG closure (p = 0.547), and graft success rate (p = 0.726) were not significantly different between the two groups. Neither wound dehiscence nor keloid formation was observed in our patients.

Conclusion:
Both MAT and TF grafts revealed satisfactory surgical and functional results. Compared with the conventional endaural approach with TF grafts, the new transmeatal approach method with an MAT graft causes relatively minimal trauma and results in better wound cosmetics. This method represents an easy, minimally invasive surgery and shows comparatively good results.
Prevalence of Helicobacter pylori virulence genes among Iranian infected patients: a systematic review and meta-analysis
Authors: Kamarehei Farideh , Taheri Mohammad , Mohammadi Younes , Shokoohizadeh Leili , Alikhani Mohammad Yousef 
Published: July 2020

Introduction:

Helicobacter pylori infection as the worldwide problem is related to many gastrointestinal disorders. Because of antithesis results among different articles; we systematically reviewed articles about the prevalence of H. pylori virulence factors among different diseases (gastritis, gastric cancer, nonulcer disease, peptic ulcer disease, duodenal ulcer) in different regions of Iran.

Methods:
We used the Preferred Reporting Items for Systematic Review and Meta-Analysis statement for reporting systematic review and meta-analysis of this study in national and international databases. We searched the cagA, vacA, oipA, babA, iceA, dupA prevalence among infected patients in Iran. We used Newcastle--Ottawa quality for assessing the quality of studies in meta-analyses. Due to significant heterogeneity of the results, random effects model to calculate pooled prevalence estimates with 95% confidence intervals, weighted by study size.

Results:
Among 1106 reports screened, 28 related articles were eligible for meta-analysis. The pooled prevalence (95% confidence interval) of cagA, vacA, oipA, babA, iceA1, iceA2, dupA were estimated as 62% (21--95), 71.2% (38–82), 71% (13–99), 61.6% (3–96), 36.2% (12–90), 26.2% (13–37), 40.8% (12–55), respectively.

Discussion:
The frequency of virulence factor genes among H. pylori strains isolated in Iranian patients to be more frequently associated with the gastrointestinal disease compared with the other countries and these data can be considered in development of eradication strategies.
Evaluation of a Proarrhythmic Repolarization Marker (Total Cosine R to T) in Patients With Uncomplicated Familial Mediterranean Fever
Authors: Nussinovitch Udi , Stahi Tomer , Livneh Avi 
Published: July 2020

Background/Objective
Familial Mediterranean fever (FMF) is a systemic autoinflammatory disorder characterized by recurrent attacks of fever and serous inflammation. The association between FMF and risk of cardiac arrhythmia is continuously questioned; some studies report abnormal cardiac repolarization, while others do not. Considering this controversy, we aim to perform in a large cohort of FMF patients a total cosine R to T (TCRT) analysis, a previously unexplored repolarization marker in this disorder.

Methods
The study group included 56 FMF patients without amyloidosis, diagnosed with FMF according to published criteria and 131 control subjects, unaffected with FMF. A 12-lead electrocardiogram (ECG) was performed according to strict standards. Electrocardiogram files were processed with Python-based computer software. Patients were followed for 10 to 12 years, and the rate of cardiac complications was evaluated.

Results
Other than FMF and prescription of colchicine, both groups had similar medical and demographic background. TCRT results were similar for a randomly selected beat (0.40 ± 0.06 vs 0.50 ± 0.04, p > 0.05) and for an averaged beat (0.39 ± 0.06 vs 0.50 ± 0.04, p > 0.05) in FMF patients and control subjects, respectively. Correction of average TCRT for heart rate also resulted in similar TCRTc values in patients and control groups (0.42 ± 0.07 s−0.5 vs 0.51 ± 0.05 s−0.5, respectively, p > 0.05). During the follow-up period, none of the patients died, and no patient developed clinical symptoms suggestive of ventricular arrhythmias.

Conclusions
Colchicine treated uncomplicated FMF patients have normal TCRT and TCRTc values, implying low risk for cardiac arrhythmias in this population. Future studies should evaluate the sensitivity and specificity of this marker in high-risk FMF populations, such as those who developed AA amyloidosis.