The ProteomeXchange consortium at 10 years: 2023 update.

Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.

Simulation analyses of the evolution of intra-inflorescence flowering patterns assuming selection on anthesis interval among individual flowers.

What conditions select flowering patterns within inflorescences, or variation in the anthesis interval within inflorescences among plants? Under what conditions are gradual blooming and simultaneous blooming, both traits related to floral display size, advantageous? We constructed a simulation model in which the opening times and longevities of individual flowers within inflorescences, the sizes of attractive structures of individual flowers, and the numbers of ovules and pollen grains produced by individual flowers evolve. Individual plants in the population compete for pollinators, and plants are selected by pollinators according to their floral display sizes and amounts of resources allocated to attractive structures. We found that, if the proportion of pollen on a pollinator deposited on a stigma was low, gradual blooming did not evolve even if inbreeding depression was greater than 0.5. This is because the amount of outcross-pollen on pollinators decreased at a low rate during flower visits within a single inflorescence, and the selfing rate was suppressed to a low level even if the floral display size was large. On the other hand, if the proportion of pollen deposition was high, gradual blooming evolved even if inbreeding depression was smaller than 0.5. This may be because gradual blooming can enhance pollen delivery to other plants by reducing the loss of self-pollen by geitonogamy. On the other hand, allocation ratios among floral organs (female and male organs and attractive structures) were independent of the degree of simultaneous and gradual blooming within inflorescences. We concluded that the evolution of gradual blooming is more strongly affected by the proportion of pollen on a pollinator deposited on a stigma than by inbreeding depression.

Prognosis of microscopic polyangiitis is well predictable in the first 2 weeks of treatment.

BACKGROUND: Kidney and life outcomes remain unsatisfactory in patients with microscopic polyangiitis (MPA). Appropriate treatment intensity must be provided to the appropriate patients. To identify severe cases early, we investigated the factors related to kidney and life outcomes. METHODS: We included patients diagnosed with MPA based on myeloperoxidase-antineutrophil cytoplasmic antibody (MPO-ANCA) positivity and kidney histopathology results after kidney biopsies between January 1, 2021, and May 11, 2023, at 10 affiliated centers, including our hospital. Death, maintenance dialysis, and estimated glomerular filtration rate (eGFR) < 15 after 6 months of treatment were defined as poor prognosis groups, and factors associated with these conditions were investigated. RESULTS: We included 84 (36 men and 48 women) patients in this study. Median age was 73.8 (interquartile range: 71-81) years. After 6 months of treatment, the proportion of patients in the poor prognosis group was 16.7 %, with a mortality of 7.1 % and a poor kidney prognosis rate of 9.5 %. Area under the receiver operating characteristic curve showed that eGFR at 2 weeks had a comparable prognostic performance equal as eGFR at 4 weeks (area under the curve: 0.875 and 0.896, respectively). After adjustment by various factors, eGFR at 2 weeks was related with prognosis significantly (p = 0.031). CONCLUSION: Kidney function 2 weeks after the start of treatment for MPA can predict prognosis.

Prognosis and incidence of infections in chronic kidney disease patients with membranous nephropathy enrolled in a large Japanese clinical claims database.

