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1.

Background

The objective of this study is the evaluation of the Masaoka-Koga and the International Association for the Study of Lung Cancer (IASLC)/International Thymic Malignancy Interest Group (ITMIG) proposal for the new TNM-staging system on clinical implementation and prognosis of thymic malignancies.

Methods

A retrospective study of 76 patients who underwent surgery between January 2005 and December 2015 for thymoma. Kaplan–Meier survival analysis was used to determine overall and recurrence-free survival rates.

Results

Indication for surgery was primary mediastinal tumor (n =?55), pleural manifestation (n =?17), or mediastinal recurrence (n =?4) after surgery for thymoma. Early Masaoka-Koga stages I (n =?9) and II (n =?14) shifted to the new stage I (n =?23). Advanced stages III (Masaoka-Koga: n =?20; ITMIG/IASLC: n =?17) and IV (Masaoka-Koga: n =?33; ITMIG/IASLC: n =?35) remained nearly similar and were associated with higher levels of WHO stages. Within each staging system, the survival curves differed significantly with the best 5-year survival in early stages I and II (91%). Survival for stage IV (70 to 77%) was significantly better compared to stage III (49 to 54%). Early stages had a significant longer recurrence-free survival (86 to 90%) than advanced stages III and IV (55 to 56%).

Conclusions

The proportion of patients with IASLC/ITMIG stage I increased remarkably, whereas the distribution in advanced stages III and IV was nearly similar. The new TNM-staging system presents a clinically useful and applicable system, which can be used for indication, stage-adapted therapy, and prediction of prognosis for overall and recurrence-free survival.
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2.

Background

The prenatal condition offers a unique possibility of examining physiological interaction between individuals. Goal of this work was to look for evidence of coordination between fetal and maternal cardiac systems.

Methods

177 magnetocardiograms were recorded in 62 pregnancies (16th–42nd week of gestation). Fetal and maternal RR interval time series were constructed and the phases, i.e. the timing of the R peaks of one time series in relation to each RR interval of the other were determined. The distributions of these phases were examined and synchrograms were constructed for real and surrogate pairs of fetal and maternal data sets. Synchronization epochs were determined for defined n:m coupling ratios.

Results

Differences between real and surrogate data could not be found with respect to number of synchronization epochs found (712 vs. 741), gestational age, subject, recording or n:m combination. There was however a preference for the occurrence of synchronization epochs in specific phases in real data not apparent in the surrogate for some n:m combinations.

Conclusion

The results suggest that occasional coupling between fetal and maternal cardiac systems does occur.
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3.

Background

There is conflicting evidence regarding the benefit of adjunctive corticosteroid therapy in patients with Mycoplasma pneumoniae pneumonia. We hypothesised that corticosteroid therapy could reduce mortality and length of stay (LOS) in such patients.

Methods

Adult patients with M. pneumoniae pneumonia from January 2010 to December 2013 were identified from the Japanese Diagnosis Procedure Combination inpatient database. The effects of low-dose and high-dose corticosteroid therapies on mortality, LOS, drug costs and hyperglycaemia requiring insulin treatment were evaluated using propensity score analyses.

Results

Eligible patients (n?=?2228) from 630 hospitals were divided into no-corticosteroid (n?=?1829), low-dose corticosteroid (n?=?267) and high-dose corticosteroid (n?=?132) groups. The propensity score-matched pairs were generated from no-corticoid and low-dose corticoid groups (251 pairs), or no-corticoid and high-dose corticosteroid groups (120 pairs). Adjunctive corticosteroid therapy did not decrease 30-day mortality. In addition, both low-dose and high-dose corticosteroid therapies were associated with increases in LOS. Furthermore, hyperglycaemia requiring insulin treatment and drug cost increased with corticosteroid use.

Conclusions

Adjunctive treatment with low-dose or high-dose corticosteroids may not be beneficial in M. pneumoniae pneumonia.
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4.

Background

Lately, biomarker discovery has become one of the most significant research issues in the biomedical field. Owing to the presence of high-throughput technologies, genomic data, such as microarray data and RNA-seq, have become widely available. Many kinds of feature selection techniques have been applied to retrieve significant biomarkers from these kinds of data. However, they tend to be noisy with high-dimensional features and consist of a small number of samples; thus, conventional feature selection approaches might be problematic in terms of reproducibility.

