bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Surgical Mask on Setup Error in Head and Neck Radiotherapy
Authors: Ding Yi , Ma Pingping , Li Wei , Wei Xueyan , Qiu Xiaoping , Hu Desheng , Wu Yuan , Wei Wei , Zeng Fanyu , Wang Xiaohong , Wang Xiao
Published: December 2020

Purpose:

With the widespread prevalence of Corona Virus Disease 2019 (COVID-19), cancer patients are suggested to wear a surgical mask during radiation treatment. In this study, cone beam CT (CBCT) was used to investigate the effect of surgical mask on setup errors in head and neck radiotherapy.

Methods:

A total of 91 patients with head and neck tumors were selected. CBCT was performed to localize target volume after patient set up. The images obtained by CBCT before treatment were automatically registered with CT images and manually fine-tuned. The setup errors of patients in 6 directions of Vrt, Lng, Lat, Pitch, Roll and Rotation were recorded. The patients were divided into groups according to whether they wore the surgical mask, the type of immobilization mask used and the location of the isocenter. The setup errors of patients were calculated. A t-test was performed to detect whether it was statistically significant.

Results:

In the 4 groups, the standard deviation in the directions of Lng and Pitch of the with surgical mask group were all higher than that in the without surgical mask group. In the head-neck-shoulder mask group, the mean in the Lng direction of the with surgical mask group was larger than that of the without surgical mask group. In the lateral isocenter group, the mean in the Lng and Pitch directions of the with surgical mask group were larger than that of the without surgical mask group. The t-test results showed that there was significant difference in the setup error between the 2 groups ( p = 0.043 and p = 0.013, respectively) only in the Lng and Pitch directions of the head-neck-shoulder mask group. In addition, the setup error of 6 patients with immobilization open masks exhibited no distinguished difference from that of the patients with regular immobilization masks.

Conclusion:

In the head and neck radiotherapy patients, the setup error was affected by wearing surgical mask. It is recommended that the immobilization open mask should be used when the patient cannot finish the whole treatment with a surgical mask.
Expression and Possible Molecular Mechanisms of microRNA-205-5p in Patients With Head and Neck Squamous Cell Carcinoma
Authors: Zhou Ziyan , Liu Chang , Liu Kang , Lv Meixin , Li Baibei , Lan Zhenrui , Chen Wei , Kang Min
Published: December 2020

Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent malignancy worldwide, with high incidence and poor survival rates. Increased expression of microRNA-205-5p (miR-205-5p) may influence the outcomes of HNSCC, but the identities of miR-205-5p target genes and the potential signaling pathways related to HNSCC remain unclear. RT-qPCR was used to detect the expression levels of miR-205-5p in the plasma of patients with HNSCC. We also performed a meta-analysis using data from relevant literature, and the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases to evaluate the expression level of miR-205-5p in HNSCC. Next, we predicted the potential miR-205-5p target genes in HNSCC. We also used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for enrichment analyses adapted to investigate the dynamics and possible mechanisms of miR-205-5p in HNSCC. Lastly, we predicted the potential miR-205-5p target genes by evaluating their expression level and using Spearman analysis. Expression of miR-205-5p was higher in HNSCC tissues compared to normal unafflicted tissue samples (P < 0.05), and the corresponding summary receiver operating characteristic (sROC) was 0.82.The pooled sensitivity, specificity, PLR, NLR, and DOR values were 0.78 (95% CI: 0.75-0.81), 0.67 (95% CI: 0.60-0.73), 2.34 (95% CI: 1.45-3.76), 0.34 (95% CI: 0.19-0.60), and 8.16 (95% CI: 4.01-16.64), respectively. Based on GO and KEGG analyses, we found that miR-205-5p was correlated with the progression of HNSCC through association with signaling pathways, including the drug metabolism-cytochrome P450 pathway. Analysis of the target genes revealed that flavin-containing monooxygenase isoform 2 (FMO2) and alcohol dehydrogenase 1B (ADH1B) may be important targets of miR-205-5p. In summary, miR-205-5p may have a significant role in the prognosis of HNSCC and may serve as a potential biomarker in HNSCC.
Analysis of regression-discontinuity designs with multiple cutoffs or multiple scores
Authors: Cattaneo Matias D. , Titiunik Rocío , Vazquez-Bare Gonzalo
Published: December 2020

In this article, we introduce the Stata (and R) package rdmulti, which consists of three commands (rdmc, rdmcplot, rdms) for analyzing regression-discontinuity (RD) designs with multiple cutoffs or multiple scores. The command rdmc applies to noncumulative and cumulative multicutoff RD settings. It calculates pooled and cutoff-specific RD treatment effects and provides robust biascorrected inference procedures. Postestimation and inference is allowed. The command rdmcplot offers RD plots for multicutoff settings. Finally, the command rdms concerns multiscore settings, covering in particular cumulative cutoffs and two running variable contexts. It also calculates pooled and cutoff-specific RD treatment effects, provides robust bias-corrected inference procedures, and allows for postestimation and inference. These commands use the Stata (and R) package rdrobust for plotting, estimation, and inference. Companion R functions with the same syntax and capabilities are provided.
Fitting partially linear functional-coefficient panel-data models with Stata
Authors: Du Kerui , Zhang Yonghui , Zhou Qiankun
Published: December 2020

