bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of dementia with immunoglobulin G N-glycans in a Chinese Han Population
Authors: Zhang Xiaoyu , Yuan Hui , Lyu Jihui , Meng Xiaoni , Tian Qiuyue , Li Yuejin , Zhang Jie , Xu Xizhu , Su Jing , Hou Haifeng , Li Dong , Sun Baoliang , Wang Wei , Wang Youxin 
Published: February 2021

AbstractImmunoglobulin G (IgG) functionality can drastically change from anti- to proinflammatory by alterations in the IgGN-glycan patterns. Our previous studies have demonstrated that IgGN-glycans associated with the risk factors of dementia, such as aging, dyslipidemia, type 2 diabetes mellitus, hypertension, and ischemic stroke. Therefore, the aim is to investigate whether the effects of IgGN-glycan profiles on dementia exists in a Chinese Han population. A case–control study, including 81 patients with dementia, 81 age- and gender-matched controls with normal cognitive functioning (NC) and 108 non-matched controls with mild cognitive impairment (MCI) was performed. Plasma IgGN-glycans were separated by ultra-performance liquid chromatography. Fourteen glycan peaks reflecting decreased of sialylation and core fucosylation, and increased bisectingN-acetylglucosamine (GlcNAc)N-glycan structures were of statistically significant differences between dementia and NC groups after controlling for confounders (p < 0.05;q < 0.05). Similarly, the differences for these 14 initial glycans were statistically significant between AD and NC groups after adjusting for the effects of confounders (p < 0.05;q < 0.05). The area under the receiver operating curve (AUC) value of the model consisting of GP8, GP9, and GP14 was determined to distinguish dementia from NC group as 0.876 [95% confidence interval (CI): 0.815–0.923] and distinguish AD from NC group as 0.887 (95% CI: 0.819–0.936). Patients with dementia were of an elevated proinflammatory activity via the significant changes of IgG glycome. Therefore, IgGN-glycans might contribute to be potential novel biomarkers for the neurodegenerative process risk assessment of dementia.
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge
Authors: Lawson Catherine L. , Kryshtafovych Andriy , Adams Paul D. , Afonine Pavel V. , Baker Matthew L. , Barad Benjamin A. , Bond Paul , Burnley Tom , Cao Renzhi , Cheng Jianlin , Chojnowski Grzegorz , Cowtan Kevin , Dill Ken A. , DiMaio Frank , Farrell Daniel P. , Fraser James S. , Herzik Mark A. , Hoh Soon Wen , Hou Jie , Hung Li-Wei , Igaev Maxim , Joseph Agnel P. , Kihara Daisuke , Kumar Dilip , Mittal Sumit , Monastyrskyy Bohdan , Olek Mateusz , Palmer Colin M. , Patwardhan Ardan , Perez Alberto , Pfab Jonas , Pintilie Grigore D. , Richardson Jane S. , Rosenthal Peter B. , Sarkar Daipayan , Schäfer Luisa U. , Schmid Michael F. , Schröder Gunnar F. , Shekhar Mrinal , Si Dong , Singharoy Abishek , Terashi Genki , Terwilliger Thomas C. , Vaiana Andrea , Wang Liguo , Wang Zhe , Wankowicz Stephanie A. , Williams Christopher J. , Winn Martyn , Wu Tianqi , Yu Xiaodi , Zhang Kaiming , Berman Helen M. , Chiu Wah 
Published: February 2021

AbstractThis paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.
Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions
Authors: Chen Min-dong , Wang Bin , Li Yong-ping , Zeng Mei-juan , Liu Jian-ting , Ye Xin-ru , Zhu Hai-sheng , Wen Qing-fang 
Published: February 2021

