bluuebunny/crossref_metadata_2025_split huggingface dataset:
i2d: an R package for simulating data from images and the implications in biomedical research
Authors: Liang Xiaoyu , Hu Ying , Yan Chunhua , Xu Ke 
Published: November 2020

Abstract

Motivation
High-quality imaging analyses have been proposed to drive innovation in biomedical and biological research. However, the application of images remains underexploited because of the limited capacity of human vision and the challenges in extracting quantitative information from images. Computationally extracting quantitative information from images is critical to overcoming this limitation. Here, we present a novel R package, i2d, to simulate data from an image based on digital convolution.

Results
The R package i2d allows users to transform an image into a simulated dataset that can be used to extract and analyze complex information in biomedical and biological research. The package also includes three novel and efficient methods for graph clustering based on simulated data, which can be used to dissect complex gene networks into sub-clusters that have similar biological functions.

Availability and implementation
The code, the documentation, a tutorial and example data are available on an open source at: github.com/XiaoyuLiang/i2d.

Supplementary information
Supplementary data are available at Bioinformatics online.
AVIA 3.0: interactive portal for genomic variant and sample level analysis
Authors: Reardon Hue V , Che Anney , Luke Brian T , Ravichandran Sarangan , Collins Jack R , Mudunuri Uma S 
Published: November 2020

Abstract

Summary
The Annotation, Visualization and Impact Analysis (AVIA) is a web application combining multiple features to annotate and visualize genomic variant data. Users can investigate functional significance of their genetic alterations across samples, genes and pathways. Version 3.0 of AVIA offers filtering options through interactive charts and by linking disease relevant data sources. Newly incorporated services include gene, variant and sample level reporting, literature and functional correlations among impacted genes, comparative analysis across samples and against data sources such as TCGA and ClinVar, and cohort building. Sample and data management is now feasible through the application, which allows greater flexibility with sharing, reannotating and organizing data. Most importantly, AVIA’s utility stems from its convenience for allowing users to upload and explore results without any a priori knowledge or the need to install, update and maintain software or databases. Together, these enhancements strengthen AVIA as a comprehensive, user-driven variant analysis portal.

Availabilityand implementation
AVIA is accessible online at https://avia-abcc.ncifcrf.gov.
Predictive value of triglyceride/high-density lipoprotein cholesterol for major clinical outcomes in advanced chronic kidney disease: a nationwide population-based study
Authors: Kim Yaerim , Lee Soojin , Lee Yeonhee , Kang Min Woo , Park Sehoon , Park Sanghyun , Han Kyungdo , Paek Jin Hyuk , Park Woo Yeong , Jin Kyubok , Han Seugyeup , Han Seung Seok , Lee Hajeong , Lee Jung Pyo , Joo Kwon Wook , Lim Chun Soo , Kim Yon Su , Kim Dong Ki 
Published: November 2020

Abstract

Background
Dyslipidemia is an essential parameter in the prediction of cardiovascular disease (CVD). We aimed to explore whether lipid profiles could predict major outcomes in patients with advanced chronic kidney disease (CKD).

Methods
We retrospectively reviewed the National Health Insurance Service database for people who received nationwide health screening in 2009. All subjects exposed to a lipid-lowering agent before screening were excluded. The population was divided into control, early [estimated glomerular filtration rate (eGFR) 45–59 mL/min/1.73 m2] and advanced (eGFR &lt;45 mL/min/1.73 m2) CKD groups. The hazard ratios (HRs) of outcomes were calculated using multivariate Cox regression models.

Results
A total of 3 634 873 participants were included in this study, with 404 298 (11.1%) and 66 805 (1.8%) having early and advanced CKD, respectively. For all populations, levels of triglyceride/high-density lipoprotein cholesterol (TG/HDL-C) showed a linear association with major cardiovascular and cerebrovascular events (MACCEs) and all-cause mortality, while low-density lipoprotein cholesterol (LDL-C) showed a different pattern of association with MACCEs (linear association) from all-cause mortality (U-shaped association). The significance between the levels of LDL-C and outcomes was attenuated in the advanced CKD group. For TG/HDL-C, although the significance was decreased, the linear patterns with both MACCEs and all-cause mortality were maintained in the advanced CKD group.

