bluuebunny/crossref_metadata_2025_split huggingface dataset:
PIC-Me: paralogs and isoforms classifier based on machine-learning approaches
Authors: Oh Jooseong , Lee Sung-Gwon , Park Chungoo 
Published: October 2021

Abstract
Background
Paralogs formed through gene duplication and isoforms formed through alternative splicing have been important processes for increasing protein diversity and maintaining cellular homeostasis. Despite their recognized importance and the advent of large-scale genomic and transcriptomic analyses, paradoxically, accurate annotations of all gene loci to allow the identification of paralogs and isoforms remain surprisingly incomplete. In particular, the global analysis of the transcriptome of a non-model organism for which there is no reference genome is especially challenging.

Results
To reliably discriminate between the paralogs and isoforms in RNA-seq data, we redefined the pre-existing sequence features (sequence similarity, inverse count of consecutive identical or non-identical blocks, and match-mismatch fraction) previously derived from full-length cDNAs and EST sequences and described newly discovered genomic and transcriptomic features (twilight zone of protein sequence alignment and expression level difference). In addition, the effectiveness and relevance of the proposed features were verified with two widely used support vector machine (SVM) and random forest (RF) models. From nine RNA-seq datasets, all AUC (area under the curve) scores of ROC (receiver operating characteristic) curves were over 0.9 in the RF model and significantly higher than those in the SVM model.

Conclusions
In this study, using an RF model with five proposed RNA-seq features, we implemented our method called Paralogs and Isoforms Classifier based on Machine-learning approaches (PIC-Me) and showed that it outperformed an existing method. Finally, we envision that our tool will be a valuable computational resource for the genomics community to help with gene annotation and will aid in comparative transcriptomics and evolutionary genomics studies, especially those on non-model organisms.
A consensus-based ensemble approach to improve transcriptome assembly
Authors: Voshall Adam , Behera Sairam , Li Xiangjun , Yu Xiao-Hong , Kapil Kushagra , Deogun Jitender S. , Shanklin John , Cahoon Edgar B. , Moriyama Etsuko N. 
Published: October 2021

AbstractBackgroundSystems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform transcriptome assembly from RNAseq data. However, assembling high quality transcriptomes is still not a trivial problem. This is especially the case for non-model organisms where adequate reference genomes are often not available. Different methods produce different transcriptome models and there is no easy way to determine which are more accurate. Furthermore, having alternative-splicing events exacerbates such difficult assembly problems. While benchmarking transcriptome assemblies is critical, this is also not trivial due to the general lack of true reference transcriptomes.ResultsIn this study, we first provide a pipeline to generate a set of the simulated benchmark transcriptome and corresponding RNAseq data. Using the simulated benchmarking datasets, we compared the performance of various transcriptome assembly approaches including both de novo and genome-guided methods. The results showed that the assembly performance deteriorates significantly when alternative transcripts (isoforms) exist or for genome-guided methods when the reference is not available from the same genome. To improve the transcriptome assembly performance, leveraging the overlapping predictions between different assemblies, we present a new consensus-based ensemble transcriptome assembly approach, ConSemble.ConclusionsWithout using a reference genome, ConSemble using four de novo assemblers achieved an accuracy up to twice as high as any de novo assemblers we compared. When a reference genome is available, ConSemble using four genome-guided assemblies removed many incorrectly assembled contigs with minimal impact on correctly assembled contigs, achieving higher precision and accuracy than individual genome-guided methods. Furthermore, ConSemble using de novo assemblers matched or exceeded the best performing genome-guided assemblers even when the transcriptomes included isoforms. We thus demonstrated that the ConSemble consensus strategy both for de novo and genome-guided assemblers can improve transcriptome assembly. The RNAseq simulation pipeline, the benchmark transcriptome datasets, and the script to perform the ConSemble assembly are all freely available from:http://bioinfolab.unl.edu/emlab/consemble/.
Hepatocellular carcinoma in nonalcoholic fatty liver disease with or without cirrhosis: a population-based study
Authors: Pinyopornpanish Kanokwan , Khoudari George , Saleh Mohannad Abou , Angkurawaranon Chaisiri , Pinyopornpanish Kanokporn , Mansoor Emad , Dasarathy Srinivasan , McCullough Arthur 
Published: October 2021

