ResearchPad - Analysis https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Exploring the Paradox of Increased Global Health and Degraded Global Environment: How Much Borrowed Time Is Humanity Living on?]]> https://www.researchpad.co/product?articleinfo=Naac92970-d402-4070-a3c1-7b4596659e95 <![CDATA[Systematic review of the prevalence of current smoking among hospitalized COVID-19 patients in China: could nicotine be a therapeutic option?]]> https://www.researchpad.co/product?articleinfo=N74e5f8c0-21f2-4a95-b2f4-5a40f36978e7 <![CDATA[Proposed Amendments to the Constitution of the International Commission on Zoological Nomenclature]]> https://www.researchpad.co/product?articleinfo=N3d84714b-929a-4275-87b8-88c22cfed338

Abstract

The International Commission on Zoological Nomenclature (ICZN, or Commission) considered amendments to Articles of its Constitution (ICZN 1999a) at a special session in Singapore, convened on June 3–7, 2019. During this meeting, Commissioners also planned revisions to the Bylaws, the current International Code of Zoological Nomenclature (ICZN 1999b, 2003, 2012, 2017) and ZooBank user policies.

]]>
<![CDATA[Systematic Review and Meta-Analysis of Sex Differences in Social Contact Patterns and Implications for Tuberculosis Transmission and Control]]> https://www.researchpad.co/product?articleinfo=Nee18d789-0b3b-40b1-b66a-3ae64454cf7f

Social contact patterns might contribute to excess burden of tuberculosis in men. We conducted a study of social contact surveys to evaluate contact patterns relevant to tuberculosis transmission. Available data describe 21 surveys in 17 countries and show profound differences in sex-based and age-based patterns of contact. Adults reported more adult contacts than children. Children preferentially mixed with women in all surveys (median sex assortativity 58%, interquartile range [IQR] 57%–59% for boys, 61% [IQR 60%–63%] for girls). Men and women reported sex-assortative mixing in 80% and 95% of surveys (median sex assortativity 56% [IQR 54%–58%] for men, 59% [IQR 57%–63%] for women). Sex-specific patterns of contact with adults were similar at home and outside the home for children; adults reported greater sex assortativity outside the home in most surveys. Sex assortativity in adult contacts likely contributes to sex disparities in adult tuberculosis burden by amplifying incidence among men.

]]>
<![CDATA[Coinfinder: detecting significant associations and dissociations in pangenomes]]> https://www.researchpad.co/product?articleinfo=N5b6aa6ad-3805-4584-b068-4ce452f6f591

The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are ‘coincident’) more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.

]]>
<![CDATA[Advancing alcohol research in low-income and middle-income countries: a global alcohol environment framework]]> https://www.researchpad.co/product?articleinfo=N6519e755-1f46-4bd5-a3a5-3ff76ee7dce6

Alcohol-related harm has gained increased attention in high-income countries (HICs) in recent years which, alongside government regulation, has effected a reduction in alcohol consumption. The alcohol industry has turned its attention to low-income and middle-income country (LMIC) markets as a new source of growth and profit, prompting increased consumption in LMICS. Alcohol use in LMICs is also increasing. There is a need to understand particularly in LMICs the impact of industry strategy in shaping local contexts of alcohol use. We draw on conceptualisations from food systems research, and research on the commercial determinants of health, to develop a new approach for framing alcohol research and discuss implications for alcohol research, particularly in LMICs, focusing on South Africa as an illustrative example. We propose a conceptualisation of the ‘alcohol environment’ as the system of alcohol provision, acquisition and consumption—including, critically, industry advertising and marketing—along with the political, economic and regulatory context of the alcohol industry that mediates people’s alcohol drinking patterns and behaviours. While each country and region is different in terms of its context of alcohol use, we contrast several broadly distinct features of alcohol environments in LMICs and HICs. Improving understanding of the full spectrum of influences on drinking behaviour, particularly in LMICs, is vital to inform the design of interventions and policies to facilitate healthier environments and reduce the harms associated with alcohol consumption. Our framework for undertaking alcohol research may be used to structure mixed methods empirical research examining the role of the alcohol environment particularly in LMICs.

