bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics
Authors: Bentley Stephen D. , Lo Stephanie W. 
Published: May 2021

AbstractVaccines are powerful agents in infectious disease prevention but often designed to protect against some strains that are most likely to spread and cause diseases. Most vaccines do not succeed in eradicating the pathogen and thus allow the potential emergence of vaccine evading strains. As with most evolutionary processes, being able to capture all variations across the entire genome gives us the best chance of monitoring and understanding the processes of vaccine evasion. Genomics is being widely adopted as the optimum approach for pathogen surveillance with the potential for early and precise identification of high-risk strains. Given sufficient longitudinal data, genomics also has the potential to forecast the emergence of such strains enabling immediate or pre-emptive intervention. In this review, we consider the strengths and challenges for pathogen genomic surveillance using the experience of the Global Pneumococcal Sequencing (GPS) project as an early example. We highlight the multifaceted nature of genome data and recent advances in genome-based tools to extract useful information relevant to inform vaccine strategies and treatment options. We conclude with future perspectives for genomic pathogen surveillance.
Shortcomings of SARS-CoV-2 genomic metadata
Authors: Gozashti Landen , Corbett-Detig Russell 
Published: May 2021

Abstract
Objective
The SARS-CoV-2 pandemic has prompted one of the most extensive and expeditious genomic sequencing efforts in history. Each viral genome is accompanied by a set of metadata which supplies important information such as the geographic origin of the sample, age of the host, and the lab at which the sample was sequenced, and is integral to epidemiological efforts and public health direction. Here, we interrogate some shortcomings of metadata within the GISAID database to raise awareness of common errors and inconsistencies that may affect data-driven analyses and provide possible avenues for resolutions.

Results
Our analysis reveals a startling prevalence of spelling errors and inconsistent naming conventions, which together occur in an estimated ~ 9.8% and ~ 11.6% of “originating lab” and “submitting lab” GISAID metadata entries respectively. We also find numerous ambiguous entries which provide very little information about the actual source of a sample and could easily associate with multiple sources worldwide. Importantly, all of these issues can impair the ability and accuracy of association studies by deceptively causing a group of samples to identify with multiple sources when they truly all identify with one source, or vice versa.
Fairness in household financial contribution to the Iran’s healthcare system from 2008 to 2018
Authors: Darvishi Ali , Amini-Rarani Mostafa , Mehrolhassani Mohammad Hossein , Yazdi-Feyzabadi Vahid 
Published: May 2021

Abstract
Objective
Enhancing financial protection in health is one of the main goals of Iran’s health transformation program (HTP), a recent reform conducted in early 2014. This study aimed to measure financial protection using the fair financial contribution index (FFCI) in urban and rural areas before (2008–2013) and after (2014–2018) the HTP implementation. Using a retrospective study on annual national cross-sectional surveys of households' income and expenditure, FFCI was measured. The total sample sizes for urban and rural areas from 2008 to 2018 were 207,980 and 212,249 households, respectively.

Results
The worst fair contributions to health expenditure in urban (FFCI = 0.684) and rural areas (FFCI = 0.530) were related to 2010 and 2009, respectively. Otherwise, the best fair contributions for urban (FFCI = 0.858) and rural (FFCI = 0.836) areas were made in 2011. Before the HTP implementation began, FFCI showed minor changes from 0.834 in 2008 to 0.833 in 2013. Following the HTP implementation, the FFCI values in urban and rural populations declined (worsened) from 0.842 to 0.836 and 0.816 to 0.809, respectively.On average more
fair financial contributions had been made following five years after the HTP, especially
in rural areas, but less than that expected in upstream documents (as
determined 0.9).
Global existence of positive periodic solutions of a general differential equation with neutral type
Authors: Liu Ming , Cao Jun , Xu Xiaofeng 
Published: May 2021

AbstractIn this paper, the dynamics of a general differential equation with neutral type are investigated. Under certain assumptions, the stability of positive equilibrium and the existence of Hopf bifurcation are obtained by analyzing the distribution of eigenvalues. And global existence of positive periodic solutions is established by using the global Hopf bifurcation result of Krawcewicz et al. Finally, by taking neutral Nicholson’s blowflies model and neutral Mackey–Glass model as two examples, some numerical simulations are carried out to illustrate the analytical results.
Exponential stability in the Lagrange sense for Clifford-valued recurrent neural networks with time delays
Authors: Rajchakit G. , Sriraman R. , Boonsatit N. , Hammachukiattikul P. , Lim C. P. , Agarwal P. 
Published: May 2021