BACKGROUND: The treatment of membranous nephropathy involves a combination of conservative approaches, steroids, and immunosuppressive agents. Infection is an adverse effect of these treatments and its incidence is a critical issue for patients with membranous nephropathy, as many of them are older adults. However, the incidence of infections remains unclear; hence, this study investigated this issue using data from a large Japanese clinical claims database. METHODS: From a database of patients with chronic kidney disease (n = 924,238), those diagnosed with membranous nephropathy from April 2008 to August 2021 with a history of one or more prescriptions and undergoing medical care were included. Patients who had undergone kidney replacement therapy were excluded. Patients were divided into three groups based on their prescriptions after diagnosis: prednisolone(PSL), who received steroids; PSL + IS, who were prescribed steroids and immunosuppressive agents; and C, who were treated without steroid or immunosuppressive agent use. The primary outcome was death or the initiation of kidney replacement therapy. The secondary outcome was death or hospitalization due to infection. Infectious diseases such as sepsis, pneumonia, urinary tract infections, cellulitis, cytomegalovirus infection, colitis, or hepatitis were defined as infections. Hazard ratios were expressed using group C as a reference. RESULTS: Of 1,642 patients, the incidence of the primary outcome occurred in 62/460 individuals in the PSL group, 81/635 individuals in the PSL + IS group, and 47/547 individuals in the C group. The Kaplan-Meier survival curve showed no significant differences (P = 0.088). The incidence of secondary outcomes occurred in 80/460 individuals, 102/635 individuals, and 37/547 individuals in the PSL, PSL + IS, and C groups, respectively. The incidence of secondary outcomes was significantly higher in the PSL group (hazard ratio [HR] 2.43 [95% confidence interval [CI] 1.64-3.62, P < 0.01]) and PSL + IS group (HR 2.23 [95% CI 1.51-3.30, P < 0.01]). CONCLUSIONS: The outcome of membranous nephropathy was not completely satisfactory. Patients who use steroids and immunosuppressive agents have a high incidence of infection and may require close monitoring during the course of treatment.High-efficacy treatment with a low incidence of infections is desirable. The significance of this study lies in the fact that the impressions of membranous nephropathy, which have been recognized as tacit knowledge, were quantified using a clinical database.

GlycoPOST realizes FAIR principles for glycomics mass spectrometry data.

For the reproducibility and sustainability of scientific research, FAIRness (Findable, Accessible, Interoperable and Re-usable), with respect to the release of raw data obtained by researchers, is one of the most important principles underpinning the future of open science. In genomics and transcriptomics, the sharing of raw data from next-generation sequencers is made possible through public repositories. In addition, in proteomics, the deposition of raw data from mass spectrometry (MS) experiments into repositories is becoming standardized. However, a standard repository for such MS data had not yet been established in glycomics. With the increasing number of glycomics MS data, therefore, we have developed GlycoPOST (https://glycopost.glycosmos.org/), a repository for raw MS data generated from glycomics experiments. In just the first year since the release of GlycoPOST, 73 projects have already been registered by researchers around the world, and the number of registered projects is continuously growing, making a significant contribution to the future FAIRness of the glycomics field. GlycoPOST is a free resource to the community and accepts (and will continue to accept in the future) raw data regardless of vendor-specific formats.

Systematic characterization of seed overlap microRNA cotargeting associated with lupus pathogenesis.

BACKGROUND: Combinatorial gene regulation by multiple microRNAs (miRNAs) is widespread and closely spaced target sites often act cooperatively to achieve stronger repression ("neighborhood" miRNA cotargeting). While miRNA cotarget sites are suggested to be more conserved and implicated in developmental control, the pathological significance of miRNA cotargeting remains elusive. RESULTS: Here, we report the pathogenic impacts of combinatorial miRNA regulation on inflammation in systemic lupus erythematosus (SLE). In the SLE mouse model, we identified the downregulation of two miRNAs, miR-128 and miR-148a, by TLR7 stimulation in plasmacytoid dendritic cells. Functional analyses using human cell lines demonstrated that miR-128 and miR-148a additively target KLF4 via extensively overlapping target sites ("seed overlap" miRNA cotargeting) and suppress the inflammatory responses. At the transcriptome level, "seed overlap" miRNA cotargeting increases susceptibility to downregulation by two miRNAs, consistent with additive but not cooperative recruitment of two miRNAs. Systematic characterization further revealed that extensive "seed overlap" is a prevalent feature among broadly conserved miRNAs. Highly conserved target sites of broadly conserved miRNAs are largely divided into two classes-those conserved among eutherian mammals and from human to Coelacanth, and the latter, including KLF4-cotargeting sites, has a stronger association with both "seed overlap" and "neighborhood" miRNA cotargeting. Furthermore, a deeply conserved miRNA target class has a higher probability of haplo-insufficient genes. CONCLUSIONS: Our study collectively suggests the complexity of distinct modes of miRNA cotargeting and the importance of their perturbations in human diseases.