Abstract
Background
There are limited data regarding the factors associated with hepatocellular carcinoma (HCC) in non-alcoholic fatty liver disease (NAFLD) patients without cirrhosis. We sought to determine the prevalence and factors associated with HCC in NAFLD patients with or without cirrhosis.

Methods
Adults with NAFLD (June 2015 to May 2020) were identified using the electronic health record database (Explorys Inc, Cleveland, OH) from 26 major integrated US healthcare systems. The prevalence of HCC was calculated. Multivariable analyses adjusting for covariates were performed to evaluate the associated risk factors and the presence of HCC.

Results
A total of 392,800 NAFLD patients were identified. Among 1110 patients with HCC, 170 (15.3%) had no cirrhosis. The prevalence of HCC in non-cirrhotic and cirrhotic NAFLD patients was 4.6/10,000 persons (95% CI 3.9–5.3), and 374.4/10,000 persons (95% CI 350.9–398.8), respectively. Age > 65 years (adjusted OR; 3.37, 95% CI 2.47–4.59), ever had elevated alanine aminotransferase (2.69; 2.14–3.37), male gender (2.57; 1.88–3.49), smoker (1.75; 1.23–2.49), and diabetes (1.56; 1.15–2.11) were associated with HCC in non-cirrhotic NAFLD (all P < 0.05). The prevalence of HCC in the non-cirrhotic with all five risk factors was 45.5/10,000 persons (95% CI 17.4–73.6). The factors associated with HCC in cirrhotic NAFLD included clinical decompensation, age > 65 years, male gender, Hispanic race, elevated alanine aminotransferase, diabetes and smoker (all P < 0.05).

Conclusions
These data identified the major risk factors for the development of HCC in NAFLD patients. In the non-cirrhotics, older male patients with smoking history, diabetes and an elevated alanine aminotransferase had highest risk and may need increased judicious monitoring.
Patterns of physical activity and their relationship with depression among community-dwelling older adults in Shanghai, China: a latent class approach
Authors: Liang Yan , Li Xinghui , Yang Tingting , Li Mengying , Ruan Ye , Yang Yinghua , Huang Yanyan , Jiang Yihua , Wang Ying 
Published: October 2021

AbstractBackgroundFew studies have explored patterns of physical activity (PA) and examined their relationship with depression among community-dwelling older adults. We aimed to identify the patterns of PA through a person-centered analytical approach and examine the association between quantity and patterns of PA, and depression among community-dwelling older adults.MethodsWe conducted a cross-sectional survey study in the Minhang district, Shanghai, China, in August 2019, and used a self-administered questionnaire to collect data through home visits. The total sample included 2525 older adults. This study used the Physical Activity Scale for the Elderly (PASE) to assess the quantity of PA in older adults. Depression was evaluated with the Geriatric Depression Scale (GDS). Latent class analysis (LCA) was used to identify subpopulations by shared item response patterns. Logistic regressions were performed to estimate the relationship between PASE score, patterns of PA, and depression. An exploratory analysis of joint levels and patterns of PA effects on depression was based on sample subgroups with combinations of levels and patterns of PA. Logistic regression was used to calculate the odds ratio for combined subgroups.ResultsFour latent classes were identified: “domestic types,” “athletic types,” “gardening/caring types,” and “walkers.” PASE scores and patterns of PA both were associated with depression. Older adults who were the most active (PASE quartile: 75–100%) and the athletic types had the strongest significant association with depression (OR = 0.19, 95% CI: 0.06–0.65), followed by those who were the most active (PASE quartile: 75–100%) and the walkers (OR = 0.28, 95% CI: 0.14–0.57) when compared with older adults with the least activity (PASE quartile: 0–25%) and domestic types.ConclusionThis study suggests both the quantity and patterns of physical activity are associated with depressive symptoms among community-dwelling older adults. Population-level intervention should encourage community-dwelling older adults to increase their quantity of PA to reduce the risk of depression. Athletics and walkers are recommended. To develop individual-level tailored interventions, more attention should be paid to older adults who are highly engaged in gardening/caring for others.
Clinical safety and efficacy of a preloaded monofocal hydrophobic acrylic intraocular lens in a real-world population
Authors: Latham Samuel Giles , Carr Francis , Ali Hala , Gangwani Vinod 
Published: October 2021