AbstractSelecting suitable internal reference genes is an important prerequisite for the application of quantitative real-time PCR (qRT-PCR). However, no systematic studies have been conducted on reference genes in luffa. In this study, seven reference genes were selected, and their expression levels in luffa plants exposed to various simulated abiotic stresses [i.e., cold, drought, heat, salt, H2O2, and abscisic acid (ABA) treatments] were analyzed by qRT-PCR. The stability of the reference gene expression levels was validated using the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The results indicated thatEF-1αwas the most stably expressed and suitable reference gene overall and for the heat, cold, and ABA treatments. Additionally,UBQexpression was stable following the salt treatment, whereasTUBwas identified as a suitable reference gene for H2O2and drought treatments. The reliability of the selected reference genes was verified by analyzing the expression of copper/zinc superoxide dismutase (Cu/Zn-SOD) gene in luffa. When the most unstable reference genes were used for data normalizations, the resulting expression patterns had obvious biases when compared with the expression patterns for the most ideal reference genes used alone or combined. These results will be conducive to more accurate quantification of gene expression levels in luffa.
A solver based on pseudo-spectral analytical time-domain method for the two-fluid plasma model
Authors: Morel B. , Giust R. , Ardaneh K. , Courvoisier F. 
Published: February 2021

AbstractA number of physical processes in laser-plasma interaction can be described with the two-fluid plasma model. We report on a solver for the three-dimensional two-fluid plasma model equations. This solver is particularly suited for simulating the interaction between short laser pulses with plasmas. The fluid solver relies on two-step Lax–Wendroff split with a fourth-order Runge–Kutta scheme, and we use the Pseudo-Spectral Analytical Time-Domain (PSATD) method to solve Maxwell’s curl equations. Overall, this method is only based on finite difference schemes and fast Fourier transforms and does not require any grid staggering. The Pseudo-Spectral Analytical Time-Domain method removes the numerical dispersion for transverse electromagnetic wave propagation in the absence of current that is conventionally observed for other Maxwell solvers. The full algorithm is validated by conservation of energy and momentum when an electromagnetic pulse is launched onto a plasma ramp and by quantitative agreement with wave conversion of p-polarized electromagnetic wave onto a plasma ramp.
Factors based on optical coherence tomography correlated with vision impairment in diabetic patients
Authors: Endo Hiroaki , Kase Satoru , Tanaka Hikari , Takahashi Mitsuo , Katsuta Satoshi , Suzuki Yasuo , Fujii Minako , Ishida Susumu , Kase Manabu 
Published: February 2021

AbstractThe aim of this study is to evaluate the relationship between retinal structures and visual acuity in diabetic patients using optical coherence tomography (OCT) and OCT angiography (OCTA). This study was a retrospective observational study conducted at a single medical center in Japan. Evaluation of retinal images was analyzed using spectral domain OCT. Twelve factors including central retinal thickness, length of disorganization of retinal inner layer (DRIL), number of inner hyperreflective foci, number of outer hyperreflective foci, height of intraretinal fluid, height of subretinal fluid, length of external limiting membrane disruption, length of external ellipsoid zone (EZ) disruption, vessel density of superficial capillary plexus (SCP), foveal avascular zone (FAZ) area, and FAZ circularity were analyzed based on OCT/OCTA findings. Multivariate analysis was used to investigate the OCT-based factors that could be correlated with poor visual acuity in treatment-naïve diabetic eyes. A total of 183 eyes of 123 diabetic patients with type 2 diabetes (mean age 61.9 ± 12.3 years, 66 men and 57 women) and 62 eyes of 55 control subjects (mean age 64.4 ± 12.5 years, 15 men and 40 women) was enrolled in this study. Multiple regression analysis showed that OCT-based factors correlated with visual acuity were length of DRIL (β = 0.24, P < 0.01), length of EZ disruption (β = 0.35, P < 0.001), and FAZ circularity (β =  − 0.14, P < 0.05). The other factors showed no significant correlation. In conclusion, the length of DRIL, length of EZ disruption, and FAZ circularity measured by OCT were identified as related factors for visual impairment in treatment-naïve diabetic eyes.
Associations between human leukocyte antigens and renal function
Authors: Lowe Marcus , Payton Antony , Verma Arpana , Worthington Judith , Gemmell Isla , Hamilton Patrick , Ollier William , Augustine Titus , Poulton Kay 
Published: February 2021