]]>
<![CDATA[Adapting Lean methods to facilitate stakeholder engagement and co-design in healthcare]]> https://www.researchpad.co/product?articleinfo=N2d94f311-d7c0-4522-bbcd-d592995deada

Quality improvement approaches drawn from industry can go beyond traditional concepts of value and deliver improvements in healthcare services, argue Iain Smith and colleagues

]]>
<![CDATA[Revitalising audit and feedback to improve patient care]]> https://www.researchpad.co/product?articleinfo=N0d4688fb-19e8-4cb5-9a05-52b74d44ca07

Audit and feedback are widely used in quality improvement. Robbie Foy and colleagues argue that their full potential to improve patient care could be realised through a more evidence based and imaginative approach

]]>
<![CDATA[Diet, nutrition, and cancer risk: what do we know and what is the way forward?]]> https://www.researchpad.co/product?articleinfo=N74193380-6ac1-4c4e-86bc-64e72d27164c

Timothy J Key and colleagues describe the evidence linking diet and nutrition to cancer risk, concluding that obesity and alcohol are the most important factors

]]>
<![CDATA[What role should the commercial food system play in promoting health through better diet?]]> https://www.researchpad.co/product?articleinfo=N88ece1c4-45da-4d18-b318-acb21539dcb1

Martin White and coauthors consider that the commercial food system has the potential to show leadership and support for dietary public health, but systemic change is needed first and this is likely to require governmental action

]]>
<![CDATA[Health benefits of policies to reduce carbon emissions]]> https://www.researchpad.co/product?articleinfo=N808031f1-d370-4dea-94ad-e44e5f2ddbb1

James Milner and colleagues argue that carefully considered policies to lower carbon emissions can also improve health, and we should use these benefits to push for strong climate action

]]>
<![CDATA[Clinical negligence costs: taking action to safeguard NHS sustainability]]> https://www.researchpad.co/product?articleinfo=N3dafb0ba-d864-4775-9bf4-f1b33bd6cad7

The NHS cannot afford to divert more and more money to litigation, and we need to tackle the problem at source. Tim Draycott and colleagues set out four principles to reduce avoidable harm

]]>
<![CDATA[Strengthening the links between planning and health in England]]> https://www.researchpad.co/product?articleinfo=Nfaa05631-0434-4afa-83d3-a1684a50e6a8

Gemma McKinnon and colleagues argue that multidisciplinary action in planning and health will contribute to more equitable communities and improved health and wellbeing

]]>
<![CDATA[WHO should declare climate change a public health emergency ]]> https://www.researchpad.co/product?articleinfo=N1c994454-5936-479e-a4d5-70718b88269e

Rapid and potentially irreversible climate change poses a direct threat to global public health. Andrew Harmer and colleagues argue that WHO should recognise this in the same way as global threats from specific diseases

]]>
<![CDATA[To include or not include: renal dialysis policy in the era of universal health coverage]]> https://www.researchpad.co/product?articleinfo=Nde3633a4-11c9-4cf7-be80-7b7d697e4681

Expensive treatments such as renal dialysis are a challenge for countries aiming for universal coverage. Yot Teerawattananon and colleagues set out a systematic approach to ensuring it is affordable

]]>
<![CDATA[Interactive Models in Synthetic Biology: Exploring Biological and Cognitive Inter-Identities]]> https://www.researchpad.co/product?articleinfo=Nd2e286ff-c6fe-4dab-881a-d65aefdb9e7a

The aim of this article is to investigate the relevance and implications of synthetic models for the study of the interactive dimension of minimal life and cognition, by taking into consideration how the use of artificial systems may contribute to an understanding of the way in which interactions may affect or even contribute to shape biological identities. To do so, this article analyzes experimental work in synthetic biology on different types of interactions between artificial and natural systems, more specifically: between protocells and between biological living cells and protocells. It discusses how concepts such as control, cognition, communication can be used to characterize these interactions from a theoretical point of view, which criteria of relevance and evaluation of synthetic models can be applied to these cases, and what are their limits.

]]>
<![CDATA[Assessment of agricultural biomass residues to replace fossil fuel and hydroelectric power energy: A spatial approach]]> https://www.researchpad.co/product?articleinfo=N7977cf9c-c014-499d-8bfe-21622fa36344

Abstract

Despite the recent discoveries of considerable fossil fuel reserves, Brazil is one of the only great economic and industrial powers with very high amounts of renewable energy in its electricity matrix. Approximately 79.3% of the electric energy supply comes from renewable resources, of which hydroelectric power represents 70.6%. The two primary concerns regarding hydroelectricity are the damage caused to the environment by the construction of dams and the uncertainty of the supply in cases of long drought seasons. This article presents an analysis on the availability and energy exploitation of sugarcane straw and forest residues derived from eucalyptus for decentralized generation using a Geographic Information System–based model. The potential bioelectricity and bioethanol production from sugarcane and eucalyptus biomass in the Administrative Region of Campinas (ARC) is higher than the demand in this region. The results provide guidelines for designing alternatives to the intended Nationally Determined Contributions in Brazil within the scope of the ARC, and they can be used to provide energy empowerment, electric matrix diversification, and new policies that address the residue availability and demand.

