bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining AMIA’s artificial intelligence principles
Authors: Solomonides Anthony E , Koski Eileen , Atabaki Shireen M , Weinberg Scott , McGreevey John D , Kannry Joseph L , Petersen Carolyn , Lehmann Christoph U 
Published: January 2022

Abstract
Recent advances in the science and technology of artificial intelligence (AI) and growing numbers of deployed AI systems in healthcare and other services have called attention to the need for ethical principles and governance. We define and provide a rationale for principles that should guide the commission, creation, implementation, maintenance, and retirement of AI systems as a foundation for governance throughout the lifecycle. Some principles are derived from the familiar requirements of practice and research in medicine and healthcare: beneficence, nonmaleficence, autonomy, and justice come first. A set of principles follow from the creation and engineering of AI systems: explainability of the technology in plain terms; interpretability, that is, plausible reasoning for decisions; fairness and absence of bias; dependability, including “safe failure”; provision of an audit trail for decisions; and active management of the knowledge base to remain up to date and sensitive to any changes in the environment. In organizational terms, the principles require benevolence—aiming to do good through the use of AI; transparency, ensuring that all assumptions and potential conflicts of interest are declared; and accountability, including active oversight of AI systems and management of any risks that may arise. Particular attention is drawn to the case of vulnerable populations, where extreme care must be exercised. Finally, the principles emphasize the need for user education at all levels of engagement with AI and for continuing research into AI and its biomedical and healthcare applications.
Burn Injuries in People Who Used Drug, 2009 to 2017: A Case–Control Study in Shiraz, Southern Iran
Authors: Hoghoughi Mohammad Ali , Marzban Mohammad Reza , Shahrbaf Mohammad Amin , Shahriarirad Reza , Kamran Hooman , Meimandi Farzaneh Zahmatkesh , Salimi Maryam , Hosseinpour Hamidreza 
Published: January 2022

Abstract
Burn injury is a critical health issue, which is associated with several morbidities and mortalities. Substance abuse, which is an important public health problem in Iran, can affect burn injury outcomes and etiologies in victims. This study was aimed to evaluate different aspects of burn injuries in people who used drug (PWUD) in two referral centers in the south of Iran. This case–control study was conducted on burn victims referred to Amir-al Momenin Hospital and Ghotb-al-din Hospital from 2009 to 2017. Patients with a history of drug consumption were selected from the database and compared to randomly selected burn victims with no history of drug use. Demographics, burn etiology, underlying disease, total body surface area, hospitalization duration, and also the outcomes were collected and recorded in both groups. Data analysis was done by SPSS software. A total of 5912 inpatients were included in this study, of which 2397 of them (40.54%) were female. The mean age of the patients was 26.12 ± 19.18. Drug history was positive in 659 patients (11.15%). Familial issues and mental disorders were significantly higher in the PWUD group compared to the control group (P &lt; .001). Explosion etiology was significantly higher in the PWUD group (P &lt; .001). Psychiatric disorders (P &lt; .001), total body surface area (P = .023), and hospital stay (P &lt; .001) were significantly higher in PWUD; however, the mortality rate had no statistically significant differences between the groups (P = .583). Substance abuse is a risk factor in burn victims, which can affect burn etiology and burn-related morbidities.
Global Externalities, Local Policies, and Firm Selection
Authors: Ahlvik Lassi , Liski Matti 
Published: January 2022

Abstract
How to fight global problems with local tools? When only firms know what externality-producing activities can be relocated, policies shape the location distribution of firm types with different social values. We find that, because of this selection effect, the optimal local policies confront firms’ mobility with elevated corrective externality prices, in contrast with the common remedies for the relocation risk. Our mechanism incentivizes also moving firms to limit the externality, and it influences strategically the distribution of moving firms that comply with policies elsewhere. The magnitude of these effects is illustrated by a quantification for the key sectors in the European Union emissions trading system.
Extrapolation of design strategies for lignocellulosic biomass conversion to the challenge of plastic waste
Authors: Jarboe Laura R , Khalid Ammara , Rodriguez Ocasio Efrain , Noroozi Kimia Fashkami 
Published: January 2022

Abstract
The goal of cost-effective production of fuels and chemicals from biomass has been a substantial driver of the development of the field of metabolic engineering. The resulting design principles and procedures provide a guide for the development of cost-effective methods for degradation, and possibly even valorization, of plastic wastes. Here, we highlight these parallels, using the creative work of Lonnie O'Neal (Neal) Ingram in enabling production of fuels and chemicals from lignocellulosic biomass, with a focus on ethanol production as an exemplar process.
Environmental Scan of Parent-Facing Health Information About Antibiotics in US Children’s Hospital Websites
Authors: Mangal Sabrina , Arcia Adriana , Carter Eileen 
Published: January 2022

