Protein Classification of Diffuse-Type Gastric Cancer Using Formalin-Fixed Paraffin-Embedded Samples

Background: Gastric cancer (GC) is the third leading cause of cancer deaths in the world. It is highly heterogeneous. Many molecular therapies for GC have entered clinical trials but, apart from trastuzumab, apatinib and ramucirumab, all have failed. One important reason is that insufficient attention is paid to the underlying subtypes and characteristics of GC, especially the diffuse-type gastric cancer (DGC) according to the Lauren classification with worst clinical outcomes. Aim: Here we firstly investigated formalin-fixed paraffin-embedded (FFPE) samples of DGC to establish clinically relevant molecular classification based on proteomics analysis. Also, we tried to generate a suitable classifier of DGC that can guide patient therapy. Methods: We screened a total of 2548 cases retrospectively, who underwent GC resection at Beijing Cancer Hospital from October 2006 to December 2011. We used a fast mass spectrometry workflow for proteome profiling. Finally we carried out proteome profiling of 99 DGC paired tumor-nearby tissues from FFPE sections. Median overall survival of the whole population was 55.0 months. Proteome profiling data from these samples were used to develop a subtype prediction model. We used consensus clustering to identify molecular subtypes based on differentially expressed proteins. The pathway enrichment was performed by GSEA, and the prediction classifier was generated by elastic-net machine learning. Kaplan-Meier survival analysis and Cox regression multivariate analysis were used. Results: A total of 8201 gene products were identified in this study, and 1249 differential expressed proteins between tumor and nearby-normal tissue was detected (FDR q-value < 0.01 by SAM). Tumor upregulated proteins mostly enriched into pathways including RNA processing, epithelial-mesenchymal transition (EMT), immune response and inflammation related pathways. Tumor downregulated proteins mostly enriched into metabolic pathways such as oxidative phosphorylation pathway. Based on proteome profiling alone, DGC can be subtyped into 3 major classes (PX1-3) that exhibit distinct proteome features and correlate with distinct clinical outcomes. PX1 (31 patients) exhibits RNA processing proteins and associates with the best prognosis; PX2 (26 patients) exhibits highly expressed cell cycle features, and the patients have poorer prognosis than those with cluster1 but better prognosis than those with cluster3; PX3 (42 patients) features EMT and the worst prognosis. We built a classifier of 12 marker proteins that can stratify DGC patients into these 3 subtypes, opening a door for protein classification in clinical application and intervention. Conclusion: Our study demonstrated that proteome profiling alone from FFPE samples was able to subtype DGC into 3 protein subtypes that were linked to distinct patterns of molecular alterations and prognosis. The prediction model need to be further verified in more clinical cohorts.

The multiple arrhythmia dataset evaluation database (M.A.D.A.E.)

The convergence between wearable and medical device technologies is a natural progression. Miniaturization has allowed the design of small, compact monitoring systems that can record physiological signals over longer periods of time. Thus, the potential for these devices to expand the understanding of disease progression and patients' clinical status is very high. The accuracy of these devices, however, is dependent upon the computer algorithms utilized in the analysis of the large volume of physiological data monitored and/or recorded by the devices. Automated interpretation of the data by these new technologies, therefore, necessitates closer examination by regulatory organizations. The current requirements for the validation of novel Ambulatory ECG (A-ECG) annotation algorithms are based on the AAMI/ANSI-EC57 and IEC60601-2-47 Standard. These standards are being updated, but they rely on a very limited set of digitized ECG recordings from a couple of ECG databases built in the first half of the 70's. These reference signals are obsolete. We are developing a validation tool for computerized methods designed to detect and monitor cardiac activities based on body-surface ECGs. We will rely on a set of existing digital high-resolution 12‑lead A-ECG recordings acquired in cardiac patients and healthy individuals. These ECG signals include a large and unique set of electrocardiographic events. This tool is being qualified by the Center for Devices and Radiological Health of the United States Food and Drug Administration (FDA) as a Medical Device Development Tool (MDDT). This document provides insights into the design of the M.A.D.A.E. database, its functionalities, and its ultimate role in enabling the next generations of automatic interpretation of ECG signals.

