bluuebunny/crossref_metadata_2025_split huggingface dataset:
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms
Authors: Scalzitti Nicolas , Jeannin-Girardon Anne , Collet Pierre , Poch Olivier , Thompson Julie Dawn 
Published: March 2020

Abstract
Background: The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed to evaluate the accuracy of gene prediction methods in the face of incomplete genome assemblies, low genome coverage and quality, complex gene structures, or a lack of suitable sequences for evidence-based annotations. Results: We describe the construction of a new benchmark, called G3PO (benchmark for Gene and Protein Prediction PrOgrams), designed to represent many of the typical challenges faced by current genome annotation projects. The benchmark is based on a carefully validated and curated set of real eukaryotic genes from 147 phylogenetically disperse organisms, and a number of test sets are defined to evaluate the effects of different features, including genome sequence quality, gene structure complexity, protein length, etc. We used the benchmark to perform an independent comparative analysis of the most widely used ab initio gene prediction programs and identified the main strengths and weaknesses of the programs. More importantly, we highlight a number of features that could be exploited in order to improve the accuracy of current prediction tools. Conclusions: The experiments showed that ab initio gene structure prediction is a very challenging task, which should be further investigated. We believe that the baseline results associated with the complex gene test sets in G3PO provide useful guidelines for future studies.
The Natural History of Infantile Neuroaxonal Dystrophy
Authors: Altuame Fadie D , Foskett Gretchen , Atwal Paldeep , Endemann Sarah , Midei Mark , Milner Peter , Salih Mustafa A , Hamad Muddathir , Al-Muhaizea Mohammad , Hashem Mais , Alkuraya Fowzan S 
Published: March 2020

Abstract
Background Infantile neuroaxonal dystrophy (INAD) is a rapidly progressive neurodegenerative disorder of early onset causing premature death. It results from biallelic pathogenic variants in PLA2G6 , which encodes a calcium‐independent phospholipase A2. Objective We aim to outline the natural history of INAD and provide a comprehensive description of its clinical, radiological, laboratory, and molecular findings. Materials and Methods We comprehensively analyzed the charts of 28 patients: 16 patients from Riyadh, Saudi Arabia, 8 patients from North and South America and 4 patients from Europe with a molecularly confirmed diagnosis of PLA2G6 ‐associated neurodegeneration (PLAN) and a clinical history consistent with INAD. Results In our cohort, speech impairment and loss of gross motor milestones were the earliest signs of the disease. As the disease progressed, loss of fine motor milestones and bulbar dysfunction were observed. Temporo-frontal function was among the last of the milestones to be lost. Appendicular spastic hypertonia, axial hypotonia, and hyperreflexia were common neurological findings. Other common clinical findings include nystagmus (60.7%), seizures (42.9%), gastrointestinal disease (42.9%), skeletal deformities (35.7%), and strabismus (28.6%). Cerebellar atrophy and elevations in serum AST and LDH levels were consistent features of INAD. There was a statistically significant difference when comparing patients with non-sense/truncating variants compared with missense/in-frame deletions in the time of initial concern (p = 0.04), initial loss of language (p = 0.001), initial loss of fine motor skills (p = 0.009), and initial loss of bulbar skills (p = 0.007). Conclusion INAD is an ultra-rare neurodegenerative disorder that presents in early childhood, with a relentlessly progressive clinical course. Knowledge of the natural history of INAD may serve as a resource for healthcare providers to develop a targeted care plan and may facilitate the design of clinical trials to treat this disease.
PGRMC1 effects on metabolism, genomic mutation and CpG methylation imply crucial roles in animal biology and disease
Authors: Thejer Bashar M. , Adhikary Partho P. , Teakel Sarah L. , Fang Johnny , Weston Paul A. , Gurusinghe Saliya , Anwer Ayad G. , Gosnell Martin , Jazayeri Jalal A. , Ludescher Marina , Gray Lesley-Ann , Pawlak Michael , Wallace Robyn H. , Pant Sameer D. , Wong Marie , Fischer Tamas , J. Elizabeth , Fehm Tanja N. , Neubauer Hans , Goldys Ewa M. , Quinn Jane C. , Weston Leslie A. , CAHILL Michael 
Published: March 2020

