Randomised clinical trial: the effects of Helicobacter pylori eradication on glandular atrophy and intestinal metaplasia after subtotal gastrectomy for gastric cancer

BACKGROUND

Helicobacter pylori eradication is recommended for early gastric cancer (GC) patients after resection.

AIM

To evaluate whether H. pylori eradication improves glandular atrophy and intestinal metaplasia (IM) in GC patients undergoing subtotal gastrectomy.

METHODS

This randomised, double-blind trial was performed in tertiary care setting. Distal GC patients with H. pylori infection were randomised to receive proton pump inhibitor-based triple therapy or placebo. The histology was evaluated using the updated Sydney system before and at 36 months after surgery. The endpoints were the comparison of atrophy and IM score changes between the allocated groups and according to final H. pylori status.

RESULTS

Overall, 190 patients were randomised to the treatment and placebo groups. For lesser curvature of the corpus, mean atrophy and IM scores did not differ between the treatment and placebo groups. However, the H. pylori-eradicated patients had significantly lower mean scores than the H. pylori-persistent patients regarding atrophy (0.55 ± 0.95 vs. 1.05 ± 1.10 respectively; P = 0.0046) and IM (0.66 ± 0.99 vs. 1.05 ± 1.16 respectively; P = 0.0284). The percentage change from baseline was more marked in the H. pylori-negative than in the H. pylori-positive groups (-58.6% vs. -11.0% for atrophy and -60.5% vs. -35.6% for IM respectively). For greater curvature, mean atrophy score was lower in the H. pylori-negative group than in the H. pylori-positive group (0.14 ± 0.50 vs. 0.41 ± 0.75 respectively; P = 0.0281). The percentage change was -36.4% vs. 86.3%.

CONCLUSION

Helicobacter pylori eradication in GC patients is beneficial, as reflected by lower scores of atrophy and IM at 36 months after subtotal gastrectomy. (ClinicalTrials.gov number, NCT01002443).

Viral genome analysis and knowledge management

One of the challenges of genetic data analysis is to combine information from sources that are distributed around the world and accessible through a wide array of different methods and interfaces. The HIV database and its footsteps, the hepatitis C virus (HCV) and hemorrhagic fever virus (HFV) databases, have made it their mission to make different data types easily available to their users. This involves a large amount of behind-the-scenes processing, including quality control and analysis of the sequences and their annotation. Gene and protein sequences are distilled from the sequences that are stored in GenBank; to this end, both submitter annotation and script-generated sequences are used. Alignments of both nucleotide and amino acid sequences are generated, manually curated, distilled into an alignment model, and regenerated in an iterative cycle that results in ever better new alignments. Annotation of epidemiological and clinical information is parsed, checked, and added to the database. User interfaces are updated, and new interfaces are added based upon user requests. Vital for its success, the database staff are heavy users of the system, which enables them to fix bugs and find opportunities for improvement. In this chapter we describe some of the infrastructure that keeps these heavily used analysis platforms alive and vital after nearly 25 years of use. The database/analysis platforms described in this chapter can be accessed at http://hiv.lanl.gov http://hcv.lanl.gov http://hfv.lanl.gov.

Epidemiology of the Foot-and-Mouth Disease Serotype O Epidemic of November 2010 to April 2011 in the Republic Of Korea