Measurement of the Absolute Branching Fraction of the Inclusive Decay Λ_{c}^{+}→Λ+X

Based on an e^{+}e^{-} collision data sample corresponding to an integrated luminosity of 567  pb^{-1} taken at the center-of-mass energy of sqrt[s]=4.6  GeV with the BESIII detector, we measure the absolute branching fraction of the inclusive decay Λ_{c}^{+}→Λ+X to be B(Λ_{c}^{+}→Λ+X)=(38.2_{-2.2}^{+2.8}±0.9)% using the double-tag method, where X refers to any possible final state particles. In addition, we search for direct CP violation in the charge asymmetry of this inclusive decay for the first time, and obtain A_{CP}≡[B(Λ_{c}^{+}→Λ+X)-B(Λ[over ¯]_{c}^{-}→Λ[over ¯]+X)]/[B(Λ_{c}^{+}→Λ+X)+B(Λ[over ¯]_{c}^{-}→Λ[over ¯]+X)]=(2.1_{-6.6}^{+7.0}±1.6)%, a statistically limited result with no evidence of CP violation.

Mixed Starter Culture Regulates Biogenic Amines Formation via Decarboxylation and Transamination during Chinese Rice Wine Fermentation

The utilization of amine-negative starter based on an understanding of nitrogen metabolism is a useful method for controlling biogenic amine (BA) in Chinese rice wine (CRW) fermentation. The contribution of brewing materials to protein degradation was analyzed; wheat Qu protein had no effect, and yeast autolysis generated 10% amino nitrogen. Milling degree of rice was strongly correlated with BAs formation ( R² = 0.99). Subsequently, Lactobacillus plantarum and Staphylococcus xylosus were coinoculated as amine-negative starter at an optimized ratio of 1:2. Coinoculation induced a significant reduction in total BAs (43.7%, 44.5 mg L^-1), putrescine (43.0%, 20.4 mg L^-1), tyramine (42.8%, 14.3 mg L^-1), and histamine (42.6%, 3.5 mg L^-1) content. Notably, BAs degradation ability of Staphylococcus xylosus was stronger than the suppression effect of Lactobacillus plantarum, and higher lactic acid bacteria (LAB) amount has a positive correlation with lower BAs content. Overall, mixed strains exerted a synergistic effect in lowering BAs accumulation via decarboxylation and transamination.

Nosocomial outbreak of Candida parapsilosis sensu stricto fungaemia in a neonatal intensive care unit in China

BACKGROUND

Candida parapsilosis is a common agent of fungaemia, but few outbreaks of Candida parapsilosis infection have been reported in China.

AIM

To elaborate an outbreak of nosocomial Candida parapsilosis sensu stricto fungaemia in a neonatal intensive care unit (NICU) of a comprehensive hospital in China from July to October 2017.

METHODS

Epidemics and characteristics of fungaemia cases were investigated. Surveillance samples were collected. Vitek 2 Compact System, internal transcribed spacer sequencing, and random amplified polymorphic DNA (RAPD) typing were conducted to identify the isolates. Antifungal susceptibility test was performed for all bloodstream isolates.

FINDINGS

Sixteen neonates were diagnosed as Candida parapsilosis sensu stricto fungaemia during this period. Presenting symptoms included leucopenia, thrombocytopenia, and respiratory crackles. Fifteen cases were cured whereas one case who suffered from severe concomitant diseases died. The isolates were susceptible to fluconazole, amphotericin B, itraconazole, voriconazole, and 5-fluorocytosine. A total of 313 surveillance samples were collected, and Candida parapsilosis sensu stricto was identified from 16 environmental samples and one sample from an ultrasonographer's hand. The colonized locations included wiping cloths, faucets, sinks, operating table, puddles in the bathroom, a ventilator, and an ultrasonic probe. The RAPD patterns of all the Candida parapsilosis sensu stricto isolates from bloodstream and surveillance samples were identical. The outbreak was controlled after a series of infection control measures.

CONCLUSION

Contaminated environment was associated with this outbreak. Close attention to immunocompromised patients, thorough environmental disinfection and hand hygiene should be strengthened in NICU.

Observations of the Interaction and Transport of Fine Mode Aerosols with Cloud and/or Fog in Northeast Asia from Aerosol Robotic Network (AERONET) and Satellite Remote Sensing

