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ABSTRACT Cirrhosis is associated with brain dysfunction known as hepatic encephalopathy (HE). The mechanisms behind HE are unclear although hyperammonemia and systemic inflammation through

gut dysbiosis have been proposed. We aimed to define the individual contribution of specific gut bacterial taxa towards astrocytic and neuronal changes in brain function using multi-modal

MRI in patients with cirrhosis. 187 subjects (40 controls, 147 cirrhotic; 87 with HE) underwent systemic inflammatory assessment, cognitive testing, stool microbiota analysis and brain MRI

analysis. MR spectroscopy (MRS) changes of increased Glutamate/glutamine, reduced myo-inositol and choline are hyperammonemia-associated astrocytic changes, while diffusion tensor imaging

(DTI) demonstrates changes in neuronal integrity and edema. Linkages between cognition, MRI parameters and gut microbiota were compared between groups. We found that HE patients had a

significantly worse cognitive performance, systemic inflammation, dysbiosis and hyperammonemia compared to controls and cirrhotics without HE. Specific microbial families (autochthonous taxa

negatively and Enterobacteriaceae positively) correlated with MR spectroscopy and hyperammonemia-associated astrocytic changes. On the other hand _Porphyromonadaceae_, were only correlated

with neuronal changes on DTI without linkages with ammonia. We conclude that specific gut microbial taxa are related to neuronal and astrocytic consequences of cirrhosis-associated brain

dysfunction. SIMILAR CONTENT BEING VIEWED BY OTHERS IMPAIRED BRAIN FUNCTION IMPROVED BY L-CARNITINE IN PATIENTS WITH CIRRHOSIS: EVALUATION USING NEAR-INFRARED SPECTROSCOPY Article Open

access 11 August 2020 CEREBRAL SMALL VESSEL DISEASE BURDEN IS ASSOCIATED WITH DECREASED ABUNDANCE OF GUT _BARNESIELLA INTESTINIHOMINIS_ BACTERIUM IN THE FRAMINGHAM HEART STUDY Article Open

access 21 August 2023 THE GUT MICROBIOME IS ASSOCIATED WITH BRAIN STRUCTURE AND FUNCTION IN SCHIZOPHRENIA Article Open access 07 May 2021 INTRODUCTION Hepatic encephalopathy (HE) or brain

dysfunction due to cirrhosis represents a major healthcare burden in subjects with cirrhosis1. Cirrhosis is associated with dysbiosis or an altered gut microbiota that potentiates a systemic

pro-inflammatory milieu2. This inflammatory environment can potentiate neuro-inflammation, brain edema and ultimately neuronal dysfunction in the setting of hyperammonemia3,4. However the

specific contribution of the gut microbiota towards neuro-inflammation, edema and hyperammonemia in cirrhosis is unclear. Brain imaging in patients with cirrhosis and HE reveals differing

impact on neuronal fibers and astrocytes. MR spectroscopy (MRS) findings reveal higher glutamine + glutamate and compensatorily lower myoinositol and choline in astrocytes while diffusion

tensor imaging of long white-matter neuronal tracts shows impaired axonal integrity and edema5. HE treatments, which mostly act on the gut milieu, have varied impacts on MRS and DTI. While

lactulose improves MRS, rifaximin and LOLA do not6,7,8. In contrast rifaximin therapy and lactulose can both favorably impact neuronal integrity as demonstrated by diffusion tensor imaging

(DTI)8,9. While smaller-scale studies have shown that gut bacteria are associated with cognitive performance as a whole, the linkage between microbial taxa and individual components of the

impaired brain response i.e. neuronal and astrocytic impairment is unclear10,11. Given the immense complexity of the gut microbiota and their specific modulation with these therapies, the

relationship between gut taxa and brain MR consequences becomes relevant in defining focused treatment targets. The aim of this study was to define the linkage between gut microbial taxa and

brain MR consequences of neuronal and astrocytic dysfunction in patients with cirrhosis. RESULTS We recruited 187 subjects for this study; 40 healthy controls and 147 cirrhotics.

