Efficacy assessment of cryostorants of donor hearts by ImageJ based image analysis

AIM

Donor organ injury during cold preservation before transplantation negatively impacts graft survival. The current study was to examine available evidences for the efficacy of different cold storage solutions that are used to preserve donor hearts in vitro prior to orthotopic transplantation.

METHODS

A systematic search of full-length articles published from 1980 to August 2012 was performed in PubMed and Google Scholar. Detailed searches were also made for availability of any sourceware for histopathology images of endomyocardial biopsies of stored hearts.

RESULTS

Not even a single controlled trial has been published relating to this topic. However, we assessed all available literature pertaining to this topic, and performed original, simple yet innovative analyses using ImageJ, a Java based image analyses program, to show the tremendous power to objectively examine the efficacy of the storage solution. Our analysis suggest that ImageJ may be conveniently used to obtain evidences (or lack of it) of ischemic injury of donor hearts during cold storage.

CONCLUSION

Even the UNOS database does not provide histopathological evidences of cardiac biopsies of orthotopically transplanted hearts. We, however, make the case of the need for image analyses and making availability of images to allow establishing evidence of the usefulness of these storage solutions. We recommend obtaining endomyocardial biopsy prior to orthotopic transplantation and create a registry of H&E stained slides. This is the only step that will direct us towards evidence based care of such highly critical patients who need the equally challenging surgical intervention of cardiac transplantation.

Ion fusion of high-resolution LC-MS-based metabolomics data to discover more reliable biomarkers

A systematic approach for the fusion of associated ions from a common molecule was developed to generate "one feature for one peak" metabolomics data. This approach guarantees that each molecule is equally selected as a potential biomarker and may largely enhance the chance to obtain reliable findings without employing redundant ion information. The ion fusion is based on low mass variation in contrast to the theoretical calculation measured by a high-resolution mass spectrometer, such as LTQ orbitrap, and a high correlation of ion pairs from the same molecule. The mass characteristics of isotopic distribution, neutral loss, and adduct ions were simultaneously applied to inspect each extracted ion in the range of a predefined retention time window. The correlation coefficient was computed with the corresponding intensities of each ion pair among all experimental samples. Serum metabolomics data for the investigation of hepatocellular carcinoma (HCC) and healthy controls were utilized as an example to demonstrate this strategy. In total, 609 and 1084 ion pairs were respectively found meeting one or more criteria for fusion, and therefore fused to 106 and 169 metabolite features of the datasets in the positive and negative modes, respectively. The important metabolite features were separately discovered and compared to distinguish the HCC from the healthy controls using the two datasets with and without ion fusion. The results show that the developed method can be an effective tool to process high-resolution mass spectrometry data in "omics" studies.

Metabolic profiling study of early and late recurrence of hepatocellular carcinoma based on liquid chromatography-mass spectrometry

The objectives of this pilot study were to predict early postoperative recurrence in hepatocellular carcinoma (HCC) patients based on metabolic features and to explore the related metabolic disturbances. Liquid chromatography-mass spectrometry-based metabolic profiling was performed on the plasma of 18 late recurrent and 22 early recurrent HCC patients. Metabolic differences were found to be related to amino acid, bile acid, cholesterol, fatty acid, phospholipid and carbohydrate metabolism. Bile acids, steroids and fatty acids showed significant variation in the early recurrent HCC group compared to the late recurrence group. Decreased levels of polyunsaturated eicosapentaenoic acid, docosahexaenoic acid and linolenic acid were found to be specific metabolic features for early recurrence. With the combination of methionine, GCDCA and cholesterol sulfate, 85% of the early recurrent HCCs can be predicted correctly with the corresponding area under the curve (AUC) equal to 0.95 in the training set, and 80% of the early recurrent HCCs can be predicted correctly with the corresponding AUC equal to 0.91 in the test set.