Analysis of sun photometer measured and satellite retrieved aerosol optical depth (AOD) data has shown that major aerosol pollution events with very high fine mode AOD (>1.0 in mid-visible) in the China/Korea/Japan region are often observed to be associated with significant cloud cover. This makes remote sensing of these events difficult even for high temporal resolution sun photometer measurements. Possible physical mechanisms for these events that have high AOD include a combination of aerosol humidification, cloud processing, and meteorological co-variation with atmospheric stability and convergence. The new development of Aerosol Robotic network (AERONET) Version 3 Level 2 AOD with improved cloud screening algorithms now allow for unprecedented ability to monitor these extreme fine mode pollution events. Further, the Spectral Deconvolution Algorithm (SDA) applied to Level 1 data (L1; no cloud screening) provides an even more comprehensive assessment of fine mode AOD than L2 in current and previous data versions. Studying the 2012 winter-summer period, comparisons of AERONET L1 SDA daily average fine mode AOD data showed that Moderate Resolution Imaging Spectroradiometer (MODIS) satellite remote sensing of AOD often did not retrieve and/or identify some of the highest fine mode AOD events in this region. Also, compared to models that include data assimilation of satellite retrieved AOD, the L1 SDA fine mode AOD was significantly higher in magnitude, particularly for the highest AOD events that were often associated with significant cloudiness.

Pharmacokinetic changes induced by focused ultrasound in glioma-bearing rats using dynamic contrast-enhanced MRI measurement

It has been shown that focused ultrasound (FUS) can be effectively used for brain tumor therapy, and as a noninvasive, targeted drug delivery technique combined with microbubbles. In this study, magnetic resonance imaging (MRI) was used to measure the kinetics of Gadolinium diethylenetriamine Penta acetic acid (Gd-DTPA) in glioma-bearing rats. Ten glioma-bearing rats (9-12 weeks, 290-340 g weight) were used in the study. After the use of dynamic contrast enhancement (DCE)-MRI, the spatial permeability of FUS-induced blood-brain barrier disruption (BBB-D) was evaluated, and the kinetic parameters by the general kinetic model (GKM) were calculated. The results show that mean trans K of the contralateral tumor was significantly lower than the mean trans K of sonicated tumor. Moreover, the transfer constant trans K in ultrasound tumors was closely related to tissue extravasation (R = 0.95), suggesting that DCE-MRI can determine drug accumulation in the brain. Except for a few small red blood cell extravasations, there was no macroscopic damage according to the histologic analysis. The study showed that the DCE-MRI can be a valuable tool in quantifying BBB permeability in tumors and monitor the kinetics of FUS-induced BBB-D processes.

Column-integrated aerosol optical properties of coarse- and fine-mode particles over the Pearl River Delta region in China

The sun-photometer data from 2011 to 2013 at Panyu site (Panyu) and from 2007 to 2013 at Dongguan site (Dg) in the Pearl River Delta region, were used for the retrieving of the aerosol optical depth (AOD), single scattering albedo (SSA), Ångström exponent (AE) and volume size distribution of coarse- and fine-mode particles. The coarse-mode particles presented low AOD (ranging from 0.05±0.03 to 0.08±0.05) but a strong absorption property (SSA ranged from 0.70±0.03 to 0.90±0.02) for the wavelengths between 440 and 1020nm. However, these coarse particles accounted for <10% of the total particles. The AOD of fine particles (AODf) was over 3 times as large as that of coarse particles (AODc). The fine particles SSA (SSAf) generally decreased as a function of wavelength, and the relatively lower SSAf value in summer was likely to be due to the stronger solar radiation and higher temperature. More than 70% of the aerosols at Panyu site were dominated by fine-mode absorbing particles, whereas about 70% of the particles at Dg site were attributed to fine-mode scattering particles. The differences of the aerosol optical properties between the two sites are likely associated with local emissions of the light-absorbing carbonaceous aerosols and the scattering aerosols (e.g., sulfate and nitrate particles) caused by the gas-phase oxidation of gaseous precursors (e.g., SO₂ and NO₂). The size distribution exhibited bimodal structures in which the accumulation mode was predominant. The fine-mode volume showed positive dependence on AOD (500nm), and the growth of peak value of the fine-mode volume was higher than that of the coarse volume. Both the AOD and SSA increased with increasing relative humidity (RH), while the AE decreased with increasing RH. These correlations imply that the aerosol properties are greatly modified by condensation growth.

The Griffiths Development Scales-Chinese (GDS-C): A cross-cultural comparison of developmental trajectories between Chinese and British children

BACKGROUND

The Griffiths Mental Development Scales (GMDS) are used in many countries to assess the development of children from birth to 8 years. There is a need for accurate and culturally appropriate developmental assessment tools for Chinese children. Here, we adapted the GMDS for use in Chinese children and compare the developmental trajectories between Chinese and British children.