In this article, we describe the implementation of fitting partially linear functional-coefficient panel models with fixed effects proposed by An, Hsiao, and Li [2016, Semiparametric estimation of partially linear varying coefficient panel data models in Essays in Honor of Aman Ullah ( Advances in Econometrics, Volume 36)] and Zhang and Zhou (Forthcoming, Econometric Reviews). Three new commands xtplfc, ivxtplfc, and xtdplfc are introduced and illustrated through Monte Carlo simulations to exemplify the effectiveness of these estimators.
Secreted Peptides for Diagnostic Trajectory Assessments in Brain Injury Rehabilitation
Authors: Patel Parantap D. , Stafflinger Jillian E. , Marwitz Jennifer H. , Niemeier Janet P. , Ottens Andrew K.
Published: December 2020

Background

Rehabilitation following traumatic brain injury (TBI) significantly improves outcomes; yet TBI heterogeneity raises the need for molecular evidence of brain recovery processes to better track patient progress, evaluate therapeutic efficacy, and provide prognostication.

Objective

Here, we assessed whether the trajectory of TBI-responsive peptides secreted into urine can produce a predictive model of functional recovery during TBI rehabilitation.

Methods

The multivariate urinary peptidome of 12 individuals with TBI was examined using quantitative peptidomics. Measures were assessed upon admission and discharge from inpatient rehabilitation. A combination of Pavlidis template matching and partial least-squares discriminant analysis was used to build models on Disability Rating Scale (DRS) and Functional Independence Measure (FIM) scores, with participants bifurcated into more or less functional improvement groups.

Results

The produced models exhibited high sensitivity and specificity with the area under the receiver operator curve being 0.99 for DRS- and 0.95 for FIM-based models using the top 20 discriminant peptides. Predictive ability for each model was assessed using robust leave-one-out cross-validation with Q2 statistics of 0.64 ( P = .00012) and 0.62 ( P = .011) for DRS- and FIM-based models, respectively, both with a high predictive accuracy of 0.875. Identified peptides that discriminated improved functional recovery reflected heightened neuroplasticity and synaptic refinement and diminished cell death and neuroinflammation, consistent with postacute TBI pathobiology.

Conclusions

Produced models of urine-based peptide measures reflective of ongoing recovery pathobiology can inform on rehabilitation progress after TBI, warranting further study to assess refined stratification across a larger population and efficacy in assessing therapeutic interventions.
Detection of an Autism EEG Signature From Only Two EEG Channels Through Features Extraction and Advanced Machine Learning Analysis
Authors: Grossi Enzo , Valbusa Giovanni , Buscema Massimo
Published: December 2020

Background and Objective

In 2 previous studies, we have shown the ability of special machine learning systems applied to standard EEG data in distinguishing children with autism spectrum disorder (ASD) from non-ASD children with an overall accuracy rate of 100% and 98.4%, respectively. Since the equipment routinely available in neonatology units employ few derivations, we were curious to check if just 2 derivations were enough to allow good performance in the same cases of the above-mentioned studies.

Methods

A continuous segment of artifact-free EEG data lasting 1 minute in ASCCI format from C3 and C4 EEG channels present in 2 previous studies, was used for features extraction and subsequent analyses with advanced machine learning systems. A features extraction software package (Python tsfresh) applied to time-series raw data derived 1588 quantitative features. A special hybrid system called TWIST (Training with Input Selection and Testing), coupling an evolutionary algorithm named Gen-D and a backpropagation neural network, was used to subdivide the data set into training and testing sets as well as to select features yielding the maximum amount of information after a first variable selection performed with linear correlation index threshold.

Results

After this intelligent preprocessing, 12 features were extracted from C3-C4 time-series of study 1 and 36 C3-C4 time-series of study 2 representing the EEG signature. Acting on these features the overall accuracy predictive capability of the best artificial neural network acting as a classifier in deciphering autistic cases from typicals (study 1) and other neuropsychiatric disorders (study 2) resulted in 100 % for study 1 and 94.95 % for study 2.

Conclusions

The results of this study suggest that also a minor part of EEG contains precious information useful to detect autism if treated with advanced computational algorithms. This could allow in the future to use standard EEG from newborns to check if the ASD signature is already present at birth.
A visual simultaneous localization and mapping approach based on scene segmentation and incremental optimization
Authors: Zhang Xiaoguo , Liu Qihan , Zheng Bingqing , Wang Huiqing , Wang Qing
Published: December 2020