Abstract
Nearly half of free-standing children’s hospital websites contain parent-facing resources about antibiotics. Most resources have information on safe antibiotic use, antibiotic resistance, and questions to ask clinicians. Accessibility can be improved by increasing readability, available languages, and multimedia. Future research should evaluate information accuracy, actionability, and comprehension with target audiences.
Determination of Glyphosate and AMPA in Blood Can Predict the Severity of Acute Glyphosate Herbicide Poisoning
Authors: Cellier M , Anthony N , Bruneau C , Descatha A 
Published: January 2022

Abstract

Objective
To evaluate a potential association between blood and urine concentration of glyphosate and its metabolite, aminomethylphosphonic acid (AMPA), with severity of acute glyphosate (herbicide) poisoning.

Methods
In our retrospective study of acute glyphosate poisoning, we examined records from the French National Database of Poisonings, dated between January 1, 2004, and December 31, 2016. We compared the severity of poisoning among case individuals using the Fisher exact test and Wilcoxon test. Also, we calculated ROC curves to determine the cutoff for blood and urine concentration.

Results
A total of 17 plasma glyphosate, 11 urine glyphosate, 13 plasma AMPA, and 10 urine AMPA specimens were included in our study, with collection dates ranging from January 1, 2004, through December 31, 2016.

Conclusion
The optimal cutoff we discovered for blood concentration of AMPA was 0.88 mg/L; for glyphosate, it was 600 mg/L. The cutoff plasma concentration of AMPA has never been described in the literature, to our knowledge.
Genomic patterns of transcription–replication interactions in mouse primary B cells
Authors: St Germain Commodore P , Zhao Hongchang , Sinha Vrishti , Sanz Lionel A , Chédin Frédéric , Barlow Jacqueline H 
Published: January 2022

Abstract
Conflicts between transcription and replication machinery are a potent source of replication stress and genome instability; however, no technique currently exists to identify endogenous genomic locations prone to transcription–replication interactions. Here, we report a novel method to identify genomic loci prone to transcription–replication interactions termed transcription–replication immunoprecipitation on nascent DNA sequencing, TRIPn-Seq. TRIPn-Seq employs the sequential immunoprecipitation of RNA polymerase 2 phosphorylated at serine 5 (RNAP2s5) followed by enrichment of nascent DNA previously labeled with bromodeoxyuridine. Using TRIPn-Seq, we mapped 1009 unique transcription–replication interactions (TRIs) in mouse primary B cells characterized by a bimodal pattern of RNAP2s5, bidirectional transcription, an enrichment of RNA:DNA hybrids, and a high probability of forming G-quadruplexes. TRIs are highly enriched at transcription start sites and map to early replicating regions. TRIs exhibit enhanced Replication Protein A association and TRI-associated genes exhibit higher replication fork termination than control transcription start sites, two marks of replication stress. TRIs colocalize with double-strand DNA breaks, are enriched for deletions, and accumulate mutations in tumors. We propose that replication stress at TRIs induces mutations potentially contributing to age-related disease, as well as tumor formation and development.
High-grade ovarian cancer associated H/ACA snoRNAs promote cancer cell proliferation and survival
Authors: Faucher-Giguère Laurence , Roy Audrey , Deschamps-Francoeur Gabrielle , Couture Sonia , Nottingham Ryan M , Lambowitz Alan M , Scott Michelle S , Abou Elela Sherif 
Published: January 2022

ABSTRACT
Small nucleolar RNAs (snoRNAs) are an omnipresent class of non-coding RNAs involved in the modification and processing of ribosomal RNA (rRNA). As snoRNAs are required for ribosome production, the increase of which is a hallmark of cancer development, their expression would be expected to increase in proliferating cancer cells. However, assessing the nature and extent of snoRNAs’ contribution to cancer biology has been largely limited by difficulties in detecting highly structured RNA. In this study, we used a dedicated midsize non-coding RNA (mncRNA) sensitive sequencing technique to accurately survey the snoRNA abundance in independently verified high-grade serous ovarian carcinoma (HGSC) and serous borderline tumour (SBT) tissues. The results identified SNORA81, SNORA19 and SNORA56 as an H/ACA snoRNA signature capable of discriminating between independent sets of HGSC, SBT and normal tissues. The expression of the signature SNORA81 correlates with the level of ribosomal RNA (rRNA) modification and its knockdown inhibits 28S rRNA pseudouridylation and accumulation leading to reduced cell proliferation and migration. Together our data indicate that specific subsets of H/ACA snoRNAs may promote tumour aggressiveness by inducing rRNA modification and synthesis.
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer
Authors: Høye Eirik , Fromm Bastian , Böttger Paul H M , Domanska Diana , Torgunrud Annette , Lund-Andersen Christin , Abrahamsen Torveig Weum , Fretland Åsmund Avdem , Dagenborg Vegar J , Lorenz Susanne , Edwin Bjørn , Hovig Eivind , Flatmark Kjersti 
Published: January 2022