Conclusions
The pattern and significance of lipid profiles were different according to the grade of kidney function. TG/HDL-C should be additionally considered as a predictive marker for CVD and mortality along with LDL-C in patients with CKD.
Consistent seismic event location and subsurface parameters inversion through slope tomography: a variable-projection approach
Authors: Sambolian S , Operto S , Ribodetti A , Virieux J 
Published: November 2020

SUMMARY
We revisit the hypocentre–velocity problem, which is of interest in different fields as for example microseismics and seismology. We develop a formulation based on kinematic migration of two picked kinematic attributes in the 2-D case, the traveltime and the slope (horizontal component of the slowness vector), from which we are able to retrieve the location and subsequently the origin time correction and the subsurface parameters mainly velocity. We show how, through a variable projection, the optimization problem boils down to a physically consistent and parsimonious form where the location estimation is projected into the subsurface parameter problem. We present in this study a proof of concept validated by a toy test in two dimensions and a synthetic case study on the Marmousi model. The method presented in this study is extendible to three dimensions by incorporating the crossline slope or the backazimuth as a supplementary attribute.
Lithospheric resistivity structure of the 2001 Bhuj earthquake aftershock zone
Authors: Azeez K K Abdul , Mohan Kapil , Veeraswamy K , Rastogi B K , Gupta Arvind K , Harinarayana T 
Published: November 2020

SUMMARY
The Bhuj area, in the Kutch region of western India, is a unique intraplate seismic zone in the world where aftershock activity associated with a large magnitude earthquake (7.7 Mw Bhuj earthquake on 26 January 2001) has persisted over a decade and up till today. We studied the lithospheric resistivity structure of the Bhuj earthquake aftershock zone to gain more insight into the structure and processes influencing the generation of intraplate seismicity in broad and, in particular, to detect the deep origin and upward migration channels of fluids linked to the crustal seismicity in the area. A lithospheric resistivity model deduced from 2-D and 3-D inversions of long-period magnetotelluric (MT) data shows low resistive lithospheric mantle, which can be best explained by a combination of a small amount of interconnected melts and aqueous fluid in the upper mantle. The MT model also shows a subvertical modestly conductive channel, spatially coinciding with the Kutch Mainland Fault, which we interpret to transport fluids from the deep lithosphere to shallow crust. We infer that pore pressure buildup aids to achieve the critical stress conditions for rock failure in the weak zones, which are pre-stressed by the compressive stress regime generated by ongoing India–Eurasia collision. The fluidized zone in the upper mantle beneath the area perhaps provides continuous fluid supply, which is required to maintain the critical stress conditions within the seismogenic crust for continued seismicity.
Comprehensive Analysis of Volatile Compounds in Mouthpiece Cigarette Adhesive by Coupling Headspace with Gas Chromatography–Mass Spectrometry
Authors: Wei Min , Zheng Feng , Song Xuyan , Li Ran , Pan Xi , Guo Guoning , Yu Qiongwei , Feng Yuqi 
Published: November 2020

Abstract

Background
Some volatile compounds in mouthpiece cigarette adhesive emit irritating odors and affect the taste of smoking cigarettes. Therefore, it is necessary to monitor the volatile compounds in mouthpiece cigarette adhesive.

Objectives
A rapid and simple analytical method of volatile compounds in mouthpiece cigarette adhesive was established.

Methods
In this study, headspace (HS) injection coupled with GC–MS was utilized for qualitative and quantitative analysis. Initially, the volatile compounds in mouthpiece cigarette adhesives were detected by HS-GC–MS, followed by spectrum library retrieval. The detected compounds with the similarity to a spectrum library of more than 85% were further identified by comparing the retention time and mass spectra of the detected volatile compounds and those of the corresponding standard samples. The quantitative analysis of nine identified volatile compounds was performed.

