DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.

SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan

Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.

Compensatory Enlargement of the Liver after Proton Beam Therapy for Hepatocellular Carcinoma

PURPOSE/OBJECTIVE(S)

Charged particle therapy (CPT) has been applied as a safe and effective treatment option for hepatocellular carcinoma (HCC). Although most HCC patients have cirrhosis, favorable treatment outcome has been achieved with CPT preserving liver function. After proton beam therapy (PBT) for patients with HCC, the liver volume in the non-irradiated area is often enlarged. Here, we evaluated whether enlargement of the non-irradiated liver affects preserving hepatic function and prognosis in HCC patients treated with PBT.

MATERIALS/METHODS

Among consecutive patients with HCC treated with PBT between April 2011 and July 2017, we retrospectively identified patients who fulfilled the following criteria: (i) receiving PBT to the right hepatic lobe, (ii) the left lateral segment was not irradiated, (iii) no local treatment was performed for liver within 12 months after PBT, and (iv) the albumin-bilirubin (ALBI) score was evaluable at 12 months after PBT. The left lateral segment was defined as the non-irradiated region and measured by contrast-enhanced CT just before and 3 months after PBT. ALBI scores just before and 12 months after PBT were compared to evaluate changes of hepatic function. Overall survival rate was estimated using the Kaplan-Meier method, and differences in survival between subgroups were examined using the log-rank test. The ALBI scores were compared using the Wilcoxon signed-rank test.

RESULTS

We identified 40 patients (male/female = 32/8). The median age at the start date of PBT was 72 (range, 54-87) years. The prescribed dose was 66.0-76.0 Gy (relative biological effectiveness) delivered in 10-38 fractions. The median follow-up was 61 (range, 12-126) months. The 5-year overall survival rates were 79.0% (95% CI: 60.4-100.0%) in the larger enlargement group (n = 16, enlarged volume of non-irradiated region 3 months after PBT ≥75 cm3) and 53.7% (95% CI: 36.0-79.9%) in the smaller enlargement group (n = 24, as above, <75 cm3), respectively (p = 0.21). The median ALBI scores just before and 12 months after PBT were -3.14 (95% CI: -3.22- (-2.53)) and -2.74 (95% CI: -3.07- (-2.42)) in the larger enlargement group (p = 0.09), and -2.91 (95% CI: -3.15- (-2.40)) and -2.59 (95% CI: -2.74- (-2.12)) in the smaller enlargement group (p = 0.006), respectively.

CONCLUSION

Our study suggests that larger enlargement of the non-irradiated liver after PBT is related to well-preserved liver function at 1 year and modestly associated with a favorable prognosis.

DNA Data Bank of Japan (DDBJ) update report 2022

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) maintains database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), our primary mission is to collect and distribute nucleotide sequence data, as well as their study and sample information, in collaboration with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute. In addition to INSDC resources, the Center operates databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank), and human genetic and phenotypic data (JGA: Japanese Genotype-Phenotype Archive). These databases are built on the supercomputer of the National Institute of Genetics, whose remaining computational capacity is actively utilized by domestic researchers for large-scale biological data analyses. Here, we report our recent updates and the activities of our services.

Advantage of POLARx over ARCTIC FRONT ADVANCE PRO during pulmonary vein isolation for paroxysmal atrial fibrillation

Introduction

The electrical pulmonary vein (PV) isolation has been established as a curative therapy for paroxysmal atrial fibrillation (AF). Arctic Front™cryoballoon has been used worldwide for AF cryoablation. Recently, a new cryoballoon, POLARxTM CRYOABLATION system have been introduced, of which material of the balloon is softer and the N2O gas flow rate is higher.

Purpose

The aim was to investigate the procedural parameter and efficacy of POLARx comparing with Arctic Front.

Methods

This retrospective single center study included 101 consecutive patients who underwent paroxysmal AF ablation using cryoballoon at Keio University hospital from April 2021 to March 2022. The procedural data including the cryoballoon temperature and the number and duration of cryoablation were compared between POLARx (POLARx group) and ARCTIC FRONT ADVANCE PRO (AFA group). After the cryoablation, we added the radiofrequency application in order to maximize the isolated area when the voltage was remained inside PV (Figure 1). The necessities of the additional radiofrequency applications were also compared.

Results

In the present study, 64 patients in AFA group and 37 patients in POLARx group were analyzed. POLARx group included younger population and less females (62.8±9.9 vs 67.5±9.4 year of age, P=0.02; 13.5 vs 32.8%, P=0.04). There was no significant difference in comorbidities and examination data such as left atrium diameter or brain natriuretic peptide level. The minimal cryoballoon temperatures reached in POLARx group were lower than AFA group (−59.3±6.2 vs −47.7±7.5°C, P&lt;0.01). No difference was found in the total number and duration of cryoablation and the time to isolate PV (6.1±2.1 vs 5.9±1.6, P=0.69; 790.2±256.1 vs 776.1±235.0 sec, P=0.69; 41.8±21.3 vs 47.1±29.6 sec, P=0.44, respectively). With regard to individual PVs, the total number and duration were tended to be larger at right superior PV in POLARx group (1.9±1.1 vs 1.4±0.7, P=0.01; 231.8±123.8 vs 193.2±83.0 sec, P=0.07), while there was no significant difference at the other PVs. The rate of successful PV isolation by a single cryo-application was not different between AFA and POLARx group (54.3 vs 61.4%, P=0.17). The additional radiofrequency applications were more frequent in AFA group (14.8 vs. 4.9%, P=0.003). There was a significant difference at right inferior PV (32.8 vs 8.1%, P=0.01), while not at left superior PV, left inferior PV and right superior PV (9.4 vs 2.9%, P=0.42; 9.4 vs 5.7%, P=0.71; 7.8 vs 2.7%, P=0.41). Phrenic nerve injury was occurred 1 case in both group and esophageal ulcer was occurred in 1 case in AFA group. No other complication including cardiac tamponade was occurred.

Conclusion

The total number and duration of cryoablation were not significantly different between AFA and POLARx group, except for right superior PV. There was an advantage in largely isolating right inferior PV in POLARx group comparing with AFA group.

Funding Acknowledgement

Type of funding sources: None.