Abstract
Background: Progesterone receptor membrane component 1 (PGRMC1) is often elevated in cancers, and exists in alternative states of phosphorylation. A motif centered on PGRMC1 Y180 was evolutionarily acquired concurrently with the embryological gastrulation organizer that orchestrates vertebrate tissue differentiation.Results: Here, we show that mutagenic manipulation of PGRMC1 phosphorylation alters cell metabolism, genomic stability, and CpG methylation. Each of several mutants elicited distinct patterns of genomic CpG methylation. Mutation of S57A/Y180/S181A led to increased net hypermethylation, reminiscent of embryonic stem cells. Pathways enrichment analysis suggested modulation of processes related to animal cell differentiation status and tissue identity, as well as cell cycle control and ATM/ATR DNA damage repair regulation. We detected different genomic mutation rates in culture.Conclusions: A companion manuscript shows that these cell states dramatically affect protein abundances, cell and mitochondrial morphology, and glycolytic metabolism. We propose that PGRMC1 phosphorylation status modulates cellular plasticity mechanisms relevant to early embryological tissue differentiation.
A Community–Based System Dynamics Approach for Understanding Factors Affecting Mental Health and Health Seeking Behaviors in Beirut and Beqaa Regions of Lebanon
Authors: Noubani Aya , Diaconu Karin , ghandour Lilian , Koussa Maria El , Loffreda Giulia , Saleh Shadi 
Published: March 2020

Abstract
Background

Available evidence on mental health and psychosocial problems in Lebanon is limited. Recent quantitative data suggests a high prevalence among Syrian refugees and their Lebanese host communities, with significant treatment gaps in both populations. This study aims to determine how Lebanese host and Syrian refugee communities perceive mental health, and identify health seeking behaviors and barriers to health access in two contrasting contexts of fragility.

Methods

A comparative qualitative study design was adopted whereas a total of 36 semi-structured interviews with Lebanese host and Syrian refugees’ community members were conducted followed by a series of four participatory group model building (GMB) sessions. Participants were recruited from two contrasting fragility contexts: Beirut and Beqaa regions. During these sessions, causal loop diagrams were elicited depicting shared understandings of factors prompting the onset of mental health and psychosocial issues; health seeking behaviors, pathways and elements affecting the rate of health improvement and maintenance were also identified.

Results

Community members in both settings had similar perceptions of factors contributing to mental health. Participants named long-term effects of exposure to wars, political and social effects of conflicts and financial constraints at the household level as precipitating factors prompting the onset of mental health and psychosocial stressors. Gender and integration related challenges between communities were identified as factors that affect condition onset and associated care seeking. Pathways for health seeking were found to be shaped by trust, the advice and support of loved ones, and the need to ensure confidentiality of affected individuals. Recurrent themes in discussion included significant delays in health seeking from the formal health system and widespread social stigma, prohibitive service costs, lack of health coverage, limited awareness of mental health service availability and trust in the quality of service as major barriers to access.

Conclusion

Mental health and psychosocial support strategies need to be gender- and integration-sensitive, primarily focused on condition prevention and awareness raising in order to strengthen health-seeking behaviors.
Deep learning-based dental plaque detection on primary teeth: a comparison with clinical assessments
Authors: You Wenzhe , Hao Aimin , Li Shuai , Wang Yong , Xia Bin 
Published: March 2020