AbstractThis paper considers the Clifford-valued recurrent neural network (RNN) models, as an augmentation of real-valued, complex-valued, and quaternion-valued neural network models, and investigates their global exponential stability in the Lagrange sense. In order to address the issue of non-commutative multiplication with respect to Clifford numbers, we divide the originaln-dimensional Clifford-valued RNN model into$2^{m}n$2mnreal-valued models. On the basis of Lyapunov stability theory and some analytical techniques, several sufficient conditions are obtained for the considered Clifford-valued RNN models to achieve global exponential stability according to the Lagrange sense. Two examples are presented to illustrate the applicability of the main results, along with a discussion on the implications.
Solution of the system of nonlinear PDEs characterizing CES property under quasi-homogeneity conditions
Authors: Alodan Haila , Chen Bang-Yen , Deshmukh Sharief , Vîlcu Gabriel-Eduard 
Published: May 2021

AbstractThe constant elasticity of substitution (CES for short) is a basic property widely used in some areas of economics that involves a system of second-order nonlinear partial differential equations. One of the most remarkable results in mathematical economics states that under homogeneity condition i.e. the production function is a homogeneous function of a certain degree, there are no other production models with the CES property apart from the famous Cobb–Douglas and Arrow–Chenery–Minhas–Solow production functions. In this paper we generalize this classification result to a much wider framework of production functions under quasi-homogeneity conditions, showing in particular the existence of three new classes of production models with the CES property.
A reduction method for magnetic disturbance caused by DC railway system
Authors: Ding Xuezhen , Li Yuguo , Wu Yunju , Duan Shuangmin , Li Zhuoxuan , Yin Yanxin , Pan Lindong 
Published: May 2021

AbstractThe stray current of direct current (DC) railway systems causes magnetic disturbance in geomagnetic measurements, which may complicate the identification of useful information. The magnetic disturbance exhibits broadband characteristics in the frequency domain. In this paper, we propose a noise reduction method based on the adaptive Kalman filter to extract useful signals from the geomagnetic data with a high level of noise. The covariance matrixes of both the process noise (Q) and measurement noise (R) can be adaptively estimated to improve the performance of the adaptive Kalman filter. The proposed method is adopted to process the geomagnetic data collected at the Beijing Geomagnetic Observatory (BJI), which is affected by the DC railway system. The magnetic disturbance is largely reduced, and the signal-to-noise ratios of the horizontal and vertical components of the geomagnetic field are improved by more than 14 dB and 27 dB, respectively. The K-indices are calculated to evaluate the performance of the adaptive Kalman filter method. To assess the influence of the adaptive Kalman filter on natural signals, the geomagnetic data that contain rapid variations are processed. The denoising results show that the adaptive Kalman filter can effectively reduce the magnetic disturbance caused by DC railway system without large impact on the natural geomagnetic rapid variations.
Teaching trainee psychiatrists a Mentalization-Based Treatment approach to personality disorder: effect on attitudes
Authors: Lee Tennyson , Grove Patrick , Garrett Chris , Whitehurst Thomas , Kanter-Bax Orestis , Bhui Kamaldeep 
Published: May 2021

Aims and methodTo evaluate whether a brief training using a Mentalization-Based Treatment (MBT) model improves attitudes of trainee psychiatrists working with patients with personality disorder. Trainee psychiatrists (n = 49) completed the Attitudes to Personality Disorder Questionnaire before and after a training consisting of two 3 h lectures on (a) theory of personality disorder and (b) practical skills using an MBT role-play.ResultsThere was a significant improvement on composite scores of attitude, with small to moderate effect size (Wilcoxon signed-rank test Z = 3.961, P < 0.001, r = 0.40).Clinical implicationsBrief MBT-informed teaching oriented to the clinical situation appears to have a positive effect on attitudes towards people with personality disorder.
Survival Outcomes of Newly Diagnosed Multiple Myeloma at a Tertiary Care Center in North India (IMAGe: 001A Study)
Authors: Yanamandra Uday , Sharma Rajni , Shankar Siddharth , Yadav Shikha , Kapoor Rajan , Pramanik Suman , Ahuja Ankur , Kumar Rajiv , Sharma Sanjeevan , Das Satyaranjan , Chatterjee Tathagata , Somasundaram Venkatesan , Verma Tarun , Mishra Kundan , Singh Jasjit , Sharma Ajay , Nair Velu 
Published: May 2021