DNA Data Bank of Japan (DDBJ) update report 2021

The Bioinformation and DDBJ (DNA Data Bank of Japan) Center (DDBJ Center; https://www.ddbj.nig.ac.jp) operates archival databases that collect nucleotide sequences, study and sample information, and distribute them without access restriction to progress life science research as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute. Besides the INSDC databases, the DDBJ Center also provides the Genomic Expression Archive for functional genomics data and the Japanese Genotype-phenotype Archive for human data requiring controlled access. Additionally, the DDBJ Center started a new public repository, MetaboBank, for experimental raw data and metadata from metabolomics research in October 2020. In response to the COVID-19 pandemic, the DDBJ Center openly shares SARS-CoV-2 genome sequences in collaboration with Shizuoka Prefecture and Keio University. The operation of DDBJ is based on the National Institute of Genetics (NIG) supercomputer, which is open for large-scale sequence data analysis for life science researchers. This paper reports recent updates on the archival databases and the services of DDBJ.

Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade

Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.

Trajectories of high-sensitivity cardiac troponin I in the two decades before cardiovascular death in Whitehall II

Background

High-sensitivity cardiac troponin may be a promising biomarker that could be used for personalised cardiovascular risk prediction and monitoring in the general population. Temporal changes in high-sensitivity cardiac troponin before cardiovascular death are largely unexplored.

Purpose

Using the longitudinal Whitehall II cohort, we evaluated whether three serial high-sensitivity cardiac troponin I measurements over 15 years improved prediction of cardiovascular death when compared to a single time point at baseline.

Methods

Whitehall II is an ongoing longitudinal observation cohort study of 10,308 civil servants, and we included participants who had at least one cardiac troponin measurement and outcome data available. We constructed time trajectories to evaluate the temporal pattern of cardiac troponin I in those who died from cardiovascular disease as compared to those who did not. Cox regression and joint models were used to investigate the association of cardiac troponin I in relation to cardiovascular death using single time point (at baseline) and repeated measurements (at baseline, 10 and 15 years), respectively. The discriminative ability was assessed by the concordance index.

Results

In total, we included 7,293 individuals (mean age of 58 years [SD 7] at baseline, 29.4% women). Of these, 5,818 (79.8%) and 4,045 (55.5%) individuals had a second and third cardiac troponin I concentration measured, respectively. Cardiovascular death occurred in 281 (3.9%) individuals during a median follow-up of 21.4 [IQR, 15.8 to 21.8] years. In the 21-year trajectories of cardiac troponin I, we observed higher baseline concentrations in those who died due to cardiovascular disease as compared to those who did not (median 5 [IQR, 2 to 9] ng/L versus 3 [IQR, 2 to 5] ng/L respectively, Figure). Cardiac troponin I was an independent predictor of cardiovascular death, and the hazard ratio (HR) derived from the joint model that included serial cardiac troponin measurements was higher than the HR derived from the single time point model (single time point model: adjusted HR 1.53, 95% Confidence Interval [CI] 1.37 to 1.70 per naturally log transformed unit of cardiac troponin I, versus repeated measurements model: adjusted HR 1.79, 95% CI 1.58 to 2.02). The discriminative ability of the cardiac troponin model improved when using repeated measurements (concordance index of unadjusted cardiac troponin models, single time point: 0.668 versus repeated measurements: 0.724).

Conclusions

Our study shows that cardiac troponin I trajectories were persistently higher among individuals who died from cardiovascular disease. Cardiac troponin I is a strong independent predictor of cardiovascular death, and incorporating repeated measurements of cardiac troponin improves cardiovascular risk prediction in the general population.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Cardiac troponin I measurements and analysis were supported by were supported by Siemens Healthineers. The study was supported by Health Data Research UK which receives its funding from HDR UK Ltd (HDR-5012) funded by the UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation and the Wellcome Trust. NLM is supported by the British Heart Foundation through a Senior Clinical Research Fellowship (FS/16/14/32023), Programme Grant (RG/20/10/34966) and a Research Excellence Award (RE/18/5/34216). The funders had no role in the study and the decision to submit this work to be considered for publication.

Troponin to risk stratify patients with suspected acute coronary syndrome for computed tomography coronary angiography

Background

Patients with suspected acute coronary syndrome in whom myocardial infarction has been ruled-out are at risk of future adverse cardiac events. However, the optimal approach to risk stratify and investigate these patients is uncertain.

Methods

We performed a prospective cohort study of 250 patients presenting to the Emergency Department with suspected acute coronary syndrome and troponin concentrations below the sex-specific 99th centile (16 ng/L for women and 34 ng/L for men). Patients were recruited in a 2:1 fashion stratified by peak high-sensitivity cardiac troponin I concentration above and below the early rule-out threshold of 5 ng/L (167 patients with intermediate troponin concentrations between 5 ng/L and the sex-specific 99th centile threshold and 83 patients with troponin concentrations &lt;5 ng/L). All patients underwent computed tomography coronary angiography after they were discharged from hospital.

Results

Overall, 37.6% (94/250) of patients had normal coronary arteries whilst 36.0% (90/250) and 26.4% (66/250) had non-obstructive and obstructive coronary artery disease, respectively. Patients with intermediate troponin concentrations were more likely to have coronary artery disease than those with troponin concentrations &lt;5 ng/L (71.9% [120/167] versus 43.4% [36/83]; odds ratio 3.33 [95% confidence interval 1.92–5.78]). This association persisted irrespective of whether patients had anginal symptoms. Conversely, there was no difference in the prevalence of coronary artery disease between those with and without anginal symptoms (63.2% [67/106] and versus 61.8% [89/144]; odds ratio 0.92 [0.48–1.76]). The majority of patients found to have coronary artery disease did not have a prior diagnosis and were not on optimal preventative medical therapy prior to undergoing computed tomography coronary angiography (50.8% [61/120] and 61.0% [22/36], versus 61.7% [74/120] and 69.4% [25/36] in patients with intermediate versus low troponin concentrations, respectively).

