bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addendum: Radiation force and torque of light-sheets (2017 J. Opt. 19 065403)
Authors: Mitri F G 
Published: September 2020

Abstract
The purpose of this Addendum is to provide some clarifications and additional discussions related to the formalism of the generalized Lorenz–Mie theories in two-dimensions presented in the manuscript (Mitri F G 2017 J. Opt.
19 065403). The generalized formalism provides exact mathematical expressions that are used to compute the optical scattering, and time-averaged radiation force and torque of any light-sheets of arbitrary wavefront illuminating a homogeneous dielectric cylindrical particle of arbitrary geometrical cross-section, suspended in a lossless medium of wave propagation. In particular, it is emphasized here that concerning the analytical derivations and calculations based on far-field limits of the scattering, the Poynting vector formalism can only be utilized to determine the optical radiation force vector and its components, a result that is commensurate with the same outcome of an analysis based on the integration of the time-averaged Maxwell stress tensor. Nevertheless, in the far-field, the Poynting vector formalism is not valid to evaluate the optical radiation torque because it is radial, and the integration of its moment over a surface of large radius enclosing the particle leads to a zero torque, not in agreement with the derivation based on Maxwell’s stress tensor. Therefore, the analytical expression required to derive the optical radiation torque component (either in the near-field or far-field limits of the scattering, which lead to equivalent expressions without any approximations in the case of a lossless medium of wave propagation) should always involve the integration of the moment of the time-averaged Maxwell stress tensor.
Atomic diffusion behavior and diffusion mechanism in Fe–Cu bimetal casting process studied by molecular dynamics simulation and experiment
Authors: Zhang Guowei , Kang Yuanyuan , Wang Mingjie , Xu Hong , Jia Hongmin 
Published: September 2020

Abstract
A molecular dynamics (MD) method with an embedded atomic method (EAM) was proposed to study the atomic diffusion behavior and diffusion mechanism in the Fe–Cu bimetal casting process. The results indicated that the diffusion coefficient of the Cu atoms was larger than that of the Fe atoms at the same temperature, but the Fe atoms predominantly diffused into the Cu side in the process of diffusion bonding. Moreover, the relationship between diffusion distance and temperature was predicted by the established model, and the optimal temperature for interface diffusion bonding of Fe–Cu bimetal ranged from 1473K to 1753 K. The diffusion behavior was mainly due to vacancies, which played a key role in the formation of the Cu cluster, and the accumulation of Cu atoms decreased the system energy. Finally, FeAcknowledgmentsCu bimetal casting was prepared to validate the simulated results of the diffusion behavior and diffusion distance, and the simulated results were consistent with the experimental ones.
Enhanced stretchable electronics made by fused-filament fabrication
Authors: Salo Teemu , Halme Aki , Lahtinen Juhani , Vanhala Jukka 
Published: September 2020

Abstract
3D printing is widely used for manufacturing complex non-functional parts, and recently, the fabrication of electronics has also attracted research attention. The commercialized process of fused-filament fabrication (FFF), which is still evolving,has been used in the preparation of basic electronic conductors and sensors but only a few studies of more complex structures with integrated circuits and passive components have been reported. Notably, the usage of FFF in wearable stretchable electronics has not been studied previously. We demonstrate that the combination of FFF printing and commonly used stretchable electronics materials and methods enables new wearable stretchable electronics. In this study, thermoplastics were extruded directly onto a stretchable substrate and their adhesion was measured using T-peel tests. The test results were further used in the fabrication of supports for meander-shaped screen-printed interconnects. The elongation of the interconnects with the supports were studied by tensile tests with simultaneous measurements of the electrical conductivity. The results were good, and the adhesion exceeded the constitution of the substrate when the filament and the substrate were of the same material type. The average bond strength was ∼2 N mm−1. Support structures placed close to the meander-shaped interconnects changed the interconnects’ deformation under elongation. The average maximum elongation of the interconnects was improved by ∼27% when the supports directed stresses away from the interconnects’ weak areas. Conversely, the results were ∼21% lower when the supports directed stresses towards the weak areas. This study demonstrates that it is possible to use direct 3D printing onto highly stretchable substrates. Currently, commercial FFF materials and methods can be used to manufacture supports, frames and other non-functional parts on wearable electronics substrates in a single process step. We believe that in the future, FFF will become a valuable tool in the manufacture of inexpensive and reliable wearable electronics.
Colour deconvolution: stain unmixing in histological imaging
Authors: Landini Gabriel , Martinelli Giovanni , Piccinini Filippo 
Published: September 2020