Existing visual simultaneous localization and mapping (V-SLAM) algorithms are usually sensitive to the situation with sparse landmarks in the environment and large view transformation of camera motion, and they are liable to generate large pose errors that lead to track failures due to the decrease of the matching rate of feature points. Aiming at the above problems, this article proposes an improved V-SLAM method based on scene segmentation and incremental optimization strategy. In the front end, this article proposes a scene segmentation algorithm considering camera motion direction and angle. By segmenting the trajectory and adding camera motion direction to the tracking thread, an effective prediction model of camera motion in the scene with sparse landmarks and large view transformation is realized. In the back end, this article proposes an incremental optimization method combining segmentation information and an optimization method for tracking prediction model. By incrementally adding the state parameters and reusing the computed results, high-precision results of the camera trajectory and feature points are obtained with satisfactory computing speed. The performance of our algorithm is evaluated by two well-known datasets: TUM RGB-D and NYUDv2 RGB-D. The experimental results demonstrate that our method improves the computational efficiency by 10.2% compared with state-of-the-art V-SLAMs on the desktop platform and by 22.4% on the embedded platform, respectively. Meanwhile, the robustness of our method is better than that of ORB-SLAM2 on the TUM RGB-D dataset.
Project of high altitude balloon launched micro glider: Aircraft design, control and flight test
Authors: Qu Zhengyu , Li Cuichun , Hao Yong , Yan Feng , Yang Yanchu
Published: December 2020

This paper presents the design details and flight tests validation of printed circuit board fabricated micro gliders. The purpose of the micro glider is to be launched from a super pressure balloon at high altitude, glide to the target position to collect data and upload data to the staying balloon. The mission demand requires the micro glider to finish precise landing with small size and low fabrication cost. To complete this concept, we designed a PCB fabricated aircraft with limited sensors including GPS and IMU. The first part of the article describes the aerodynamic design methods. The second part introduced the control and guidance system design by controlling the roll angle and flight path angle to complete the precise landing. In the simulation results presented in the third part, launch with no wind condition shows desirable precise landing ability. As a contrast, wind direction and magnitude have significant effects on the guidance ability and accuracy. In the last part, two real flight tests conducted in Inner Mongolia of China are described to compare the flight performance with the current aerodynamics and control system design. Returned data indicated the micro gliders could successfully fly at high altitude. The control algorithm can compute the command roll angle only with GPS and IMU, but some design details still need to be improved to achieve precise landing ability.
Identifying Wildlife Corridors Using Local Knowledge and Occupancy Methods along the San Buenaventura-Ixiamas Road, La Paz, Bolivia
Authors: Wallace Robert , Ayala Guido , Negroes Nuno , O’Brien Timothy , Viscarra Maria , Reinaga Ariel , Márquez Robert , Strindberg Samantha
Published: December 2020

In 2013, we conducted a baseline study on the presence, distribution and occupancy of medium- to large-sized mammals in Bolivia along the San Buenaventura-Ixiamas road that runs parallel to the Madidi National Park and Natural Area of Integrated Management boundary and cuts through the Tacana Indigenous Territory and a number of neighboring private properties. Establishing a 3 km buffer on each side of the road, we studied an 865 km2 area divided into 1 km2 cells and sampled a total of 356 of these cells. In each cell, we established one 300 m transect divided into 25 m sections and registered wildlife sign, mainly footprints, from eight wildlife species or species groups. The transects were placed either along streams (75% of cells) or within forest (25% of cells). Using single-season single-species occupancy models we estimated occupancy (ψ) for Tapirus terrestris (ψ = 0.39), Pecari tajacu (ψ = 0.5), Mazama americana (ψ = 0.56), Dasyprocta spp. (ψ = 0.59), Cuniculus paca (ψ = 0.56), Leopardus spp. (ψ = 0.33), and use for Tayassu pecari (ψ = 0.17) and Panthera onca (ψ = 0.11). Occupancy and use results verified community perceived wildlife corridors between Madidi and its area of influence. We identified additional corridors along many streams crossing the San Buenaventura-Ixiamas road. This connectivity is not only important for wildlife, but also from a food security perspective for the indigenous communities that depend on wildlife as an important source of protein. The results will be used to mitigate the impact of road improvements through the identification of priority areas for maintaining connectivity between Madidi and the surrounding landscape.
Decellularized pulp matrix as scaffold for mesenchymal stem cell mediated bone regeneration
Authors: Lee Dong Joon , Miguez Patricia , Kwon Jane , Daniel Renie , Padilla Ricardo , Min Samuel , Zalal Rahim , Ko Ching-Chang , Shin Hae Won
Published: December 2020

Scaffolds that are used for bone repair should provide an adequate environment for biomineralization by mesenchymal stem cells (MSCs). Recently, decellularized pulp matrices (DPM) have been utilized in endodontics for their high regenerative potential. Inspired by the dystrophic calcification on the pulp matrix known as pulp stone, we developed acellular pulp bioscaffolds and examined their potential in facilitating MSCs mineralization for bone defect repair. Pulp was decellularized, then retention of its structural integrity was confirmed by histological, mechanical, and biochemical evaluations. MSCs were seeded and proliferation, osteogenic gene expression, and biomineralization were assessed to verify DPM’s osteogenic effects in vitro. MicroCT, energy-dispersive X-ray (EDX), and histological analyses were used to confirm that DPM seeded with MSCs result in greater mineralization on rat critical-sized defects than that without MSCs. Overall, our study proves DPM’s potential to serve as a scaffolding material for MSC-mediated bone regeneration for future craniofacial bone tissue engineering.
The Psychometric Properties of the Turkish Version of the Riverside Life Satisfaction Scale–Adult Form
Authors: Alıcı Bedriye , Seçim Gürcan
Published: December 2020