The largest epidemic of foot-and-mouth disease (FMD) in Korea since the first record in 1911 occurred between November 2010 and April 2011. The outbreak was confirmed in 153 farms, and more than three million animals were destroyed. This study presents the temporal and spatial distribution patterns, epidemiological investigation and the control measures for the 2010/2011 epidemic in Korea. The index case of this 2010/2011 FMD epidemic was reported in a pig-farming complex with five piggeries in Andong, GyeongBuk Province, on 28 November 2010, and the outbreak lasted 145 days. The largest number of new detection of the infected farms per day was recorded in mid-January. Epidemiological investigation revealed that the FMD virus had spread from farm to farm through routine movements associated with animal husbandry operations. In contrast to FMD epidemics in other countries in which movement of the infected animals largely contributed to the spread of the disease, human behaviours were major factors in the spread of the FMD virus in the Korean epidemic. The 2010/2011 epidemic was first confirmed in a local small and medium city where share of smallholder producers is higher than that of other provinces. Although Korea had a well-developed emergent response system with the experience of controlling infection and re-obtaining FMD-free status after the previous epidemics, Korea was prompted to revise their contingency plan by tailoring it to its unique livestock environment. Practical contingency plans tailored to Korea for control of FMD can be fully effective when farmers, livestock-related agencies, veterinary service providers and the general public work together.

Predictive factors for gastroduodenal toxicity based on endoscopy following radiotherapy in patients with hepatocellular carcinoma

PURPOSE

The aim of this work was to determine predictive factors for gastroduodenal (GD) toxicity in hepatocellular carcinoma (HCC) patients who were treated with radiotherapy (RT).

PATIENTS AND METHODS

A total of 90 HCC patients who underwent esophagogastroduodenoscopy (EGD) before and after RT were enrolled. RT was delivered as 30-50 Gy (median 37.5 Gy) in 2-5 Gy (median 3.5 Gy) per fraction. All endoscopic findings were reviewed and GD toxicities related to RT were graded by the Common Toxicity Criteria for Adverse Events, version 3.0. The predictive factors for the ≥ grade 2 GD toxicity were investigated.

RESULTS

Endoscopic findings showed erosive gastritis in 14 patients (16 %), gastric ulcers in 8 patients (9 %), erosive duodenitis in 15 patients (17 %), and duodenal ulcers in 14 patients (16 %). Grade 2 toxicity developed in 19 patients (21 %) and grade 3 toxicity developed in 8 patients (9 %). V25 for stomach and V35 for duodenum (volume receiving a RT dose of more than x Gy) were the most predictive factors for ≥ grade 2 toxicity. The gastric toxicity rate at 6 months was 2.9 % for V25 ≤ 6.3 % and 57.1 % for V25 > 6.3 %. The duodenal toxicity rate at 6 months was 9.4 % for V35 ≤ 5.4 % and 45.9 % for V35 > 5.4 %. By multivariate analysis including the clinical factors, V25 for stomach and V35 for duodenum were the significant factors.

CONCLUSION

EGD revealed that GD toxicity is common following RT for HCC. V25 for the stomach and V35 for the duodenum were the significant factors to predict ≥ grade 2 GD toxicity.

miR-206 regulates brain-derived neurotrophic factor in Alzheimer disease model

OBJECTIVE

Alzheimer disease (AD) brains are deficient in brain-derived neurotrophic factor (BDNF), which regulates synaptic plasticity and memory. MicroRNAs (miRNAs) are ∼22-nucleotide small noncoding RNAs that control a variety of physiological and disease processes. Here, we show that miR-206 regulates BDNF and memory function in AD mice.

METHODS

Expression of miRNAs was analyzed in Tg2576 AD transgenic mice and human AD brain samples. Regulation of BDNF by a selected miRNA was validated by in silico prediction, target gene luciferase assay, and dendritic spine responses in neurons. AM206, a neutralizing inhibitor of miR-206 (antagomir), was injected into the third ventricle of Tg2576 mice, after which memory function, synaptogenesis, neurogenesis, and target gene expression were assessed. For noninvasive delivery, antagomirs were administered intranasally.

RESULTS

The brains of Tg2576 mice and the temporal cortex of human AD brains had increased levels of miR-206. This miRNA targeted BDNF transcripts, and AM206 prevented the detrimental effects of amyloid-β42 on BDNF and dendritic spine degeneration in Tg2576 neurons. Injection of AM206 into the cerebral ventricles of AD mice increased the brain levels of BDNF and improved their memory function. In parallel, AM206 enhanced the hippocampal synaptic density and neurogenesis. Furthermore, intranasally administered AM206 also reached the brain and increased BDNF levels and memory function in AD mice.

