- Is higher resilience predictive of lower stress and better mental health among corporate executives? [Journal Article]
- PlosPLoS One 2019; 14(6):e0218092
- CONCLUSIONS: In this cross-sectional survey of a large cohort of corporative executives, the lower-resilience cohort had a 4-fold higher prevalence of depression and an almost 3-fold higher prevalence of anxiety compared with the higher-resilience cohort. High resilience was positively associated with well-being and negatively associated with perceived stress. Our findings suggest that higher resilience in the executive workplace environment is associated with better mental health, reduced stress, and greater well-being.
- Coding algorithms for defining Charlson and Elixhauser co-morbidities in Read-coded databases. [Journal Article]
- BMBMC Med Res Methodol 2019 Jun 06; 19(1):115
- CONCLUSIONS: The comorbidity code lists may be used by future researchers to calculate CCI and EM using records from Read coded databases. The EM is preferable to the CCI but only marginal gains should be expected from incorporating comorbidities over a period longer than 1 year.
- Translation and cultural adaptation into Spanish of the Low Vision Quality of Life Questionnaire. [Journal Article]
- ASArch Soc Esp Oftalmol 2019 May 30
- CONCLUSIONS: The results obtained suggest that the Spanish version of this tool is understandable for patients with visual impairment. Its properties as a measuring tool will be evaluated in a later study to determine its validity, reliability, and sensitivity to changes.
- Reading and writing: the evolution of molecular pain genetics. [Journal Article]
- PAINPain 2019 May 22
- The diverse etiologies of conditions characterized by chronic pain require molecular assessment. Over recent decades, progress in research has enabled studying of the genetic mechanisms underlying pa…
The diverse etiologies of conditions characterized by chronic pain require molecular assessment. Over recent decades, progress in research has enabled studying of the genetic mechanisms underlying pain and consequently realistic clinical solutions. Genetic linkage has unveiled rare single-gene contributions to pain disorders, whilst advances in genome-wide association studies (GWAS) define multigenic mechanisms in conditions such as back pain and migraine. Advances in DNA sequencing now additionally allow us to efficiently identify mutations underlying congenic pain syndromes and diagnose individuals at risk of developing ongoing pain. In the laboratory, targeted modulation of gene expression with RNA interference, as well as the development of transgenic mouse models, has exponentially expanded our ability to interrogate the molecular cascades behind nociceptive and chronic pain. Furthermore, the recent evolution of CRISPR/Cas9 mediated gene editing has produced a simple yet effective method of altering the genome to alleviate ongoing pain. This genetic revolution will undoubtedly lead to more personalized therapeutics, which with consideration of environmental risk factors should combat clinical pain. We believe these improvements will occur in the next few decades. A video accompanying this abstract is available online as Supplemental Digital Content at http://links.lww.com/PAIN/A804.
- Spinal manipulation frequency and dosage effects on clinical and physiological outcomes: a scoping review. [Journal Article]
- CMChiropr Man Therap 2019; 27:23
- CONCLUSIONS: The results of this study showed that SM dosage and frequency effects have been mostly studied over the past two decades. Definitions for these two concepts however differ across studies. Overall, the results showed that treatment frequency does not significantly affect clinical outcomes during and following a SM treatment period. Dosage effects clearly influence short-term physiological responses to SM treatment, but relationships between these responses and clinical outcomes remains to be investigated.
- Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs. [Journal Article]
- RBRNA Biol 2019 Jun 03; :1-15
- To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splici…
To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 (SMARCA5) as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. Abbreviations: PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone.
- GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. [Journal Article]
- SRSci Rep 2019 May 20; 9(1):7580
- The vast amount of RNA-seq data deposited in Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly underutilized resource for biomedical research. To remove technical roadb…
The vast amount of RNA-seq data deposited in Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly underutilized resource for biomedical research. To remove technical roadblocks for reusing these data, we have developed a web-application GREIN (GEO RNA-seq Experiments Interactive Navigator) which provides user-friendly interfaces to manipulate and analyze GEO RNA-seq data. GREIN is powered by the back-end computational pipeline for uniform processing of RNA-seq data and the large number (>6,500) of already processed datasets. The front-end user interfaces provide a wealth of user-analytics options including sub-setting and downloading processed data, interactive visualization, statistical power analyses, construction of differential gene expression signatures and their comprehensive functional characterization, and connectivity analysis with LINCS L1000 data. The combination of the massive amount of back-end data and front-end analytics options driven by user-friendly interfaces makes GREIN a unique open-source resource for re-using GEO RNA-seq data. GREIN is accessible at: https://shiny.ilincs.org/grein , the source code at: https://github.com/uc-bd2k/grein , and the Docker container at: https://hub.docker.com/r/ucbd2k/grein .