Results
Eleven volatile compounds in the mouthpiece cigarette adhesive were accurately identified. The quantitative analytical method of nine volatile compounds in mouthpiece cigarette adhesive was validated to have good linearities (R2 &gt; 0.9932) within the range of 20–5000 ng/g. The detection limits of 9 compounds were within the range of 3.1–147.7 ng/g. The intra- and inter-day relative standard deviations were less than 19.8%. The recoveries of these 9 compounds spiked into mouthpiece cigarette adhesive were 68.1–108.3%.

Conclusions
The proposed method is rapid, simple, and accurate for qualitative and quantitative analysis of volatile compounds in the mouthpiece cigarette adhesive.

Highlights
The developed analytical method is expected to be used to monitor volatile compounds in various adhesives.
Cephalothin: Review of Characteristics, Properties, and Status of Analytical Methods
Authors: Nascimento Patrícia Aleixa do , Kogawa Ana Carolina , Salgado Hérida Regina Nunes 
Published: November 2020

Abstract

Background
Cephalothin (CET), a first generation cephalosporin, is the most efficient cephalosporin against resistant microorganisms. Many studies found in literature and pharmacopeias propose analytical methods which are most commonly HPLC and microbiological assays.

Objective
This paper shows a brief review of analytical methods to quantify CET with a green analytical chemistry approach.

Method
The research data were collected from the literature and official compendia.

Results
Most of the analytical methods to determine CET were performed by HPLC and agar diffusion in pharmaceuticals, blood, urine, or water. Other analytical methods were found, such as UV-Vis, iodometry, fluorimetry, IR/Raman, electrochemical, and others in less quantity. One important aspect is that these methods use organic and toxic solvents like methanol and acetonitrile and only about 4% of the methods found use water as solvent.

Conclusions
Research about analytical methods for CET focusing on green analytical chemistry is of great importance and could optimize its analysis in pharmaceutical industries and help to guarantee the quality of the product. More than just the development of new techniques, it is possible to enhance the ones that already exist, applying the green analytical chemistry principles. In this way, it will be possible to reduce the environmental impacts caused by other analytical procedures.

Highlights
This work shows a brief review of literature and pharmacopeias of analytical methods to quantify CET. Its quality control can be updated to meet the needs of current analytical chemistry and to fit into sustainable and eco-friendly analysis.
Automated and qualitative structural evaluation of floor plans for remodeling of apartment housing
Authors: Kim Seongah , Ryu Hyeongmin , Kim Jinyoung 
Published: November 2020

Abstract
Many floor plans are proposed during the early stage of an apartment housing remodeling project as it involves a multitude of entities with different stakes. Consequently, the process to converge the opinions per the individual's preference on an agreed remodeling floor plan becomes repetitive and time consuming. For these reasons, structural evaluation of each proposed conceptual plan is often bypassed and postponed until a finalized floor plan is determined. An automated structural evaluation application for architectural floor plans of apartment housing with the load-bearing wall system is developed on this necessity. The application reads the conceptual drawings and returns various supportive information regarding structural performance, almost instantly. The outputs from the application include the amount of removed, remaining, and new bearing walls, 3D views of each wall component overlaid on the floor plans and their dimensions, area moment of inertia (AMOI) of the walls, torsional resistance of the floor plans, and other supportive indices. For easy and intuitive communication with the users, an abstract and simple quantitative value, structural index (SI), is suggested and included as one of the outputs in the application. In order to validate the developed automated application, a case study is conducted with an ongoing remodeling project, and the results, accuracy, and processing time are compared with the conventional hand calculation method. The application is accurate with errors of less than 1.3%, while the processing speed is nearly seven times faster. With the developed application, the designers could evaluate their conceptual drawings in almost real time. In addition, the stakeholders would communicate in a more straightforward language with the outputs of the application, such as the AMOI evaluation and SI results. Consequently, it is anticipated that the decision-making process during the early stage of a remodeling project would be expedited with the help of the developed automated application.
Invasion Biology and Management of Sweetpotato Whitefly (Hemiptera: Aleyrodidae) in China
Authors: Guo Chen-liang , Zhu Yong-zhe , Zhang You-jun , Keller Michael A , Liu Tong-Xian , Chu Dong 
Published: November 2020