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.

The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.

Gene expression profiling of α-gustducin-expressing taste cells in mouse fungiform and circumvallate papillae.

Taste buds are complex sensory organs embedded in the epithelium of fungiform papillae (FP) and circumvallate papillae (CV). The sweet, bitter, and umami tastes are sensed by type II taste cells that express taste receptors (Tas1rs and Tas2rs) coupled with the taste G-protein α-gustducin. Recent studies revealed that the taste response profiles of α-gustducin-expressing cells are different between FP and CV, but which genes could generate such distinctive cell characteristics are still largely unknown. We performed a comprehensive transcriptome analysis on α-gustducin-expressing cells in mouse FP and CV by single-cell RNA sequencing combined with fluorescence-activated cell sorting. Transcriptome profiles of the α-gustducin-expressing cells showed various expression patterns of taste receptors. Our clustering analysis defined the specific cell populations derived from FP or CV based on their distinct gene expression. Immunohistochemistry confirmed the specific expression of galectin-3, encoded by Lgals3, which was recognized as a differentially expressed gene in the transcriptome analysis. Our work provides fundamental knowledge toward understanding the genetic heterogeneity of type II cells, potentially revealing differential characterization of FP and CV taste bud cells.

The jPOST environment: an integrated proteomics data repository and database.

Rapid progress is being made in mass spectrometry (MS)-based proteomics, yielding an increasing number of larger datasets with higher quality and higher throughput. To integrate proteomics datasets generated from various projects and institutions, we launched a project named jPOST (Japan ProteOme STandard Repository/Database, https://jpostdb.org/) in 2015. Its proteomics data repository, jPOSTrepo, began operations in 2016 and has accepted more than 10 TB of MS-based proteomics datasets in the past two years. In addition, we have developed a new proteomics database named jPOSTdb in which the published raw datasets in jPOSTrepo are reanalyzed using standardized protocol. jPOSTdb provides viewers showing the frequency of detected post-translational modifications, the co-occurrence of phosphorylation sites on a peptide and peptide sharing among proteoforms. jPOSTdb also provides basic statistical analysis tools to compare proteomics datasets.

Clinical outcome of condoliase injection treatment for lumbar disc herniation: Indications for condoliase therapy.

BACKGROUND: Condoliase is a novel, potent chemonucleolytic drug available for clinical use for lumbar disc herniation (LDH) in Japan. The aim of this study was to assess the clinical outcome of condoliase therapy in patients with LDH, as well as factors affecting the clinical outcome. METHODS: We enrolled patients with LDH who were receiving condoliase injection. The following baseline data were collected: symptom duration; herniation level and type; T2 signal intensity of herniation; adverse events; rates of spondylolisthesis, posterior intervertebral angle of ≥5°, and vertebral body translation of ≥3 mm. Change in disc height, disc degeneration, herniation size, visual analog scale (VAS) for leg and back pain, and Oswestry Disability Index (ODI) were evaluated at the baseline, and 3-month follow-up. These data were compared between patients with efficacious (VAS improvement of ≥20 mm; group E) and inefficacious (VAS improvement <20 mm or required operation; group I) for condoliase treatment. RESULTS: Forty-seven patients (20 women, 27 men; mean age 48 years) were included. The herniation level was L2/3 in one patient, L3/4 in two, L4/5 in 23, and L5/S1 in 21. Median symptom duration was 8 months. The mean VAS and ODI improved significantly from the baseline to 3-month follow-up (p < 0.01). Group E included 33 patients (70.2%) and group I included 14, three of whom had a history of discectomy. The rates of spondylolisthesis and posterior intervertebral angle ≥5° were significantly higher in group I than in group E. However, the rates of trans-ligamentous type and herniation with high signal intensity on T2-weighted images (highT2) were significantly higher in group E. Reduction of disc herniation was more frequently observed in group E. CONCLUSIONS: Condoliase injection resulted in significantly improved symptoms in patients with LDH. Condoliase therapy was less effective for patients with a history of discectomy, spondylolisthesis, or those with a posterior intervertebral angle ≥5°, while trans-ligamentous type and high T2 herniation were associated with increased efficacy.

