Mapping nanoscale carrier confinement in polycrystalline graphene by terahertz spectroscopy.

Terahertz time-domain spectroscopy (THz-TDS) can be used to map spatial variations in electrical properties such as sheet conductivity, carrier density, and carrier mobility in graphene. Here, we consider wafer-scale graphene grown on germanium by chemical vapor deposition with non-uniformities and small domains due to reconstructions of the substrate during growth. The THz conductivity spectrum matches the predictions of the phenomenological Drude-Smith model for conductors with non-isotropic scattering caused by backscattering from boundaries and line defects. We compare the charge carrier mean free path determined by THz-TDS with the average defect distance assessed by Raman spectroscopy, and the grain boundary dimensions as determined by transmission electron microscopy. The results indicate that even small angle orientation variations below 5° within graphene grains influence the scattering behavior, consistent with significant backscattering contributions from grain boundaries.

Characterization of local gut microbiome and intestinal transcriptome responses to rosiglitazone treatment in diabetic db/db mice.

The gut microbiota has been implicated in the therapeutic effects of antidiabetics. It is unclear if antidiabetics directly influences gut microbiome-host interaction. Oral peroxisome proliferator-activated receptor-γ (PPAR-γ) agonists, such as rosiglitazone, are potent insulin sensitizers used in the treatment of type 2 diabetes (T2D). PPAR-γ is abundantly expressed in the intestine, making it possible that PPAR-γ agonists directly influences gut microbiome-host homeostasis. The presented study therefore aimed to characterize local gut microbiome and intestinal transcriptome responses in diabetic db/db mice following rosiglitazone treatment. Diabetic B6.BKS(D)-Leprdb/J (db/db) mice (8 weeks of age) received oral dosing once daily with vehicle (n = 12) or rosiglitazone (3 mg/kg, n = 12) for 8 weeks. Gut segments (duodenum, jejunum, ileum, caecum, and colon) were sampled for paired analysis of gut microbiota and host transcriptome signatures using full-length bacterial 16S rRNA sequencing and RNA sequencing (n = 5-6 per group). Treatment with rosiglitazone improved glucose homeostasis without influencing local gut microbiome composition in db/db mice. In contrast, rosiglitazone promoted marked changes in ileal and colonic gene expression signatures associated with peroxisomal and mitochondrial lipid metabolism, carbohydrate utilization and immune regulation. In conclusion, rosiglitazone treatment markedly affected transcriptional markers of intestinal lipid metabolism and immune regulation but had no effect on the gut microbiome in diabetic db/db mice.

Metabolic and gut microbiome changes following GLP-1 or dual GLP-1/GLP-2 receptor agonist treatment in diet-induced obese mice.

Enteroendocrine L-cell derived peptide hormones, notably glucagon-like peptide-1 (GLP-1) and glucagon-like peptide-2 (GLP-2), have become important targets in the treatment of type 2 diabetes, obesity and intestinal diseases. As gut microbial imbalances and maladaptive host responses have been implicated in the pathology of obesity and diabetes, this study aimed to determine the effects of pharmacologically stimulated GLP-1 and GLP-2 receptor function on the gut microbiome composition in diet-induced obese (DIO) mice. DIO mice received treatment with a selective GLP-1 receptor agonist (liraglutide, 0.2 mg/kg, BID) or dual GLP-1/GLP-2 receptor agonist (GUB09-145, 0.04 mg/kg, BID) for 4 weeks. Both compounds suppressed caloric intake, promoted a marked weight loss, improved glucose tolerance and reduced plasma cholesterol levels. 16S rDNA sequencing and deep-sequencing shotgun metagenomics was applied for comprehensive within-subject profiling of changes in gut microbiome signatures. Compared to baseline, DIO mice assumed phylogenetically similar gut bacterial compositional changes following liraglutide and GUB09-145 treatment, characterized by discrete shifts in low-abundant species and related bacterial metabolic pathways. The microbiome alterations may potentially associate to the converging biological actions of GLP-1 and GLP-2 receptor signaling on caloric intake, glucose metabolism and lipid handling.

Genome-Wide Comparison of Next-Generation Sequencing and qPCR Platforms for microRNA Profiling in Serum.

This study compares next-generation sequencing (NGS) technologies that have been optimized specifically for biofluid samples, with more established qPCR-based methods for profiling microRNAs in biofluids. The same patient serum samples were analyzed by NGS and qPCR, and differences in the serum microRNA profile between HBV and HCV infected patients were investigated. While there was overall good agreement between NGS and qPCR, there were some differences between the platforms, highlighting the importance of validation.