Abstract
Background: Dental plaque is the cause of many common oral diseases (e.g., caries, gingivitis, and periodontitis). Therefore, the detection and control of dental plaque are of great significance to children’s oral health. The objectives of this study are to design an artificial intelligence (AI) model based on deep learning to detect dental plaque on primary teeth and evaluate the diagnostic accuracy of the AI model.Methods: A conventional neural network (CNN) framework was adopted, and a total of 886 photos of primary teeth taken by an intraoral camera (1280×960 pixels; TPC Ligang, Shenzhen, China) were used to train the AI model. To validate the clinical feasibility, 98 photos of primary teeth taken by the intraoral camera were assessed by the AI model. Additionally, tooth photos were acquired using a digital camera (3216×2136 pixels, Canon EOS 60D, Japan). One experienced pediatric dentist looked at these photos and marked the regions the photos containing dental plaque. Then, a plaque-disclosing agent was applied, and the areas of dental plaque were identified. After a week, the dentist drew the dental plaque area on the 98 photos taken by the digital camera a second time to evaluate the consistency of manual diagnosis. In another round of comparison, 102 photos of primary teeth taken by the same intraoral camera were marked to denote the dental plaque area obtained both by the AI model and by the pediatric dentist to evaluate the diagnostic ability of each approach based on photos with lower-resolution (fewer pixels) than those taken by the digital camera. The mean intersection-over-union (MIoU) metric was employed to indicate the detection accuracy.Results: The MIoU for the detection of dental plaque on the tested tooth photos was 0.726 ± 0.165.The MIoU of the dentist when diagnosing the 98 photos taken by the digital camera for the first time was 0.695 ± 0.269, while after one week, the MIoU of the dentist was 0.689 ± 0.253. Compared to the dentist, the AI model demonstrated a higher MIoU (0.736 ± 0.174), and the results did not change after a week. When both the dentist and the AI model assessed the 102 photos taken by the intraoral camera. the MIoU of the pediatric dentist was 0.652 ± 0.195, and the MIoU of the AI model was 0.724 ±0.159. The results of a paired t-test found no significant difference between the AI model and human specialist (P > .05) in diagnosing dental plaque on primary teeth.Conclusions: The AI model showed clinically acceptable performance in detecting dental plaque on primary teeth compared with an experienced pediatric dentist. This finding illustrates the potential application in adopting such AI technology for helping children improve their oral health.
CD59 receptor targeted delivery of miRNA-1284 and Cisplatin-loaded liposomes for effective therapeutic efficacy against cervical cancer cells
Authors: Wang Li , Liang Ting-Ting 
Published: March 2020

Abstract
Co-delivery of two different therapeutics (miRNA-1284 and cisplatin (CDDP)) into the cancer cells in a single nanocarrier provides new dimension to the cancer treatment. In this study, we have designed the CD59sp-conjugated miRNA-1284/cisplatin(CDDP)-loaded liposomes for the enhanced therapeutic effect against cervical cancers. Compared with miRNA-1284/CDDP-loaded liposomes (LP-miCDDP), CD59 antibody-conjugated LP-miCDDP (CD/LP-miCDDP) showed a significantly higher cytotoxicity in HeLa cells. Notably, MiR-1284 showed a typical concentration-dependent cell killing effect in the cervical cancer cells owing to the downregulation of HMGB1. Flow cytometer analysis showed that CD/LP-miCDDP resulted in maximum apoptosis effect (~60%) compared to CDDP (~20%) or miR-1284 (~12%) treated cells indicating the superior anticancer effect in the cancer cells. Importantly, CD/LP-miCDDP significantly prolonged the blood circulation of encapsulated drug in rats with significantly higher AUC (o-t) , t 1/2 and lower CL compared to that of free CDDP. Overall, results demonstrated that targeted and synergistic co-delivery of therapeutic components could be promising in cervical cancer therapy.
Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov.
Authors: Ward Lewis M , Bertran Emma , Johnston David T. 
Published: March 2020

Abstract
Here, we report the draft genome sequence of Dissulfurirhabdus thermomarina SH388. Improved phylogenetic and taxonomic analysis of this organism using genome-level analyses supports assignment of this organism to a novel family within the Desulfobacterota phylum. Additionally, comparative genomic and phylogenetic analyses contextualize the convergent evolution of sulfur disproportionation and potential extracellular electron transfer in this organism relative to other members of the Desulfobacterota.
Spatial Differences of Overweight and Obesity among Schoolchildren in Shandong Province, China
Authors: Han Lizhen , Fu Maosun , Liu Yihua , Jia Jinzhu , Wang Lu 
Published: March 2020