PURPOSE The outcomes of patients with myeloma from developing countries are often lacking because of poor record maintenance. Publications from such settings are also limited because of the retrospective nature of the data collection. Information technology can bridge these gaps in developing countries with real-time data maintenance. We present the real-time survival data of the patients with myeloma from a tertiary care center in North India using one such indigenously built software. PATIENTS AND METHODS These are real-time data of all patients with myeloma presenting to a tertiary care center from North India. The patient characteristics (demographics, baseline disease characteristics, risk stratification, and outcomes) were recorded contemporaneously. The survival of the study population was analyzed and grouped based on various disease characteristics at diagnosis. RESULTS The median age of the study population (N = 696) was 65.9 (34.9-94.9) years with male predominance (65%). The median follow-up was 3.7 years (0-18.6 years) with the median overall survival (OS) not achieved. The OS of the study population at 1, 3, and 5 years was 94% (n = 558), 87.5% (n = 394), and 83.1% (n = 267), respectively. Most of the patients presented in advanced stages based on International Staging System (III:70%). On Kaplan-Meier analysis, the presence of weight loss ( P = .01), renal dysfunction ( P = .047), and anemia at diagnosis ( P = .004) had a significant impact on survival. On Cox proportional model univariate analysis, the presence of renal dysfunction, anemia, and weight loss had the significant hazard ratio of 1.68 (1-2.82, P = .049), 3.18 (1.39-7.29, P = .0063), and 2.81 (1.22-6.42, P = .014), respectively, whereas on multivariate analysis of hypercalcemia, renal disease, anemia, and bone disease (CRAB) features, only anemia was found to have a significant hazard ratio of 2.56 (1.01-6.47, P = .046). CONCLUSION The real-world data show OS comparable with the published western literature. Only anemia was found to have significant impact on survival. The use of such software can aid in better data-keeping in resource-constrained settings.
Feasibility and Acceptability of Smartphone-Based Cervical Cancer Screening Among HIV-Positive Women in Western Kenya
Authors: Mungo Chemtai , Osongo Cirilus Ogollah , Ambaka Jeniffer , Randa Magdalene A. , Samba Benard , Ochieng Catherine A. , Barker Emily , Guliam Anagha , Omoto Jackton , Cohen Craig R. 
Published: May 2021

PURPOSE Adjunct cervical cancer screening methods are under evaluation to improve the diagnostic accuracy of human papillomavirus (HPV)-based screening in low- and middle-income countries. We evaluated the feasibility and acceptability of smartphone-based cervicography among HPV-positive women living with HIV (WLWH) in Western Kenya. METHODS HPV-positive WLWH of 25-49 years of age enrolled in a clinical trial (ClinicalTrials.gov identifier: NCT04191967 ) had digital images of the cervix taken using a smartphone by a nonphysician provider following visual inspection with acetic acid. All participants had colposcopy-directed biopsy before treatment. Cervical images were evaluated by three off-site colposcopists for quality, diagnostic utility, and assigned a presumed diagnosis. We determined the proportion of images rates as low, medium, or high quality, interobserver agreement using Cohen’s Kappa statistic, and the off-site colposcopist’s sensitivity and specificity for diagnosis of cervical intraepithelial neoplasia grade 2 or worse (CIN2+) compared with histopathology. Acceptability was evaluated using a questionnaire. RESULTS One hundred sixty-four HPV-positive WLWH underwent cervicography during the study period. Mean age was 37.3 years. Images from the first 94 participants were evaluated by off-site colposcopists, with a majority (70.9%) rated as high quality. Off-site colposcopists had a sensitivity ranging from 21.4% (95% CI, 0.06 to 0.43) to 35.7% (95% CI, 0.26 to 0.46) and a specificity between 85.5% (95% CI, 0.81 to 0.90) to 94.9% (95% CI, 0.92 to 0.98) for diagnosis of CIN2+ based compared with histopathology. The majority of women, 99.4%, were comfortable having an image of their cervix taken as part of screening. CONCLUSION Cervicography by a nonphysician provider as an adjunct to HPV-based screening among WLWH in a low- and middle-income country setting is feasible and acceptable. However, low sensitivity for diagnosis of CIN2+ by off-site expert colposcopists highlights the limitations of cervicography.
Active engines: Thermodynamics moves forward
Authors: Fodor Étienne , Cates Michael E. 
Published: May 2021