Eighty-five cirrhotic patients had HE, which was controlled on lactulose and rifaximin. All subjects underwent MRS and 74 subjects underwent DTI. The subjects were age-balanced but controls

had a significantly better cognitive performance and lower systemic inflammation than cirrhotic patients (Table 1), especially those with HE. CIRRHOTIC PATIENTS AND THOSE WITH HE HAD WORSE

COGNITION, INFLAMMATION AND BRAIN MR FINDINGS On MRS, there were significant differences between controls and cirrhotics on creatine ratios of Glx (WM: 1.7 ± 0.3 vs. 2.5 ± 0.8, p < 

0.0001; PGM: 1.9 ± 0.2 vs. 2.3 ± 0.7, p = 0.001; ACC: 2.1 ± 0.3 vs. 2.7 ± 0.7, p = 0.004) and mI (WM: 1.0 ± 0.1 vs. 0.5 ± 0.4, p < 0.0001; PGM: 0.8 ± 0.1 vs. 0.5 ± 0.3, p < 0.0001;

ACC: 0.7 ± 0.1 vs. 0.5 ± 0.3, p = 0.001) but not on Choline levels, indicating the impact of hyperammonemia. Cirrhotics with HE were significantly more advanced from the cirrhosis severity

and cognitive impairment perspective compared to cirrhotics without HE (Table 1). Using the PHES and ICT cut-offs separately based on our published healthy control data12, a significantly

higher proportion of prior HE patients had evidence of covert HE by PHES (n = 75, 88% vs. n = 15, 24%,p < 0.001) and by ICT (n = 68, 80% vs n = 20, 32%). Cirrhotics with HE subjects had

higher Glx and lower mI in all three volumes of interest and reduced Cho in all volumes apart from gray matter. In the 74 subjects who underwent DTI, 42 patients had prior HE and had similar

overall demographic and cirrhosis severity characteristics compared to the entire HE group. HE patients had a higher CS and lower FA compared to no-HE patients (Table 2). No changes in MD

between groups were identified. CIRRHOTICS, ESPECIALLY HE PATIENTS, DEMONSTRATED DYSBIOSIS AND ALTERED MICROBIAL FUNCTIONALITY As expected there were significant differences in the

microbiota composition between cirrhotics with and without HE as well as between controls and cirrhotic subjects on UNIFRAC (all p values < = 1.0e − 02). Specifically controls had a

significantly higher proportion of autochthonous bacterial families than cirrhotics (Fig. 1A). Similarly cirrhotic patients with HE had a higher relative abundance of these autochthonous

families and a higher abundance pattern of _Staphylococcaceae, Enterococcaceae, Porphyromonadaceae_ and _Lactobacillaceae_ compared to controls and cirrhotics without HE(Table 3/Fig. 1B). On

PiCRUST, significant differences in predicted stool bacterial functionality was found related to functions of endotoxin and endotoxin-protein synthesis and a shift towards an ammoniagenic

amino acid profile (degradation of branched-chain and metabolism of aromatic amino acids) in controls compared to cirrhotics and in HE patients compared to no-HE cirrhotic patients

(Supplementary Fig. 1A,B). BRAIN MRS AND DTI ARE CORRELATED WITH DIFFERENT GUT MICROBIAL FAMILIES On MRS, there were consistent negative linkages between autochthonous families and positive

ones between potentially pathogenic ones to brain consequences of hyperammonemia i.e. increased Glx and lower mI and Cho, in controls and cirrhotic patients (Figs 2, 3, 4, 5). These brain

changes were also linked with MELD score and serum ammonia levels. These interactions were significantly more complex in patients with HE in whom the non-autochthonous families were

positively linked with poor cognition, brain MRS findings and ammonia. On DTI, a different picture emerged with respect to the families. The family _Porphyromonadaceae_ was linked with all

aspects of DTI. On FA, _Porphyromonadaceae_ relative abundance was correlated negatively with corpus callosum splenium (r = −0.5, p = 0.01), right inferior longitudinal fasciculus (r = −0.4,

p = 0.05), posterior internal capsule (left r = −0.5, p = 0.01, right r = −0.5, p = 0.02), posterior white matter (left r = −0.5, p = 0.01, right p = 0.6, p=0.004). In contrast,

_Prevotellaceae_ relative abundance was positively related with right posterior white matter (r = 0.5, p = 0.04). On spherical isotropy, we found positive correlations between