Genome-wide association study of primary dentition pit-and-fissure and smooth surface caries

Dental caries continues to be the most common chronic disease in children today. Despite the substantial involvement of genetics in the process of caries development, the specific genes contributing to dental caries remain largely unknown. We performed separate genome-wide association studies of smooth and pit-and-fissure tooth surface caries experience in the primary dentitions of self-reported white children in two samples from Iowa and rural Appalachia. In total, 1,006 children (ages 3-12 years) were included for smooth surface analysis, and 979 children (ages 4-14 years) for pit-and-fissure surface analysis. Associations were tested for more than 1.2 million single nucleotide polymorphisms, either genotyped or imputed. We detected genome-wide significant signals in KPNA4 (p value = 2.0E-9), and suggestive signals in ITGAL (p value = 2.1E-7) and PLUNC family genes (p value = 2.0E-6), thus nominating these novel loci as putative caries susceptibility genes. We also replicated associations observed in previous studies for MPPED2 (p value = 6.9E-6), AJAP1 (p value = 1.6E-6) and RPS6KA2 (p value = 7.3E-6). Replication of these associations in additional samples, as well as experimental studies to determine the biological functions of associated genetic variants, are warranted. Ultimately, efforts such as this may lead to a better understanding of caries etiology, and could eventually facilitate the development of new interventions and preventive measures.

Electron transport enhanced by electrode surface reconstruction: a case study of C60-based molecular junctions

At the C₆₀–Cu(111) interface, electrode surface reconstruction (Rec) increases electrical current compared to that for the unreconstructed (Unrec) surface.

The investigation of transition metal doped CuGaS2 for promising intermediate band materials

Metal (Fe, Co and Ni) doped CuGaS₂ systems are systematically investigated by using a screened-exchange hybrid density functional theory, which shows that Fe and Ni doped CuGaS₂ systems are potential candidates for the photovoltaic area.

Tuning the electron transport properties of boron-nitride nanoribbons with electron and hole doping

C chain doped BN nanoribbons can be either metallic or semiconducting, depending on how the C chains are located.

Abstract PD3-8: Whole exome sequencing reveals early mutational change on endocrine and targeted therapy in estrogen receptor (ER)-positive breast cancer

Background: Breast cancer treatment is guided by baseline tumor tissue which does not take into account tumor interaction with therapy. We hypothesized that mutational change may occur early after treatment initiation and that “on-treatment” tumor profiling may be more informative of tumor behavior and, ultimately, patient outcome.

Methods: We conducted whole exome sequencing on 49 tumor samples from 2 clinical trials of combined endocrine and targeted therapy (NCT00570921: with fulvestrant/everolimus, and NCT00525161: with tamoxifen/sorafenib). Tumor DNA was subjected to exome capture using Agilent V4+UTR 71Mb and Illumina's HiSeq2000 sequencer was used to generate 2×100bp paired-end reads. After mapping reads to the reference human genome (GRCh37), point mutations and insertions/deletions were detected using the Genome Analysis Tool Kit (GATK 2.6-5). We then retained breast somatic mutations from TCGA and COSMIC databases and excluded germline mutations from dbSNP. Further filtration was then done by removing modifier impact and synonymous mutations based on SnpEff, as well as removing mutations with <15X coverage depth.

Results: Across 8 paired tumors on day 28 vs. day 1, 4-pairs on fulvestrant/everolimus and 4 on tamoxifen/sorafenib, there were a total of 50 mutations lost and 77 gained for an average of 6.25 and 9.6 per tumor pair, respectively. This represented, on average, <5% of the total mutations detected, with >95% similarity in the mutational profile of paired tumors. One consistent mutational change in response to treatment was the gain of MUC2 single nucleotide polymorphisms (SNPs) in all 8 paired day-28 vs. day-1 biopsies. This MUC2 mutation pattern persisted even with removal of the coverage depth filter. Other MUC genes had SNPs gained or lost on day 28 but these were infrequent events. Additional notable changes were the gain of HLA-DRB1 SNP's in 2/4 everolimus-treated patients, loss of NCOA3 in one, and loss of TP53 in another. Interestingly, across 5-paired primary and metastatic tumors treated with endocrine therapy alone prior to enrollment, there were more mutations lost than gained (68 vs. 34) for an average of 13.6 and 6.8 per tumor pair, respectively. This represented only slightly over 5% of the mutations detected across these tumors with no consistent genomic event observed. One patient with lobular carcinoma on tamoxifen developed a contralateral lobular associated with metastasis and gain of PIK3CA and NCOR2 SNPs in the new tumor.