Conclusions

In patients with suspected acute coronary syndrome who have myocardial infarction ruled out, those with intermediate cardiac troponin concentrations are three-times more likely to have coronary artery disease than those with low troponin concentrations. Conversely anginal symptoms did not discriminate between those with and without coronary artery disease. Further studies are required to determine if targeting computed tomography coronary angiography to those with intermediate cardiac troponin concentrations can improve the use of preventative medical therapies and clinical outcomes.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): The British Heart Foundation Odds ratio of coronary artery diseaseCumulative proportion with CAD

DDBJ update: streamlining submission and access of human data

The Bioinformation and DDBJ Center (DDBJ Center, https://www.ddbj.nig.ac.jp) provides databases that capture, preserve and disseminate diverse biological data to support research in the life sciences. This center collects nucleotide sequences with annotations, raw sequencing data, and alignment information from high-throughput sequencing platforms, and study and sample information, in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI). This collaborative framework is known as the International Nucleotide Sequence Database Collaboration (INSDC). In collaboration with the National Bioscience Database Center (NBDC), the DDBJ Center also provides a controlled-access database, the Japanese Genotype–phenotype Archive (JGA), which archives and distributes human genotype and phenotype data, requiring authorized access. The NBDC formulates guidelines and policies for sharing human data and reviews data submission and use applications. To streamline all of the processes at NBDC and JGA, we have integrated the two systems by introducing a unified login platform with a group structure in September 2020. In addition to the public databases, the DDBJ Center provides a computer resource, the NIG supercomputer, for domestic researchers to analyze large-scale genomic data. This report describes updates to the services of the DDBJ Center, focusing on the NBDC and JGA system enhancements.

Complete sequence and structure of the genome of the harmful algal bloom-forming cyanobacterium Planktothrix agardhii NIES-204T and detailed analysis of secondary metabolite gene clusters

Planktothrix species are distributed worldwide, and these prevalent cyanobacteria occasionally form potentially devastating toxic blooms. Given the ecological and taxonomic importance of Planktothrix agardhii as a bloom species, we set out to determine the complete genome sequence of the type strain Planktothrix agardhii NIES-204. Remarkably, we found that the 5S ribosomal RNA genes are not adjacent to the 16S and 23S ribosomal RNA genes. The genomic structure of P. agardhii NIES-204 is highly similar to that of another P. agardhii strain isolated from a geographically distant site, although they differ distinctly by a large inversion. We identified numerous gene clusters that encode the components of the metabolic pathways that generate secondary metabolites. We found that the aeruginosin biosynthetic gene cluster was more similar to that of another toxic bloom-forming cyanobacterium Microcystis aeruginosa than to that of other strains of Planktothrix, suggesting horizontal gene transfer. Prenyltransferases encoded in the prenylagaramide gene cluster of Planktothrix strains were classified into two phylogenetically distinct types, suggesting a functional difference. In addition to the secondary metabolite gene clusters, we identified genes for inorganic nitrogen and phosphate uptake components and gas vesicles. Our findings contribute to further understanding of the ecologically important genus Planktothrix.

Change of the pulmonary vein anatomy after cryoballoon ablation reflecting left atrial reverse remodeling

Background

Cryoballoon ablation (CBA) is a widely used procedure for atrial fibrillation (AF). However, the anatomical change of pulmonary veins (PVs) and the risk factors of PV stenosis is less clear. We aimed to decipher the prevalence and the predictive factors for PV stenosis after CBA.

Methods

We analyzed the data of 320 PVs from 80 patients who underwent CBA for AF (age: 62±10 years, 59 males, 75 paroxysmal AF). All patients underwent pre- and post-procedural cardiac computed tomography (mean 6.7±3.3 months after ablation). We defined the PV stenosis when the cross sectional area of PV was less than 50% compared with that of PV before the CBA.

Results

The average cross sectional PV area decreased significantly after CBA (pre- vs. post-CBA; 2.4±1.0cm2 vs. 2.3±1.1cm2, P&lt;0.001), whereas the volume of left atrium (LA) also decreased significantly (pre- vs. post-CBA; 75.0±23.2cm3 vs. 70.7±21.9cm3, P&lt;0.001). There was a weak but significant correlation between the reduction rate of PV area and that of LA volume (Pearson's correlation coefficient 0.411, p&lt;0.001). Only 6 PV stenosis were revealed, in which area reduction of more than 75% and 50–75% were observed in 2 PVs and 4 PVs, respectively. The incidence of PV stenosis was greater in female (male vs. female; 0.8% vs. 4.8%, P=0.043) and tend to be frequent in left PVs (left PVs vs. right PVs; 3.1% vs. 0.6%: P=0.107). Moreover, patients who developed PV stenosis tended to have lower weight and shorter height (PV stenosis group vs. non-PV stenosis group; 58.2±12.4kg vs. 67.7±13.0kg: P=0.078, 161.2±9.1cm vs. 167.2±8.8cm: P=0.094). There were no significant differences in the number of freezing, minimum temperature and total freezing time between PV stenosis group and non-PV stenosis group.

Conclusions

The ostial PV area decreased significantly but little after CBA, possibly due to LA reverse remodeling. The PV stenosis was more common in women and tend to be frequent in left PVs, lower weight, and shorter height patients, though severe stenosis after CBA was not observed in this study.

Funding Acknowledgement

Type of funding source: None

Cost-effectiveness analysis for preventing hepatitis B virus reactivation-related death in Japan

Background

There is no worldwide standard recommendation for preventing hepatitis B virus (HBV) reactivation for patients with resolved infection treated with an anti-CD20 antibody for B-cell non-Hodgkin lymphoma. This study aims to compare the cost-effectiveness between two commonly used strategies to prevent HBV reactivation-related death.

Methods

The two strategies compared were prophylactic antiviral therapy (Pro NAT) and HBV DNA monitoring followed by on-demand antiviral therapy (HBV DNA monitoring) using entecavir (Entecavir, a generic drug for Baraclude). Effectiveness was defined as the prevention of death due to HBV reactivation and costs were calculated under the health insurance system of Japan as of April 2018 using Markov model. A cost-minimization analysis, one of the cost-effectiveness analyses, was applied, since the effectiveness was the same between the two strategies according to a meta-analysis. To consider the effect of uncertainty for each parameter, probabilistic sensitivity analysis (PSA) was performed. In the scenario analysis, costs were calculated using lamivudine (Zefix) or tenofovir alafenamide (Vemlidy) instead of entecavir. All analyses were done using TreeAge Pro 2019 (TreeAge Software, Inc., MA, USA).

Results

Estimated costs per patient during the 30 months after initiation of chemotherapy for lymphoma were 1,513 USD with Pro NAT and 1,265 USD with HBV DNA monitoring. A PSA revealed that HBV DNA monitoring was more consistently cost-effective compared with Pro NAT when some parameters were set randomly according to probability distributions. In our scenario analysis, costs of Pro NAT and HBV DNA monitoring were calculated as 2,762 and 1,401 USD using lamivudine, 4,857 and 1,629 USD using tenofovir alafenamide.