Abstract
The study of thermal heat engines was pivotal to establishing the principles of equilibrium thermodynamics, with implications far wider than only engine optimization. For nonequilibrium systems, which by definition dissipate energy even at rest, how to best convert such dissipation into useful work is still largely an outstanding question, with similar potential to illuminate general physical principles. We review recent theoretical progress in studying the performances of engines operating with active matter, where particles are driven by individual self-propulsion. We distinguish two main classes, either autonomous engines exploiting a particle current, or cyclic engines applying periodic transformation to the system, and present the strategies put forward so far for optimization. We delineate the limitations of previous studies, and propose some future perspectives, with a view to building a consistent thermodynamic framework far from equilibrium.
Running vacuum against the H
0 and σ8
tensions
Authors: Solà Peracaula Joan , Gómez-Valent Adrià , de Cruz Pérez Javier , Moreno-Pulido Cristian 
Published: May 2021

Abstract
The cosmological term, Λ, was introduced 104 years ago by Einstein in his gravitational field equations. Whether Λ is a rigid quantity or a dynamical variable in cosmology has been a matter of debate for many years, especially after the introduction of the general notion of dark energy (DE). Λ is associated to the vacuum energy density,

, and one may expect that it evolves slowly with the cosmological expansion. Herein we present a devoted study testing this possibility using the promising class of running vacuum models (RVMs). We use a large string SNIa+BAO+H(z)+LSS+CMB of modern cosmological data, in which for the first time the CMB part involves the full Planck 2018 likelihood for these models. We test the dependence of the results on the threshold redshift

at which the vacuum dynamics is activated in the recent past and find positive signals up to

for

. The RVMs prove very competitive against the standard ΛCDM model and give a handle for solving the

tension and alleviating the H
0 one.
A Systematic Review and Meta-Analysis of Preoperative Frailty Instruments Derived From Electronic Health Data
Authors: Alkadri Jamal , Hage Dima , Nickerson Leigh H. , Scott Lia R. , Shaw Julia F. , Aucoin Sylvie D. , McIsaac Daniel I. 
Published: May 2021

BACKGROUND:
Frailty is a strong predictor of adverse outcomes in the perioperative period. Given the increasing availability of electronic medical data, we performed a systematic review and meta-analysis with primary objectives of describing available frailty instruments applied to electronic data and synthesizing their prognostic value. Our secondary objectives were to assess the construct validity of frailty instruments that have been applied to perioperative electronic data and the feasibility of electronic frailty assessment.

METHODS:
Following protocol registration, a peer-reviewed search strategy was applied to Medline, Excerpta Medica dataBASE (EMBASE), Cochrane databases, and the Comprehensive Index to Nursing and Allied Health literature from inception to December 31, 2019. All stages of the review were completed in duplicate. The primary outcome was mortality; secondary outcomes included nonhome discharge, health care costs, and length of stay. Effect estimates adjusted for baseline illness, sex, age, procedure, and urgency were of primary interest; unadjusted and adjusted estimates were pooled using random-effects models where appropriate or narratively synthesized. Risk of bias was assessed.

RESULTS:
Ninety studies were included; 83 contributed to the meta-analysis. Frailty was defined using 22 different instruments. In adjusted data, frailty identified from electronic data using any instrument was associated with a 3.57-fold increase in the odds of mortality (95% confidence interval [CI], 2.68–4.75), increased odds of institutional discharge (odds ratio [OR], 2.40; 95% CI, 1.99–2.89), and increased costs (ratio of means, 1.54; 95% CI, 1.46–1.63). Most instruments were not multidimensional, head-to-head comparisons were lacking, and no feasibility data were reported.