Conclusion: ER-positive breast tumors undergo early mutational change in response to therapy but the bulk of their mutational profile remains stable, even over long periods of time. MUC2 mutations emerge as a consistent early event which may reflect functional tumor differentiation in response to treatment pressure. Early emergence of mutational events suggests the need for a preoperative treatment window in future trials of this disease in order to interrogate tumor interaction with therapy prior to prolonged adjuvant therapy, which is currently based solely on pretreatment tumor assessment.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD3-8.

Pharmacokinetic/pharmacodynamic relationship of cefquinome against Pasteurella multocida in a tissue-cage model in yellow cattle

The cephalosporin antimicrobial drug cefquinome was administered to yellow cattle intravenously (i.v.) and intramuscularly (i.m.) at a dose of 1 mg/kg of body weight in a two-period crossover study. The pharmacokinetic (PK) properties of cefquinome in serum, inflamed tissue-cage fluid (exudate), and noninflamed tissue-cage fluid (transudate) were studied using a tissue-cage model. The in vitro and ex vivo activities of cefquinome in serum, exudate, and transudate against a pathogenic strain of Pasteurella multocida (P. multocida) were determined. A concentration-independent antimicrobial activity of cefquinome was confirmed for levels lower than 4 × MIC. Integration of in vivo pharmacokinetic data with the in vitro MIC provided mean values for the time that drug levels remain above the MIC (T > MIC) in serum was 14.10 h after intravenous and 14.46 h after intramuscular dosing, indicating a likely high level of effectiveness in clinical infections caused by P. multocida of MIC 0.04 μg/mL or less. These data may be used as a rational basis for setting dosing schedules, which optimize clinical efficacy and minimize the opportunities for emergence of resistant organisms.

Pharmacokinetic/pharmacodynamic relationship of marbofloxacin against Pasteurella multocida in a tissue-cage model in yellow cattle

The fluoroquinolone antimicrobial drug marbofloxacin was administered to yellow cattle intravenously and intramuscularly at a dose of 2 mg/kg of body weight in a two-period crossover study. The pharmacokinetic properties of marbofloxacin in serum, inflamed tissue-cage fluid (exudate), and noninflamed tissue-cage fluid (transudate) were studied by using a tissue-cage model. The in vitro and ex vivo activities of marbofloxacin in serum, exudate, and transudate against a pathogenic strain of Pasteurella multocida (P. multocida) were determined. Integration of in vivo pharmacokinetic data with the in vitro MIC provided mean values for the area under the curve (AUC)/MIC for serum, exudate, and transudate of 155.75, 153.00, and 138.88, respectively, after intravenous dosing and 160.50, 151.00, and 137.63, respectively, after intramuscular dosing. After intramuscular dosing, the maximum concentration/MIC ratios for serum, exudate, and transudate were 21.13, 9.13, and 8.38, respectively. The ex vivo growth inhibition data after intramuscular dosing were fitted to the inhibitory sigmoid Emax equation to provide the values of AUC/MIC required to produce bacteriostasis, bactericidal activity, and elimination of bacteria. The respective values for serum were 17.25, 31.29, and 109.62, and slightly lower values were obtained for transudate and exudate. It is proposed that these findings might be used with MIC50 or MIC90 data to provide a rational approach to the design of dosage schedules which optimize efficacy in respect of bacteriological as well as clinical cures.

Pseudotargeted metabolomics method and its application in serum biomarker discovery for hepatocellular carcinoma based on ultra high-performance liquid chromatography/triple quadrupole mass spectrometry

Untargeted analysis performed using full-scan mass spectrometry (MS) coupled with liquid chromatography (LC) is commonly used in metabolomics. Although they are commonly employed, full-scan MS methods such as quadrupole-time-of-flight (Q-TOF) MS have been restricted by various factors including their limited linear range and complicated data processing. LC coupled with triple quadrupole (QQQ) MS operated in the multiple reaction monitoring (MRM) mode is the gold standard for metabolite quantification; however, only known metabolites are generally quantified, limiting its applications in metabolomic analysis. In this study, a pseudotargeted approach was proposed to perform serum metabolomic analysis using an ultra high-performance liquid chromatography (UHPLC)/QQQ MS system operated in the MRM mode, for which the MRM ion pairs were acquired from the serum samples through untargeted tandem MS using UHPLC/Q-TOF MS. The UHPLC/QQQ MRM MS-based pseudotargeted method displayed better repeatability and wider linear range than the traditional UHPLC/Q-TOF MS-based untargeted metabolomics method, and no complicated peak alignment was required. The developed method was applied to discover serum biomarkers for patients with hepatocellular carcinoma (HCC). Patients with HCC had decreased lysophosphatidylcholine, increased long-chain and decreased medium-chain acylcarnitines, and increased aromatic and decreased branched-chain amino acid levels compared to healthy controls. The novelty of this work is that it provides an approach to acquire MRM ion pairs from real samples, is not limited to metabolite standards, and it provides a foundation to achieve pseudotargeted metabolomic analysis on the widely used LC/QQQ MS platform.