- The E-Cigarette Debate: What Counts as Evidence? [Journal Article]
- AJAm J Public Health 2019; 109(7):1000-1006
- Two major public health evaluations of e-cigarettes-one from the National Academies of Science, Engineering, and Medicine (NASEM), the other from Public Health England (PHE)-were issued back to back …
Two major public health evaluations of e-cigarettes-one from the National Academies of Science, Engineering, and Medicine (NASEM), the other from Public Health England (PHE)-were issued back to back in the winter of 2018. While some have read these analyses as broadly consistent, providing support for the view that e-cigarettes could play a role in smoking harm reduction, in every major respect, they come to very different conclusions about what the evidence suggests in terms of public health policy. How is that possible? The explanation rests in what the 2 reports see as the central challenge posed by e-cigarettes, which helped to determine what counted as evidence. For NASEM, the core question was how to protect nonsmokers from the potential risks of exposure to nicotine and other contaminants or from the risk of smoking combustible cigarettes through renormalization. A precautionary standard was imperative, making evidence that could speak most conclusively to the question of causality paramount. For PHE, the priority was how to reduce the burdens now borne by current smokers, burdens reflected in measurable patterns of morbidity and mortality. With a focus on immediate harms, PHE turned to evidence that was "relevant and meaningful." Thus, competing priorities determined what counted as evidence when it came to the impact of e-cigarettes on current smokers, nonsmoking bystanders, and children and adolescents. A new clinical trial demonstrating the efficacy of e-cigarettes as a cessation tool makes understanding how values and framing shape core questions and conclusive evidence imperative.
- Self-Imposed Exile, Marginality, and Homosexuality in the Novels of Abdellah Taïa, Rachid O., and Eyet-Chékib Djaziri. [Journal Article]
- JHJ Homosex 2019 May 13; :1-16
- A burgeoning canon of Maghrebian writers in self-imposed exiled in France has in the last decade begun to openly broach the subject of homosexuality in Arab-Muslim communities of the Maghreb. Novels …
A burgeoning canon of Maghrebian writers in self-imposed exiled in France has in the last decade begun to openly broach the subject of homosexuality in Arab-Muslim communities of the Maghreb. Novels of writers like Abdellah Taïa, Rachid O. and Eyet-Chékib Djaziri reflect a fascinating trans-Mediterranean construction of homosexual identity. Drawing on Svetlana Boym's critical work, particularly her observation that nostalgia "charts an affective geography of the native land that often mirrors the melancholic landscapes" of the exiled, this paper analyzes the construction of homosexuality against the notions of exile, nostalgia, and marginality. The novels of these Maghrebian writers highlight nostalgia as both cathartic and paralyzing for "gay" migrant protagonists who find themselves trapped in the subtle seam between a cherished Maghreb that is framed as homophobic in the sexual clash of civilizations and a more liberal yet inauspicious France. The nostalgic contemplation of the constitution of a homosexual subjectivity is read as a critical performance and mainstreaming of hitherto marginalized voices that now subvert and fight back against normalizing discourses of ethnicity, sexual and gender identity as well as nationality.
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- Splice-Aware Multiple Sequence Alignment of Protein Isoforms. [Journal Article]
- ABACM BCB 2018 Aug-Sep; 2018:200-210
- Multiple sequence alignment (MSA) is a classic problem in computational genomics. In typical use, MSA software is expected to align a collection of homologous genes, such as orthologs from multiple s…
Multiple sequence alignment (MSA) is a classic problem in computational genomics. In typical use, MSA software is expected to align a collection of homologous genes, such as orthologs from multiple species or duplication-induced paralogs within a species. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need to create MSAs that more effectively accommodate isoforms. MSAs are traditionally constructed using scoring criteria that prefer alignments with occasional mismatches over alignments with long gaps. Alternatively spliced protein isoforms effectively contain exon-length insertions or deletions (indels) relative to each other, and demand an alternative approach. Some improvements can be achieved by making indel penalties much smaller, but this is merely a patchwork solution. In this work we present Mirage, a novel MSA software package for the alignment of alternatively spliced protein isoforms. Mirage aligns isoforms to each other by first mapping each protein sequence to its encoding genomic sequence, and then aligning isoforms to one another based on the relative genomic coordinates of their constitutive codons. Mirage is highly effective at mapping proteins back to their encoding exons, and these protein-genome mappings lead to extremely accurate intra-species alignments; splice site information in these alignments is used to improve the accuracy of inter-species alignments of isoforms. Mirage alignments have also revealed the ubiquity of dual-coding exons, in which an exon conditionally encodes multiple open reading frames as overlapping spliced segments of frame-shifted genomic sequence.