Abstract

Motivation
Microscopy images of stained cells and tissues play a central role in most biomedical experiments and routine histopathology. Storing colour histological images digitally opens the possibility to process numerically colour distribution and intensity to extract quantitative data. Among those numerical procedures are colour deconvolution, which enable decomposing an RGB image into channels representing the optical absorbance and transmittance of the dyes when their RGB representation is known. Consequently, a range of new applications become possible for morphological and histochemical segmentation, automated marker localization and image enhancement.

Availability and implementation
Colour deconvolution is presented here in two open-source forms: a MATLAB program/function and an ImageJ plugin written in Java. Both versions run in Windows, Macintosh and UNIX-based systems under the respective platforms. Source code and further documentation are available at: https://blog.bham.ac.uk/intellimic/g-landini-software/colour-deconvolution-2/.

Supplementary information
Supplementary data are available at Bioinformatics online.
BarleyVarDB: a database of barley genomic variation
Authors: Tan Cong , Chapman Brett , Wang Penghao , Zhang Qisen , Zhou Gaofeng , Zhang Xiao-qi , Barrero Roberto A , Bellgard Matthew I , Li Chengdao 
Published: September 2020

Abstract
Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website at http://146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57 754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley accessions from 3 barley evolutionary original centers and 13 barley landraces from different continents. Second, it uses the latest barley genome reference and its annotation information publicly accessible, which has been achieved by the International Barley Genome Sequencing Consortium (IBSC). Third, 522 212 whole genome-wide microsatellites/simple sequence repeats (SSRs) were also included in this database, which were identified in the reference barley pseudo-molecular genome sequence. Additionally, several useful web-based applications are provided including JBrowse, BLAST and Primer3. Users can design PCR primers to asses polymorphic variants deposited in this database and use a user-friendly interface for accessing the barley reference genome. We envisage that the BarleyVarDB will benefit the barley genetic research community by providing access to all publicly available barley genomic variation information and barley reference genome as well as providing them with an ultra-high density of SNP and InDel markers for molecular breeding and identification of functional genes with important agronomic traits in barley.
Database URL: http://146.118.64.11/BarleyVar
Does contracting-out of primary health care services to non-state providers reduce child mortality in South Sudan? A synthetic control analysis
Authors: Bol Juliana , Trujillo Antonio J 
Published: September 2020

Abstract
Contracting-out is increasingly utilized as a health system strengthening strategy in lower- and middle-income countries (LMICs), to expand access to health interventions known to reduce child mortality. Existing scholarship suggests its effect has been mixed, limiting a definitive conclusion on its magnitude and direction. There are few studies assessing the impact on under-five mortality rate (U5MR) and fewer evaluations to-date have focused on Sub-Saharan Africa. We test the hypothesis that the contracting-out approach implemented in South Sudan in 2012 led to an observable reduction in U5MR. We use a novel approach, the synthetic control method to construct a synthetic South Sudan from a panel of LMICs using data from the World Bank Developmental Indicators (WDI) database. The analysis shows on average, contracting-out had a limited effect on the rate of decline of U5MR; U5MR declined by 5.2% annually between 2000 and 2011, and by 2.58% between 2012 and 2014. Relative to its synthetic control, U5MR is 2% and 5% higher in 2012 and 2013, continuing to diverge during the observation period. These findings suggest limitations in the contracting approach, and we discuss the possible policy implications of these findings.
Socioeconomic inequality in premiums for a community-based health insurance scheme in Rwanda
Authors: Chirwa Gowokani Chijere , Suhrcke Marc , Moreno-Serra Rodrigo 
Published: September 2020