_Porphyromonadaceae_ and corpus callosum splenium (r = 0.5, p = 0.009), right inferior longitudinal fasciculus (r = 0.4, p = 0.04) and posterior white matter (left r = 0.45, p = 0.03, right

r = 0.6, p = 0.005). There was a significant positive correlation on mean diffusivity between _Porphyromonadaceae_ on corpus callosum genu (r = 0.44, p = 0.03), corpus callosum splenium (r =

 0.58, p=0.003), left and right posterior white matter (r = 0.7, p < 0.001 for both), left and right frontal white matter (r = 0.4,p = 0.05 for both)and the right uncinate fasciculus (r =

 0.4, p = 0.05). Similarly significant positive correlations were found between _Veillonellaceae_ and mean diffusivity in the bilateral anterior internal capsule (r = 0.4, p = 0.03), corpus

callosum splenium (r = 0.4, p = 0.04), right cingulum (r = 0.5, p = 0.03), external capsule (left r = 0.5, p = 0.03, right r = 0.4, p = 0.05), posterior internal capsule (left r = 0.5, p = 

0.02, right r = 0.4, p = 0.05)and the right uncinate fasciculus (r = 0.5, p = 0.004). DISCUSSION The current study is the largest experience of the altered gut-liver-brain axis in humans

with cirrhosis. We found that specific gut microbial changes are linked with systemic inflammation, ammonia and ultimately with neuronal and astrocytic dysfunction in cirrhotic patients,

especially those with HE. Although there is mounting evidence from human and animal studies that gut microbiota modification can impact brain function in cirrhosis, specific linkages between

brain MRI and individual bacterial taxa have not been fully elucidated. While therapies for HE are overwhelmingly gut-based, there is often an additive role for synergistic, systemic

ammonia-scavenging treatments in humans1. There is patho-physiologic evidence supporting both hyperammonemia and inflammation in the causation of HE, with differing effects on neurons and

astrocytes13,14. It has been hypothesized that in humans the dysbiotic gut microbiota is the major source of both ammonia and the systemic pro-inflammatory milieu15. Specifically with the

progression of cirrhosis, the relative reduction in autochthonous commensals and the increase in microbiota such as those belonging to _Enterobacteriaceae_ and _Streptococcaceae_ that can

produce endotoxin and ammonia through their urease activity respectively11. We found indeed that in the human context, the brain MRS, which is largely related to hyperammonemia-associated

astrocytic changes, was related to one set of microbiota while brain DTI, which is related to neuronal integrity and edema, was related to another group of bacteria8. However in patients

with HE there is concurrent hyperammonemia and systemic inflammation, therefore differentiating their individual impact on brain MRI results is not possible. The microbial families that were

negatively linked with brain glial MRS manifestations of ammonia (high Glx and low mI and Cho) were autochthonous families (_Lachospiraceae, Ruminococcaeae_ and Clostridiales XIV). In

contrast families such as _Streptococcacae, Enterobacteriaceae, Lactobacillaceae_ and _Peptostreptococcaceae_ were related positively with ammonia, MELD score and brain MRS manifestations.

These autochthonous taxa are predominant in healthy control studies and mediate several important benefits, such as production of short-chain fatty acids and 7-α de-hydroxylation of bile

acids in hosts16,17. With the progression of cirrhosis in humans, their reduction parallels an increase in potentially harmful taxa such as _Streptococcacae_ and _Enterobacteriaceae_2.

Interestingly, taxa that were associated with DTI were distinct i.e. _Porphyromonadaceae_ relative abundance, from that associated with MRS. Relative abundance of _Porphyromonadaceae_

mirrors a situation of increasing diffuse white matter interstitial edema that is often seen in HE, due to negative associations with FA and positive ones with spherical isotropy and mean

diffusivity6. _Porphyromonadaceae_ have been implicated in cognitive dysfunction and progression of fatty liver disease in prior human and animal studies10,18. They are predominantly oral in

origin but have been implicated in systemic and hepatic inflammation in animal studies that extend beyond the local oral milieu18,19. Our findings now associate this family with neuronal