We validated the psychometric properties of the Riverside Life Satisfaction Scale for Turkish culture. A standard back-translation procedure was performed. A stratified sample ( N = 493; age range = 18–70 years) was selected from North Cyprus. Results showed that one-factor model for the Riverside Life Satisfaction Scale was a good fit. Composite reliability was .77 and factor loadings were significant (.515–.825). Significant correlations were found between the scale and the Satisfaction With Life Scale, Psychological Well-Being Scale–Short Form, Positive and Negative Affect Schedule, and extraversion, agreeableness, conscientiousness, and neuroticism subscales of the Big Five Inventory. The Riverside Life Satisfaction Scale is an up-to-date, standard, and powerful alternative scale that is statistically strong, easy-to-apply, and its reversed items were free from measurement bias. It is thus valid and reliable to use in Turkish culture, indicating the cross-cultural value of the current study.
Bargaining Power or Specialization? Determinants of Household Decision Making in Chinese Rural Migrant Families
Authors: Wang Zicheng , Lou Yun , Zhou Yi
Published: December 2020

Family migration is a common integration process for rural migrants in contemporary China. However, discussions on intra-household decision making in dual-earner migrant families are limited. This study aims to address this gap. The data set from the Rural Urban Migration in China (RUMiC2008–2010) is employed to explore the determinants of household decision making. In addition, logit regression is performed to estimate the probability of wives acting as head of the household under different specifications, and the Blinder–Oaxaca–Fairlie decomposition is utilized to discuss gender differentials in decision-making responsibilities. Income and migration duration differentials between a wife and husband have important influences on the probability of being responsible for household decision making. The squared terms of wives’ and husbands’ income have inverted effects. The gender gap between household decision makers can be largely attributed to structural factors rather than observable characteristics, though bargaining power acts as the main contributor in explained parts. Bargaining theory can account for the probability of wives becoming the household decision maker, and the claim of the specialization approach is also confirmed. Gender inequality among household decision makers is largely attributed to structural factors, such as cultural/social norms, obstacles, or gender discrimination. The establishment of long-term effective mechanisms to improve employment quality for female migrants, the supply of basic public services, and protection of women’s legal rights in the household should be strengthened in the future to elevate the status of female migrants.
Credit Rating Strategies: A Study of GCC Banks
Authors: Murthy Y. Sree Rama , Al-Muharrami Saeed
Published: December 2020

Identifying financial strategies, which help a bank to survive a crisis, is the main purpose of the article. Low oil prices and the COVID-19 pandemic is the latest crisis being faced by the Gulf Cooperation Council (GCC) banks. This article examines the financial strategies of those banks that managed to retain good credit ratings both before and after the global financial crisis, so as to throw light on the characteristics of banks that managed to remain steady and stable. This article analyzes the Fitch credit ratings of 51 Islamic and conventional banks, operating in the GCC, divided into pre–global financial crisis (2002–2007) and post–global financial crisis (2008–2013) periods. Trend and behavior of average ratios of top-rated banks in both the periods is first attempted before moving to the “Ordered Choice Logit” regression method to further analyze the data. Regression results indicate that size and cost management are very important factors in ratings both before and after the financial crisis. As long as asset quality is under control, liquidity is the focal point in achieving good ratings. Top-rated Islamic banks seem to be following a strategy of allowing capital ratios to trend down during a crisis as long as capital is well above the regulatory requirements. The article is the first of its kind, which examines credit rating strategies of GCC Islamic banks and conventional banks. The findings of the article are useful for banks as they throw light on appropriate strategies to be adopted by banks during crises.
Impact of Microfinance on Economic, Social, Political and Psychological Empowerment: Evidence from Women’s Self-help Groups in Kashmir Valley, India
Authors: Khan Shagufta Tariq , Bhat Mohd Abass , Sangmi Mohi-Ud-Din
Published: December 2020

The present study attempts to examine the impact of microfinance on certain dimensions of women empowerment, namely economic, social, political and psychological. Quasi-experimental design comprising of control group (180) and treatment group (190) has been employed to assess the impact of microfinance on women empowerment. The findings revealed positively significant but moderate level of impact of microfinance on economic, political and psychological dimensions of women empowerment and only smaller overall impact on social empowerment. In addition, case studies further supported microfinance programme has substantially empowered women in terms of economic, political, social and psychological dimensions. More importantly, ambiguity over social empowerment was cleared.
The Queensland Birth Cohort Study for Early Childhood Caries: Results at 7 Years
Authors: Harrison-Barry L. , Elsworthy K. , Pukallus M. , Leishman S.J. , Boocock H. , Walsh L.J. , Seow W.K.
Published: December 2020

Aims:

This study investigated caries predictors in 378 children remaining from a birth cohort of 1,052 at 7 y and compared the efficacy of home visits (HVs) and telephone contacts (TCs) for early childhood caries (ECC) prevention.