Abstract
Community-based health insurance (CBHI) has gained popularity in many low- and middle-income countries, partly as a policy response to calls for low-cost, pro-poor health financing solutions. In Africa, Rwanda has successfully implemented two types of CBHI systems since 2005, one of which with a flat rate premium (2005–10) and the other with a stratified premium (2011–present). Existing CBHI evaluations have, however, tended to ignore the potential distributional aspects of the household contributions made towards CBHI. In this paper, we investigate the pattern of socioeconomic inequality in CBHI household premium contributions in Rwanda within the implementation periods. We also assess gender differences in CBHI contributions. Using the 2010/11 and 2013/14 rounds of national survey data, we quantify the magnitude of inequality in CBHI payments, decompose the concentration index of inequality, calculate Kakwani indices and implement unconditional quantile regression decomposition to assess gender differences in CBHI expenditure. We find that the CBHI with stratified premiums is less regressive than CBHI with a flat rate premium system. Decomposition analysis indicates that income and CBHI stratification explain a large share of the inequality in CBHI payments. With respect to gender, female-headed households make lower contributions towards CBHI expenditure, compared with male-headed households. In terms of policy implications, the results suggest that there may be a need for increasing the premium bracket for the wealthier households, as well as for the provision of more subsidies to vulnerable households.
Assessing the practice of data quality evaluation in a national clinical data research network through a systematic scoping review in the era of real-world data
Authors: Bian Jiang , Lyu Tianchen , Loiacono Alexander , Viramontes Tonatiuh Mendoza , Lipori Gloria , Guo Yi , Wu Yonghui , Prosperi Mattia , George Thomas J , Harle Christopher A , Shenkman Elizabeth A , Hogan William 
Published: September 2020

Abstract

Objective
To synthesize data quality (DQ) dimensions and assessment methods of real-world data, especially electronic health records, through a systematic scoping review and to assess the practice of DQ assessment in the national Patient-centered Clinical Research Network (PCORnet).

Materials and Methods
We started with 3 widely cited DQ literature—2 reviews from Chan et al (2010) and Weiskopf et al (2013a) and 1 DQ framework from Kahn et al (2016)—and expanded our review systematically to cover relevant articles published up to February 2020. We extracted DQ dimensions and assessment methods from these studies, mapped their relationships, and organized a synthesized summarization of existing DQ dimensions and assessment methods. We reviewed the data checks employed by the PCORnet and mapped them to the synthesized DQ dimensions and methods.

Results
We analyzed a total of 3 reviews, 20 DQ frameworks, and 226 DQ studies and extracted 14 DQ dimensions and 10 assessment methods. We found that completeness, concordance, and correctness/accuracy were commonly assessed. Element presence, validity check, and conformance were commonly used DQ assessment methods and were the main focuses of the PCORnet data checks.

Discussion
Definitions of DQ dimensions and methods were not consistent in the literature, and the DQ assessment practice was not evenly distributed (eg, usability and ease-of-use were rarely discussed). Challenges in DQ assessments, given the complex and heterogeneous nature of real-world data, exist.

Conclusion
The practice of DQ assessment is still limited in scope. Future work is warranted to generate understandable, executable, and reusable DQ measures.
Nitric oxide function during oxygen deprivation in physiological and stress processes
Authors: Manrique-Gil Isabel , Sánchez-Vicente Inmaculada , Torres-Quezada Isabel , Lorenzo Oscar 
Published: September 2020