dysfunction and brain edema. Of note _Porphyromonadaceae_ abundance was not related to ammonia in this dataset. We have reported earlier in a smaller sample size that cognitive dysfunction

in cirrhosis is related with decrease in autochthonous families and increase in _Porphyromonadaceae_10. However our aggregate results indicate that the individual impact of microbial

families may be mediated through impact on different cell types i.e. neurons and astrocytes, in the ultimate pathogenesis of HE-related cognitive dysfunction. Despite prior smaller studies

linking cognition with stool microbiota, this is the largest experience linking gut microbiota with brain MRI results that gives us an understanding of the impaired gut-liver-brain axis in

cirrhosis. This is an association study that helps in hypothesis generation, specifically related to the differences in linkages between bacteria related and unrelated to ammonia in the

pathogenesis of cognitive dysfunction. Given that this was a clinical sample, all of our patients were on treatment with lactulose or rifaximin. However, it would have been unethical to

withdraw this therapy and in a cross-sectional manner, use of these medications did not appreciably reduce systemic inflammation or endotoxemia. We also used the clinically reproducible

definition of prior HE instead of covert HE definitions that are variable based on gold standards1,12. Also as expected, most prior HE patients indeed had evidence of covert HE. It is also

interesting that prior HE treatment studies are varied in their impact on DTI and MRS based on the agent employed, however concurrent microbiota analysis was not performed in most

studies7,8,9. Therefore linking changes in microbiota with changes in brain MRI over time is needed in further studies. Interestingly, _Lactobacillaceae_, which often have probiotic species,

had an increased relative abundance in the stool of HE patients. It was assumed in past human studies that the increased _Lactobacillaceae_ abundance was due to the use of lactulose for HE

therapy20. However, our prior and current human results and prior animal CCL4 studies demonstrate that _Lactobacillaceae_ increase may be a part of an expansion of selected urease-producing

Firmicutes in humans and mouse cirrhosis models2,21,22. An increased cerebral lactate, which has now been hypothesized to be synergistic with glutamine for HE development in some animal

models, could also be precipitated by _Lactobacillaceae_ spp23. We conclude that specific bacterial taxa are associated with astrocytic changes and neuronal changes on brain MRI in humans

with cirrhosis and HE. Specific alterations, which provide potential novel therapeutic targets to restore intestinal and neuronal homeostasis, in the gut microbial milieu could impact

different aspects of brain function in cirrhotic individuals. MATERIALS AND METHODS Outpatients with cirrhosis and age-matched healthy controls were recruited prospectively from Liver

Clinics and the community at Virginia Commonwealth University and McGuire VA Medical Centers. Cirrhosis was diagnosed using biopsy, history of frank decompensation (ascites, HE, variceal

bleeding, jaundice) or varices in a patient with chronic liver disease or those with radiological features of cirrhosis24. We excluded subjects who were unable to provide informed consent,

those with a mini-mental status exam result <25, those who had an uncertain diagnosis of cirrhosis, those with recent (<6 months history) of alcohol or illicit drug misuse and those on

absorbable antibiotics within the last 6 weeks. We only included those with prior type C HE who were controlled on lactulose or rifaximin for at least 3 months with good adherence per

clinic notes and interview before enrollment1. Healthy controls were subjects without chronic diseases who were not receiving any regular medications. All subjects gave written informed

consent and underwent a cognitive assessment consisting of a standard paper-pencil battery of psychometric hepatic encephalopathy score (PHES, number connection tests A and B, digit symbol,

serial dotting and line tracing tests) and the inhibitory control test (lures and targets are outcomes)25. Cirrhotic patients were also divided into covert HE or not using 2 gold standard

tests (PHES and ICT) based on our published control performance12. Blood was drawn for analysis of venous ammonia, endotoxin, inflammatory cytokines (IL-1β, TNF-α, and IL-6) and the MELD

score (validated logarithmic index of serum bilirubin, creatinine and INR)26. Endotoxin and cytokine analysis was performed using validated methods at Assaygate (Ijamsville, MD)27. Subjects

were asked to provide a fresh stool sample for analysis of microbiota relative abundance in a container with RNAlater as described in prior studies28. This protocol was approved by the