INTERPRETATION

Our findings demonstrate a novel miRNA-dependent regulation of BDNF in AD and suggest possible therapeutic approaches, such as noninvasive intranasal delivery of AM206.

Attenuating astrocyte activation accelerates plaque pathogenesis in APP/PS1 mice

The accumulation of aggregated amyloid-β (Aβ) in amyloid plaques is a neuropathological hallmark of Alzheimer's disease (AD). Reactive astrocytes are intimately associated with amyloid plaques; however, their role in AD pathogenesis is unclear. We deleted the genes encoding two intermediate filament proteins required for astrocyte activation-glial fibrillary acid protein (Gfap) and vimentin (Vim)-in transgenic mice expressing mutant human amyloid precursor protein and presenilin-1 (APP/PS1). The gene deletions increased amyloid plaque load: APP/PS1 Gfap(-/-)Vim(-/-) mice had twice the plaque load of APP/PS1 Gfap(+/+)Vim(+/+) mice at 8 and 12 mo of age. APP expression and soluble and interstitial fluid Aβ levels were unchanged, suggesting that the deletions had no effect on APP processing or Aβ generation. Astrocyte morphology was markedly altered by the deletions: wild-type astrocytes had hypertrophied processes that surrounded and infiltrated plaques, whereas Gfap(-/-)Vim(-/-) astrocytes had little process hypertrophy and lacked contact with adjacent plaques. Moreover, Gfap and Vim gene deletion resulted in a marked increase in dystrophic neurites (2- to 3-fold higher than APP/PS1 Gfap(+/+)Vim(+/+) mice), even after normalization for amyloid load. These results suggest that astrocyte activation limits plaque growth and attenuates plaque-related dystrophic neurites. These activities may require intimate contact between astrocyte and plaque.

Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage

We report the rational design and in vivo testing of mosaic proteins for a polyvalent pan-filoviral vaccine using a computational strategy designed for the Human Immunodeficiency Virus type 1 (HIV-1) but also appropriate for Hepatitis C virus (HCV) and potentially other diverse viruses. Mosaics are sets of artificial recombinant proteins that are based on natural proteins. The recombinants are computationally selected using a genetic algorithm to optimize the coverage of potential cytotoxic T lymphocyte (CTL) epitopes. Because evolutionary history differs markedly between HIV-1 and filoviruses, we devised an adapted computational technique that is effective for sparsely sampled taxa; our first significant result is that the mosaic technique is effective in creating high-quality mosaic filovirus proteins. The resulting coverage of potential epitopes across filovirus species is superior to coverage by any natural variants, including current vaccine strains with demonstrated cross-reactivity. The mosaic cocktails are also robust: mosaics substantially outperformed natural strains when computationally tested against poorly sampled species and more variable genes. Furthermore, in a computational comparison of cross-reactive potential a design constructed prior to the Bundibugyo outbreak performed nearly as well against all species as an updated design that included Bundibugyo. These points suggest that the mosaic designs would be more resilient than natural-variant vaccines against future Ebola outbreaks dominated by novel viral variants. We demonstrate in vivo immunogenicity and protection against a heterologous challenge in a mouse model. This design work delineates the likely requirements and limitations on broadly-protective filoviral CTL vaccines.