Abstract
Plants are aerobic organisms that have evolved to maintain specific requirements for oxygen (O2), leading to a correct respiratory energy supply during growth and development. There are certain plant developmental cues and biotic or abiotic stress responses where O2 is scarce. This O2 deprivation known as hypoxia may occur in hypoxic niches of plant-specific tissues and during adverse environmental cues such as pathogen attack and flooding. In general, plants respond to hypoxia through a complex reprogramming of their molecular activities with the aim of reducing the impact of stress on their physiological and cellular homeostasis. This review focuses on the fine-tuned regulation of hypoxia triggered by a network of gaseous compounds that includes O2, ethylene, and nitric oxide. In view of recent scientific advances, we summarize the molecular mechanisms mediated by phytoglobins and by the N-degron proteolytic pathway, focusing on embryogenesis, seed imbibition, and germination, and also specific structures, most notably root apical and shoot apical meristems. In addition, those biotic and abiotic stresses that comprise hypoxia are also highlighted.
RMVar: an updated database of functional variants involved in RNA modifications
Authors: Luo Xiaotong , Li Huiqin , Liang Jiaqi , Zhao Qi , Xie Yubin , Ren Jian , Zuo Zhixiang 
Published: September 2020

Abstract
Distinguishing the few disease-related variants from a massive number of passenger variants is a major challenge. Variants affecting RNA modifications that play critical roles in many aspects of RNA metabolism have recently been linked to many human diseases, such as cancers. Evaluating the effect of genetic variants on RNA modifications will provide a new perspective for understanding the pathogenic mechanism of human diseases. Previously, we developed a database called ‘m6AVar’ to host variants associated with m6A, one of the most prevalent RNA modifications in eukaryotes. To host all RNA modification (RM)-associated variants, here we present an updated version of m6AVar renamed RMVar (http://rmvar.renlab.org). In this update, RMVar contains 1 678 126 RM-associated variants for 9 kinds of RNA modifications, namely m6A, m6Am, m1A, pseudouridine, m5C, m5U, 2′-O-Me, A-to-I and m7G, at three confidence levels. Moreover, RBP binding regions, miRNA targets, splicing events and circRNAs were integrated to assist investigations of the effects of RM-associated variants on posttranscriptional regulation. In addition, disease-related information was integrated from ClinVar and other genome-wide association studies (GWAS) to investigate the relationship between RM-associated variants and diseases. We expect that RMVar may boost further functional studies on genetic variants affecting RNA modifications.
Update on congenital cytomegalovirus infection: Prenatal prevention, newborn diagnosis, and management
Authors: Barton Michelle , Forrester A Michael , McDonald Jane 
Published: September 2020

Abstract
Cytomegalovirus (CMV) is the leading cause of congenital infection and the most common cause of non-genetic sensorineural hearing loss (SNHL) in childhood. Although most infected infants are asymptomatic at birth, the risk for SNHL and other neurodevelopmental morbidity makes congenital CMV (cCMV) a disease of significance. Adherence to hygienic measures in pregnancy can reduce risk for maternal CMV infection. The prompt identification of infected infants allows early initiation of surveillance and management. A multidisciplinary approach to management is critical to optimize outcomes in affected infants.
Improving Access to Banking: Evidence from Kenya*
Authors: Allen Franklin , Carletti Elena , Cull Robert , Qian Jun QJ , Senbet Lemma , Valenzuela Patricio 
Published: September 2020

Abstract
We explore the relationship between bank branch expansion, financial inclusion, and profitability for Equity Bank. Unlike traditional banks, including foreign and government owned banks in Kenya, Equity Bank targets less developed territories and less privileged households. Its presence increased financial inclusion by 31% of the adult population between 2006 and 2015, especially for Kenyans who were less educated, did not own their own home, and lived in less-developed areas. The bank’s business model proves to be highly effective, with branch-level profits rising in areas with a smaller number of operating banks. Overall, the growth of Equity Bank demonstrates that financial inclusion can be achieved and sustained through profitable branching and service strategies that also serve the needs of underserved regions and populations. Thus, financial inclusion need not come at the sacrifice of bank profitability.
Tokyo and New York: A Study in the Contrasting Effects of Socioeconomic Status on Coronavirus Disease 2019 Outcomes
Authors: Hifumi Toru , Ishikawa Yohei , Otani Norio , Ishimatsu Shinichi , Urashima Mitsuyoshi 
Published: September 2020

Objectives:
It is still not known why cases of coronavirus disease 2019 during the first wave in Tokyo have fallen without lockdown restrictions. People with low socioeconomic status are not dominant among coronavirus disease 2019 patients in Tokyo in contrast with New York, where the opposite demographics have been in play. Thus, we set out to examine the association between socioeconomic status and the rate of coronavirus disease 2019 infections using public data from Tokyo.