Abstract
Background
This study was designed to evaluate visual, refractive and safety outcomes in eyes after they underwent phacoemulsification and implantation of a preloaded monofocal hydrophobic acrylic intraocular lens.

Methods
This was a single center observational study conducted at Ashford and St Peter’s Hospitals NHS Foundation Trust, United Kingdom. Patients were included if they had cataract extraction with in-the-bag implantation of the EyeCee® One preloaded intraocular lens from August to October 2019. Pre-operative, surgery-related and 2 weeks and 3 months post-operative data was collected. Surgeons at this trust were then asked to complete a feedback form to evaluate their experience of implanting the EyeCee® One.

Results
One hundred fifty-two eyes were included in the study. Ninety-four (62%) of these eyes had cataract but no concomitant ocular pathology that could potentially affect visual acuity. Three months post-operatively, 98.7% of all eyes had monocular CDVA ≤0.3 logMAR. 100% of the eyes without concomitant ocular pathology achieved this target. The mean CDVA of all eyes in this study improved from 0.43 ± 0.43 logMAR pre-operatively, to 0.05 ± 0.11 logMAR post-operatively (p < 0.05). The mean sphere and spherical equivalent values showed significant improvements (p < 0.05) and (p < 0.05). There were no intraoperative complications and 1.3% of patients reported complications 2 weeks post-operatively. All of the participating surgeons said they would use the EyeCee® One again with 64% providing an overall rating of ‘excellent’ for their experience of implanting this intraocular lens.

Conclusions
This study indicates excellent post-operative visual acuity and refractive outcomes in eyes after EyeCee® One implantation. This is accompanied with very little risk of intraoperative and post-operative complications.
Spatial analysis of colorectal cancer outcomes and socioeconomic factors in Virginia
Authors: Thatcher Esther J. , Camacho Fabian , Anderson Roger T. , Li Li , Cohn Wendy F. , DeGuzman Pamela B. , Porter Kathleen J. , Zoellner Jamie M. 
Published: October 2021

Abstract
Background
Colorectal cancer (CRC) disparities vary by country and population group, but often have spatial features. This study of the United States state of Virginia assessed CRC outcomes, and identified demographic, socioeconomic and healthcare access contributors to CRC disparities.

Methods
County- and city-level cross-sectional data for 2011–2015 CRC incidence, mortality, and mortality-incidence ratio (MIR) were analyzed for geographically determined clusters (hotspots and cold spots) and their correlates. Spatial regression examined predictors including proportion of African American (AA) residents, rural-urban status, socioeconomic (SES) index, CRC screening rate, and densities of primary care providers (PCP) and gastroenterologists. Stationarity, which assesses spatial equality, was examined with geographically weighted regression.

Results
For incidence, one CRC hotspot and two cold spots were identified, including one large hotspot for MIR in southwest Virginia. In the spatial distribution of mortality, no clusters were found. Rurality and AA population were most associated with incidence. SES index, rurality, and PCP density were associated with spatial distribution of mortality. SES index and rurality were associated with MIR. Local coefficients indicated stronger associations of predictor variables in the southwestern region.