Methods:

The HVs or TCs were made at ages 6, 12, 18, 30, and 42 mo with annual dental clinic examinations at ages 2 to 7 y. At every visit, the parents completed validated questionnaires regarding the children’s family, medical, dental, and dietary histories.

Results:

The caries prevalence increased from 2% and 6% at ages 2 and 3 y to 15%, 33%, 42%, and 52% at ages 4 to 7 y. The mean caries experience (decayed, missing, and teeth extracted due to caries) of the total cohort increased from 0.1 ± 0.5 at age 2 y to 0.2 ± 1.1 at 3 y, 0.5 ± 1.6 at 4 y, 1.1 ± 2.4 at 5 y, 1.6 ± 2.6 at 6 y, and 2.0 ± 2.7 at 7 y. The prevalence of mutans streptococci (MS) in the total cohort at years 2 to 7 was 22%, 36%, 42%, 42%, 39%, and 44%, respectively. MS was strongly correlated with caries prevalence for all years (all P < 0.001). Statistical modeling employing the generalized estimating equations identified caries predictors as holding a Health Care Card (low socioeconomic status) ( P = 0.009; odds ratio [OR] = 2.05; confidence interval [CI]: 1.20–3.52), developmental defects of enamel (DDEs) ( P < 0.001; OR = 1.09; CI: 1.05–1.14), and MS counts ≤105/mL ( P = 0.001; OR = 1.63; CI: 1.24–2.14). By contrast, HVs were more protective than TCs for caries ( P = 0.008; OR = 0.42; CI: 0.22–0.80).

Conclusions:

This study provides prospective, clinical evidence that MS, DDEs, and low socioeconomic status are strongly correlated with early childhood caries and that HVs are more efficacious than TCs in ECC prevention.

Knowledge Transfer Statement:

This 7-y birth cohort study provides longitudinal clinical evidence that mutans streptococci, developmental defects of enamel, and low socioeconomic status are key risk indicators of early childhood caries.
Lower-Third SLOE Rankings Impede, But Do Not Prevent, A Match in Emergency Medicine Residency Training
Authors: Hansroth Joseph A , Davis Kristin H , Quedado Kimberly D , Davis Stephen M , Kiefer Autumn S , Shaver Erica B , Kiefer Christopher S , Cottrell Scott , Ferrari Norman D
Published: December 2020

Objective:

Emergency medicine program directors (PD) value the standardized letter of evaluation (SLOE) as the most important aspect of a residency application when making both invitation and ranking decisions. This study aims to determine whether the presence of any lower-third in either SLOE global assessment (GA) question impacted the ability of an applicant to match into EM. We hypothesized that any lower-third ranking would be associated with increased odds of not matching into EM.

Methods:

We conducted a retrospective cohort study evaluating allopathic applicants from medical schools in the United States (US allopathic applicants) to a single EM residency program during the 2018/2019 match cycles. GA SLOE rankings from all applications were tabulated and compared to the applicant’s National Resident Matching Program (NRMP) match outcome. Comparative analyses were conducted between SLOE groupings and odds ratios (OR) were calculated.

Results:

A total of 2,017 SLOEs from 781 US allopathic applicants were analyzed during the study period. Of the total, 277 (35%) applicants in our sample had any lower-third GA ranking, which significantly decreased an applicant’s odds of matching in EM by 79% (OR 0.21, 95% CI, 0.12-0.34). Having more than one lower-third GA ranking did not further statistically decrease the odds of a successful EM match (OR 0.60, 95% CI 0.31-1.17). As a secondary finding of the study, results demonstrate that those applicants having no lower-third GA rankings had a nearly 5 times increased odds of an EM match (OR 4.84, 95% CI, 2.91-8.03).

Conclusion:

Having any lower-third GA ranking significantly reduced an applicant’s chances of matching into an EM program. Faculty advisors should be aware of the increased risk of not matching for any applicant with any lower-third GA ranking and advise students appropriately, while maintaining the integrity of the SLOE and not divulging the confidential information contained within.
Poverty and Food Insecurity Disparities and Their Causes in the Eastern Indian State of Odisha
Authors: Mohapatra Bidhan K.
Published: December 2020

This article discusses the key factors that influence poverty and food insecurity. The study involved 645 households in 4 villages of 2 districts (one developed and one undeveloped) in Odisha, an eastern Indian state. Odisha’s per capita income was taken as the dividing line for the segregation of districts into developed (more than average) and undeveloped (less than average). Poverty and food insecurity composite indices and probit and logit analyses revealed that: (a) in the developed district, education and caste are significant factors in determining the household poverty level, whereas education plays a vital role in the undeveloped district in deciding poverty level; (b) food insecurity is significantly affected by education, caste and assets in the developed district and by education and agriculture as the primary occupation in the undeveloped district; (c) education is derived as the common determinant of poverty as well as food insecurity; and (d) the inference drawn from the results is that, whatever the economy (developed or undeveloped), education was the most significant and common factor in determining both poverty and/or food insecurity at household level of the areas studied. However, it should not be misinterpreted that education is the only indicator that can resolve the complex issues of poverty and food insecurity. Based on area needs, a comprehensive approach with special focus on these significant indicators revealed from this research would be helpful in addressing poverty and food insecurity.
Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure
Authors: Deng Lei , Liu Youzhi , Shi Yechuan , Zhang Wenhao , Yang Chun , Liu Hui
Published: December 2020