In vivo human apolipoprotein E isoform fractional turnover rates in the CNS

Apolipoprotein E (ApoE) is the strongest genetic risk factor for Alzheimer's disease and has been implicated in the risk for other neurological disorders. The three common ApoE isoforms (ApoE2, E3, and E4) each differ by a single amino acid, with ApoE4 increasing and ApoE2 decreasing the risk of Alzheimer's disease (AD). Both the isoform and amount of ApoE in the brain modulate AD pathology by altering the extent of amyloid beta (Aβ) peptide deposition. Therefore, quantifying ApoE isoform production and clearance rates may advance our understanding of the role of ApoE in health and disease. To measure the kinetics of ApoE in the central nervous system (CNS), we applied in vivo stable isotope labeling to quantify the fractional turnover rates of ApoE isoforms in 18 cognitively-normal adults and in ApoE3 and ApoE4 targeted-replacement mice. No isoform-specific differences in CNS ApoE3 and ApoE4 turnover rates were observed when measured in human CSF or mouse brain. However, CNS and peripheral ApoE isoform turnover rates differed substantially, which is consistent with previous reports and suggests that the pathways responsible for ApoE metabolism are different in the CNS and the periphery. We also demonstrate a slower turnover rate for CSF ApoE than that for amyloid beta, another molecule critically important in AD pathogenesis.

The embryo lethality of Escherichia coli isolates and its relationship to the presence of virulence-associated genes

The aims of this study were to determine if the chicken embryo lethality assay and the presence of 9 virulence-associated genes of Escherichia coli were correlated and to discover which virulence genes contributed most to embryo lethality. We examined 58 E. coli strains isolated from visceral organs of chickens with colibacillosis for the presence of 9 virulence genes (fimC, tsh, fyuA, irp2, iucD, cvi/cva, iss, astA, and vat) by PCR. The gene FimC (type I fimbriae) was detected with the highest prevalence in 93.1% of the isolates, followed by iucD (67.24%), iss (58.62%), tsh (34.48%), cvi/cva (34.48%), fyuA (32.76%), astA (31.0%), irp2 (27.59%), and vat (17.24%). The embryo mortality ranged from 5 to 100%; however, most of the isolates were moderately or highly virulent. High positive correlations were observed between the presence of virulence genes and chicken embryo lethality. In addition, presence of the iucD (aerobactin) gene was the trait that best contributed to embryo mortality by using the multivariate model. These results suggest that expression frequency of these 9 virulence genes is associated with embryo mortality, and the gene that best predicted embryo mortality was iucD.

Low-density lipoprotein receptor represents an apolipoprotein E-independent pathway of Aβ uptake and degradation by astrocytes

Accumulation of the amyloid β (Aβ) peptide within the brain is hypothesized to be one of the main causes underlying the pathogenic events that occur in Alzheimer disease (AD). Consequently, identifying pathways by which Aβ is cleared from the brain is crucial for better understanding of the disease pathogenesis and developing novel therapeutics. Cellular uptake and degradation by glial cells is one means by which Aβ may be cleared from the brain. In the current study, we demonstrate that modulating levels of the low-density lipoprotein receptor (LDLR), a cell surface receptor that regulates the amount of apolipoprotein E (apoE) in the brain, altered both the uptake and degradation of Aβ by astrocytes. Deletion of LDLR caused a decrease in Aβ uptake, whereas increasing LDLR levels significantly enhanced both the uptake and clearance of Aβ. Increasing LDLR levels also enhanced the cellular degradation of Aβ and facilitated the vesicular transport of Aβ to lysosomes. Despite the fact that LDLR regulated the uptake of apoE by astrocytes, we found that the effect of LDLR on Aβ uptake and clearance occurred in the absence of apoE. Finally, we provide evidence that Aβ can directly bind to LDLR, suggesting that an interaction between LDLR and Aβ could be responsible for LDLR-mediated Aβ uptake. Therefore, these results identify LDLR as a receptor that mediates Aβ uptake and clearance by astrocytes, and provide evidence that increasing glial LDLR levels may promote Aβ degradation within the brain.