AbstractThe sweetpotato whitefly, Bemisia tabaci Gennadius (Hemiptera: Aleyrodidae), is a broadly invasive pest of great economic significance to agricultural and horticultural systems in the world. Bemisia tabaci contains more than 44 cryptic species, among which B. tabaci Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED) are the most invasive and destructive, and have spread to many countries. Research on B. tabaci cryptic species increased dramatically in China following the introduction of MEAM1 in the middle-late 1990s. Our report discussed significant advances over the past two decades to understand the invasive genetics of B. tabaci in China. We reviewed the main findings including changes in the cryptic species composition and invasion characteristics of B. tabaci, also summarizing the factors that affect the displacement of dominant cryptic species. Finally, the integrated management of B. tabaci in China was discussed. We hope that this review can stimulate interest in and deepen understanding of B. tabaci, which will lay a foundation for further research in this field.
Learning to denoise astronomical images with U-nets
Authors: Vojtekova Antonia , Lieu Maggie , Valtchanov Ivan , Altieri Bruno , Old Lyndsay , Chen Qifeng , Hroch Filip 
Published: November 2020

ABSTRACT
Astronomical images are essential for exploring and understanding the Universe. Optical telescopes capable of deep observations, such as the Hubble Space Telescope (HST), are heavily oversubscribed in the Astronomical Community. Images also often contain additive noise, which makes denoising a mandatory step in post-processing the data before further data analysis. In order to maximize the efficiency and information gain in the post-processing of astronomical imaging, we turn to machine learning. We propose Astro U-net, a convolutional neural network for image denoising and enhancement. For a proof-of-concept, we use HST images from Wide Field Camera 3 instrument UV/visible channel with F555W and F606W filters. Our network is able to produce images with noise characteristics as if they are obtained with twice the exposure time, and with minimum bias or information loss. From these images, we are able to recover $95.9{{\ \rm per\ cent}}$ of stars with an average flux error of $2.26{{\ \rm per\ cent}}$. Furthermore, the images have, on average, 1.63 times higher signal-to-noise ratio than the input noisy images, equivalent to the stacking of at least three input images, which means a significant reduction in the telescope time needed for future astronomical imaging campaigns.
The contribution of N-rich stars to the Galactic stellar halo using APOGEE red giants
Authors: Horta Danny , Mackereth J Ted , Schiavon Ricardo P , Hasselquist Sten , Bovy Jo , Allende Prieto Carlos , Beers Timothy C , Cunha Katia , García-Hernández D A , Kisku Shobhit S , Lane Richard R , Majewski Steven R , Mason Andrew C , Nataf David M , Roman-Lopes Alexandre , Schultheis Mathias 
Published: November 2020

