Abstract:
:The impacts of environmental chemicals on the decline of kidney function have been suggested by a limited number of statistical and animal studies. Thus, those exposures may be modifiable risk factors for chronic kidney disease. Some of the chemicals, such as Perfluoroalkyl acid (PFA), are pervasive throughout our environment, determining their health effects is an important public health concern. In this study, we examined cross-sectional data from the 2009-2010 cycle of the National Health and Nutrition Examination Survey (NHANES) using a statistical causal inference method-generalized propensity score method, to determine the links between concentrations of several major environmental chemicals and kidney function measured by the estimated glomerular filtration rate (eGFR). Various generalized propensity score estimation methods including Hirano-Imbens, additive spline, and a generalized additive model were compared. Among the examined environmental chemicals, each of the statistical models used associated an increase in PFA concentration with a decline in eGFR. We conclude that PFA is a modifiable risk factor for chronic kidney disease and the statistical causal method produces credible results in estimating the effect of chemical exposures on a continuous measure of kidney functions with an observational dataset.
journal_name
Comput Struct Biotechnol Jjournal_title
Computational and structural biotechnology journalauthors
Zhao J,Hinton P,Chen J,Jiang Jdoi
10.1016/j.csbj.2019.12.001subject
Has Abstractpub_date
2019-12-17 00:00:00pages
93-99issn
2001-0370pii
S2001-0370(19)30172-2journal_volume
18pub_type
杂志文章abstract::Runs of Homozygosity (RoHs) are popular among geneticists as the footprint of demographic processes, evolutionary forces and inbreeding in shaping our genome, and are known to confer risk of Mendelian and complex diseases. Notwithstanding growing interest in their study, there is unmet need for reliable and rapid meth...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.07.003
更新日期:2020-07-14 00:00:00
abstract::Infectious diseases, including vector-borne diseases transmitted by arthropods, are a leading cause of morbidity and mortality worldwide. In the era of big data, addressing broad-scale, fundamental questions regarding the complex dynamics of these diseases will increasingly require the integration of diverse datasets ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.06.031
更新日期:2020-06-25 00:00:00
abstract::The high mutation rate in retroviruses is one of the leading causes of drug resistance. In human immunodeficiency virus type-1 (HIV-1), synergistic mutations in its protease and the protease substrate - the Group-specific antigen (Gag) polyprotein - work together to confer drug resistance against protease inhibitors a...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.12.022
更新日期:2020-12-23 00:00:00
abstract::The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulat...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.11.028
更新日期:2020-11-19 00:00:00
abstract::Allosteric modulation provides an effective avenue for selective and potent enzyme inhibition. Here, we summarize and critically discuss recent advances on the mechanisms of allosteric partial agonists for three representative signalling enzymes activated by cyclic nucleotides: the cAMP-dependent protein kinase (PKA),...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.10.026
更新日期:2020-11-11 00:00:00
abstract::Natural products (NPs) are an indispensable source of drugs and they have a better coverage of the pharmacological space than synthetic compounds, owing to their high structural diversity. The prediction of their interaction profiles with druggable protein targets remains a major challenge in modern drug discovery. Ex...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2019.08.008
更新日期:2019-10-28 00:00:00
abstract::Coronaviruses are a group of enveloped RNA viruses that are diversely found in humans and now declared a global pandemic by the World Health Organization in March 2020. The population's susceptibility to these highly pathogenic coronaviruses has contributed to large outbreaks, evolved into public health events, and ra...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.11.011
更新日期:2020-01-01 00:00:00
abstract::Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2019.09.010
更新日期:2019-10-25 00:00:00
abstract:Motivation:With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thu...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.08.011
更新日期:2020-08-27 00:00:00
abstract::Buried active sites of enzymes are connected to the bulk solvent through a network of hydrophobic channels. We developed a discretized model that can accurately predict ligand transport along hydrophobic channels up to six orders of magnitude faster than any other existing method. The non-dimensional nature of the mod...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2019.06.001
更新日期:2019-06-11 00:00:00
abstract::With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2015.10.006
更新日期:2015-11-30 00:00:00
abstract::Lung cancer is the leading worldwide cause of cancer mortality, however, neither curative treatments nor substantial prolonged survival has been achieved, highlighting the need for investigating new proteins responsible for its development and progression. IKKα is an essential protein for cell survival and differentia...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2019.02.003
更新日期:2019-02-07 00:00:00
abstract::Basic chemometric methods for making empirical regression models for QSPR/QSAR are briefly described from a user's point of view. Emphasis is given to PLS regression, simple variable selection and a careful and cautious evaluation of the performance of PLS models by repeated double cross validation (rdCV). A demonstra...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.5936/csbj.201302007
更新日期:2013-03-02 00:00:00
abstract::Although the potential advantages of clinical germline genome editing (GGE) over currently available methods are limited, the implementation of GGE in the clinic has been proposed and discussed. Ethical issues related to such an application have been extensively debated, meanwhile, seemingly less attention has been pa...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.03.014