Background

RNA binding proteins (RBPs) play a vital role in post-transcriptional processes in all eukaryotes, such as splicing regulation, mRNA transport, and modulation of mRNA translation and decay. The identification of RBP binding sites is a crucial step in understanding the biological mechanism of post-transcriptional gene regulation. However, the determination of RBP binding sites on a large scale is a challenging task due to high cost of biochemical assays. Quite a number of studies have exploited machine learning methods to predict binding sites. Especially, deep learning is increasingly used in the bioinformatics field by virtue of its ability to learn generalized representations from DNA and protein sequences.

Results

In this paper, we implemented a novel deep neural network model, DeepRKE, which combines primary RNA sequence and secondary structure information to effectively predict RBP binding sites. Specifically, we used word embedding algorithm to extract features of RNA sequences and secondary structures, i.e., distributed representation of k-mers sequence rather than traditional one-hot encoding. The distributed representations are taken as input of convolutional neural networks (CNN) and bidirectional long-term short-term memory networks (BiLSTM) to identify RBP binding sites. Our results show that deepRKE outperforms existing counterpart methods on two large-scale benchmark datasets.

Conclusions

Our extensive experimental results show that DeepRKE is an efficacious tool for predicting RBP binding sites. The distributed representations of RNA sequences and secondary structures can effectively detect the latent relationship and similarity between k-mers, and thus improve the predictive performance. The source code of DeepRKE is available athttps://github.com/youzhiliu/DeepRKE/.
Novel risk scoring system for predicting acute respiratory distress syndrome among hospitalized patients with coronavirus disease 2019 in Wuhan, China
Authors: Liang Mengyuan , He Miao , Tang Jian , He Xinliang , Liu Zhijun , Feng Siwei , Chen Ping , Li Hui , Xue Yu’e , Bai Tao , Ma Yanling , Zhang Jianchu
Published: December 2020

Background

The mortality rate from acute respiratory distress syndrome (ARDS) is high among hospitalized patients with coronavirus disease 2019 (COVID-19). Hence, risk evaluation tools are required to immediately identify high-risk patients upon admission for early intervention.

Methods

A cohort of 220 consecutive patients with COVID-19 were included in this study. To analyze the risk factors of ARDS, data obtained from approximately 70% of the participants were randomly selected and used as training dataset to establish a logistic regression model. Meanwhile, data obtained from the remaining 30% of the participants were used as test dataset to validate the effect of the model.

Results

Lactate dehydrogenase, blood urea nitrogen, D-dimer, procalcitonin, and ferritin levels were included in the risk score system and were assigned a score of 25, 15, 34, 20, and 24, respectively. The cutoff value for the total score was > 35, with a sensitivity of 100.00% and specificity of 81.20%. The area under the receiver operating characteristic curve and the Hosmer–Lemeshow test were 0.967 (95% confidence interval [CI]: 0.925–0.989) and 0.437(P Value = 0.437). The model had excellent discrimination and calibration during internal validation.

Conclusions

The novel risk score may be a valuable risk evaluation tool for screening patients with COVID-19 who are at high risk of ARDS.
A non-synonymous variant rs12614 of complement factor B associated with risk of chronic hepatitis B in a Korean population
Authors: Seo Jung Yeon , Shin Joong-Gon , Youn Byeong Ju , Namgoong Suhg , Cheong Hyun Sub , Kim Lyoung Hyo , Kim Ji On , Shin Hyoung Doo , Kim Yoon Jun
Published: December 2020

Background

Hepatitis B is known to cause several forms of liver diseases including chronic hepatitis B (CHB), and hepatocellular carcinoma. Previous genome-wide association study of CHB risk has demonstrated that rs12614 of complement factor B (CFB) was significantly associated with CHB risk. In this study, fine-mapping study of previously reported GWAS single nucleotide polymorphism (SNP; CFB rs12614) was performed to validate genetic effect of rs12614 on CHB susceptibility and identify possible additional causal variants around rs12614 in a Korean population. This association study was conducted in order to identify genetic effects of CFB single nucleotide polymorphisms (SNPs) and to identify additional independent CHB susceptible causal markers within a Korean population.

Methods

A total of 10 CFB genetic polymorphisms were selected and genotyped in 1716 study subjects comprised of 955 CHB patients and 761 population controls.

Results

A non-synonymous variant, rs12614 (Arg32Trp) in exon2 of CFB, had significant associations with risk of CHB (odds ratio = 0.43, P = 5.91 × 10− 10). Additional linkage disequilibrium and conditional analysis confirmed that rs12614 had independent genetic effect on CHB susceptibility with previously identified CHB markers. The genetic risk scores (GRSs) were calculated and the CHB patients had higher GRSs than the population controls. Moreover, OR was found to increase significantly with cumulative GRS.