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis.

The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72 individuals using only 24 barcoded libraries.

Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics.

RESULTS: of sequencing of whole mitochondrial genome, HV1 and HV2 DNA with the second generation system (SGS) Roche 454 GS Junior were compared with results of Sanger sequencing and SNP typing with SNaPshot single base extension detected with MALDI-TOF and capillary electrophoresis. We investigated the performance of the software analysis of the data, reproducibility, ability to sequence homopolymeric regions, detection of mixtures and heteroplasmy as well as the implications of the depth of coverage. We found full reproducibility between samples sequenced twice with SGS. We found close to full concordance between the mtDNA sequences of 26 samples obtained with (1) the 454 SGS method using a depth of coverage above 100 and (2) Sanger sequencing and SNP typing. The discrepancies were primarily observed in homopolymeric regions. The 454 SGS method was able to sequence 95% of the reads correctly in homopolymers up to 4 bases, and up to 6 bases could be sequenced with similar success if the results were carefully, visually inspected. The 454 technology was able to detect mixtures or heteroplasmy of approximately 10%. We detected previously unreported heteroplasmy in the GM9947A component of the NIST human mitochondrial DNA SRM-2392 standard reference material.

Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing.

We sequenced the D21S11 locus in 77 individuals from Danish paternity cases using 454 FLX next generation sequencing (NGS) technology. All samples were also typed with the AmpFlSTR Profiler Plus or the AmpFlSTR Identifiler PCR Amplification kits as part of paternity investigations. In 18 of the confirmed trios, a genetic inconsistency was observed between one of the parents and the child at the D21S11 locus. NGS of the D21S11 locus revealed which allele had mutated from which parent to the child in 13 of these trios. All characterized mutations could be explained by single-step mutations in the longest sub-repeat of D21S11. A total of 53 of the 77 sequenced samples originated from unrelated individuals. Twenty different D21S11 alleles were detected by NGS in these individuals whereas only 13 different alleles were observed with fragment analysis. Several alleles had the same lengths but different sequences, e.g. four and three different alleles were detected by NGS with lengths determined by CE corresponding to allele 30 and allele 31, respectively.

Post-operative acute kidney injury and five-year risk of death, myocardial infarction, and stroke among elective cardiac surgical patients: a cohort study.

INTRODUCTION: The prognostic impact of acute kidney injury (AKI) on long-term clinical outcomes remains controversial. We examined the five-year risk of death, myocardial infarction, and stroke after elective cardiac surgery complicated by AKI. METHODS: We conducted a cohort study among adult elective cardiac surgical patients without severe chronic kidney disease and/or previous heart or renal transplant surgery using data from population-based registries. AKI was defined by the Acute Kidney Injury Network (AKIN) criteria as a 50% increase in serum creatinine from baseline level, acute creatinine rise of ≥26.5 µmol/L (0.3 mg/dL) within 48 hours, and/or initiation of renal replacement therapy within five days after surgery. We followed patients from the fifth post-operative day until myocardial infarction, stroke or death within five years. Five-year risk was computed by the cumulative incidence method and compared with hazards ratios (HR) from a Cox proportional hazards regression model adjusting for propensity score. RESULTS: A total of 287 (27.9%) of 1,030 patients developed AKI. Five-year risk of death was 26.5% (95% CI: 21.2 to 32.0) among patients with AKI and 12.1% (95% CI: 10.0 to 14.7) among patients without AKI. The corresponding adjusted HR of death was 1.6 (95% CI: 1.1 to 2.2). Five-year risk of myocardial infarction was 5.0% (95% CI: 2.9 to 8.1) among patients with AKI and 3.3% (95% CI: 2.1 to 4.8) among patients without AKI. Five-year risk of stroke was 5.0% (95% CI: 2.8 to 7.9) among patients with AKI and 4.2% (95% CI: 2.9 to 5.8) among patients without AKI. Adjusted HRs were 1.5 (95% CI: 0.7 to 3.2) of myocardial infarction and 0.9 (95% CI: 0.5 to 1.8) of stroke. CONCLUSIONS: AKI, within five days after elective cardiac surgery, was associated with increased five-year mortality and a statistically insignificant increased risk of myocardial infarction. No association was seen with the risk of stroke.

Kinship Analysis with Diallelic SNPs - Experiences with the SNPforID Multiplex in an ISO17025 Accreditated Laboratory.