Abstract
Background The spatial differences and related factors of overweight and obesity among schoolchildren in Shandong province were analyzed, aiming to provide scientific basis for prevention of childhood obesity and the adoption of targeted intervention policies. Methods The sample came from Shandong province's physical examination data in 2017. A total of 10.27 million schoolchildren aged 6-18 years were included. ArcGIS software (hot spot analysis) was used to explore the spatial differences, and regional influencing factors were analyzed by multinomial logistic regression. Results The prevalence of overweight and obesity among schoolchildren aged 6-18 years were 17.93% and 6.79%, respectively. Moreover, boys/girls, urban/rural areas both showed that the former rate was higher than the latter, and the 9-11 age group was confirmed to have the highest prevalence. Regional distribution illustrated that, in Shandong province, the areas with high prevalence of overweight and obesity were mainly concentrated in the central, northern and eastern parts, and the hot spots clusters were located in Yantai and Weihai, while the low-value areas were aggregated in the western (boys) and southern (girls) regions. Further exploration revealed that total retail sales of consumer goods (CGTRS) and per capita disposable income (PCDI) were confirmed as risk factors for regional obesity level, while number of full-time teachers (FTT) was a protective factor. Conclusions The spatial differences of overweight and obesity are statistically significant and influenced by some regional factors, suggesting that relevant departments should adopt targeted interventions when relevant strategies are made.
Media Reporting on Air Pollution: Health risk and precautionary measures in national and regional newspapers
Authors: Ramondt Steven , Ramirez A. Susana 
Published: March 2020

Abstract
Background Exposure to air pollution is one of the primary global health risk factors, yet individuals lack the knowledge to engage in individual risk mitigation and the skills to mobilize for change necessary to reduce such risks. The news media are an important tool for influencing individual actions and support for public policies to reduce environmental threats; thus, a lack of news coverage of such issues may exacerbate knowledge deficits. This study examines the reporting of health risk and precautionary measures regarding air pollution in national and regional print news using an environmental health literacy perspective.Methods We conducted a content analysis of two national (New York Times and Washington Post) and two local newspapers (Fresno Bee and Bakersfield Californian) newspapers covering the country’s most polluted region, California’s San Joaquin Valley, during a 5-year period (2011-2015). Using a constructed week sampling approach, 276 newspaper articles were coded for information on threat, efficacy information, and information sources.Results News coverage of air pollution mostly failed to mention human health risks. Moreover, fewer than 10 percent of news stories about air pollution provided information on the precautionary measures necessary for individuals to take action to mitigate their risk. Despite being located in one of the most polluted areas in the US, local newspapers did not report significantly more threat and efficacy information. News coverage of air pollution consistently missed opportunities to raise environmental health literacy.Conclusions Although air pollution levels are high and continue to rise at alarming rates, our findings suggest that news media reporting is not conducive to raising environmental health literacy. Public health advocates and health promotion experts must develop more effective strategies for disseminating information about the health risks of air pollution, balancing the need for recognizing the structural causes of poor air quality and the actions individuals and communities can take to reduce air pollution related morbidity and mortality. National and local news media may be useful partners for such dissemination.
Uptake of provider-initiated HIV and syphilis testing among Heterosexual STD Clinic attendees in Southern China: Results from a Cross-sectional Study
Authors: Zhao Peizhen , Zheng Heping , Tang Weiming , Cheng Huanhuan , Huang Shujie , Yang Bin , Wang Cheng 
Published: March 2020

Abstract
Background Provider-initiated HIV and syphilis testing and counseling (PITC) services are important components of HIV and syphilis prevention programs. However, PITC guidelines have neither been formalized nor widely implemented in China. Limited studies conducted to identify the barriers to offering PITC services from sexually transmitted diseases (STD) clinic attendees’ perspective. We conducted a cross-sectional survey on heterosexual STD clinic attendees to evaluate this in China.Methods A cross-sectional survey was conducted in 2016 in Southern China. Participants completed a validated questionnaire including social-demographic information, reasons for not conducting HIV and syphilis testing, and HIV and STD infection history. In this study, we limited the participants as individuals who self-identified as heterosexual.Results A total of 1943 participants were recruited in this study. Among those participants, 60.6% (1177/1943) and 74.3% (1443/1943) conducted HIV testing and syphilis testing during the study, respectively. Of whom, 2.2% (26/1177) and 21.5% (310/1443) are found to be HIV-positive and syphilis-positive, respectively. The most common barrier to HIV and syphilis testing is a lack of awareness of HIV and syphilis infection. Condom use in the last sexual act, having paid sex during the last 6 months, and receiving HIV and STD related knowledge were positively associated with uptake of both HIV and syphilis testing.Conclusions This study highlights the need and importance of promoting provider-initiated HIV and syphilis testing and counseling services in China. Future studies on exploring innovative methods to improve the knowledge and awareness of HIV and syphilis infection among STD clinic attendees is warranted.
Predictors of lost to follow-up in a “test and treat” programme among adult women with high-risk sexual behavior in Kampala, Uganda.
Authors: Kamacooko Onesmus , Mayanja Yunia , Bagiire Daniel , Namale Gertrude , Hansen Christian Holm , Seeley Janet 
Published: March 2020