Results

In this article, we propose a stable feature selection method for high-dimensional datasets. We apply an ensemble L 1 -norm support vector machine to efficiently reduce irrelevant features, considering the stability of features. We define the stability score for each feature by aggregating the ensemble results, and utilize backward feature elimination on a purified feature set based on this score; therefore, it is possible to acquire an optimal set of features for performance without the need to set a specific threshold. The proposed methodology is evaluated by classifying the binary stage of renal clear cell carcinoma with RNA-seq data.

Conclusion

A comparison with established algorithms, i.e., a fast correlation-based filter, random forest, and an ensemble version of an L 2 -norm support vector machine-based recursive feature elimination, enabled us to prove the superior performance of our method in terms of classification as well as stability in general. It is also shown that the proposed approach performs moderately on high-dimensional datasets consisting of a very large number of features and a smaller number of samples. The proposed approach is expected to be applicable to many other researches aimed at biomarker discovery.
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5.

Background

No drugs have been approved for the treatment of patients with pulmonary hypertension (PH) secondary to idiopathic pulmonary fibrosis (IPF), particularly those with idiopathic honeycomb lung. This study was conducted to investigate the long-term efficacy and safety of bosentan for PH based on changes in prognosis and respiratory failure.

Methods

IPF patients with borderline or less severe PH and completely organized honeycomb lung were randomized (1:1) to bosentan or no treatment for PH for 2 years and assessed at baseline and every 6 months for respiratory failure, activities of daily living (ADL), lung and heart functions by right cardiac catheterization, and other parameters. An interim analysis was performed, however, following detection of a significant survival benefit favoring bosentan therapy.

Results

Significant differences were noted for the bosentan-treated (n?=?12) vs. untreated (n?=?12) groups in hospital-free survival (603.44?±?50.074 days vs. 358.87?±?68.65 days; hazard ratio [HR], 0.19; P?=?0.017) and overall survival (671 days vs. 433.78?±?66.98 days; HR, 0.10; P?=?0.0082). Again, significant improvements were noted for the bosentan-treated group from baseline to month 6 or 12 in several indices in ADL, pulmonary circulation, and %DLCO. Without requiring O2 inhalation, bosentan was associated with no increase but a trend toward a decrease in adverse events and an improvement in respiratory status.

Conclusions

Bosentan tended to improve prognosis and ADL without worsening respiratory failure in IPF patients with borderline or less severe PH and completely organized honeycomb lung alone.

Trial registration

This study was registered on December 18, 2010 with UMIN-CTR Clinical Trial as UMIN000004749 to investigate the long-term influence of bosentan on cardiac function, as well as its cardioprotective efficacy and safety, in patients with pulmonary hypertension secondary to concurrent COPD and IPF, respectively.
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6.

Introduction

Urinary pteridines are putative molecular biomarkers for noninvasive cancer screening and prognostication. Central to their translational biomarker development is the need to understand the sources and extent of their non-epidemiological variation.

Objectives

This study was designed to characterize the two primary sources of urinary pteridine variance: daily variation and the effect of dietary folate.

Methods

Daily variation was studied by collecting urine specimens (n = 81) three times daily for 3 days. The effect of dietary folate was investigated in a treatment study in which urine specimens (n = 168) were collected daily during a control week and a treatment week during which participants received dietary folate supplements. Measurements of six urinary pteridines were made using high-performance liquid chromatography–tandem mass spectrometry. Coefficients of variation were calculated to characterize daily variance between and within subjects, while nearest neighbor non-parametric analyses were used to identify diurnal patterns and measure dietary folate effects.

Results

Daily variance was approximately 35 % RSD for both within-day and between-day periods for most pteridines. Diurnal patterns in response to circadian rhythms were similarly observed for urinary pteridines. Folate supplementation was shown to alter urinary pteridine profiles in a pathway dependent manner, suggesting that dietary folate may regulate endogenous neopterin and biopterin biosynthesis.

Conclusions

Urinary pteridine levels were found to be responsive to both daily variation and folate supplementation. These findings provide new insights into pteridine biosynthesis and regulation as well as useful information for the design of future clinical translational research.
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7.

Introduction

Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.

Objectives

We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.

Methods

massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.

Results

Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.

Conclusion

massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.
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8.

Objectives

To investigate the contribution of direct electron transfer mechanisms to electricity production in microbial fuel cells by physically retaining Shewanella oneidensis cells close to or away from the anode electrode.

Results

A maximum power output of 114 ± 6 mWm?2 was obtained when cells were retained close to the anode using a dialysis membrane. This was 3.5 times more than when the cells were separated away from the anode. Without the membrane the maximum power output was 129 ± 6 mWm?2. The direct mechanisms of electron transfer contributed significantly to overall electron transfer from S. oneidensis to electrodes, a result that was corroborated by another experiment where S. oneidensis cells were entrapped in alginate gels.