BACKGROUND: The mutation rate of single nucleotide polymorphisms (SNPs) is estimated to be 100,000 times lower than that of short tandem repeats (STRs), which makes SNPs very suitable for relationship testing. The SNPforID multiplex assay was the first SNP typing assay that was a real alternative to the commonly used STR kits in kinship and crime case work and the first SNP assay to be validated in a forensic laboratory accredited according to the ISO17025 standard. METHODS: A total of 54 crime case samples were typed with the SNPforID multiplex assay. 30 samples from relationship cases were sequenced in selected SNP loci. RESULTS: It was demonstrated that mixtures were easily detected with the SNPforID assay by analyzing the signal strengths of the detected alleles. Unusual imbalances in signal strengths that were observed in a few individuals could be explained by unexpected SNPs in one of the primer binding sites. A complicated relationship case with four closely related individuals is presented. CONCLUSION: Mixtures can be detected with bi-allelic SNPs. The SNPforID assay is a very useful supplement to the STR kits in relationship testing.

Forensic and phylogeographic characterisation of mtDNA lineages from Somalia.

The African mitochondrial (mt) phylogeny is coarsely resolved but the majority of population data generated so far is limited to the analysis of the first hypervariable segment (HVS-1) of the control region (CR). Therefore, this study aimed on the investigation of the entire CR of 190 unrelated Somali individuals to enrich the severely underrepresented African mtDNA pool. The majority (60.5 %) of the haplotypes were of sub-Saharan origin with L0a1d, L2a1h and L3f being the most frequently observed haplogroups. This is in sharp contrast to previous data reported from the Y-chromosome, where only about 5 % of the observed haplogroups were of sub-Saharan provenance. We compared the genetic distances based on population pairwise F (st) values between 11 published East, Central and North African as well as western Asian populations and the Somali sequences and displayed them in a multi-dimensional scaling plot. Genetic proximity evidenced by clustering roughly reflected the relative geographic location of the populations. The sequences will be included in the EMPOP database ( www.empop.org ) under accession number EMP00397 upon publication (Parson and Dür Forensic Sci Int Genet 1:88-92, 2007).

The EuroSCORE in western Denmark: a population-based study.

OBJECTIVE: The present study aimed to examine the predictive performance of the logistic European System for Cardiac Operative Risk Evaluation (EuroSCORE) in a large cohort of patients undergoing cardiac surgery from 1999 through 2010 because methodologic shortcomings have hampered many previous studies questioning its predictive performance. DESIGN: Population-based prospectively registered data. SETTING: The Western Denmark Heart Registry, a multi-institutional registry. PARTICIPANTS: Twenty-one thousand six hundred sixty-four patients. INTERVENTIONS: On-pump cardiac surgery. MEASUREMENTS AND MAIN RESULTS: The predictive ability of the logistic EuroSCORE was assessed using the area under the curve (AUC) for the discrimination test, the Hosmer-Lemeshow (HL) calibration test, and the mean estimated-to-observed mortality ratio (E/O). The overall AUC was 0.79 (95% confidence interval [CI] 0.77-0.81; HL test, p < 0.01; E/O 1.9). For coronary artery bypass grafting, the AUC was 0.78 (95% CI 0.75-0.81; HL test, p < 0.01; E/O 2.3). For coronary artery bypass grafting plus valve replacement, the AUC was 0.69 (95% CI 0.65-0.73; HL test, p = 0.02; E/O 1.5). For aortic valve replacement, the AUC was 0.76 (95% CI 0.72-0.80; HL test, p < 0.01; E/O 2.5). The overall and procedural specific E/O ratios tended to increase from 1999 to 2010. Mortality was overestimated across all levels of estimated risk, and in low-to-medium-risk patients, this overestimation increased most notably with time. CONCLUSIONS: The EuroSCORE provides moderate-to-good discrimination and poor calibration. Despite substantial changes in risk factors during the study period, the EuroSCORE consistently overestimated 30-day mortality independent of the preoperative risk level and surgical procedure performed, indicating improved quality of surgery and patient care.

Microalbuminuria is associated with high adverse event rate following cardiac surgery.