Conclusions

rs12614 showed significant genetic effect on CHB risk within the Korean population. As such rs12614 may be used as a possible causal genetic variant for CHB susceptibility.
Brimonidine-associated uveitis – a descriptive case series
Authors: Hopf Susanne , Mercieca Karl , Pfeiffer Norbert , Prokosch-Willing Verena
Published: December 2020

Background

Anterior uveitis secondary to topical brimonidine administration is rare and not well-defined. In glaucoma patients using brimonidine, one must consider this phenomenon to avoid mis-diagnosis and over-treatment with topical steroids which in turn may increase intraocular pressure (IOP). This is the largest case series including the longest patient follow-up in the current literature.

Methods

Sixteen patients (26 eyes) with consultant diagnosed brimonidine-associated anterior uveitis in a tertiary referral glaucoma clinic presenting between 2015 and 2019 were included in this retrospective case series. Clinical records were taken for descriptive analysis. Main outcome measures were the key clinical features, and disease course (therapy, IOP control, patient outcome).

Results

Key features were conjunctival ciliary injection and mutton fat keratic precipitation in all eyes. The findings were bilateral in 10 patients. Time between initiation of brimonidine treatment and presentation was 1 week to 49 months. Glaucoma sub-types were mostly pseudo-exfoliative and primary open angle glaucoma. Brimonidine treatment was stopped immediately. Additionally, topical corticosteroids were prescribed in 18 eyes and tapered down during the following 4 weeks. Thirteen eyes did not need surgical or laser treatment (median follow-up time 15 months). No patient showed recurrence of inflammation after cessation of brimonidine.

Conclusions

This type of anterior uveitis is an uncommon but important manifestation which should always be considered in glaucoma patients on brimonidine treatment. Although treatable at its root cause, problems may persist, especially with respect to IOP control. The latter may necessitate glaucoma surgery after the resolved episode of the uveitis.
Changes in evidence for studies assessing interventions for COVID-19 reported in preprints: meta-research study
Authors:   the COVID-19 NMA Consortium, Oikonomidi Theodora , Boutron Isabelle , Pierre Olivier , Cabanac Guillaume , Ravaud Philippe
Published: December 2020

Background

The increasing use of preprints to disseminate evidence on the effect of interventions for the coronavirus disease 2019 (COVID-19) can lead to multiple evidence sources for a single study, which may differ in the reported evidence. We aim to describe the proportion of evidence on the effect of interventions for COVID-19 from preprints and journal articles and map changes in evidence between and within different sources reporting on the same study.

Methods

Meta-research study. We screened the Cochrane living systematic review and network meta-analysis (COVID-NMA) database to identify all preprints and journal articles on all studies assessing interventions for COVID-19 published up to 15 August 2020. We compared all evidence sources (i.e., preprint and associated journal article) and the first and latest versions of preprints for each study to identify changes in two evidence components: study results (e.g., numeric change in hazard ratio, odds ratio, event rate, or change in p value > or < 0.05 in any outcome) and abstract conclusions (classified as positive, negative or neutral regarding the intervention effect, and as reporting uncertainty in the findings or not). Changes in study results were further classified as important changes if they (1) represented a change in any effect estimate by ≥ 10% and/or (2) led to a change in the p value crossing the threshold of 0.05.

Results

We identified 556 studies. In total, 338 (61%) had been reported in a preprint: 66 (20%) of these had an associated journal article (median time to publication 76 days [interquartile range (IQR) 55–106]) and 91 (27%) had > 1 preprint version. A total of 139 studies (25% of the overall sample) were reported in multiple evidence sources or versions of the same source: for 63 (45%), there was a change in at least one evidence component between or within sources (42 [30%] had a change in study results, and in 29 [21%] the change was classified as important; 33 [24%] had a change in the abstract conclusion). For studies with both a preprint and an article, a median of 29% (IQR 14–50) of total citations were attributed to the preprint instead of the article.

Conclusions

Results on the effect of interventions for COVID-19 are often reported in multiple evidence sources or source versions for a single study. Evidence is not stable between and within evidence sources. Real-time linkage of all sources per study could help to keep systematic reviews up-to-date.
Reporting and valuing one’s own health: a think aloud study using EQ-5D-5L, EQ VAS and a time trade-off question among patients with a chronic condition
Authors: Ernstsson Olivia , Burström Kristina , Heintz Emelie , Mølsted Alvesson Helle
Published: December 2020

Background

The EQ-5D-5L, the EQ VAS, and the time trade-off (TTO) are commonly used to report and value health. Still, there is a need to better understand how these questionnaires and methods are perceived by the respondents, as well as the thoughts and motives behind their responses. The aim of this study was to increase knowledge of how individuals think and reason when reporting and valuing their own current health, using EQ-5D-5L, EQ VAS, and an open-ended TTO question.

Methods

Twenty patients with type 1 diabetes participated in qualitative individual think aloud interviews in Stockholm, Sweden. Participants were asked to describe their thoughts when responding to three assessments. The interviews were transcribed verbatim and analyzed using thematic analysis.