Conclusions
Rurality, low SES, and racial distribution were important predictors of CRC incidence, mortality, and MIR. Regions with concentrations of one or more factors of disparities face additional hurdles to improving CRC outcomes. A large cluster of high MIR in southwest Virginia region requires further investigation to improve early cancer detection and support survivorship. Spatial analysis can identify high-disparity populations and be used to inform targeted cancer control programming.
Youth susceptibility to tobacco use: is it general or specific?
Authors: Cheng Hui G. , Lizhnyak Pavel N. , Knight Natasha A. , Vansickel Andrea R. , Largo Edward G. 
Published: October 2021

Abstract
Background
Susceptibility to tobacco use predicts tobacco use onset among youth. The current study aimed to estimate the extent of overlap in susceptibilities across various tobacco products, investigate sociopsychological correlates with susceptibilities, and examine whether the relationship linking susceptibility with the onset of use is product-specific or is accounted for by a general susceptibility-onset relationship.

Methods
The study population consisted of US youth 12–17 years old who had never used a tobacco product, sampled in the longitudinal Population Assessment of Tobacco and Health study wave 4 (Dec. 2016-Jan. 2018; n = 10,977). Tobacco product-specific susceptibility at wave 4 was assessed via questions about curiosity, likelihood to try, and likelihood of use if a best friend offered. The onset of use of various tobacco products was defined as first use occurring between the wave 4 and wave 4.5 (Dec. 2017-Dec. 2018) assessments (n = 8841). Generalized linear regression and structural equation models were used for data analysis.

Results
There is a large degree of overlap in susceptibilities across tobacco products (65% of tobacco-susceptible youth were susceptible to more than one tobacco product). Tobacco-susceptible youths were more likely to have recently used cannabis, consumed alcohol, or to have been associated with tobacco-using peers. Structural equation models suggest that the susceptibility-onset relationship largely operates in a non-product-specific manner after accounting for the general susceptibility-to-tobacco-onset relationship.

Conclusions
Youth susceptibility to tobacco use overlaps widely across different tobacco products and other risky behaviors. Findings from this study support a holistic approach towards the prevention of risk behaviors, supplemented by product-specific strategies when needed.
Ramadan daily intermittent fasting reduces objectively assessed habitual physical activity among adults
Authors: Farooq Abdualziz , Chamari Karim , Sayegh Suzan , El Akoum Maha , Al-Mohannadi Abdulla Saeed 
Published: October 2021

Abstract
Background
Muslims around the world practice intermittent fasting during the month of Ramadan each year. We hypothesized that daily physical activity could be reduced among Muslims due to the inability to refuel and rehydrate in the fasting state.

Methods
A cohort study design among adults registered with national physical activity community program. Data from a pedometer-based community program was used to extract 3 months of daily step counts before, during, and after Ramadan for the past years (2013–2019). A survey was conducted among participants to determine fasting practice and other health and environmental factors.

Results
A total of 209 participants completed the survey and provided valid data on physical activity. During Ramadan, the average steps per day decreased significantly (− 385 ± SE 158) among participants who fasted (n = 151) p = 0.046 and increased (+ 731 ± SE 247) for the non- fasting participants (n = 58) p = 0.010. Fasting participants preferred before sunset (33.8%) or evening (39.7%) for physical activity. Whereas, non-fasting participants preferred early morning (34.5%).

Conclusion
Fasting during Ramadan impacts the daily physical activity behavior among Muslims. Interventions should focus on creating awareness of the importance of maintenance of adequate physical activity for adults fasting during Ramadan.
A RE-AIM evaluation in early adopters to iteratively improve the online BeUpstanding™ program supporting workers to sit less and move more
Authors: Healy Genevieve N. , Winkler Elisabeth A. H. , Goode Ana D. 
Published: October 2021

Abstract
Background
The web-based BeUpstanding program supports desk workers to sit less and move more. Successfully translated from a research-delivered intervention, BeUpstanding has gone through iterative development and evaluation phases in preparation for wide-scale implementation. In the third planned “early-adopters” phase (01/09/2017–11/06/2019), the program was made freely-available online. An integrated delivery and evaluation platform was also developed to enable workplace champions to run and evaluate the intervention within their work team independent of researcher support. Using the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) framework, this study reports on the extent to which the program and processes were “fit-for-purpose” for a national implementation trial across the indicators of uptake (reach and adoption), implementation and engagement, and effectiveness for behaviour change.