Conclusions

Our cost-effectiveness analysis shows that an HBV DNA monitoring strategy using entecavir should be recommended for preventing HBV reactivation-related death in Japan.

Key messages

Cost-effectiveness analysis demonstrated that HBV DNA monitoring was more cost-effective compared to Pro NAT; this result was consistent with PSA. HBV DNA monitoring strategy should be recommended to prevent HBV reactivation-related death for the patients with resolved HBV infection in Japan.

Comprehensive assessment of multiple tryptophan metabolites as potential biomarkers for immune checkpoint inhibitors in patients with non-small cell lung cancer

Purpose

Tryptophan metabolites have immunomodulatory functions, suggesting possible roles in cancer immunity.

Methods

Plasma tryptophan metabolites were measured using liquid chromatography/mass spectrometry before immune checkpoint inhibitors (ICIs) in patients with non-small cell lung cancer (NSCLC).

Results

The 19 patients with NSCLC had significantly lower levels of tryptophan (p = 0.002) and xanthurenic acid (p = 0.032), and a significantly higher level of 3-hydroxyanthranilic acid (3-HAA) (p = 0.028) compared with the 10 healthy volunteers. The patients achieving objective responses had significantly lower levels of 3-HAA than those who did not (p = 0.045). Receiver operating characteristic analyses determined that the cutoff value of 3-HAA for objective response was 35.4 pmol/mL (sensitivity: 87.5% and specificity: 83.3%). The patients with 3-HAA < 35.4 pmol/mL had significantly longer median progression-free survival (7.0 months) than those without (1.6 months, p = 0.022).

Conclusions

Tryptophan metabolites may have a potential for predicting the efficacy of ICIs.

Registration number

University Hospital Medical Information Network Clinical Trial Registry 000026140.

Electronic supplementary material

The online version of this article (10.1007/s12094-020-02421-8) contains supplementary material, which is available to authorized users.

DDBJ Data Analysis Challenge: a machine learning competition to predict Arabidopsis chromatin feature annotations from DNA sequences

Recently, the prospect of applying machine learning tools for automating the process of annotation analysis of large-scale sequences from next-generation sequencers has raised the interest of researchers. However, finding research collaborators with knowledge of machine learning techniques is difficult for many experimental life scientists. One solution to this problem is to utilise the power of crowdsourcing. In this report, we describe how we investigated the potential of crowdsourced modelling for a life science task by conducting a machine learning competition, the DNA Data Bank of Japan (DDBJ) Data Analysis Challenge. In the challenge, participants predicted chromatin feature annotations from DNA sequences with competing models. The challenge engaged 38 participants, with a cumulative total of 360 model submissions. The performance of the top model resulted in an area under the curve (AUC) score of 0.95. Over the course of the competition, the overall performance of the submitted models improved by an AUC score of 0.30 from the first submitted model. Furthermore, the 1^st- and 2^nd-ranking models utilised external data such as genomic location and gene annotation information with specific domain knowledge. The effect of incorporating this domain knowledge led to improvements of approximately 5%-9%, as measured by the AUC scores. This report suggests that machine learning competitions will lead to the development of highly accurate machine learning models for use by experimental scientists unfamiliar with the complexities of data science.

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

DDBJ Database updates and computational infrastructure enhancement

The Bioinformation and DDBJ Center (https://www.ddbj.nig.ac.jp) in the National Institute of Genetics (NIG) maintains a primary nucleotide sequence database as a member of the International Nucleotide Sequence Database Collaboration (INSDC) in partnership with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The NIG operates the NIG supercomputer as a computational basis for the construction of DDBJ databases and as a large-scale computational resource for Japanese biologists and medical researchers. In order to accommodate the rapidly growing amount of deoxyribonucleic acid (DNA) nucleotide sequence data, NIG replaced its supercomputer system, which is designed for big data analysis of genome data, in early 2019. The new system is equipped with 30 PB of DNA data archiving storage; large-scale parallel distributed file systems (13.8 PB in total) and 1.1 PFLOPS computation nodes and graphics processing units (GPUs). Moreover, as a starting point of developing multi-cloud infrastructure of bioinformatics, we have also installed an automatic file transfer system that allows users to prevent data lock-in and to achieve cost/performance balance by exploiting the most suitable environment from among the supercomputer and public clouds for different workloads.

P3598Cardiac Cycle - The effect of exercise on cardiac troponin release

Introduction

International guidelines recommend the use of low concentrations of high-sensitivity cardiac troponin to risk stratify patients with suspected acute coronary syndrome, however, troponin concentration may also rise due to physical exercise. Interpreting cardiac troponin concentration in this context is challenging because the magnitude and duration of troponin elevation following physical exercise is uncertain.

Purpose

To determine the effect of intensity and duration of physical exercise on cardiac troponin concentration.

Methods

We invited 10 physically active healthy volunteers (7 male and 3 female; mean age: 34±7) to attend 3 study visits, during which they underwent exercise on a stationary bicycle at prespecified intensities and durations. The first visit involved low intensity cycling (50–60% of the participant's lactate threshold [LT]) for 60 minutes. During the second visit, participants cycled at high intensity (80–90% LT) for 60 minutes and during the third study visit, participants cycled at moderate intensity (60–70% LT) for 4 hours. High-sensitivity cardiac troponin I (hs-cTnI) concentration was measured at the start of exercise and every hour up to 6 hours during each study visit and subsequently at 1, 2 and 7 days after each exercise visit.

Results

Study participants had a median hs-cTnI concentration of 1.8 ng/L (interquartile range [IQR] 0.8–5.7 ng/L) at baseline. Cardiac troponin concentration was elevated following moderate- and high-intensity exercise (P=0.006 and P<0.001, respectively) but not following low-intensity exercise (P=0.137). Troponin concentrations were significantly higher following the shorter duration of high-intensity exercise (peak hs-cTnI concentration = 13 ng/L [IQR 6.5–27.1 ng/L]) compared to the longer duration moderate-intensity exercise (peak hs-cTnI concentration = 6.9 ng/L [2.9–7.9 ng/L]; P-value <0.001). Following both moderate- and high-intensity exercise, cardiac troponin concentration returned to baseline within 48 hours (Figure 1).

Troponin concentrations ng/L / time

Conclusions

Our study suggests that elevation in cardiac troponin concentration is associated with the intensity rather than duration of physical exercise, and that exercise-induced troponin elevations resolve within 48 hours. These findings have important implications for the interpretation of cardiac troponin in the risk stratification and diagnosis of patients who present with symptoms suggestive of acute coronary syndrome following physical exercise.