OBJECTIVE: To examine if preoperative microalbuminuria is associated with an increased risk of long-term adverse outcomes following elective cardiac surgery and if it provides additional prognostic information beyond the European System for Cardiac Operative Risk Evaluation (EuroSCORE). METHODS: In a prospective follow-up study, we included 1049 patients undergoing elective cardiac surgery from 1 April 2005 to 30 September 2007. Microalbuminuria (urine albumin/creatinine ratio between 2.5 and 25 mg mmol(-1)) was assessed preoperatively in a morning spot-urine sample. We used population-based medical registries for follow-up from day 31 until day 365 postoperatively, and compared all-cause death, myocardial infarction, cerebral stroke and a composite outcome of severe infections including septicaemia, deep or superficial sternal wound infection, or leg wound infection among patients with or without microalbuminuria using Cox proportional hazard and competing risk regressions. RESULTS: Microalbuminuria was found in 175 (18.5%) out of 947 patients available for follow-up. The adjusted risks of all-cause death (adjusted hazard ratio 2.3 (95% confidence interval 1.1-4.9)), stroke (adjusted hazard ratio 2.9 (95% confidence interval 1.1-7.8)) and severe infection composite outcome (adjusted hazard ratio 2.4 (95% confidence interval 1.2-4.9)) were doubled to tripled in patients with preoperative microalbuminuria. The risk of myocardial infarction was not increased. Adding information on microalbuminuria improved the predictive accuracy of the EuroSCORE regarding mortality (areas under receiver operating characteristic curves were: for the EuroSCORE 0.73 (95% confidence interval 0.65-0.81) and for EuroSCORE+microalbuminuria 0.76 (95% confidence interval 0.68-0.83). CONCLUSIONS: Preoperative microalbuminuria is associated with an increased risk of long-term adverse outcomes in patients undergoing elective cardiac surgery, and it appears to provide prognostic information on mortality.

No excess surgical blood loss in patients with acquired type 2A von Willebrand disease.

OBJECTIVES: Acquired type 2A von Willebrand disease may develop as a consequence of aortic valve stenosis and is associated with varying degrees of bleeding tendency. It remains unknown, whether it portends excess blood loss during aortic valve replacement. DESIGN: We consecutively enrolled 45 patients with severe aortic valve stenosis undergoing aortic valve replacement. Patients with acquired type 2A von Willebrand disease were identified measuring the von Willebrand factor high molecular weight multimer. Data on the intraoperative, early postoperative, and the total blood loss within 24 hours of surgery was obtained and compared between groups. RESULTS: Acquired type 2A von Willebrand disease was found in 33% (n = 15/45) of the patients. Baseline characteristics were similar between groups. Patients with acquired type 2A von Willebrand disease neither had excess median intraoperative blood loss (375 ml (interquartile range 100-450 ml) vs. 350 ml (interquartile range 250-500 ml), p = 0.59) nor increased median total blood loss (695 ml (interquartile range 450-850 ml) vs. 752 ml (interquartile range 575-1035 ml), p = 0.41) as compared to patients without acquired type 2A von Willebrand disease. CONCLUSION: Acquired type 2A von Willebrand disease was not associated with increased blood loss during aortic valve replacement in patients with severe aortic valve stenosis.

Insulin resistance, adiponectin and adverse outcomes following elective cardiac surgery: a prospective follow-up study.

BACKGROUND: Insulin resistance and adiponectin are markers of cardio-metabolic disease and associated with adverse cardiovascular outcomes. The present study examined whether preoperative insulin resistance or adiponectin were associated with short- and long-term adverse outcomes in non-diabetic patients undergoing elective cardiac surgery. METHODS: In a prospective study, we assessed insulin resistance and adiponectin levels from preoperative fasting blood samples in 836 patients undergoing cardiac surgery. Population-based medical registries were used for postoperative follow-up. Outcomes included all-cause death, myocardial infarction or percutaneous coronary intervention, stroke, re-exploration, renal failure, and infections. The ability of insulin resistance and adiponectin to predict clinical adverse outcomes was examined using receiver operating characteristics. RESULTS: Neither insulin resistance nor adiponectin were statistically significantly associated with 30-day mortality, but adiponectin was associated with an increased 31-365-day mortality (adjusted odds ratio 2.9 [95% confidence interval 1.3-6.4]) comparing the upper quartile with the three lower quartiles. Insulin resistance was a poor predictor of adverse outcomes. In contrast, the predictive accuracy of adiponectin (area under curve 0.75 [95% confidence interval 0.65-0.85]) was similar to that of the EuroSCORE (area under curve 0.75 [95% confidence interval 0.67-0.83]) and a model including adiponectin and the EuroSCORE had an area under curve of 0.78 [95% confidence interval 0.68-0.88] concerning 31-365-day mortality. CONCLUSIONS: Elevated adiponectin levels, but not insulin resistance, were associated with increased mortality and appear to be a strong predictor of long-term mortality. Additional studies are warranted to further clarify the possible clinical role of adiponectin assessment in cardiac surgery. TRIAL REGISTRATION: The Danish Data Protection Agency; reference no. 2007-41-1514.