Abstract
Background: Immediate uptake of antiretroviral therapy (ART) after an HIV-positive diagnosis (Test and Treat) is now being implemented in Uganda. Data are limited on lost to follow-up (LTFU) in high-risk cohorts that have initiated ‘Test and Treat’. We describe LTFU in a cohort of women of high-risk sexual behaviour who initiated ART under “Test and Treat”. Methods: We performed a retrospective cohort study of participant records at the Good Health for Women Project (GHWP) clinic, a clinic in Kampala for women at high-risk of HIV-infection. We included HIV positive women ≥ 18 years who initiated ART at GHWP between August 2014 and March 2018. We defined LTFU as not taking an ART refill for ≥3 months from the last clinic appointment among those not registered as dead or transferred to another clinic. We used the Kaplan-Meier technique to estimate time to LTFU after ART initiation. Predictors of LTFU were assessed using a multivariable Cox proportional hazards model. Results: The mean (±SD) age of the 293 study participants was 30.3 (± 6.5) years, with 274 (94%) reporting paid sex while 38 (13%) had never tested for HIV before enrolment into GHWP. LTFU within the first year of ART initiation was 16% and the incidence of LTFU was estimated at 12.7 per 100 person-years (95%CI 9.90-16.3). In multivariable analysis, participants who reported sex work as their main job at ART initiation (Adjusted Hazards Ratio [aHR] =1.95, 95%CI 1.10–3.45), having baseline WHO clinical stage III or IV (aHR= 2.75, 95% CI 1.30–5.79) were more likely to be LTFU. Conclusion LTFU in this cohort is high. Follow up strategies are required to support women on Test and Treat to remain on treatment, especially those who engage in sex work and those who initiate ART at a later stage of disease. Keywords: Universal Test and Treat, Women at high-risk, lost to follow-up, loss to follow-up; sub-Saharan Africa.
Evaluation of the effect of an "Internet plus medical"-based health management service model in patients with nonalcoholic fatty liver disease
Authors: Yang Yan , Tian Cui-Huan , Dai Jun , Zhang Wei , Li Shu-Qing , Min Xiang , Wang Yan-Yan , Cao Juan 
Published: March 2020

Abstract
Objectives To observe the effect of an "Internet plus medical"-based health management service model in patients with nonalcoholic fatty liver disease (NAFLD) and to explore an effective model for NAFLD health management to provide a reference for NAFLD treatment and nursing.Methods A total of 519 patients with NAFLD were randomly assigned to a routine health education group (N=258) or a health management platform group (N=261). The routine health education group received routine health education, and the health management platform group was treated with the "Internet plus medical"-based health management service model to manage NAFLD. The new model provides closed-loop services for the prevention and rehabilitation of NAFLD through the process of grouping, filing, evaluating, planning, intervening, assessing stage and following up. The two groups were observed for 24 weeks. The results of basic indicators, laboratory indicators, body composition analyses, controlled attenuation parameters (CAP) and quality of life assessment questionnaires were used as evaluation indices. All data of the participants were collected and analyzed prior to and following the intervention, and the differences between the two groups were compared.Results Compared with the routine health education group, the NAFLD health management service model based on “Internet plus medical” treatment effectively reduced the weight, body mass index (BMI), CAP, aspartate transaminase (AST)/alanine aminotransferase (ALT) value, body fat content and visceral fat area of NAFLD patients (P =0.047, 0.031, 0.044, 0.037 and 0.047, respectively) and improve the quality of life of NAFLD patients in terms of physiological role, energy and general health (P=0.027, 0.001 and 0.044, respectively).Conclusions The results of the present study preliminarily confirm the validity and development prospects of the new NAFLD management service model. This finding suggests that the model is an evidence-based model of health education and management for NAFLD prevention in China.