Acknowledgement/Funding

British Heart Foundation

Risk of heat illness in men and women: A systematic review and meta-analysis

BACKGROUND

Heat illness (HI) is a growing global concern; its incidence has risen dramatically across the world in recent years. The individual factors whereby elevated core temperature produces HI are not well-understood. Given known physiological differences between men and women pertaining to temperature regulation, we hypothesized that women would be at increased risk of HI than men.

OBJECTIVES

We aimed to determine the relative risk of HI in women compared with men through an exhaustive literature review and meta-analysis.

METHODS

We search PubMed and Ovid Medline databases from inception to Apr 2017. Search terms included all permutations of sex and heat illness (including heatstroke and exertional heat illness) with no language restrictions. We included adult or adolescent human data reporting comparable male and female HI rates. One reviewer identified and screened titles and abstracts. Two independent reviewers applied eligibility criteria. Disagreements were resolved with a third reviewer.

RESULTS

Of 5888 articles identified by searches, 36 were included in the systematic review and 22 in the meta-analysis. The mean (standard deviation) quality score was 3.31(1.25)/5. Overall the rate among women was consistently lower than men across the lifespan. The male: female pooled IRR was 2.28 (p < 0.001, 95% CI: 1.66-3.16). There was modest heterogeneity (between-studies variance (τ²) = 0.02). The rates did not differ significantly when corrected for severity or occupation.

DISCUSSION

The rate of HI was significantly increased in men compared with women. Risk for HI might be conferred by psychological and behavioral factors rather than physiological ones. Further research is required to delineate which groups are at greatest risk, leading to the development of mitigation strategies against HI.

OTHER

No funding was received. The authors acknowledge the support of the UK Women in Ground Close Combat Review. The Study was registered with PROSPREO CRD42017064739.

Abstract P3-03-18: Invasive lobular carcinoma does not fit to axillary lymph node management according to NCCN guideline influenced by ACOSOG Z0011 criteria

[Introduction] Surgery for breast cancer (BC) became less invasion, from radical mastectomy to modified or breast conserving surgery (BCS). Axillary lymph node (ALN) management for cN0 also became less, from ALN dissection (ALND) to sentinel lymph node (SLN) biopsy. In some cases, management without ALND is allowed even if ALN macro-metastasis exist.

[Background] ALND for SLN metastasis positive case is useful for local control, staging and decision making for post-operative treatment. Since the ACOSOG Z0011 trial (Z11) result was reported, however, the necessity of ALND, even if SLN metastasis, became less. In the NCCN guideline (NCCN), strongly influenced by Z11, for cN0 BC with SLN metastasis, operations without ALND are allowed in cases of T1 or T2, the number of metastatic ALN 1 or 2, BCS with whole breast radiation and no-neoadjuvant therapy. This does not mean ALND was abolished but the position of ALND changed, from the perspective that over invasive procedure must be prohibited with appropriate pre-operative and intra-operative diagnosis. If there are some discordance between clinical and pathological diagnosis of tumor size or ALN metastasis, however, the criteria for axillary operation by NCCN will not be recommended. We have major two types of invasive carcinoma, ductal (IDC) and lobular (ILC). Z11 or NCCN did not describe about these two phenotypes. We compared these at the point of suitable axillary management.

[Subjects] Out of 1320 invasive BC (IDC; 1212, ILC; 108) cases in our hospital from January 2008 to January 2018, 1210 cases (IDC; 1113, ILC; 97) with T1/T2 and cN0 were reviewed in two points, the judgment of the competence for BCS was appropriate or not, and cN0 reflected the condition for the omission of ALND (ALN metastasis within 2) or not.

[Results] The difference of diameter between cT and pT; dT (=pT-cT) were measured significantly larger in ILC (0.68±1.97cm) than IDC (0.01±1.08cm)(p&lt;0.01, t-test) with the wide scattering. We can make proper evaluation for the cT of IDC, but underestimate for ILC. The conversion rate from cN0 to pN1 was significantly higher in ILC (33/97; 34.0%) than IDC (238/1113; 21.4%)(p&lt;0.01, χ2 test). In addition, the cases with 3 or more ALN metastasis, this means ALND is necessary, was observed with significantly higher frequent in ILC (13/97; 13.4%) than IDC (74/1113; 7.1%)(p=0.02, χ2 test). Clinical evaluation for ALN in ILC was difficult and inaccurate.

[Discussion] Commonly, ILC makes diffuse spread into the breast tissue. This feature will make it difficult to evaluate the clinical appropriate tumor size. Because of not only underestimation but wide scattering, the diagnosis for safety BCS may not be guaranteed in ILC. For ALN, cN0 did not reflect adequately the condition of omission for ALND in ILC compared with IDC. ILC patients with SLN metastasis have to be performed ALND at higher risk. These facts will mean that ILC does not fit to ALN management according to NCCN. Few guidelines separate ILC from IDC for the axillary management. The validation of clinical trials for ALND should be done in histological subtype as well as intrinsic again. Clinically, we must observe carefully in cases of ILC without ALND according to Z11.

Citation Format: Miyamoto T, Fujisawa T, Morishita A, Yanagita Y, Fujii T-A. Invasive lobular carcinoma does not fit to axillary lymph node management according to NCCN guideline influenced by ACOSOG Z0011 criteria [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-03-18.

Abstract P1-14-07: Randomized phase 3 study of anthracycline-containing regimens versus S-1 as first-line treatment for metastatic breast cancer (SELECT BC-CONFIRM)–A combined analysis of two randomized phase 3 studies (SELECT BC-CONFIRM and SELECT BC)–

Background: Anthracycline-containing regimens and taxane have been standard as the first-line chemotherapy for metastatic breast cancer (MBC). We conducted SELECT BC (randomized phase 3 study of taxane versus S-1 as first-line treatment for MBC) for evaluating the efficacy of S-1 for patients with HER2-negative MBC from 2006 to 2010 in Japan. This study demonstrated non-inferiority of S-1 in overall survival (OS) (median OS was 37.2 months in taxes group and 35.0 months in S-1 group (HR 1.05, 95% CI 0.86–1.27, p=0.015)), and superiority in health-related quality of life (HRQOL) to taxanes. S-1 was also shown as less toxic than taxane (Lancet Oncol 2016; 17: 90-98). S-1 might provide clinical benefit as first-line treatment for patients with HER2-negative MBC. To confirm this suggestion, we have conducted further study (randomized phase 3 study of anthracycline-containing regimens versus S-1 as first-line treatment for HER2-negative MBC: SELECT BC-CONFIRM) from 2011 to present, and a combined analysis of two randomized studies (SELECT-BC CONFIRM and SELECT-BC).