AbstractHuman leukocyte antigens (HLA) have been associated with renal function, but previous studies report contradictory findings with little consensus on the exact nature or impact of this observation. This study included 401,307 white British subjects aged 39–73 when they were recruited by UK Biobank. Subjects’ HLA types were imputed using HLA*IMP:02 software. Regression analysis was used to compare 362 imputed HLA types with estimated glomerular filtration rate (eGFR) as a primary outcome and clinical indications as secondary outcome measures. 22 imputed HLA types were associated with increased eGFR (and therefore increased renal function). Decreased eGFR (decreased renal function) was associated with 11 imputed HLA types, seven of which were also associated with increased risk of end-stage renal disease and/or chronic kidney disease. Many of these HLA types are commonly inherited together in established haplotypes, for example: HLA-A*01:01, B*08:01, C*07:01, DRB1*03:01, DQB1*02:01. This haplotype has a population frequency of 9.5% in England and each allele was associated with decreased renal function. 33 imputed HLA types were associated with kidney function in white British subjects. Linkage disequilibrium in HLA heritance suggests that this is not random and particularly affects carriers of established haplotypes. This could have important applications for the diagnosis and treatment of renal disease and global population health.
Combining expert knowledge and machine-learning to classify herd types in livestock systems
Authors: Brock Jonas , Lange Martin , Tratalos Jamie A. , More Simon J. , Graham David A. , Guelbenzu-Gonzalo Maria , Thulke Hans-Hermann 
Published: February 2021

AbstractA detailed understanding of herd types is needed for animal disease control and surveillance activities, to inform epidemiological study design and interpretation, and to guide effective policy decision-making. In this paper, we present a new approach to classify herd types in livestock systems by combining expert knowledge and a machine-learning algorithm called self-organising-maps (SOMs). This approach is applied to the cattle sector in Ireland, where a detailed understanding of herd types can assist with on-going discussions on control and surveillance for endemic cattle diseases. To our knowledge, this is the first time that the SOM algorithm has been used to differentiate livestock systems. In compliance with European Union (EU) requirements, relevant data in the Irish livestock register includes the birth, movements and disposal of each individual bovine, and also the sex and breed of each bovine and its dam. In total, 17 herd types were identified in Ireland using 9 variables. We provide a data-driven classification tree using decisions derived from the Irish livestock registration data. Because of the visual capabilities of the SOM algorithm, the interpretation of results is relatively straightforward and we believe our approach, with adaptation, can be used to classify herd type in any other livestock system.
The evolution of humanitarian mapping within the OpenStreetMap community
Authors: Herfort Benjamin , Lautenbach Sven , Porto de Albuquerque João , Anderson Jennings , Zipf Alexander 
Published: February 2021

AbstractIn the past 10 years, the collaborative maps of OpenStreetMap (OSM) have been used to support humanitarian efforts around the world as well as to fill important data gaps for implementing major development frameworks such as the Sustainable Development Goals. This paper provides a comprehensive assessment of the evolution of humanitarian mapping within the OSM community, seeking to understand the spatial and temporal footprint of these large-scale mapping efforts. The spatio-temporal statistical analysis of OSM’s full history since 2008 showed that humanitarian mapping efforts added 60.5 million buildings and 4.5 million roads to the map. Overall, mapping in OSM was strongly biased towards regions with very high Human Development Index. However, humanitarian mapping efforts had a different footprint, predominantly focused on regions with medium and low human development. Despite these efforts, regions with low and medium human development only accounted for 28% of the buildings and 16% of the roads mapped in OSM although they were home to 46% of the global population. Our results highlight the formidable impact of humanitarian mapping efforts such as post-disaster mapping campaigns to improve the spatial coverage of existing open geographic data and maps, but they also reveal the need to address the remaining stark data inequalities, which vary significantly across countries. We conclude with three recommendations directed at the humanitarian mapping community: (1) Improve methods to monitor mapping activity and identify where mapping is needed. (2) Rethink the design of projects which include humanitarian data generation to avoid non-sustainable outcomes. (3) Remove structural barriers to empower local communities and develop capacity.
Incidence of diabetes mellitus and associated risk factors in the adult population of the Basque country, Spain
Authors: Urrutia Inés , Martín-Nieto Alicia , Martínez Rosa , Casanovas-Marsal J Oriol , Aguayo Anibal , del Olmo Juan , Arana Eunate , Fernandez-Rubio Elsa , Castaño Luis , Gaztambide Sonia ,   The Diabetes Epidemiology Group, García-Castaño Alejandro , Gómez-Conde Sara , Larrauri Sara , Martínez de LaPiscina Idoia , Saso Laura , Velasco Olaia 
Published: February 2021