METHODS

Children with typical development were recruited from 7 urban cities in China between 2009 and 2013. The Griffiths Mental Development Scales-Chinese (GDS-C) were adapted and used to assess the development of urban Chinese children. Developmental curves were computed for 6 subscales using learning management system methods and compare against the British curves from the Griffiths Mental Development Scales-Extended Revised (GMDS-ER).

RESULTS

The GDS-C were used to assess the developmental status of 815 Chinese children. Plots of the 1st, 5th, 10th, 25th, 50th, 75th, 90th, 95th, and 99th percentiles, and full percentile tables were obtained, which showed similar trends to data from the British GMDS-ER.

CONCLUSIONS

The Chinese developmental curves obtained from the GDS-C showed similarities and differences to the developmental curves from the British GMDS-ER. The development of urban Chinese children should be assessed with the culturally appropriate GDS-C.

Systematic review and meta-analysis of the genetic association between protamine polymorphism and male infertility

While several previous studies have proposed an association between male infertility and protamine polymorphism, the reported findings have shown some inconsistency. To evaluate the potential association between the two most common single nucleotide polymorphisms (rs2301365 and rs1646022) in protamine and male infertility, we performed a meta-analysis involving 2713 cases and 2086 controls from 15 published case-controlled studies. Overall, our analysis showed significant associations between the specific protamine single-nucleotide polymorphism (rs2301365) and male infertility, and this association was indicated by all of the models we tested. Subgroup analysis revealed significant associations with a Caucasian background, PCR sequence, population-based, case size of > 150 and case size of < 150 subgroups. Similarly, significant associations were found between rs1646022 and male infertility in the hospital population and case size of < 200 subgroups. However, trial sequential analysis showed that the number of patients in the study did not reach optimal information size. Further studies with larger sample sizes are now warranted to clarify the potential roles of the two protamine polymorphisms in the pathogenesis of male infertility. This may help us to understand the precise molecular mechanisms underlying the effect of protamines upon male infertility.

[Stability enhancement of urethanase from Lysinibacillus fusiformis by site-directed mutagenesis]

Ethyl carbamate as a potential carcinogen commonly exists in traditional fermented foods and beverages. Enzymatic removal of ethyl carbamate from fermented foods and beverages is an efficient and safe method. In this study, we mutated urethanase from Lysinibacillus fusiformis SC02 on the Q328 site through computer aided design approaches. The half-life of resulting mutants Q328C and Q328V was detected to be 7.46 and 1.96 folds higher than that of the original enzyme, and Q328R presented better thermal-tolerance than the original urethanase when incubated at high temperature. The tolerance of Q328C to ethanol and acid also increased when compared with that of the original enzyme. The stability and tolerance to acid and ethanol of urethanase could be improved by modification on its Q328 site.

HPV16 DNA and integration in normal and malignant epithelium: implications for the etiology of laryngeal squamous cell carcinoma

Background

Molecular evidence suggests that human papillomavirus (HPV) has a role in the etiology of oropharyngeal squamous cell carcinoma. However, the role of HPV in laryngeal squamous cell carcinoma (LSCC) is unclear.

Patients and methods

We conducted a case–control study using tumor tissue specimens from 300 LSCC patients and vocal cord polyp specimens from 300 cancer-free controls. HPV genotype, HPV16 viral load and viral integration status, and p16 expression were determined.

Results

The prevalence of HPV (all types) was higher in cases than controls [21 (7.0%) versus 10 (3.3%), adjusted odds ratio (aOR) 2.37, 95% CI 1.08–5.21]. The prevalence of HPV16 was higher in cases than controls [20 (6.7%) versus 8 (2.7%), aOR 2.84, 95% CI 1.21–6.68]. The risk of LSCC associated with HPV16 DNA positivity was even higher in patients aged 55 years or younger (aOR 3.52, 95% CI 1.07–11.54), males (aOR 4.74, 95% CI 1.33–16.90), never-smokers (aOR 5.57, 95% CI 1.41–22.10), and never-drinkers (aOR 3.72, 95% CI 1.09–12.72). HPV DNA was partly or fully integrated in all 20 HPV16-positive cases but was episomal in all 8 HPV16-positive controls; however, the HPV16-positive cases and controls had similar viral loads (P = 0.28). P16 immunostaining was positive in 31 of the 300 cases (10.3%) and negative in all 300 controls.

Conclusion

These results suggest that prior infection with HPV16 may play a role in the etiology of some LSCC. This larger case–control study will offer for the first time the possibility to address in depth the understanding of a tissue-specific role of HPV in laryngeal carcinogenesis. Further studies with larger samples are needed to confirm these findings.