ABSTRACT
The contribution of dissolved globular clusters (GCs) to the stellar content of the Galactic halo is a key constraint on models for GC formation and destruction, and the mass assembly history of the Milky Way. Earlier results from APOGEE pointed to a large contribution of destroyed GCs to the stellar content of the inner halo, by as much as 25 ${{\ \rm per\ cent}}$, which is an order of magnitude larger than previous estimates for more distant regions of the halo. We set out to measure the ratio between nitrogen-rich (N-rich) and normal halo field stars, as a function of distance, by performing density modelling of halo field populations in APOGEE DR16. Our results show that at 1.5 kpc from the Galactic Centre, N-rich stars contribute a much higher 16.8$^{+10.0}_{-7.0}\, {{\ \rm per\ cent}}$ fraction to the total stellar halo mass budget than the 2.7$^{+1.0}_{-0.8}\, {{\ \rm per\ cent}}$ ratio contributed at 10 kpc. Under the assumption that N-rich stars are former GC members that now reside in the stellar halo field, and assuming the ratio between first and second population GC stars being 1:2, we estimate a total contribution from disrupted GC stars of the order of 27.5$^{+15.4}_{-11.5}\, {{\ \rm per\ cent}}$ at r = 1.5 kpc and 4.2$^{+1.5}_{-1.3}\, {{\ \rm per\ cent}}$ at r = 10 kpc. Furthermore, since our methodology requires fitting a density model to the stellar halo, we integrate such density within a spherical shell from 1.5 to 15 kpc in radius, and find a total stellar mass arising from dissolved and/or evaporated GCs of MGC,total = 9.6$^{+4.0}_{-2.6}\, \times$ 107 M⊙.
Feasibility, acceptability and change in health following a telephone-based cognitive behaviour therapy intervention for patients with axial spondyloarthritis
Authors: Pedley Rebecca , Dean Linda E , Choy Ernest , Gaffney Karl , Ijaz Tanzeel , Kay Lesley , Lovell Karina , Molloy Christine , Martin Kathryn , Packham Jonathan , Siebert Stefan , Sengupta Raj , Macfarlane Gary J , Hollick Rosemary J 
Published: November 2020

Abstract

Objective
The aim was to assess the feasibility and acceptability of a telephone-based cognitive behaviour therapy (tCBT) intervention for individuals with axial SpA (axSpA), with and without co-morbid FM, and to measure the change in patient-reported health outcomes.

Methods
A convenience sample of individuals recruited from British Society for Rheumatology Biologics Registry for AS (BSRBR-AS) sites were offered a course of tCBT (framed as coaching). Patient-reported outcomes were measured at baseline and on course completion. Semi-structured qualitative interviews assessed intervention acceptability. Thematic analysis was informed by the theoretical framework of acceptability.

Results
Forty-two participants attended for initial assessment. Those completing at least one tCBT session (n = 28) were younger, more likely to meet classification criteria for FM (57 vs 29%) and reported higher disease activity. Modest improvements were reported across a range of disease activity and wider health measures, with 62% of patients self-rating their health as improved (median 13 weeks post-intervention). Twenty-six participants were interviewed (including six who discontinued after initial assessment). tCBT was widely acceptable, offering a personalized approach. Despite low or unclear expectations, participants described improved sleep and psychological well-being and gained new skills to support self-management. Reasons for non-uptake of tCBT centred on lack of perceived need and fit with individual value systems. Many felt that tCBT would be most useful closer to diagnosis.

Conclusion
Higher uptake among axSpA patients with co-morbid FM suggests that these individuals have additional needs. The findings are helpful in identifying patients most likely to engage with and benefit from tCBT and to maximize participation.
Rapid Rule-Based Reward Reversal and the Lateral Orbitofrontal Cortex
Authors: Rolls Edmund T , Vatansever Deniz , Li Yuzhu , Cheng Wei , Feng Jianfeng 
Published: November 2020

AbstractHumans and other primates can reverse their choice of stimuli in one trial when the rewards delivered by the stimuli change or reverse. Rapidly changing our behavior when the rewards change is important for many types of behavior, including emotional and social behavior. It is shown in a one-trial rule-based Go-NoGo deterministic visual discrimination reversal task to obtain points, that the human right lateral orbitofrontal cortex and adjoining inferior frontal gyrus is activated on reversal trials, when an expected reward is not obtained, and the non-reward allows the human to switch choices based on a rule. This reward reversal goes beyond model-free reinforcement learning. This functionality of the right lateral orbitofrontal cortex shown here in very rapid, one-trial, rule-based changes in human behavior when a reward is not received is related to the emotional and social changes that follow orbitofrontal cortex damage, and to depression in which this non-reward system is oversensitive and over-connected.