Mitochondrial DNA HV1 and HV2 variation in Danes.

Sequences from the two hypervariable regions (HV1 and HV2) of the control region of the mitochondrial DNA were obtained from a total of 201 Danes and five individuals who later were recognized to be of non-West European origin. Two fractions of each region were amplified separately and sequenced at least twice. The samples were sequenced using flanking sequencing primes and both terminator and primer chemistry. Sequence evaluation was performed by two independent scientists. The haplogroup distribution of the samples resembles that found in other European population. All the sequences have been made available in the EMPOP database.

Microalbuminuria and short-term prognosis in patients undergoing cardiac surgery.

OBJECTIVES: To examine if preoperative microalbuminuria (MA) is associated with in increased risk of adverse outcomes in patients undergoing elective cardiothoracic surgery, and if adding information on MA could improve the accuracy of the additive EuroSCORE. METHODS: In a follow-up study we included 962 patients undergoing elective cardiothoracic surgery from 1 April 2005 to 30 September 2007 at our department. MA (urine albumin/creatinine ratio between 2.5-25 mg/mmol) was assessed in a morning spot-urine sample. We used population-based medical registries for 30-day follow-up and compared the length of stay and adverse outcomes including (i) all-cause death, myocardial infarction, stroke, or atrial fibrillation, (ii) surgical reintervention, renal insufficiency, sternal wound infection, or septicaemia among patients with and without MA. RESULTS: MA was found in 180 (18.7%) patients. The risk of both combined outcomes (adjusted odds ratios (ORs): 1.00 (95% confidence interval (CI): 0.77-1.30) and 1.18 (95% CI: 0.79-1.75), respectively) and most individual outcomes did not differ between the micro- and normoalbuminuric patients. The patients with MA and an additive EuroSCORE of 5 had a significantly prolonged median length of intensive care unit (ICU) stay (0.15 days [95% CI: 0.04-0.26]) and total hospital stay (0.5 days [95% CI: 0.04-0.96]). Patients with MA had a higher risk of postoperative septicaemia (OR: 12.1 [95% CI: 3.2-45.9]). Area under receiver operating characteristics curves of the EuroSCORE with regard to 30-day mortality was 0.86 both with and without MA. CONCLUSIONS: Preoperative MA in patients undergoing elective cardiothoracic surgery was not associated with most early adverse outcomes. However, risk of septicaemia was higher and patients with MA also had a marginally longer length of ICU and hospital stay. Information on preoperative MA did not improve the accuracy of the additive EuroSCORE.

Practical regimen for amiodarone use in preventing postoperative atrial fibrillation.

BACKGROUND: Postoperative atrial fibrillation occurs in 5% to 65% of patients undergoing cardiac surgery. Although postoperative atrial fibrillation is often regarded as a temporary, benign, operation-related problem, it is associated with a twofold to threefold increase in risk of adverse events, including permanent or transient stroke, acute myocardial infarction, and death. METHODS: This randomized, controlled, double-blinded trial included 250 eligible consecutively enrolled patients undergoing coronary artery bypass grafting (CABG). They received 300 mg of amiodarone/placebo administered intravenously over 20 minutes on the first postoperative day and an oral dose of 600 mg of amiodarone or placebo twice daily for the first 5 postoperative days. RESULTS: The patients in amiodarone prophylaxis experienced a reduction in risk of atrial fibrillation of 14% (95% confidence interval [CI], 5.0% to 24%), with the number needed to treat at 6.9 (95% CI, 4.2 to 20), and the results for symptomatic atrial fibrillation showed a risk reduction of 18% (95% CI, 9.4% to 26), with the number needed to treat at 5.7 (95% CI, 3.9 to 11). Of the patients who developed atrial fibrillation in the placebo group, 84% experienced a symptomatic attack versus only 43% in the amiodarone group. CONCLUSIONS: Postoperative prophylaxis with a high dose of oral amiodarone after an intravenous bolus infusion is a safe, practical, feasible, and effective regimen for CABG patients. It significantly diminishes the occurrence of postoperative atrial fibrillation.