Drinking Ice-Cold Water Reduces the Severity of Anticancer Drug-Induced Taste Dysfunction in Mice.

Taste disorders are common adverse effects of cancer chemotherapy that can reduce quality of life and impair nutritional status. However, the molecular mechanisms underlying chemotherapy-induced taste disorders remain largely unknown. Furthermore, there are no effective preventive measures for chemotherapy-induced taste disorders. We investigated the effects of a combination of three anticancer drugs (TPF: docetaxel, cisplatin and 5-fluorouracil) on the structure and function of mouse taste tissues and examined whether the drinking of ice-cold water after TPF administration would attenuate these effects. TPF administration significantly increased the number of cells expressing apoptotic and proliferative markers. Furthermore, TPF administration significantly reduced the number of cells expressing taste cell markers and the magnitudes of the responses of taste nerves to tastants. The above results suggest that anticancer drug-induced taste dysfunction may be due to a reduction in the number of taste cells expressing taste-related molecules. The suppressive effects of TPF on taste cell marker expression and taste perception were reduced by the drinking of ice-cold water. We speculate that oral cryotherapy with an ice cube might be useful for prophylaxis against anticancer drug-induced taste disorders in humans.

Contrast Mechanisms of Solution-Dispersed Graphene Compounds in Twilight Fluorescence Microscopy.

Twilight fluorescence microscopy is a newly developed technique that is capable of imaging a single-layer graphene compound dispersed in a liquid. A graphene solution mixed with a highly concentrated dye is placed on a glass plate and is irradiated by the excitation beam with an incident angle that has a finite width around the total internal reflection angle. Both the evanescence field and the faint refracted beam decay exponentially as they travel from the glass surface. The dye fluorescence excited by both beams is used as illumination. A simplified theory for dark contrast of graphene compounds is developed based on absorption and Förster resonance energy transfer (FRET), assuming that (1) FRET has a sharp cutoff distance, (2) FRET is independent of the number of layers, and (3) Dexter electron transfer is negligible. The contrast of a reduced graphene oxide multilayer, whose layer heights have been determined by atomic force microscopy, shows good agreement with the simplified theory under various dye concentrations. The FRET cutoff distance is found to be much shorter than one expected for graphene and similar to the distance between two small molecules. This short cutoff distance is the main reason for the assumption to be valid.

Donor-Acceptor Core-Shell Nanoparticles and Their Application in Non-Volatile Transistor Memory Devices.

Donor-acceptor crosslinked poly[poly(ethylene glycol) methyl ether-methacrylate]-block-poly[1,1'-bis(2-ethylpentyl)-6-methyl-6'-(5-methyl-3-vinylthiophen-2-yl)-[3,3'-biindoline]-2,2'-dione] (poly(PEGMA)m -b-poly(VTIID)n ) nanoparticles with various vinylthiophene donor/isoindigo acceptor ratios are synthesized successfully. The prepared nanoparticles have uniform sizes and well-defined core-shell nanostructures. The intramolecular charge transfer is effectively enhanced due to the incorporation of acceptor groups after the crosslinking reaction. A transistor memory device is assembled using the synthesized polymer and has nonvolatile flash-type memory and amphiphilic trapping behavior. The optimized devices exhibit a significant memory window of approximately 38 V, a retention ability of over 104 s, and an endurance of at least 100 cycles. This study examines multiple applications of crosslinked core-shell nanoparticles, which demonstrates their promise as charge-storage dielectric materials for use in organic memory devices.

jPOSTrepo: an international standard data repository for proteomes.

Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository.jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region.

Direct visualization of diffuse unoccupied molecular orbitals at a rubrene/graphite interface.

Spectroscopic and nanoscale imaging investigations concerning the spatial extent of molecular orbitals at organic/substrate interfaces have been of intense interest to understand charge dynamics. Here, the spatial extent of unoccupied molecular orbitals of ultrathin rubrene [5,6,11,12-tetraphenyltetracene] films has been investigated with scanning tunneling microscopy and spectroscopy. Based on constant-current distance (z)-voltage (V) measurements, the unoccupied energy levels are elucidated and found to be consistent with previously reported macroscopic two-photon photoemission (2PPE) spectroscopy. In the diffuse unoccupied molecular orbitals reported with 2PPE (J. Phys. Chem. C, 2013, 117, 20098), nanoscale dz/dV spatial maps reveal that the local density of states of the orbitals extends over the rubrene molecules. Delocalization is also observed for the image potential states, which are inherently free-electron-like. This is in contrast to the localized nature of other unoccupied molecular orbitals. A nanoscale understanding of diffuse and delocalized molecular orbitals provides a fundamental insight into low-lying Rydberg states in polycyclic aromatic hydrocarbons.

Ferrokinetics is associated with the left ventricular mass index in patients with chronic kidney disease.

Background Patients with chronic kidney disease (CKD) often have the complication of anaemia. Usage of an erythropoietin-stimulating agent accelerates iron deficiency because it promotes iron utilization. Recently, iron administration was reported to be effective for patients with cardiac failure. We examined the association between ferrokinetics and cardiac function in patients with CKD. Methods In this cross-sectional study, we examined 558 patients (424 men and 134 women; mean age, 68.9 ± 13.1 years) with CKD who were admitted to our hospital. We assessed cardiac function by ultrasonography and ferrokinetics through transferrin saturation (TSAT) and ferritin levels. Results The primary diseases of CKD were nephrosclerosis (n = 247), diabetic nephropathy (n = 154), chronic glomerulonephritis (n = 73), and others. The mean estimated glomerular filtration rate was 16.9 ± 9.3 mL/min/1.7 m2, and the haemoglobin (Hb) level was 11.0 ± 1.7 g/dL. The median of TSAT was 28.05%, and patients were divided into two groups: below (L-Ts) and above (H-Ts) the median. The median of ferritin was 122 ng/mL, and patients were divided into two groups: below (L-f) and above (H-f) the median. We categorized four groups as H-Ts + H-F, H-Ts + L-F, L-Ts + H-F, and L-Ts + L-F. The Hb levels were 11.1 ± 1.8, 11.3 ± 1.4, 10.9 ± 1.6, and 10.8 ± 1.5 g/dL, respectively, and there was no difference between groups. However, the left ventricular mass indices (LVMIs) were 122.6 ± 46.6, 110.8 ± 32.0, 118.3 ± 36.0, 126.7 ± 46.9, respectively (P = 0.0291). This tendency was stronger in patients without cardiovascular events. Conclusion In patients with CKD, there is an association between ferrokinetics and LVMI. We have to be mindful not only of anaemia but also of ferrokinetics.

[THE POTENTIAL ROLE OF SOCIAL NETWORK ANALYSIS IN TUBERCULOSIS CONTACT INVESTIGATION].