Methods: In SELECT BC-CONFIRM, 230 patients receiving first-line treatment for MBC were randomly assigned to either anthracycline group (n=115) or S-1 group (n=115). Anthracycline group patients received anthracycline-containing regimens (AC, EC, FAC, FEC, q3w) at the discretion of the treating physician. S-1 group patients received S-1 40–60 mg twice daily based on the patient's body surface area for 28 days on, 14-day off. The primary endpoint was OS, and secondary endpoints were progression-free survival (PFS), time to treatment failure (TTF), adverse events, HRQOL, and cost-effectiveness. The results were combined with SELECT-BC, to confirm the hypothesis that S-1 treatment is not inferior to the standard therapy (taxanes / anthracycline) for HER2-negative MBC.

Results: A combined analysis of the two studies showed that HR was 1.06, 95%CI 0.90-1.253, and p=0.0071 between the standard therapy group and S-1 group. In addition, the Bayesian posterior probability for which HR would be less than 1.333 was about 99.6%.

Conclusions: A combined analysis of SELECT BC-CONFIRM and SELECT BC clearly demonstrated that OS with S-1 was not inferior to that with the standard therapy in patients receiving first-line treatment for HER2-negative MBC. S-1 could become a standard therapy for this patient population.

Citation Format: Park Y, Akabane H, Watanabe T, Takahashi M, Sagara Y, Nishimura R, Tsurutani J, Takashima T, Fujisawa T, Hozumi Y, Uemura Y, Mukai H. Randomized phase 3 study of anthracycline-containing regimens versus S-1 as first-line treatment for metastatic breast cancer (SELECT BC-CONFIRM)–A combined analysis of two randomized phase 3 studies (SELECT BC-CONFIRM and SELECT BC)– [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-14-07.

Abstract P4-13-09: Sequential second line endocrine therapy is still an effective strategy for postmenopausal ER+ and HER2- advanced breast cancer with low sensitivity to initial endocrine therapy

Background:It is unclear how to define responsiveness to endocrine therapy (ET) during the clinical course of advanced breast cancer (ABC), especially in evaluation of the effect of sequential ET. Objective:The goal of the study was to evaluate the efficacy of second line treatment of physician's choice (2nd-line TPC) for estrogen receptor-positive (ER+) and HER2-negative postmenopausal ABC with very low or low sensitivity to initial ET. Methods:A multicenter prospective observational cohort study was performed for 2nd-line TPCs. ABC with low sensitivity to initial ET was defined as recurrence within 5 years (yrs) during adjuvant ET or progression within 9 months (mo.) of initial ET. Similarly, ABC with very low sensitivity to initial ET was defined as recurrence within 2 yrs during adjuvant ET or progression within 3 mo. of initial ET. The expected clinical benefit rate (CBR: defined as patients who achieved CR, PR or SD for 24 weeks) was 50%. The null hypothesis of a CBR of 30% was tested with a one-sided α of 5%. 90% confidence intervals (CIs) were calculated for hypothesis tests. Results: A total of 56 patients (pts) were enrolled, but 7 were ineligible and one discontinued before starting the protocol treatment. The median age was 66 yrs (range: 41-88) and the median BMI was 23.4 kg/m2 (16.4-31.9). All pts were ER+ and 80% were PgR+. Most of pts had a baseline PS of 0 or 1, 90% had invasive ductal carcinoma, and 10% had invasive lobular carcinoma. Postoperative recurrence was detected in 84% and these pts had a median duration of adjuvant ET of 30.5 mo. (5.3-58.9). De novo stage IV ABC was present in 16%, with a median duration of first-line ET of 5 mo. (2.3-10.8). Adjuvant chemotherapy including anthracycline- and/or a taxane-containing regimen was administered in 58% (29/49). As adjuvant ET before initial recurrence, 34 pts received non-steroidal aromatase inhibitors (AIs) (88.0%), 1 received a steroidal AI (2.3%), and 3 received a selective estrogen receptor modulator (SERM). As first line ET in de novo stage IV, 7 pts (14%) were treated with AIs or a SERM (1 case). 2nd-line TPCs were also used, with 40 pts receiving fulvestrant (82%), 5 receiving SERMs (10%), 3 receiving a mTOR inhibitor plus a steroidal AI (6%), and one patient receiving an AI alone. The overall CBR was 44.9% (90% CI: 34.6-57.6, p=0.009), and CBR was similar across following subgroups (PgR+: n=39, 51.3%, 90% CI: 39.6-65.2, p=0.0016; very low sensitivity group: n=17, 58.8%, 90% CI: 42.0-78.8, p=0.003; non-visceral metastases: n=25, 40%, 90% CI; 34.1-65.9, p=0.0175). However, there were not statistically significant CBR in PgR- (n=10, 20.0%, 90% CI; 8.73-50.7, p=0.617), fulvestrant subgroup (n=40, 40.0 %, 90% CI; 29.2-54.2, p=0.063), low sensitive group (n=32, 37.5%, 90% CI; 26.0-53.6, p=0.1326), and visceral metastases (n=24, 48%, 90%CI; 28.2-60.3 p=0.072). The median PFS was 7.1 mo. (95% CI: 5.6-10.6). Conclusion:This study shows that 2nd line ETs was effective and might be a valid option in the sequence of treatments for postmenopausal women with ABC with low sensitivity to initial ET. It was suggested that PgR and visceral metastasis were significant predictive factors for CBR.

Citation Format: Araki K, Fujisawa T, Sakamaki K, Kikawa Y, Iwamoto T, Sangai T, Shien T, Takao S, Nishimura R, Takahashi M, Aihara T, Mukai H, Taira N. Sequential second line endocrine therapy is still an effective strategy for postmenopausal ER+ and HER2- advanced breast cancer with low sensitivity to initial endocrine therapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-13-09.