Conclusion

S. oneidensis transfers electrons primarily by direct electron transfer as opposed to mediated electron transfer.
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9.

Introduction

Botanicals containing iridoid and phenylethanoid/phenylpropanoid glycosides are used worldwide for the treatment of inflammatory musculoskeletal conditions that are primary causes of human years lived with disability, such as arthritis and lower back pain.

Objectives

We report the analysis of candidate anti-inflammatory metabolites of several endemic Scrophularia species and Verbascum thapsus used medicinally by peoples of North America.

Methods

Leaves, stems, and roots were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and partial least squares-discriminant analysis (PLS-DA) was performed in MetaboAnalyst 3.0 after processing the datasets in Progenesis QI.

Results

Comparison of the datasets revealed significant and differential accumulation of iridoid and phenylethanoid/phenylpropanoid glycosides in the tissues of the endemic Scrophularia species and Verbascum thapsus.

Conclusions

Our investigation identified several species of pharmacological interest as good sources for harpagoside and other important anti-inflammatory metabolites.
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10.

Introduction

Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.

Objective

The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.

Methods

Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.

Results

Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.

Conclusions

The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.
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11.
12.

Background

Riociguat is a soluble guanylate cyclase stimulator approved for pulmonary arterial hypertension (PAH) and chronic thromboembolic pulmonary hypertension (CTPEH). The objective of this study was to evaluate right heart size and function assessed by echocardiography during long term treatment with riociguat.

Methods

Patients who started riociguat treatment (1.0–2.5?mg tid) within the trials phase II, PATENT, PATENTplus, EAS, CHEST and continued treatment for 3–12?months were included in this study. Echocardiography was analysed off-line at baseline, after 3, 6 and 12?months by investigators who were blinded to clinical data. Last and baseline observation carried forward method (LOCF, BOCF) were performed as sensitivity analysis.

Results

Seventy-one patients (45% PAH, 55% CTEPH; 53.5% female; 60?±?13?years, mean pulmonary arterial pressure 46?±?10?mmHg, mean PVR 700?±?282dynes·sec·cm-5) were included. After 6?months, RA and RV area, RV thickness tricuspid regurgitation velocity showed a significant reduction. After 12?months, patients receiving riociguat therapy showed a significant reduction in right atrial (??2.6?±?4.4?cm2, 95% CI -3.84, ??1.33; p?<?0.001, n?=?49) and right ventricular (RV) area (??3.5?±?5.2?cm2, 95% CI -5.1, ??1.9; p?<?0.001; n?=?44), RV thickness (??0.76?±?2.2?mm, 95% CI -1.55, 0.03; n?=?32), and a significant increase in TAPSE (2.95?±?4.78?mm, 95% CI 1.52, 4.39; n?=?45) and RV fractional area change (8.12?±?8.87?mm, 95% CI 4.61, 11.62; n?=?27).Both LOCF and BOCF showed similar results but lower effect sizes.

Conclusion

Patients under long-term treatment with riociguat show significantly reduced right heart size and improved RV function in PAH and CTEPH. Further controlled prospective studies are needed to confirm these results.
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13.

Background

Thalassemia is known as the commonest monogenic disorder with an imbalanced rate of globin chains production of adult hemoglobin. Despite the available information about the thalassemia etiology, its phenotype varies from each patient to another. This study aimed to evaluate the hematological parameters of patients with the same -α3.7 homozygote and heterozygote genotypes to amend screening programs.

Methods

In this observational study, we evaluated 1301 thalassemia suspected patients who referred to the Thalassemia and Hemoglobinopathy Research Center of Ahvaz University of Medical Sciences, Khuzestan, Iran during 2014–2016. According to the genotyping studies, patients divided into 2 groups with -α3.7/αα (n = 646) and -α3.7/-α3.7 (n = 181) genotypes. Thereafter, distribution of hematological parameters evaluated in both groups.

Results

The mean age in heterozygous and homozygous groups was 25.7±4.5 and 26±4.4 years old, respectively. The degree of anemia was considerably varied in patients with the same genotype. MCV, RBC and MCH showed a wide distribution in patients.

Conclusion

The findings presented here suggest that other molecular mechanisms along with α-globin gene mutations could be involved in determining the phenotypes of alpha thalassemia patients.
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14.