Methods
Data were collected via the online surveys embedded in the program and through program access analytics. Descriptive data (with linearized variance for the clustered staff-level data) and results from mixed models (repeated data and clustering for pre-post changes) are reported.

Results
Despite purposeful limited promotion, uptake was good, with 182 Australian users initially registering (208 total) and 135 (from 113 organisations) then completing the sign-up process. Recruitment reached users across Australia and in 16 of 19 Australian industries. Implementation was inconsistent and limited, with signed-up users completing 0 to 14 of the program’s 14 steps and only 7 (5.2%) completing all seven core steps. Many champions (n = 69, 51.1%) had low engagement (1 day toolkit usage) and few (n = 30, 22%) were highly engaged (> 1 day toolkit usage and surveyed staff). Although only 18 users (7 organisations) performed the pre- and post-program staff evaluations (337 and 167 staff, respectively), pre-post changes showed the program effectively reduced workplace sitting by − 9.0% (95% CI -12.0, − 5.9%).

Discussion
The program had uptake across industries and across Australia, but implementation and engagement varied widely. Few workplaces completed the evaluation components. In those that did, the program was effective for the primary outcome (workplace sitting). Conducting a planned early adopters phase and a comprehensive evaluation according to RE-AIM helped highlight necessary program improvements to make it more suitable for wide-scale implementation and evaluation.

Trial registration
Australian and New Zealand Clinic Trials Registry ACTRN12617000682347. Date registered: 12/05/2017.
Comparison of thyroid function in different emotional states of drug-naïve patients with bipolar disorder
Authors: Zhao Shengnan , Zhang Xu , Zhou Yaling , Xu Hao , Li Yuwei , Chen Yuexin , Zhang Bo , Sun Xueli 
Published: October 2021

Abstract
Background
Previous studies have shown that bipolar disorder is closely related to thyroid dysfunction. Psychiatric drugs have a large or small effect on thyroid function, and thyroid hormone levels can also affect the effect of drug treatment. Therefore, the purpose of this study is assessment the thyroid function of drug-naive bipolar disorder across different mood states, with the expectation of providing support for treatment options.

Methods
The present study is a cross-sectional study. Patients diagnosed with bipolar disorder according to the International Classification of Diseases diagnostic Criteria, Edition 10 (ICD 10) and who had never received medication were included in the study. The Montgomery Depression Scale (MADRS) was used to assess depressive symptoms and the Young Mania Rating Scale (YMRS) for manic symptoms. Thyroid function indicators include thyroid-stimulating hormone (TSH), free triiodothyronine (FT3), total triiodothyronine (TT3), free thyroxine (FT4), and total thyroxine (TT4). Levels of TSH, TT4, FT4, TT3, and FT3 were measured within 48 h of hospitalization, between 06:00 and 08:00.

Results
The data analysis finally covered the data of 291 subjects (136 in a bipolar manic group, 128 in a bipolar depressive group, and 27 in a bipolar mixed group), including 140 males and 151 females, with an average age of 27.38 ± 8.01. There was no significant difference in age, sex, marital status, work status, family history, and course of illness among the manic group, depressive group, and mixed group. The level of FT3, the rate of thyroid hormone increased secretion, and the total abnormality rate of thyroid hormone secretion in the manic group were significantly higher than those in the depressive group.

Conclusion
These findings indicate that thyroid functions were significantly different between depressive and manic episodes in BD patients. In clinical practice, it is necessary to take into account the differences in thyroid hormone levels in patients with BD across different emotional states in choosing drug.