CONCLUSIONS:
Frailty status derived from electronic data provides prognostic value as it is associated with adverse outcomes, even after adjustment for typical risk factors. However, future research is required to evaluate multidimensional instruments and their head-to-head performance and to assess their feasibility and clinical impact.
Metabolic programming and monitoring tools in pre-weaned dairy calves
Authors: Plate Peter 
Published: May 2021

The current knowledge on the effects of nutritional and environmental factors in the late embryonic and neonatal phase of dairy calves on performance later in life is summarised. The importance of epigenetic factors is increasingly recognised in this context. Prolonged colostrum feeding, discouraged on most farms to prevent the spread of Johne's disease, can have beneficial effects on the calf's immune system and has been shown to give protection against rotavirus. The importance of colostrum hygiene for uptake of antibodies is explained. Intensive milk or milk replacer feeding leads to a more productive animal while reducing the rearing costs. Iron deficiency anaemia is a common condition in whole milk fed dairy calves, and monitoring haemoglobin and supplementing iron where necessary leads to higher growth rates in calves. Other monitoring tools like lung ultrasound scanning, and beta-hydroxy-butyrate testing at weaning are briefly introduced. In conclusion, the benefits of many early intervention measures are likely to be underestimated.
GNAQ knockdown promotes bone metastasis through epithelial-mesenchymal transition in lung cancer cells
Authors: Choi Ji-Yoon , Lee Yun Sun , Shim Da Mi , Lee Young Keun , Seo Sung Wook 
Published: May 2021

Aims Bone metastasis ultimately occurs due to a complex multistep process, during which the interactions between cancer cells and bone microenvironment play important roles. Prior to colonization of the bone, cancer cells must succeed through a series of steps that will allow them to gain migratory and invasive properties; epithelial-to-mesenchymal transition (EMT) is known to be integral here. The aim of this study was to determine the effects of G protein subunit alpha Q (GNAQ) on the mechanisms underlying bone metastasis through EMT pathway. Methods A total of 80 tissue samples from patients who were surgically treated during January 2012 to December 2014 were used in the present study. Comparative gene analysis revealed that the GNAQ was more frequently altered in metastatic bone lesions than in primary tumour sites in lung cancer patients. We investigated the effects of GNAQ on cell proliferation, migration, EMT, and stem cell transformation using lung cancer cells with GNAQ-knockdown. A xenograft mouse model tested the effect of GNAQ using micro-CT analyses and histological analyses. Results GNAQ-knockdown showed down-regulation of tumour growth through mitogen-activated protein kinase (MAPK) signalling in lung cancer cells, but not increased apoptosis. We found that GNAQ-knockdown induced EMT and promoted invasiveness. GNAQ-knockdown cells injected into the bone marrow of murine tibia induced tumour growth and bone-to-lung metastasis, whereas it did not in control mice. Moreover, the knockdown of GNAQ enhanced cancer stem cell-like properties in lung cancer cells, which resulted in the development of resistance to chemotherapy. Conclusion The present study reveals that the GNAQ-knockdown induced cancer stem cell-like properties. Cite this article: Bone Joint Res 2021;10(5):310–320.
40 GHz high-efficiency Michelson interferometer modulator on a silicon-rich nitride and thin-film lithium niobate hybrid platform
Authors: Huang Xingrui , Liu Yang , Li Zezheng , Guan Huan , Wei Qingquan , Tan Manqing , Li Zhiyong 
Published: May 2021

We propose and demonstrate a Michelson interferometer modulator with integrated Bragg reflectors on a silicon-rich nitride–thin-film lithium niobate hybrid platform. High-reflectivity Bragg reflectors are placed at the ends of both arms, which double the electro-optic (E-O) interaction length and reduce the velocity mismatch between the microwave and optical wave. The presented Michelson interferometer modulator achieves a measured half-wave voltage length product as low as 1.06 V cm and high-speed modulation up to 70 Gbps. A 3-dB E-O bandwidth beyond 40 GHz is also achieved, which is, to the best of our knowledge, the highest modulation bandwidth of Michelson interferometer modulators.