Results

The analysis showed that participants conducted the assessments by contextualizing and interpreting instructions, relating the questions to their own health, using different recall periods and time perspectives, and using personal, interpersonal, or normative comparators. It was challenging to reduce the experience of everyday life into a response option, and the thoughts behind the responses differed between the assessments. Before deciding on what to include, participants thought of the purpose and context of the assessments. Current health or past experiences of health were applied in the EQ-5D descriptive system and in EQ VAS, while participants focused on the future in the TTO. Thoughts about the impact on others, personal goals, and expectations on future health were more clearly integrated in the TTO assessment. All participants considered the trade-off between life years and health. However, despite the use of different comparators, the concept of ‘full health’ was found difficult to imagine or relate to.

Conclusions

This study provides insights as to how responses to the EQ-5D-5L, EQ VAS, and TTO assessments are complementary and where these assessments differ in adults with a chronic condition. The findings may contribute to a better understanding when interpreting the quantitative results and contribute to the literature pertaining to possible explanations for differences in health state values depending on the valuation method.
Predicting survival in anaplastic astrocytoma patients in a single-center cohort of 108 patients
Authors: Wahner Helena C. W. , Träger Malte , Bender Katja , Schweizer Leonille , Onken Julia , Senger Carolin , Ehret Felix , Budach Volker , Kaul David
Published: December 2020

Background

Current guidelines for the treatment of anaplastic astrocytoma (AA) recommend maximal safe resection followed by radiotherapy and chemotherapy. Despite this multimodal treatment approach, patients have a limited life expectancy. In the present study, we identified variables associated with overall survival (OS) and constructed a model score to predict the OS of patients with AA at the time of their primary diagnosis.

Methods

We retrospectively evaluated 108 patients with newly diagnosed AA. The patient and tumor characteristics were analyzed for their impact on OS. Variables significantly associated with OS on multivariable analysis were included in our score. The final algorithm was based on the 36-month survival rates corresponding to each characteristic.

Results

On univariate analysis, age, Karnofsky performance status, isocitrate dehydrogenase status, and extent of resection were significantly associated with OS. On multivariable analysis all four variables remained significant and were consequently incorporated in the score. The total score ranges from 20 to 33 points. We designated three prognostic groups: A (20–25), B (26–29), and C (30–33 points) with 36-month OS rates of 23%, 71%, and 100%, respectively. The OS rate at 5 years was 8% in group A, 61% in group B and 88% in group C.

Conclusions

Our model score predicts the OS of patients newly diagnosed with AA and distinguishes patients with a poor survival prognosis from those with a greater life expectancy. Independent and prospective validation is needed. The upcoming changes of the WHO classification of brain tumors as well as the practice changing results from the CATNON trial will most likely require adaption of the score.
Successfully treatment of application awake extracorporeal membrane oxygenation in critical COVID-19 patient: a case report
Authors: Tang Junyi , Li Wencan , Jiang Fanli , Wang Tao
Published: December 2020

Background

A newly infectious diseases named coronavirus disease 2019 (COVID-19) emerged in China and now has spread in many countries, and constituted a public health emergency of international concern. Extracorporeal membrane oxygenation (ECMO) is used as salvage therapies in critical COVID-19 patients with respiratory/cardiac failure.

Case presentation

A 49-year-old female patient was diagnosed with COVID-19 and progressed to critical cases, she was successfully treated with the application of awake extracorporeal membrane oxygenation. This case is the first reported successfully treatment of application awake ECMO in critical COVID-19 patient in China.

Conclusions

Here we present the first reported successfully treatment of application awake ECMO in critical COVID-19 patient, however, whether awake ECMO can be widely used in the treatment of critical COVID-19 patients need more practice.
Confined placental mosaicism of Duchenne muscular dystrophy: a case report
Authors: Winerdal Max , Westenius Eini , Granfors Michaela , Pettersson Maria , Iwarsson Erik
Published: December 2020

Background

Small copy number variations confined to the placenta are extremely rare findings in chorionic villus sampling, nonetheless of great clinical importance. To the best of our knowledge, this is the first reported case of confined placental mosaicism for an intragenic Duchenne muscular dystrophy (DMD) gene deletion.

Case presentation

We describe a pregnant woman where confined placental mosaicism for an intragenic DMD deletion was detected. She was referred for a chorionic villus sampling due to an increased risk of trisomy 21 derived from combined first trimester screening. Rapid aneuploidy detection showed a male fetus with normal results for chromosomes 13, 18 and 21. A chromosomal microarray demonstrated a deletion of exons 61–62 in the DMD gene in approximately 50% of the cells. A follow-up analysis on amniotic cells showed a normal result for the DMD gene. Hence, confined placental mosaicism was confirmed.

Conclusions

We propose tissue specific fragile sites as a possible theoretical mechanism for the formation of submicroscopic copy number variations and highlight that the finding of DMD deletion mosaicism in a chorionic villus sample might be isolated to the placenta. Therefore, confirmation by amniocentesis is of crucial clinical importance to avoid misdiagnosis of the fetus.