Background

Evidence suggests that epicardial adipose tissue (EAT) is closely related to coronary artery stenosis (CAS). However, sexual dimorphism may be present in adipose tissue, and its influence on CAS between men and women is controversial. We assessed the relationship between EAT and CAS by sex and menopausal status in patients with suspected angina.

Methods

Six hundred twenty-eight consecutive patients (men/women n?=?257/371; mean age = 59.9?±?10.2?years) who had chest pain for angina and underwent coronary angiography were included. CAS was defined as >?50% luminal narrowing of at least one epicardial coronary artery. EAT thickness was measured by transthoracic echocardiography.

Results

Of the 628 patients, 52.1% (n?=?134) of men and 35.3% (n?=?131) of women had CAS. The mean EAT thickness was not different between men and women and was larger in patients with CAS (8.04?±?2.39 vs 6.58?±?1.88?mm, P?<?0.001). EAT thickness was independently associated with CAS in both sexes (P?<?0.001). The odds ratio (OR) of EAT for the presence of CAS was higher in men (OR?=?1.43, 95% confidence interval [CI] 1.21–1.69) than in women (OR?=?1.24, 95% CI 1.10–1.40). EAT thickness was larger in postmenopausal women than in premenopausal women (7.59?±?2.25 vs 5.80?±?1.57?mm, P?<?0.001) and was independently related with CAS (OR?=?1.24, 95% CI 1.09–1.41). This was not the case in premenopausal women.

Conclusion

In patients with suspected angina, an increase in EAT thickness was independently related to the presence of CAS in both men and women, with it being stronger in men. According to menopausal status in women, EAT thickness is significantly associated with CAS only in postmenopausal women.
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15.

Background

Although the majority of solitary fibrous tumors of the pleura (SFTP) follow a benign course, 10–25% of patients suffer from recurrence or metastatic disease. Several scoring models have been proposed to predict the outcome. However, none of these included immunohistochemical (IHC) markers as possible prognosticators.

Methods

In this multicenter study, we collected clinical data and formalin-fixed and paraffin-embedded (FFPE) tissue blocks of patients with histologically proven SFTP which had been surgically resected between 2000 und 2015. After systematic and extensive IHC staining on tissue microarrays, the results were analyzed and compared to histomorphological and clinical data for their possible prognostic value.

Results

In total, 78 patients (mean age 61?±?11 years) were included. Of these, 9 patients (11%) had an adverse outcome including SFTP recurrence (n?=?6) or SFTP-related death (n?=?3). Mean overall survival was 172?±?13 months. 1 and 10-year event-free survival rates were 99% and 93%. In the multivariable analysis only MIB-1 proliferation index (Ki-67) ≥10% (HR 12.3, CI 1.1–139.5, p?=?0.043), ≥4 mitoses per 10 high power fields (HR 36.5, CI 1.2–1103.7, p?=?0.039) and tumor size larger than 10 cm (HR 81.8, CI 1.7–4016.8, p?=?0.027) were independently associated with adverse outcome.

Conclusion

A high proliferation rate by MIB-1 IHC was associated with impaired outcome. Upon this, we established a new score using mitosis, necrosis, size of the tumor and MIB-1, which performed better than the traditional scores in our data set. This prognostic score could help to better evaluate outcome of SFTP, but requires external validation.
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16.

Introduction

Genotype and metabolomic variation are important for bacterial survival and adaptation to environmental changes.

Objectives

In this study, we compared the relationship among Klebsiella pneumoniae strains based on their genotypic and metabolic profiles. In addition, we also evaluated the association of the relationship with beta-lactamase production.

Methods

A total of 53 K. pneumoniae strains isolated in 2013–2014 from a tertiary teaching hospital in Malaysia were subjected to antimicrobial susceptibility testing (AST) via disk diffusion method and beta-lactamase production confirmation. The bacterial strains were also typed genotypically and metabolically via REP-PCR and 1H-NMR spectroscopy respectively. The concordance of the matrices derived based on genotypic and metabolic characterization was measured based on Spearman’s rank correlation.

Results

Spearman’s correlation rank showed that there is a weak but significant negative correlation between the genetic fingerprints and metabolic profiles of K. pneumoniae. Specifically, K. pneumoniae strains were clustered into five major clusters based on REP-PCR where most of the carbapenem resistant K. pneumoniae (CRKP) strains made up the major cluster. In contrast, metabolic patterns of the three groups (i.e. CRKP, extended spectrum beta-lactamase producing K. pneumoniae (ESBL), susceptible) of K. pneumoniae were clearly differentiated on PLS-DA score plots derived from 1H-NMR spectroscopy.