Clinical manifestations of foot-and-mouth disease during the 2010/2011 epidemic in the Republic of Korea

We reviewed the clinical signs of the foot-and-mouth disease (FMD) incidences in the Republic of Korea occurring from November 2010 to April 2011. Profuse salivation, vesiculation, lameness or ataxia, and ulceration were the most commonly observed clinical signs of FMD among the infected animals, irrespective of the species. The clinical signs of FMD manifested more clearly in the dairy cattle and pigs compared to the beef cattle, deer and goats on infected farms. About 54% of the infected dairy farms reported vesicles on the teats as the primary clinical sign, while vesiculation on the nose, including the snout and muzzle, was the major lesion observed in infected beef cattle and pig farms. The teat and feet were the second most frequently vesiculated body parts on infected pigs. Although the average age of the first-to-appear clinical lesion in the animals in the beef and dairy cattle farms subjected to vaccination was higher than that observed in the animals in the farms not subjected to vaccination, a reverse pattern was observed in the pig farms. In this study, the clinical signs of FMD were described on the basis of the subjective observations by the farm workers. The present results highlight the clinical signs expected on specific body parts of different types of susceptible animals, and therefore, they may be useful for generating public awareness, particularly among farm workers, as well as for early detection of future FMD outbreaks.

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.

Contrast-enhanced computed tomography angiography and volume-rendered imaging for evaluation of cellophane banding in a dog with extrahepatic portosystemic shunt

A 4-year-old, 1.8 kg, male, castrated Maltese was presented for evaluation of urolithiasis. Urinary calculi were composed of ammonium biurate. Preprandial and postprandial bile acids were 44.2 and 187.3 μmol/ , respectively (reference ranges 0–10 and 0–20 μmol/ , respectively). Single-phase contrast-enhanced computed tomography angiography (CTA) with volume-rendered imaging (VRI) was obtained. VRI revealed a portocaval shunt originating just cranial to a tributary of the gastroduodenal vein and draining into the caudal vena cava at the level of the epiploic foramen. CTA revealed a 3.66 mm-diameter shunt measured at the level of the termination of the shunt and a 3.79 mm-diameter portal vein measured at the level between the origin of the shunt and the porta of the liver. Surgery was performed using cellophane banding without attenuation. Follow-up single-phase CTA with VRI was obtained 10 weeks after surgery. VRI revealed no evidence of portosystemic communication on the level of a cellophane band and caudal to the cellophane band. CTA demonstrated an increased portal vein diameter (3.79–5.27 mm) measured at the level between the origin of the shunt and the porta of the liver. Preprandial and postprandial bile acids were 25 and 12.5 μmol/ , respectively (aforementioned respective reference ranges), 3 months post-surgery. No problems were evident at 6 months.

A Systematic Study of the Structural and Luminescence Properties of P-Type Porous Silicon

The structural and luminescence properties of (001) p-type porous silicon samples (p∼0.1-0.2 Ω•cm) fabricated electrochemically under various conditions were investigated using high resolution double and triple axis diffraction and photoluminescence spectroscopy. We show the sensitivity of the structure of the porous silicon to the current density in the range of 10-50 mA/cm2, HF acid concentration in the range of 15% - 30%, and the evolution of the structure with time. We have found a systematic dependence of the amount of strain in the porous silicon layer (PSL) on the current density. The effect of the HF concentration is such that at 25% and 30% HF, PSLs are formed which are crystalline and strained, but at a lower HF concentration (15%), strained layers are not formed. The perpendicular strain in the layer increases linearly with storage time but the in-plane lattice constant of the porous silicon remains matched to the substrate. Further, we utilized x-ray reciprocal space maps to observe that, with storage time, there is an increase in the diffuse scattering from the PSL due to an increase in the range of tilts in the layer. Room temperature photoluminescence emission was observed for all 15% and 25% HF samples, but not for all 30% HF samples. Higher peak luminescence energy was obtained with lower HF concentration. Finally, we note the relationship between the strain in the PSL and the luminescence properties.

Non-Linear Optical Polymers for Active Optical Devices

Second order non-linear optical (NLO) polymers have been the focus of intense research effort in recent years [1]. This effort is justified by the potential value of these materials in a range of attractive optical signal processing applications with lower device costs and enhanced device performance.