AbstractThe aim of this study was to estimate the incidence of diabetes mellitus in the Basque Country and the risk factors involved in the disease by reassessing an adult population after 7 years of follow-up. In the previous prevalence study, 847 people older than 18 years were randomly selected from all over the Basque Country and were invited to answer a medical questionnaire, followed by a physical examination and an oral glucose tolerance test. In the reassessment, the same variables were collected and the resulting cohort comprised 517 individuals of whom 43 had diabetes at baseline. The cumulative incidence of diabetes was 4.64% in 7 years and the raw incidence rate was 6.56 cases/1000 person-years (95%CI: 4.11–9.93). Among the incident cases, 59% were undiagnosed. The most strongly associated markers by univariate analyses were age > 60 years, dyslipidaemia, prediabetes and insulin resistance. We also found association with hypertension, obesity, family history of diabetes and low education level. Multivariate analysis adjusted for age and sex showed that a set of risk factors assessed together (dyslipidaemia, waist-to-hip-ratio and family history of diabetes) had great predictive value (AUC-ROC = 0.899, 95%CI: 0.846–0.953, p = 0.942), which suggests the need for early intervention before the onset of prediabetes.
Decoupling the metal insulator transition and crystal field effects of VO2
Authors: Hwang In-Hui , Park Chang-In , Yeo Sunmog , Sun Cheng-Jun , Han Sang-Wook 
Published: February 2021

AbstractVO2 is a highly correlated electron system which has a metal-to-insulator transition (MIT) with a dramatic change of conductivity accompanied by a first-order structural phase transition (SPT) near room temperature. The origin of the MIT is still controversial and there is ongoing debate over whether an SPT induces the MIT and whether the Tc can be engineered using artificial parameters. We examined the electrical and local structural properties of Cr- and Co-ion implanted VO2 (Cr-VO2 and Co-VO2) films using temperature-dependent resistance and X-ray absorption fine structure (XAFS) measurements at the V K edge. The temperature-dependent electrical resistance measurements of both Cr-VO2 and Co-VO2 films showed sharp MIT features. The Tc values of the Cr-VO2 and Co-VO2 films first decreased and then increased relative to that of pristine VO2 as the ion flux was increased. The pre-edge peak of the V K edge from the Cr-VO2 films with a Cr ion flux ≥ 1013 ions/cm2 showed no temperature-dependent behavior, implying no changes in the local density of states of V 3d t2g and eg orbitals during MIT. Extended XAFS (EXAFS) revealed that implanted Cr and Co ions and their tracks caused a substantial amount of structural disorder and distortion at both vanadium and oxygen sites. The resistance and XAFS measurements revealed that VO2 experiences a sharp MIT when the distance of V–V pairs undergoes an SPT without any transitions in either the VO6 octahedrons or the V 3d t2g and eg states. This indicates that the MIT of VO2 occurs with no changes of the crystal fields.
Increased C reactive protein, cardiac troponin I and GLS are associated with myocardial inflammation in patients with non-ischemic heart failure
Authors: Schwuchow-Thonke S. , Göbel S. , Emrich T. , Schmitt V. H. , Fueting F. , Klank C. , Escher F. , Schultheiss H. P. , Münzel T. , Keller K. , Wenzel P. 
Published: February 2021