ABSTRACT
Although microRNAs (miRNAs) contribute to all hallmarks of cancer, miRNA dysregulation in metastasis remains poorly understood. The aim of this work was to reliably identify miRNAs associated with metastatic progression of colorectal cancer (CRC) using novel and previously published next-generation sequencing (NGS) datasets generated from 268 samples of primary (pCRC) and metastatic CRC (mCRC; liver, lung and peritoneal metastases) and tumor adjacent tissues. Differential expression analysis was performed using a meticulous bioinformatics pipeline, including only bona fide miRNAs, and utilizing miRNA-tailored quality control and processing. Five miRNAs were identified as up-regulated at multiple metastatic sites Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [mir-141–3p], Mir-1307_5p and Mir-155_5p. Several have previously been implicated in metastasis through involvement in epithelial-to-mesenchymal transition and hypoxia, while other identified miRNAs represent novel findings. The use of a publicly available pipeline facilitates reproducibility and allows new datasets to be added as they become available. The set of miRNAs identified here provides a reliable starting-point for further research into the role of miRNAs in metastatic progression.
InterTADs: integration of multi-omics data on topologically associated domains, application to chronic lymphocytic leukemia
Authors: Tsagiopoulou Maria , Pechlivanis Nikolaos , Maniou Maria Christina , Psomopoulos Fotis 
Published: January 2022

ABSTRACTThe integration of multi-omics data can greatly facilitate the advancement of research in Life Sciences by highlighting new interactions. However, there is currently no widespread procedure for meaningful multi-omics data integration. Here, we present a robust framework, called InterTADs, for integrating multi-omics data derived from the same sample, and considering the chromatin configuration of the genome, i.e. the topologically associating domains (TADs). Following the integration process, statistical analysis highlights the differences between the groups of interest (normal versus cancer cells) relating to (i) independent and (ii) integrated events through TADs. Finally, enrichment analysis using KEGG database, Gene Ontology and transcription factor binding sites and visualization approaches are available. We applied InterTADs to multi-omics datasets from 135 patients with chronic lymphocytic leukemia (CLL) and found that the integration through TADs resulted in a dramatic reduction of heterogeneity compared to individual events. Significant differences for individual events and on TADs level were identified between patients differing in the somatic hypermutation status of the clonotypic immunoglobulin genes, the core biological stratifier in CLL, attesting to the biomedical relevance of InterTADs. In conclusion, our approach suggests a new perspective towards analyzing multi-omics data, by offering reasonable execution time, biological benchmarking and potentially contributing to pattern discovery through TADs.
A comparison on predicting functional impact of genomic variants
Authors: Wang Dong , Li Jie , Wang Yadong , Wang Edwin 
Published: January 2022

ABSTRACT
Single-nucleotide polymorphism (SNPs) may cause the diverse functional impact on RNA or protein changing genotype and phenotype, which may lead to common or complex diseases like cancers. Accurate prediction of the functional impact of SNPs is crucial to discover the ‘influential’ (deleterious, pathogenic, disease-causing, and predisposing) variants from massive background polymorphisms in the human genome. Increasing computational methods have been developed to predict the functional impact of variants. However, predictive performances of these computational methods on massive genomic variants are still unclear. In this regard, we systematically evaluated 14 important computational methods including specific methods for one type of variant and general methods for multiple types of variants from several aspects; none of these methods achieved excellent (AUC ≥ 0.9) performance in both data sets. CADD and REVEL achieved excellent performance on multiple types of variants and missense variants, respectively. This comparison aims to assist researchers and clinicians to select appropriate methods or develop better predictive methods.
Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability
Authors: Roberts Aedan G K , Catchpoole Daniel R , Kennedy Paul J 
Published: January 2022

ABSTRACTThere is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a difference in mean are ignored by traditional differential expression-based analyses. Using a Bayesian hierarchical model that provides tests for both differential variability and differential distribution for bulk RNA-seq data, we report here an investigation into differential variability and distribution in cancer. Analysis of eight paired tumour–normal datasets from The Cancer Genome Atlas confirms that differential variability and distribution analyses are able to identify cancer-related genes. We further demonstrate that differential variability identifies cancer-related genes that are missed by differential expression analysis, and that differential expression and differential variability identify functionally distinct sets of potentially cancer-related genes. These results suggest that differential variability analysis may provide insights into genetic aspects of cancer that would not be revealed by differential expression, and that differential distribution analysis may allow for more comprehensive identification of cancer-related genes than analyses based on changes in mean or variability alone.
High-scale random access on DNA storage systems
Authors: El-Shaikh Alex , Welzel Marius , Heider Dominik , Seeger Bernhard 
Published: January 2022