Design:
We obtained data from each of the 23 wards of Tokyo, showing population size, density, age, sex, number of graduates, income, and hospital attendance numbers. Coronavirus disease 2019 infections were gathered for 2 separate days: April 9, 2020, when new daily coronavirus disease 2019 infections were at their peak during the first wave in Japan; and May 9, 2020, to observe any changes in incidence over the preceding month.

Setting:
The primary outcome was set as the number of coronavirus disease 2019 infections per 100,000 population.

Interventions:
None.

Measurements and Main Results:
By conducting simple linear regression modeling, the incidence of cases on April 9 was associated significantly with four variables: population age greater than 65 years (%), university rate, hospital, and income. Using these four variables, multivariate linear regression analyses demonstrated that only income remained significant (p = 0.006 at April 9 and p = 0.03 at May 9). This indicates that the highest case numbers were dominant in high-income areas, and affected fewer patients in districts in the low-income areas.

Conclusions:
The result of the current study is exactly opposite to the data from New York. This may be considered one of the main reasons why the rate of death and new patients of coronavirus disease 2019 has been so low in Tokyo. That is, appropriate hygienic status, free access to hospital by ambulance, and universal health insurance system may contribute to the outcome in such low-income areas.
Lack of Cellular Inflammation in a Non-human Primate Model of Radiation Nephropathy
Authors: Cohen Eric P. , Farese Ann M. , Parker George A. , Kane Maureen A. , MacVittie Thomas J. 
Published: September 2020

Abstract
Inflammation is commonly cited as a mechanism of delayed effects of acute radiation exposure (DEARE). Confirmation of its presence could provide significant insight to targeted use of treatments or mitigators of DEARE. We sought to quantify the presence of cellular inflammation in kidneys of non-human primates that developed acute and chronic kidney injury after a partial body irradiation exposure. We show herein that cellular inflammation is not found as a component of either acute or chronic kidney injury. Other mechanistic pathways of injury must be sought.
Patency of Anterior Epitympanic Space and Surgical Outcomes After Endoscopic Ear Surgery for the Attic Cholesteatoma
Authors: Mizutari Kunio , Takihata Saki , Kimura Eiko , Inuzuka Eri , Shiotani Akihiro 
Published: September 2020

Objective:
To reveal the patency of the anterior epitympanic space (AES) and the surgical outcomes after transcanal endoscopic ear surgery (TEES) for attic cholesteatoma with a classification of anatomical variation of the AES.

Study Design:
Retrospective case review.

Setting:
Tertiary referral center.

Patients:
Seventy-four ears (72 patients with early-stage (I or II) attic cholesteatoma) aged between 16 and 85 years (mean: 48.9 yr) who underwent TEES between 2015 and 2017 were analyzed.

Intervention:
Tympanoplasty with atticoantrotomy was performed with TEES. TEES was performed using a rigid endoscope with an outer diameter of 2.7 mm.

Main Outcome Measure:
The tensor fold in the AES anatomical classification, the postoperative patency of the AES evaluated by computer tomography images, and hearing outcomes based on the American Academy of Otolaryngology and Head and Neck Surgery criteria were evaluated after TEES for early-stage attic cholesteatoma.

Results:
There were 14 (18.9%) ears with a vertical tensor fold orientation, 29 (39.2%) ears with an oblique orientation, and 29 (39.2%) ears with a horizontal orientation. The total postoperative patency rate in the AES was 81.0%, without any significant difference in the anatomical variation in the AES, whereas the rate of preoperative complete tensor fold was 90.5%. Cholesteatoma recurrence was observed in three cases (4.1%), and all recurrent cases had obstructed AES. No significant difference was found in the postoperative air-bone gap regardless of the patency of the AES.

Conclusion:
Our findings indicate that TEES is useful in restoring ventilation in the AES, resulting in favorable management of cholesteatoma.