Institutional Review Boards at VCU Medical Center and Richmond VA Medical Center and all research activities were carried out in accordance with approved guidelines. SAMPLE ANALYSIS

MICROBIOTA Stool was collected and DNA extracted using published techniques27. We first used Length Heterogeneity PCR (LH-PCR) fingerprinting of the 16S rRNA to rapidly survey our samples

and standardize the community amplification. We then interrogated the microbial taxa associated using Multitag Pyrosequencing (MTPS)29. This technique allows the rapid sequencing of multiple

samples at one time. Microbiome Community Fingerprinting: About 10 ng of extracted DNA was amplified by PCR using a fluorescently labeled forward primer 27F (5′-(6FAM) AGAGTTTGATCCTGGCTCA

G-3′) and unlabeled reverse primer 355R′ (5′-GCTGCCTCCCGTAGGAGT-3′). Both primers are universal primers for bacteria. The LH-PCR products were diluted according to their intensity on agarose

gel electrophoresis and mixed with ILS-600 size standards (Promega) and HiDi Formamide (Applied Biosystems, Foster City, CA). The diluted samples were then separated on a ABI 3130xl

fluorescent capillary sequencer (Applied Biosystems, Foster City, CA) and processed using the Genemapper™ software package (Applied Biosystems, Foster City, CA). Normalized peak areas were

calculated using a custom PERL script and operational taxonomic units (OTUs) constituting less than 1% of the total community from each sample were eliminated from the analysis to remove the

variable low abundance components within the communities. MTPS Specifically, we have generated a set of 96 emulsion PCR fusion primers that contain the 454 emulsion PCR linkers on the 27F

and 355R primers and a different 8 base “barcode” between the A adapter and 27F primer. Thus, each fecal sample was amplified with unique bar-coded forward 16S rRNA primers and then up to 96

samples were pooled and subjected to emulsion PCR and pyrosequenced using a GS-FLX pyrosequencer (Roche). Data from each pooled sample were “deconvoluted” by sorting the sequences into bins

based on the barcodes using custom PERL scripts. Thus, we were able to normalize each sample by the total number of reads from each barcode. We have noted that ligating tagged primers to

PCR amplicons distorts the abundances of the communities and thus it is critical to incorporate the tags during the original amplification step29. MICROBIOME COMMUNITY ANALYSIS We identified

the taxa present in each sample using the Bayesian analysis tool in Version 10 of the Ribosomal Database Project (RDP10). The abundances of the bacterial identifications were then

normalized using a custom PERL script and genera present at >1% of the community were tabulated. We chose this cutoff because of our _a priori_ assumption that genera present in <1% of

the community vary between individuals and have minimal contribution to the functionality of that community and 2,000 reads per sample will only reliably identify community components that

are greater than 1% in abundance. ANALYSIS OF MICROBIOTA QIIME analysis, LEFSe and Kruskal-Wallis tests were used to evaluate changes in overall microbial abundance30. We also performed

Metastats to evaluate changes in relative abundance between groups with correction for the false discovery rate (FDR)31.Predicted bacterial functions were then assessed using PiCRUST

(phylogenetic investigation of communities by reconstruction of unobserved states)32. BRAIN MRI EVALUATION A subset then underwent multi-modal brain MRI assessment on the day of the

cognitive testing and sample collection. All images were acquired on a 3T GE Signa scanner using a quadrature birdcage RF head coil. We tested two strategies to study the impact of cirrhosis

in astrocytes and neurons8,33. For the impact of hyperammonemia-associated astrocytic changes, MR spectroscopy was performed while neuronal white matter integrity was studied using

diffusion tensor imaging (DTI). For MRS, 1H-single voxel spectra were acquired for pre-specified separate volumes of interest (2 × 2 × 2 cm) in the Right Posterior White Matter (RPWM),

anterior cingulate cortex (ACC) and Posterior Gray Matter (PGM) using point-resolved spectroscopy with automated shimming and water suppression (TE/TR/NS/Volume = 35/1500/128/8 cm3). These

specific voxels have been used in several prior studies and have a representation of largely white matter (RPWM), gray matter (PGM) and those with both (ACC)33,34. DTI was performed using a