Conclusion

Overall, this study showed that metabolomic profiling using 1H-NMR spectroscopy is able to discriminate K. pneumoniae strains based on their beta-lactamase production status.
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17.

Introduction

Digestion resistant carbohydrates (DRC) are complex carbohydrates that resist digestion and absorption in the small bowel. Diets high in DRC can have wide ranging impacts on the health of the host, which include changes to immunity and allergy, incidence of cardiovascular disease, and obesity.

Objectives

The aim of this study was to characterise the effects of DRC (inulin, konjac or resistant starch) on large intestinal short-chain fatty acid (SCFA) concentrations and serum metabolite and lipid profiles.

Methods

A rat model was used to compare the effects of feeding a basal diet or the basal diet containing 5 % inulin, konjac or resistant starch for 14 days.

Results

Of the three DRC, inulin had the greatest effect; ten serum phospholipids differed significantly in abundance between inulin-treated and control rats. In particular phosphatidylcholines and lysophosphatidylcholines containing fatty acyl chains 22:5, 22:4, 20:4, 18:0 and 16:0 were increased in the inulin-fed group, whereas phosphocholines containing fatty acyls 20:5 and 22:6 were decreased.

Conclusion

These results indicated an impact on both n-3 and n-6 fatty acid metabolism as a result of inulin dietary intake. Increased intestinal concentrations of SCFA were detected in rats fed DRC, but only inulin caused appreciable changes to serum lipid profiles.
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18.

Objective

To improve the production of welan gum and obtain a carotenoid-free strain while reducing the fermentation and post-treatment costs.

Results

The vitreoscilla globin (vgb) gene combined with the β-galactosidase (lacZ) promoter was inserted into the phytoene synthase (crtB) gene region of the chromosome in Alcaligenes sp. ATCC31555. When the recombinant strain was grown in a 5 l fermentor, welan gum was produced at 24 ± 0.4 g l?1 compared to 21 g ± 0.4 g l?1 in the wild type. Furthermore, the carotenoid-free welan gum produced using Alcaligenes sp. ATCC31555 VHb strain was less expensive with improved properties.

Conclusions

Alcaligenes sp. ATCC31555 VHb strain was a better neutral welan-producing strain with a higher production than the wild-type strain.
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19.

Objective

To generate Candida antarctica lipase A (CAL-A) mutants with modified fatty acid selectivities and improved lipolytic activities using error-prone PCR (epPCR).

Results

A Candida antarctica lipase A mutant was obtained in three rounds of epPCR. This mutant showed a 14 times higher ability to hydrolyze triacylglycerols containing conjugated linoleic acids, and was 12 and 14 times more selective towards cis-9, trans-11 and trans-10, cis-12 isomers respectively, compared to native lipase. Lipolytic activities towards fatty acid esters were markedly improved, in particular towards butyric, lauric, stearic and palmitic esters.

Conclusion

Directed molecular evolution is an efficient method to generate lipases with desirable selectivity towards CLA isomers and improved lipolytic activities towards esters of fatty acids.
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20.

Introduction

Metamorphosis is a complicated process in which cell proliferation, differentiation, and death are orchestrated to form the mature structures of insects. In Drosophila, this process is controlled by ecdysone, a steroid hormone responsible for tissue remodeling and organogenesis that gives rise to the adult fly.

Objective

By using a metabolomics approach, this study aimed to elucidate global changes in the central metabolic pathways in Drosophila throughout metamorphosis and then further examine the effects of temperature and origin on metabolic profiles.

Methods

Targeted and non-targeted metabolic profiling of time-course samples from Drosophila were constructed to cover a wide range of cellular metabolites during metamorphosis.

Results

This was the first wide-scale metabolomics study of Drosophila metamorphosis focusing on central metabolism. The abundance of detected metabolites changed drastically and correlated strongly with the development of Drosophila pupae. In non-stress conditions, temperature affected the developmental time, but the metabolic state at a certain stage of metamorphosis remained stable. Between D. melanogaster Canton S and Oregon R, similar metabolic profiles throughout metamorphosis was observed. However, there were still differences in purine and pyrimidine metabolism at an early stage in the pupal period, which was matched by differences in ecdysteroid levels.

Conclusion

This study supported the strength of metabolomics in the field of developmental biology. The results provided a general view on the metabolic profile of Drosophila during metamorphosis, which provides basic 3 knowledge for future metabolomics studies using Drosophila.
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