Material Requirements for a Boron Phosphide Thermal Neutron Counter

Electrical characterization (current versus voltage and capacitance versus voltage) of nonstoichiometric amorphous boron phosphide Schottky diodes for neutron detection is presented. These results are incorporated in a Monte Carlo model of detector response to determine material requirements for a boron phosphide neutron counter.

Comparison Between Cadmium Zinc Telluride Crystals Grown in Russia and in the Ukraine

A comparative analysis of different Cd1−xZnxTe (CZT) crystals grown by a vertical high pressure Bridgman (VHPB) method is reported. The results of several analytical techniques, such as triple axis x-ray diffraction (TAD), rocking curves, low temperature photoluminescence (PL), scanning electron microscopy (SEM), and proton induced x-ray emission (PIXE) are discussed. Segregated carbon inclusions were identified by SEM and energy dispersive x-ray fluorescence (EDXRF), and the results are interpreted in terms of constitutional supercooling of the solidifying CZT melt. The carbon inclusions significantly decrease the resistivity, and in some cases, the noise is too large for the fabrication of radiation detectors. Combining these results with other measurements reported by our research team [1], we identify correlations between the growth and the defects identified in these CZT crystals.

Survival rate of H5N1 highly pathogenic avian influenza viruses at different temperatures

The survival rate of Korean H5N1 highly pathogenic avian influenza (HPAI) viruses was investigated at different temperatures under the laboratory conditions. The estimated survival days for a starting viral concentration of 10(6.5) 50% egg infectious dose/0.1 mL were 930, 1,042, and 3,213 d at 4 degrees C; 226, 232, and 293 d at 20 degrees C; and 51, 55, and 58 d at 30 degrees C for A/chicken/Korea/ES/03, A/chicken/Korea/IS/06, and A/chicken/Korea/Gimje/08 (Gimje/08) viruses, respectively. The stability of the Gimje/08 virus was statistically significant compared with the other 2 viruses except for the data between Gimje/08 and A/chicken/Korea/IS/06 virus at 30 degrees C. This result indicated that the survival rate of 3 Korean HPAI viruses is different at various temperatures, which might have partially influenced the large scale of HPAI outbreak in Korea in 2008.

Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity

Immunological control of hepatitis C virus (HCV) is possible and is probably mediated by host T-cell responses, but the genetic diversity of the virus poses a major challenge to vaccine development. We considered monovalent and polyvalent candidates for an HCV vaccine, including natural, consensus and synthetic 'mosaic' sequence cocktails. Mosaic vaccine reagents were designed using a computational approach first applied to and demonstrated experimentally for human immunodeficiency virus type 1 (HIV-Delta). Mosaic proteins resemble natural proteins, but are assembled from fragments of natural sequences via a genetic algorithm and optimized to maximize the coverage of potential T-cell epitopes (all 9-mers) found in natural sequences and to minimize the inclusion of rare 9-mers to avoid vaccine-specific responses. Genotype 1-specific and global vaccine cocktails were evaluated. Among vaccine candidates considered, polyvalent mosaic sequences provided the best coverage of both known and potential epitopes and had the fewest rare epitopes. A global vaccine based on conserved proteins across genotypes may be feasible, as a five-antigen mosaic cocktail provided 90, 77 and 70% coverage of the Core, NS3 and NS4 proteins, respectively; protein coverage diminished with increased protein variability, dropping to 38% for NS2. For the genotype 1-specific vaccine, the H77 prototype vaccine sequence matched only 50% of the potential epitopes in the population, whilst a polyprotein three-antigen mosaic cocktail increased potential epitope coverage to 83%. More than 75% coverage of all HCV proteins was achieved with a three-antigen mosaic cocktail, suggesting that genotype-specific vaccines could also include the more variable proteins.