Microscopic gain analysis of modulation-doped GeSn/SiGeSn quantum wells: epitaxial design toward high-temperature lasing

Threshold carrier densities of GeSn quantum well (QW) lasers and the physical reason of low-temperature lasing of current GeSn laser are investigated through the comparison of threshold carrier densities of conventional III-V QW lasers. Electrons distributed over L-band is the main cause of decreased gain for GeSn QWs. To increase the gain (and improve the laser characteristics), a modulation-doped GeSn QW is proposed and the material gain is analyzed based on many-body theory for both qualitative and quantitative simulation. Significant gain increase can be expected for n-type modulation doping QWs. The doping condition for elevated temperature lasing is discussed and it was found that material gain curve similar to III-V QW is obtained for GeSn QW with n-type modulation doping of 6 × 10¹⁸ cm^-3. It was also found that unlike III-V QW lasers, n-type modulation doping is more effective for high-speed operation in terms of differential gain than p-type modulation doping.

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Summary

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 min, with rich information such as pseudogenes, translation exceptions and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4—on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Supplementary information

Supplementary data are available at Bioinformatics online.

TogoGenome/TogoStanza: modularized Semantic Web genome database

TogoGenome is a genome database that is purely based on the Semantic Web technology, which enables the integration of heterogeneous data and flexible semantic searches. All the information is stored as Resource Description Framework (RDF) data, and the reporting web pages are generated on the fly using SPARQL Protocol and RDF Query Language (SPARQL) queries. TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies. TogoGenome also serves as an interface to conduct semantic comparative genomics by which a user can observe pan-organism or organism-specific genes based on the functional aspect of gene annotations and the combinations of organisms from different taxa. The TogoGenome database exhibits a modularized structure, and each module in the report pages is separately served as TogoStanza, which is a generic framework for rendering an information block as IFRAME/Web Components, which can, unlike several other monolithic databases, also be reused to construct other databases. TogoGenome and TogoStanza have been under development since 2012 and are freely available along with their source codes on the GitHub repositories at https://github.com/togogenome/ and https://github.com/togostanza/, respectively, under the MIT license.

Generating Publication-Ready Prokaryotic Genome Annotations with DFAST

DDBJ Fast Annotation and Submission Tool (DFAST) is a genome annotation pipeline for prokaryotes, which also assists data submission to the public sequence database. It is available both as a web service and as a stand-alone tool that runs on local machines. DFAST can annotate a typical-sized bacterial genome within 5 min. The default annotation workflow contains a gene prediction phase for protein coding sequence, rRNA, tRNA, and CRISPR, and a functional annotation phase to infer protein functions. DFAST generates result files in standard annotation formats and data files for submission to DNA Data Bank of Japan (DDBJ). In this chapter, the annotation workflow and applications of DFAST are introduced.

Evaluation of serum IgE in peach-allergic patients with systemic reaction by using recombinant Pru p 7 (gibberellin-regulated protein)

BACKGROUND

Lipid transfer protein (LTP) is a major fruit allergen. It has, however, recently been revealed that the systemic reaction in peach-allergic patients is related not only to LTP (Pru p 3) but also to gibberellin-regulated protein (Pru p 7). We investigated recombinant Pru p 7 (rPru p 7) for its potential use in worldwide standardization for the diagnosis of peach allergy.

METHODS

Natural Pru p 7 (nPru p 7) was purified from peach crude extract using a monoclonal antibody affinity column. Complementary DNA for Pru p 7 was cloned and expressed in Escherichia coli and Pichia pastoris. Serum immunoglobulin (Ig) E in peach-allergic patients was examined by enzyme-linked immunosorbent assay (ELISA) using nPru p 7 and rPru p 7 (E. coli product: erPru p 7 and P. pastoris product: prPru p 7).

RESULTS

Peach-allergic patients (n=27) were diagnosed and categorized into oral reaction (n=10) or systemic reaction (n=17). The nPru p 7 positivity based on serum IgE levels was 52% in the systemic-reaction group and 0% in the oral-reaction group (P<0.05). In the systemic-reaction group, there was no significant difference in reactivity between nPru p 7 and prPru p 7, but the reactivity of erPru p 7 was significantly lower than those of nPru p 7 and prPru p 7 (P<0.05).

CONCLUSIONS

We found that prPru p 7 exhibited reactivity in ELISA comparable to that of nPru p 7 for the diagnosis of peach allergy with systemic reaction.

Indications for partial parotidectomy using retrograde dissection of the marginal mandibular branch of the facial nerve for benign tumours of the parotid gland

The aims of this study were to evaluate the efficacy of partial parotidectomy using retrograde dissection of the marginal mandibular branch of the facial nerve for benign tumours of the parotid gland and to establish the indications for its use. We examined 106 consecutive patients with previously untreated benign tumours in the lower portion of the parotid gland who were treated by parotidectomy. The first group (anterograde group, n=52) consisted of those who had standard anterograde parotidectomy. The remaining patients, who underwent retrograde parotidectomy, were further divided into two groups: those in whom the upper edge of the tumour was located below the mastoid tip (below mastoid group, n=46) or those in whom it was above the mastoid tip (above mastoid group, n=8). The operating time was significantly shorter in the below mastoid group (141.2, 127.5, and 98.1minutes, respectively) as was intraoperative blood loss (41.1, 53.0, and 24.4ml, respectively), compared with the other two groups. There was a higher incidence of facial nerve dysfunction in the above mastoid group postoperatively (4/8) than in the other two groups. The results suggested that the presence of a tumour of any size located below the mastoid tip is a good indication for parotidectomy using retrograde dissection of the marginal mandibular branch of the facial nerve.

Temperature-dependent thermal behavior of impurity hydrogen trapped in vacancy-type defects in single crystal ZnO

Interacting nature between impurity hydrogen atoms and vacancy-type defects in single crystal ZnO was investigated by means of positron annihilation lifetime spectroscopy. In order to clarify the observation of their thermal behavior, the sample was implanted with ¹H⁺ using an electrostatic accelerator. After the implantation, the positron lifetime became shorter, which suggests that the hydrogen atoms were captured by zinc vacancies (V_Zn) to form vacancy-hydrogen complexes (V_Zn + nH). The complexes decompose by heat treatment: most of the hydrogen atoms gradually dissociate from V_Zn + nH in the temperature range 393-773 K. It was also suggested that large vacancy clusters were formed by the agglomeration of smaller clusters during the process of stepwise isochronal annealings at temperatures from 773 to 1073 K, and their decomposition took place at 1173-1373 K. Temperature-dependent thermal behaviors of hydrogen atoms and vacancy-type defects in ZnO are discussed.