更新日期:2020-03-21 00:00:00
abstract:Purpose:Mutation-induced variation of protein-ligand binding affinity is the key to many genetic diseases and the emergence of drug resistance, and therefore predicting such mutation impacts is of great importance. In this work, we aim to predict the mutation impacts on protein-ligand binding affinity using efficient s...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.02.007
更新日期:2020-02-20 00:00:00
abstract:Purpose:Visceral fat is an independent risk factor for metabolic and cardiovascular disease. The study aimed to investigate the associations between gut microbiome and visceral fat. Methods:We recruited 32 obese adults and 30 healthy controls at baseline. Among the obese subjects, 14 subjects underwent laparoscopic sl...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.09.026
更新日期:2020-09-20 00:00:00
abstract::Membrane fatty acid desaturases are a diverse superfamily of enzymes that catalyze the introduction of double bonds into fatty acids. They are essential in a range of metabolic processes, such as the production of omega-3 fatty acids. However, our structure-function understanding of this superfamily is still developin...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2016.08.003
更新日期:2016-09-12 00:00:00
abstract::Numerous bioactive natural products are synthesised by modular polyketide synthases. These compounds can be made in high yield by native multienzyme assembly lines. However, formation of analogues by genetically engineered systems is often considerably less efficient. Biochemical studies on intact polyketide synthase ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.5936/csbj.201210010
更新日期:2012-11-17 00:00:00
abstract::Post-transcriptional RNA modification occurs on all types of RNA and plays a vital role in regulating every aspect of RNA function. Thanks to the development of high-throughput sequencing technologies, transcriptome-wide profiling of RNA modifications has been made possible. With the accumulation of a large number of ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.06.010
更新日期:2020-06-13 00:00:00
abstract::ChIP-seq experiments identify genome-wide profiles of DNA-binding molecules including transcription factors, enzymes and epigenetic marks. Biological replicates are critical for reliable site discovery and are required for the deposition of data in the ENCODE and modENCODE projects. While early reports suggested two r...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.5936/csbj.201401002
更新日期:2014-01-31 00:00:00
abstract::Interactions between their transmembrane domains (TMDs) frequently support the assembly of single-pass membrane proteins to non-covalent complexes. Yet, the TMD-TMD interactome remains largely uncharted. With a view to predicting homotypic TMD-TMD interfaces from primary structure, we performed a systematic analysis o...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.09.035
更新日期:2020-10-07 00:00:00
abstract::As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molec...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.08.004
更新日期:2020-08-06 00:00:00
abstract::Tolypocladium guangdongense has a similar metabolite profile to Ophiocordyceps sinensis, a highly regarded fungus used for traditional Chinese medicine with high nutritional and medicinal value. Although the genome sequence of T. guangdongense has been reported, relatively little is known about the regulatory networks...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.07.014
更新日期:2020-07-25 00:00:00
abstract::Immunotherapy is the revolution in cancer treatment of this last decade. Among multiple approaches able to harness the power of the immune system against cancer, T cell based immunotherapies represent one of the most successful examples. In particular, biotechnological engineering of protein structures, like the T cel...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2016.09.003
更新日期:2016-09-28 00:00:00
abstract::Metabolomics is a relatively new high-throughput technology that aims at measuring all endogenous metabolites within a biological sample in an unbiased fashion. The resulting metabolic profiles may be regarded as functional signatures of the physiological state, and have been shown to comprise effects of genetic regul...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.5936/csbj.201301009
更新日期:2013-03-22 00:00:00
abstract::Microsatellite instability (MSI) is a genomic property of the cancers with defective DNA mismatch repair and is a useful marker for cancer diagnosis and treatment in diverse cancer types. In particular, MSI has been associated with the active immune checkpoint blockade therapy response in cancer. Most of computational...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2020.03.007
更新日期:2020-03-19 00:00:00
abstract::Understanding the pathogenesis of disease is instrumental in delineating its progression mechanisms and for envisioning ways to counteract it. In the process, animal models represent invaluable tools for identifying disease-related loci and their genetic components. Amongst them, the laboratory rat is used extensively...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2015.11.006
更新日期:2015-11-26 00:00:00
abstract::This mini review addresses recent developments in computational enzyme design. Successful protocols as well as known issues and limitations are discussed from an energetic perspective. It will be argued that improved results can be obtained by including a dynamic treatment in the design protocol. Finally, a molecular ...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.5936/csbj.201209009
更新日期:2012-10-23 00:00:00
abstract::Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing these processes. Biomed...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章,评审
doi:10.1016/j.csbj.2020.05.017
更新日期:2020-06-02 00:00:00
abstract::Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players...
journal_title:Computational and structural biotechnology journal
pub_type: 杂志文章
doi:10.1016/j.csbj.2016.02.001
更新日期:2016-02-10 00:00:00