[Aim] To explore the possible role of social network analysis (SNA) in identifying infected contacts and visualizing data in a tuberculosis (TB) contact investigation. [Method] We analyzed TB contact investigation data from an outbreak in a Japanese language school in Tokyo, Japan, in 20XX. Information on places which the index case and his contacts commonly shared was collected in line with the data collected routinely in contact investigation. Average hours of exposure to the index case were calculated for each contact by using SNA software, and the relationship to the index case via commonly shared places was visualized as a sociogram. Statistical analysis was performed to. compare the exposure hours and TB infection statuses, between those . infected, including active TB and latent TB infection (LTBI), and non- infected contacts. [Result] The data on the index TB case and 41 contacts, of whom 5 and 10 were diagnosed with active TB and LTBI, were analyzed. Contacts with active TB and LTBI had 12.5 and 11.5 times longer median hours of exposure, which were significantly longer compared to non-infected contacts. The sociogram summarized the network of index TB case, contacts characterized by exposure hours and infection statuses, and the places shared by the index case and the contacts. [Discussion] SNA analysis was considered to be useful in prioritizing contacts in a TB contact investigation, in assisting interpretation of indeterminate Interferon-Gamma release assay test results, in estimating places where transmission occurred, and visualizing data accrued in TB contact inves- tigations.

[Scintigraphic imaging in the diagnosis of failed intrathecal baclofen therapy: a case report of a 7-year-old boy with ventriculoperitoneal shunt].

Intrathecal baclofen (ITB) therapy is popular for the management of intractable spasticity. In 2007, the indications of ITB therapy expanded to include spasticity of children in Japan. In this report, we assessed the utility of radioisotopic scintigraphy in the diagnosis of failed ITB therapy. A 7-year-old boy with schizencephaly, hydrocephalus, and spastic quadriplegia had an ITB pump implanted. In his infancy, he had undergone ventriculoperitoneal shunt implantation. One month after the ITB operation, the ITB therapeutic effect diminished. Several examinations confirmed that the pump function was normal and catheter failure had not occurred. However, radioisotopic scintigraphy revealed that the baclofen had been washed out to blood circulation more rapidly than is typically observed. We considered two possible causes for this; obstruction of the cerebrospinal space due to kyphosis and excessive washout of celebrospinal fluid through the ventriculoperitoneal shunt. The catheter was moved to a more caudal site surgically, and his spasticity improved. The use of radioisotopic scintigraphy to identify the distribution of baclofen is an effective technique for investigation of baclofen pump system malfunction.

The 2011 measles outbreak in Tokyo. An analysis of surveillance data.

OBJECTIVES: The study was conducted with the intention of establishing a strategy to eliminate measles on the basis of an analysis of the epidemiological profile of measles cases reported in Tokyo during the year 2011. METHODS: We investigated measles cases reported to the Tokyo Metropolitan Government in 2011, recorded as part of the National Epidemiological Surveillance of Infectious Diseases. Factors analyzed included age, vaccination status for each patient, cases for which records were discarded after laboratory confirmation, genotype of the measles virus and relationships between dates of specimen collection and results of polymerase chain reaction (PCR) and IgM antibody tests. RESULTS: A total of 178 measles cases were reported in Tokyo during 2011, and the majority of cases (128, 71.9%) were reported during the peak period from epiweeks 13 to 24. The largest age group reported was one to four years of age (40, 22.5%) followed by groups of 20-29 and 30-39 years of age (both 34, 19.1%). Most cases were sporadic, with only six outbreaks occurring. Even then, the numbers of cases for each outbreak was less than five. More than half of the patients in all age groups, except for the 1-4-year-old group, had not been vaccinated or did not have a record of vaccination. Genotypes D4 and D9 of measles virus were detected in most cases. However, genotype D5, which had been circulating in Japan before 2008, was not detected. CONCLUSION: Imported viruses were the cause of measles cases reported in Tokyo during 2011. The disease control was better than that in 2007 and 2008 because of the swift and appropriate responses to the occurrences. It is also possible that there has been an increase in the proportion of people with immunity to measles. Increasing the rate of immunization, performing effective surveillance, and confirming suspicious measles cases by using molecular methods are important for achieving the elimination of measles.