AbstractInflammatory cardiomyopathy diagnosed by endomyocardial biopsy (EMB) is common in non-ischemic heart failure (HF) and might be associated with adverse outcome. We aimed to identify markers predicting myocardial inflammation in HF. We screened 517 patients with symptomatic non-ischemic HF who underwent EMB; 397 patients (median age 54 [IQR 43/64], 28.7% females) were included in this study. 230 patients were diagnosed with myocardial inflammation, defined as ≥ 7.0 CD3+ lymphocytes/mm2 and/or ≥ 35.0 Mac1 macrophages/mm2 and were compared to 167 inflammation negative patients. Patients with myocardial inflammation were more often smokers (52.4% vs. 39.8%, p = 0.013) and had higher C-reactive protein (CRP) levels (5.4 mg/dl vs. 3.7 mg/dl, p = 0.003). In logistic regression models CRP ≥ 8.15 mg/dl (OR 1.985 [95%CI 1.160–3.397]; p = 0.012) and Troponin I (TnI) ≥ 136.5 pg/ml (OR 3.011 [1.215–7.464]; p = 0.017) were independently associated with myocardial inflammation, whereas no association was found for elevated brain natriuretic peptide (OR 1.811 [0.873–3.757]; p = 0.111). In prognostic performance calculation the highest positive predictive value (90%) was detected for the combination of Global longitudinal strain (GLS) ≥ -13.95% and TnI ≥ 136.5 pg/ml (0.90 (0.74–0.96)). Elevated CRP, TnI and GLS in combination with TnI can be useful to detect myocardial inflammation. Smoking seems to predispose for myocardial inflammation.
Early alterations in retinal microvasculature on swept-source optical coherence tomography angiography in acute central serous chorioretinopathy
Authors: Podkowinski Dominika , Foessl Bernhard , de Sisternes Luis , Beka Sophie , Mursch-Edlmayr Anna-Sophie , Strauss Rupert W. , Bolz Matthias 
Published: February 2021

AbstractThe purpose of the study was to evaluate the retinal blood flow in patients with acute central serous chorioretinopathy (CSC) over an observational period of 1 month using swept-source optical coherence tomography (SS-OCTA), focusing especially on changes in the area of subretinal fluid (A-SRF). We correlated these findings with conventional indocyanine green angiography (ICGA). ICGA and SS-OCTA images were collected and analyzed of 12 eyes of 12 patients. The A-SRF was annotated and a qualitative analysis of choriocapillaris, the vessel density (VD) and perfusion density (PD) of the retinal superficial capillary plexus (SCP) and the deep capillary plexus (DCP) was performed in A-SRF and the unaffected remaining area (RA). The VD and PD in the DCP were statistically significantly lower in A-SRF than in the RA at baseline. (VD: p = 0.014; PD: p = 0.036). After 1 month, there was a statistically significant difference in the VD and PD of the DCP (VD: p = 0.015; PD: p = 0.014), and for the PD of the SCP between the A-SRF and the RA (p = 0.015), with lower values in the A-SRF. We found low perfused areas in choriocapillaris corresponding to hypofluorescent areas on ICGA. In conclusion there is a difference in VD and VD of the DCP in the area of SRF in acute CSC. These alterations may lead to a chronic change in the microvasculature and potentially to morphological changes.
Polychlorinated biphenyls and risk of hepatocellular carcinoma in the population living in a highly polluted area in Italy
Authors: Donato Francesco , Moneda Marco , Portolani Nazario , Rossini Angelo , Molfino Sarah , Ministrini Silvia , Contessi Giovanni Battista , Pesenti Silvia , De Palma Giuseppe , Gaia Alice , Zanardini Elena , Sileo Claudio Vito , Magoni Michele 
Published: February 2021

AbstractPolychlorinated biphenyls (PCBs) are human carcinogens, based on sufficient evidence for melanoma and limited evidence for non-Hodgkin lymphoma and breast cancer. Few data are available for liver cancer, although PCBs cause it in rats and determined liver damage in poisoned people. We investigated the association between PCB serum levels and hepatocellular carcinoma (HCC) with a case–control study in a PCB-polluted area in North Italy. We enrolled prospectively 102 HCC incident cases and 102 age and gender-matched hospital controls. Serum concentrations of 33 PCB congeners were determined by a gas chromatograph coupled to mass spectrometry. Of 102 HCC cases, 62 who had lost < 3 kg of body weight in past 3 years were included in the analysis (67.7% males, mean age 68 years). The odds ratio (OR) for HCC for 3rd compared to 1st tertile of PCB distribution was 1.76 (95% confidence interval 0.62–5.03) for total PCB, adjusting for socio-demographic variables and risk factors for HCC by logistic regression. For most PCB congeners, ORs > 1.5 or 2 were found, although the 95% CIs included the null value for almost all of them. This preliminary study suggests that PCBs might play a role in HCC development.