Conscious sedation with midazolam intravenously for a patient with Parkinson's disease and unpredictable chorea-like dyskinesia

Oral surgery can be difficult in patients with chorea-like dyskinesia, which is common in those on long-term levodopa medication for Parkinson's disease, and we know of no conclusive evidence to indicate whether conscious sedation with midazolam is effective in such cases. We report a patient in whom levodopa-induced chorea-like dyskinesia disappeared when midazolam was given intravenously for conscious sedation.

Si-based Mach-Zehnder wavelength/mode multi/demultiplexer for a WDM/MDM transmission system

We propose and experimentally demonstrate a low-loss and low-crosstalk Mach-Zehnder mode/wavelength multi/demultiplexer for WDM/MDM transmission based on a Si-photonics platform. A broadband 3-dB mode divider, which is also newly devised here, makes it possible to compose a Mach-Zehnder filter for "mode" and "wavelength" simultaneously. Transmission characteristics of fabricated 3-dB mode dividers are in excellent agreement with theoretical results. Mach-Zehnder filters using the 3-dB mode divider with a free spectral range (FSR) of 20 and 1 nm are also fabricated and the modal crosstalk is less than -24 dB in the 40-nm wavelength range for the MZ filter with an FSR of 20 nm. The tuning of the peak wavelength position by the TiN heater is also demonstrated.

Type-1 polarised dendritic cells are a potent immunogen against Mycobacterium tuberculosis

OBJECTIVE

Application of immunotherapy using dendritic cells (DCs) is considered an effective treatment strategy against persistent Mycobacterium tuberculosis infection. With the goal of developing improved therapeutic vaccination strategies for patients with tuberculosis (TB), we tested the ability of ex vivo-generated DCs to induce an effective TB antigen-specific type-1 immune response.

METHODS

Monocyte-derived DCs from TB patients were induced to mature using a 'standard' cytokine cocktail (interleukin [IL] 1β, tumour necrosis factor alpha [TNF-α], IL-6 and prostaglandin E2) or a type 1-polarised DC (DC1) cocktail (IL-1β, TNF-α, interferon [IFN] α, IFN-γ and polyinosinic:polycytidylic acid), and were loaded with the established TB antigen 6-kDa early secretory antigenic target protein (ESAT-6).

RESULTS

Although DC1s from TB patients expressed the same levels of multiple co-stimulatory molecules (CD83, CD86, CD80 and CD40) as the standard DCs (sDCs), DC1s secreted substantially higher levels of IL-12p70. Furthermore, when DCs pulsed with or without ESAT-6 were cultured with lymphocytes from the same patients, DC1s induced much higher numbers of ESAT-6-specific IFN-γ-producing T-cells than sDCs, as manifested by their superior induction of natural killer cell activation and antigen-independent suppression of regulatory T-cells.

CONCLUSION

TB antigen-loaded DC1s are potent inducers of antigen-specific T-cells, which could be used to develop improved immunotherapies of TB.

Abstract P3-13-03: NEOS: A randomized, open label, phase 3 trial of adjuvant chemotherapy for postmenopausal breast cancer patients who responded to neoadjuvant letrozole: First report of long-term outcome and prognostic value of response to neoadjuvant endocrine therapy

Background: Whether adjuvant chemotherapy is required for patients (pts) with intermediate-risk endocrine-responsive postmenopausal breast cancer (BC) remains unknown. Sufficient data have not been available about the long-term prognosis of patients with neoadjuvant endocrine therapy (ET). NEOS is a randomized phase III study that assessed the long-term prognosis of estrogen receptor positive (ER+) primary breast cancer (PBC) pts who received neoadjuvant ET with/without adjuvant chemotherapy.

Methods: Postmenopausal BC pts with ER +/HER2 negative, T1c-2, clinically node negative, under 76 years old were enrolled at primary registration. Pts were treated by leterozole (LET) in weeks 24-28 after primary enrollment. Pts experienced progression (PD) during neoadjuvant phase were excluded at randomization and received any systemic therapy driven by investigators before or after surgery. The long-term prognosis was followed in all registered pts including PD pts. Response to neoadjuvant ET was evaluated as complete response (CR), partial response (PR) or stable disease (SD) using calipers, ultrasound and MRI (or CT) at the baseline and end of treatment before surgery. Pts who met eligibility criteria were randomized 1:1 to LET for 4.5-5 years after chemotherapy or LET alone for 4.5-5 years without chemotherapy after surgery. Pts excluded at second registration were treated any systemic therapies driven by investigators. The primary endpoint was disease-free survival (DFS) and secondary endpoints included overall survival (OS), clinical response rate in neoadjuvant phase, pathological response, and breast-conserving surgery rate. The randomization code have been blinded to the investigators.

Results: Between May 2008 and June 2013, 904 patients were enrolled at primary registration from 100 institutions in Japan (median follow-up: 4.0 years) and 24 pts were withdrawn during neoadjuvant phase. The median age was 63 years, T1c:37%, T2:63%, and PgR+:78%. Clinical response rates (CR, PR, SD and PD) were2% (16pts), 48% (421pts), 45% (400pts) and 5% (43pts), respectively and, in each response category, 0% (0/16), 5.5% (23/421), 7.8% (31/400), and 20.9% (9/43) experienced DFS events. DFS in PD pts to neoadjuvant ET were statistically significantly worse than CR, PR, SD pts (p&lt;0.0001, hazard ratio 4.7 (95% CI:2.3-9.5). The prognosis after surgery in 669 randomized pts was good regardless with/without chemotherapy, forty four pts (6.6%) experienced DFS events after surgery. The predictive markers of PD for neoadjuvant ET were yet unclear among evaluated clinical factors.

Conclusion: This is the first report of DFS in the largest neoadjuvant ET trial (NEOS). The DFS of postmenopausal, ER+/HER2-, PBC pts excluding PD pts to neoadjuvant ET is highly good regardless with/without chemotherapy. Neoadjuvant ET with utilization of PD response as a prognostic marker can be considered as a standard treatment option for these patients. Clinical trial information: UMIN000001090.

Citation Format: Iwata H, Masuda N, Fujisawa T, Toyama T, Ohtani S, Yamamoto Y, Kashiwaba M, Taira N, Sakai T, Hasegawa Y, Nakamura R, Akabane H, Shibahara Y, Sasano H, Yamaguchi T, Ohashi Y. NEOS: A randomized, open label, phase 3 trial of adjuvant chemotherapy for postmenopausal breast cancer patients who responded to neoadjuvant letrozole: First report of long-term outcome and prognostic value of response to neoadjuvant endocrine therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-13-03.