Limits on spin-independent couplings of WIMP dark matter with a p-type point-contact germanium detector

We report new limits on a spin-independent weakly interacting massive particle (WIMP)-nucleon interaction cross section using 39.5 kg days of data taken with a p-type point-contact germanium detector of 840 g fiducial mass at the Kuo-Sheng Reactor Neutrino Laboratory. Crucial to this study is the understanding of the selection procedures and, in particular, the bulk-surface events differentiation at the sub-keV range. The signal-retaining and background-rejecting efficiencies were measured with calibration gamma sources and a novel n-type point-contact germanium detector. Part of the parameter space in the cross section versus WIMP-mass implied by various experiments is probed and excluded.

Stable isotope-assisted lipidomics combined with nontargeted isotopomer filtering, a tool to unravel the complex dynamics of lipid metabolism

Investigations of complex metabolic mechanisms and networks have become a focus of research in the postgenomic area, thereby creating an increasing demand for sophisticated analytical approaches. One such tool is lipidomics analysis that provides, a detailed picture of the lipid composition of a system at a given time. Introducing stable isotopes into the studied system can additionally provide information on the synthesis, transformation and degradation of individual lipid species. However, capturing the entire dynamics of lipid networks is still a challenge. We developed and evaluated a novel strategy for the in-depth analysis of the dynamics of lipid metabolism with the capacity for high molecular specificity and network coverage. The general workflow consists of stable isotope-labeling experiments, ultrahigh-performance liquid chromatography (UHPLC)/high-resolution Orbitrap-mass spectrometry (MS) lipid profiling and data processing by a software tool for global isotopomer filtering and matching. As a proof of concept, this approach was applied to the network-wide mapping of dynamic lipid metabolism in primary human skeletal muscle cells cultured for 4, 12, and 24 h with [U-(13)C]-palmitate. In the myocellular lipid extracts, 692 isotopomers were detected that could be assigned to 203 labeled lipid species spanning 12 lipid (sub)classes. Interestingly, some lipid classes showed high turnover rates but stable total amounts while the amount of others increased in the course of palmitate treatment. The novel strategy presented here has the potential to open new detailed insights into the dynamics of lipid metabolism that may lead to a better understanding of physiological mechanisms and metabolic perturbations.

Genome-wide association studies of pit-and-fissure- and smooth-surface caries in permanent dentition

While genetics clearly influences dental caries risk, few caries genes have been discovered and validated. Recent studies have suggested differential genetic factors for primary dentition caries and permanent dentition caries, as well as for pit-and-fissure- (PF) and smooth- (SM) surface caries. We performed separate GWAS for caries in permanent-dentition PF surfaces (1,017 participants, adjusted for age, sex, and the presence of Streptococcus mutans) and SM surfaces (1,004 participants, adjusted for age, education group, and the presence of Streptococcus mutans) in self-reported whites (ages 14 to 56 yrs). Caries scores were derived based on visual assessment of each surface of each tooth; more than 1.2 million SNPs were either successfully genotyped or imputed and were tested for association. Two homologous genes were suggestively associated: BCOR (Xp11.4) in PF-surface caries (p value = 1.8E-7), and BCORL1 (Xq26.1) in SM-surface caries (p value = 1.0E-5). BCOR mutations cause oculofaciocardiodental syndrome, a Mendelian disease involving multiple dental anomalies. Associations of other plausible cariogenesis genes were also observed for PF-surface caries (e.g., INHBA, p value = 6.5E-6) and for SM-surface caries (e.g., CXCR1 and CXCR2, p value = 1.9E-6). This study supports the notion that genes differentially affect cariogenesis across the surfaces of the permanent dentition, and nominates several novel genes for investigation.