ABSTRACT
Due to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA and enable random access (predominantly random reads) by primers, which serve as unique identifiers for directly accessing data. However, primers come with a significant limitation regarding the maximum available number per DNA library. The number of different primers within a library is typically very small (e.g. ≈10). We propose a method to overcome this deficiency and present a general-purpose technique for addressing and directly accessing thousands to potentially millions of different data objects within the same DNA pool. Our approach utilizes a fountain code, sophisticated probe design, and microarray technologies. A key component is locality-sensitive hashing, making checks for dissimilarity among such a large number of probes and data objects feasible.
Perceived racial discrimination and eating habits: a systematic review and conceptual models
Authors: Rodrigues Ylana Elias , Fanton Marcos , Novossat Ricardo Suñé , Canuto Raquel 
Published: January 2022

AbstractContextThere is no systematic review on the relationship between racial discrimination and eating habits.ObjectiveA systematic review was conducted to synthesize evidence on the association between perceived racial discrimination (PRD) and eating habits. A conceptual model was developed to depict the most common mechanisms used to explain this association.Data SourcesArticles were retrieved from the PubMed, Embase, LILACS, and PsycINFO databases from inception to January 2021.Study SelectionOnly observational studies were included, and there were no restrictions on age, racial group, or country. Two reviewers selected the articles independently.Data ExtractionData were extracted independently by 2 reviewers. The assessment of methodological quality was conducted using the Newcastle-Ottawa Scale.ResultsAll studies retrieved were conducted among the US population. Nineteen studies were included. On average, the studies showed a methodological quality of 66%. Forty-six associations were evaluated: 38 between PRD and negative eating habits, 29 between PRD and eating behavior, and 17 between PRD and food consumption.ConclusionsPRD negatively affects eating habits. A conceptual framework based on ecosocial theory is suggested as a guide for future research. Further studies in different countries (beyond the United States) should be conducted to understand how racial discrimination affects eating habits within different ethnic, cultural, social, and economic contexts.Systematic Review RegistrationPROSPERO registration no. CRD42019142605
Pathways of parental influence on adolescent diet and obesity: a psychological stress–focused perspective
Authors: Dimitratos Sarah M , Swartz Johnna R , Laugero Kevin D 
Published: January 2022

Abstract
Youth obesity has become increasingly prevalent, with 34.5% of US adolescents 12–19 years old estimated to have overweight or obesity. Disordered eating and weight concern peak in adolescence, and overeating to cope with negative emotions can affect long-term health and obesity risk. Parents significantly influence adolescent diet quality, and parental stress may influence parenting behaviors that increase the risk for stress-motivated eating and obesity in adolescents. Chronic or repeated exposure to parental stress may lead to stress-related neurophysiological changes that promote consumption of palatable foods and obesogenic eating habits in adolescents. Understanding how parental stress influences adolescents’ eating behavior may reveal novel access points for reducing adolescent obesity. Here, we aim to provide a new stress-focused framework for developing intervention strategies targeted at obesity prevention in adolescents.
Western and ketogenic diets in neurological disorders: can you tell the difference?
Authors: Habashy Karl John , Ahmad Fatima , Ibeh Stanley , Mantash Sarah , Kobeissy Fatima , Issa Hawraa , Habis Ralph , Tfaily Ali , Nabha Sanaa , Harati Hayat , Reslan Mohammad Amine , Yehya Yara , Barsa Chloe , Shaito Abdullah , Zibara Kazem , El-Yazbi Ahmed F , Kobeissy Firas H 
Published: January 2022

AbstractThe prevalence of obesity tripled worldwide between 1975 and 2016, and it is projected that half of the US population will be overweight by 2030. The obesity pandemic is attributed, in part, to the increasing consumption of the high-fat, high-carbohydrate Western diet, which predisposes to the development of the metabolic syndrome and correlates with decreased cognitive performance. In contrast, the high-fat, low-carbohydrate ketogenic diet has potential therapeutic roles and has been used to manage intractable seizures since the early 1920s. The brain accounts for 25% of total body glucose metabolism and, as a result, is especially susceptible to changes in the types of nutrients consumed. Here, we discuss the principles of brain metabolism with a focus on the distinct effects of the Western and ketogenic diets on the progression of neurological diseases such as epilepsy, Parkinson’s disease, Alzheimer’s disease, and traumatic brain injury, highlighting the need to further explore the potential therapeutic effects of the ketogenic diet and the importance of standardizing dietary formulations to assure the reproducibility of clinical trials.