]]>
<![CDATA[FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals]]> https://www.researchpad.co/product?articleinfo=N0870a0ef-ad7f-485c-8234-e0ef66109b19

Abstract

Motivation

MicroRNA (miRNA) target prediction algorithms do not generally consider biological context and therefore generic target prediction based on seed binding can lead to a high level of false-positive predictions. Here, we present FilTar, a method that incorporates RNA-Seq data to make miRNA target prediction specific to a given cell type or tissue of interest.

Results

We demonstrate that FilTar can be used to: (i) provide sample specific 3′-UTR reannotation; extending or truncating default annotations based on RNA-Seq read evidence and (ii) filter putative miRNA target predictions by transcript expression level, thus removing putative interactions where the target transcript is not expressed in the tissue or cell line of interest. We test the method on a variety of miRNA transfection datasets and demonstrate increased accuracy versus generic miRNA target prediction methods.

Availability and implementation

FilTar is freely available and can be downloaded from https://github.com/TBradley27/FilTar. The tool is implemented using the Python and R programming languages, and is supported on GNU/Linux operating systems.

Supplementary information

Supplementary data are available at Bioinformatics online.

]]>
<![CDATA[PheGWAS: a new dimension to visualize GWAS across multiple phenotypes]]> https://www.researchpad.co/product?articleinfo=N596deaae-a8ce-4fc4-9255-0a794300adb7

Abstract

Motivation

PheGWAS was developed to enhance exploration of phenome-wide pleiotropy at the genome-wide level through the efficient generation of a dynamic visualization combining Manhattan plots from GWAS with PheWAS to create a 3D ‘landscape’. Pleiotropy in sub-surface GWAS significance strata can be explored in a sectional view plotted within user defined levels. Further complexity reduction is achieved by confining to a single chromosomal section. Comprehensive genomic and phenomic coordinates can be displayed.

Results

PheGWAS is demonstrated using summary data from Global Lipids Genetics Consortium GWAS across multiple lipid traits. For single and multiple traits PheGWAS highlighted all 88 and 69 loci, respectively. Further, the genes and SNPs reported in Global Lipids Genetics Consortium were identified using additional functions implemented within PheGWAS. Not only is PheGWAS capable of identifying independent signals but also provides insights to local genetic correlation (verified using HESS) and in identifying the potential regions that share causal variants across phenotypes (verified using colocalization tests).

Availability and implementation

The PheGWAS software and code are freely available at (https://github.com/georgeg0/PheGWAS).

Supplementary information

Supplementary data are available at Bioinformatics online.

]]>
<![CDATA[Bioinformatics Analysis for Multiple Gene Expression Profiles in Sepsis]]> https://www.researchpad.co/product?articleinfo=Nbda98e63-9ed8-47a0-a3a5-0e78b2a3b7c2

Background

This work aimed to screen key biomarkers related to sepsis progression by bioinformatics analyses.

Material/Methods

The microarray datasets of blood and neutrophils from patients with sepsis or septic shock were downloaded from Gene Expression Omnibus database. Then, differentially expressed genes (DEGs) from 4 groups (sepsis versus normal blood samples; septic shock versus normal blood samples; sepsis neutrophils versus normal controls and septic shock neutrophils versus controls) were respectively identified followed by functional analyses. Subsequently, protein–protein network was constructed, and key functional sub-modules were extracted. Finally, receiver operating characteristic analysis was conducted to evaluate diagnostic values of key genes.

Results

There were 2082 DEGs between blood samples of sepsis patients and controls, 2079 DEGs between blood samples of septic shock patients and healthy individuals, 6590 DEGs between neutrophils from sepsis and controls, and 1056 DEGs between neutrophils from septic shock patients and normal controls. Functional analysis showed that numerous DEGs were significantly enriched in ribosome-related pathway, cell cycle, and neutrophil activation involved in immune response. In addition, TRIM25 and MYC acted as hub genes in protein–protein interaction (PPI) analyses of DEGs from microarray datasets of blood samples. Moreover, MYC (AUC=0.912) and TRIM25 (AUC=0.843) had great diagnostic values for discriminating septic shock blood samples and normal controls. RNF4 was a hub gene from PPI analyses based on datasets from neutrophils and RNF4 (AUC=0.909) was capable of distinguishing neutrophil samples from septic shock samples and controls.

Conclusions

Our findings identified several key genes and pathways related to sepsis development.

]]>