single shot, spin-echo echoplanar imaging sequence (FOV = 256 mm, slice thickness = 2.0 mm, 70 contiguous axial slices, 128 × 128 matrix, TR = 9000 ms, TE = 80 ms, b-value = 1000 s/mm2, #b0

images = 6, #Diffusion Directions = 64). MRI ANALYSIS MRS The choline (Cho), creatine (Cr), myo-inositol (mI) and glutamate + glutamine (Glx) complex peak areas were computed using LCModel

software and their creatine ratios were used as in prior studies35,36,37. A high Glx and low mI and Cho creatine ratios are associated with cirrhosis and hyperammonemia. DTI: Whole brain

voxel-wise maps of Fractional Anisotropy (FA), mean diffusivity (MD) and spherical isotropy (CS) were constructed from pre-processed DTI images using tools in FSL 5.0.2 (FMRIB’s Software

Library, www.fmrib.ox.ac.uk/fsl)38,39,40,41. These maps were then transformed to standard space using a combination of nonlinear and affine registration tools. The _a priori_ ROIs for major

white matter tracts (Corpus callosum, internal capsule, inferior and superior longitudinal fasciculi, frontal and posterior white matter, uncinate fasciculi, insula and corticospinal tracts)

were created using the DTI-based probabilistic white matter atlases42,43 using a probability threshold of 40%. Mean FA, MD and CS values were extracted from individual maps. A low FA and

high CS and MD indicate interstitial edema. CORRELATION NETWORK ANALYSIS We created correlation networks using tools in the Galaxy Portal at the Microbiome Analysis Center and only included

nodes consisting of microbiota, MELD score, cognitive tests and creatine ratios of mI, Cho and Glx in all three regions of interest which had a p value <0.01 and correlation coefficient

of >0.6 or <−0.6. These networks were created for controls and cirrhotic subjects and then also within cirrhotic subjects into those with and without prior HE44. We then analyzed

correlation differences between cirrhotics with and without HE and these were then visualized in Cytoscape45. ADDITIONAL INFORMATION HOW TO CITE THIS ARTICLE: Ahluwalia, V. _et al_. Impaired

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Google Scholar  Download references ACKNOWLEDGEMENTS Funded partly using grants from NIDDK Grant R01DK089713, VA Merit Review grant CX10076, and the McGuire Research Institute (JSB). The

authors acknowledge Mary Beatty-Brooks from McGuire VAMC for help with figures. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Gastroenterology, Hepatology and Nutrition, Virginia

Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA , Vishwadeep Ahluwalia, Melanie B White, Ariel B Unser, Andrew Fagan, Kalyani Daita, Douglas M Heuman & 

Jasmohan S Bajaj * Microbiome Analysis Center, George Mason University, Manassas, Virginia, USA Naga S Betrapally, Patrick M Gillevet & Masoumeh Sikaroodi * Microbiology and Immunology,

Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA Phillip B Hylemon & Huiping Zhou Authors * Vishwadeep Ahluwalia View author publications You can

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Scholar * Andrew Fagan View author publications You can also search for this author inPubMed Google Scholar * Kalyani Daita View author publications You can also search for this author

inPubMed Google Scholar * Douglas M Heuman View author publications You can also search for this author inPubMed Google Scholar * Huiping Zhou View author publications You can also search

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You can also search for this author inPubMed Google Scholar CONTRIBUTIONS J.S.B., P.M.G. and P.B.H. were involved in conceptualization of the study and in all aspects, P.M.G., K.D., H.Z.,

M.S. and N.S.B. were involved in microbiota and systems biology analysis, J.S.B., V.A., M.B.W., A.B.U., A.F. and D.M.H. were involved in recruitment and human study activities, all authors

were involved in critical revision of this manuscript. CORRESPONDING AUTHOR Correspondence to Jasmohan S Bajaj. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing

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http://creativecommons.org/licenses/by/4.0/ Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Ahluwalia, V., Betrapally, N., Hylemon, P. _et al._ Impaired Gut-Liver-Brain Axis in

Patients with Cirrhosis. _Sci Rep_ 6, 26800 (2016). https://doi.org/10.1038/srep26800 Download citation * Received: 26 February 2016 * Accepted: 10 May 2016 * Published: 26 May 2016 * DOI:

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