Flexible Scan Statistics for Detecting Spatial Disease Clusters: The rflexscan R Package

The spatial scan statistic is commonly used to detect spatial disease clusters in epidemiological studies. Among the various types of scan statistics, the flexible scan statistic proposed by Tango and Takahashi (2005) is one of the most promising methods to detect arbitrarily-shaped clusters. In this paper, we introduce a new R package, rflexscan (Otani and Takahashi 2021), that provides efficient and easy-to-use methods for analyses of spatial count data using the flexible spatial scan statistic. The package is designed for any of the following interrelated purposes: to evaluate whether reported spatial disease clusters are statistically significant, to test whether a disease is randomly distributed over space, and to perform geographical surveillance of disease to detect areas of significantly high rates. The functionality of the package is demonstrated through an application to a public-domain small-area cancer incidence dataset in New York State, USA, between 2005 and 2009

多次元階層混合モデルとoptimal discovery procedureによる遺伝子-治療交互作用の検出

Open House, ISM in Tachikawa, 2017.6.16統計数理研究所オープンハウス（立川）、H29.6.16ポスター発

ゲノムワイド関連解析における多重検定手法の比較評価

Open House, ISM in Tachikawa, 2016.6.17統計数理研究所オープンハウス（立川）、H28.6.17ポスター発

Potential Biases of the Transmission Risks of COVID-19 estimated by Contact Tracing Surveys in Japan

Introduction: Contact tracing surveys are being conducted to identify and isolate close contacts of an identified patient to reduce the spread of coronavirus disease (COVID-19). However, the estimates of risk indexes based on information obtained from the surveys and normally used in practice can have biases comparing with true magnitude of risks of infection and spread.Method: We evaluated whether the estimates of the risk indexes obtained from information of the active epidemiological surveillance, contact tracing surveys in Japan, are suitable for quantitative assessment of the risk factors of COVID-19, using pseudo data via a simulation study. We discussed two types of risks considered in the issue of infectious disease, the probability of infection and that of spreading, and the estimates of these risks.Results and Discussion: A naive method to estimate the risks of infection and spreading of COVID-19 is to calculate the ratio of infected patients to close contacts and the ratio of patients who infected others to all the confirmed patients, respectively. However, these estimates could possibly have significant biases and result in being ineffective for both the exploration and the quantitative assessment of the risk factors in the following ordinary cases: a person contacts closely with many confirmed patients, or a confirmed patient contact closely with many people. Then, some steps are needed to reduce such possible biases for the estimation the risks of both the infection and spreading of COVID-19

Respiratory complex I in mitochondrial membrane catalyzes oversized ubiquinones

NADH-ubiquinone (UQ) oxidoreductase (complex I) couples electron transfer from NADH to UQ with proton translocation in its membrane part. The UQ reduction step is key to triggering proton translocation. Structural studies have identified a long, narrow, tunnel-like cavity within complex I, through which UQ may access a deep reaction site. To elucidate the physiological relevance of this UQ-accessing tunnel, we previously investigated whether a series of oversized UQs (OS-UQs), whose tail moiety is too large to enter and transit the narrow tunnel, can be catalytically reduced by complex I using the native enzyme in bovine heart submitochondrial particles (SMPs) and the isolated enzyme reconstituted into liposomes. Nevertheless, the physiological relevance remained unclear because some amphiphilic OS-UQs were reduced in SMPs but not in proteoliposomes, and investigation of extremely hydrophobic OS-UQs was not possible in SMPs. To uniformly assess the electron transfer activities of all OS-UQs with the native complex I, here we present a new assay system using SMPs, which were fused with liposomes incorporating OS-UQ and supplemented with a parasitic quinol oxidase to recycle reduced OS-UQ. In this system, all OS-UQs tested were reduced by the native enzyme, and the reduction was coupled with proton translocation. This finding does not support the canonical tunnel model. We propose that the UQ reaction cavity is flexibly open in the native enzyme to allow OS-UQs to access the reaction site, but their access is obstructed in the isolated enzyme as the cavity is altered by detergent-solubilizing from the mitochondrial membrane

Impact of chronic lung allograft dysfunction, especially restrictive allograft syndrome, on the survival after living-donor lobar lung transplantation compared with cadaveric lung transplantation in adults: a single-center experience

PURPOSE: The differences in chronic lung allograft dysfunction (CLAD) between living-donor lobar lung transplantation (LDLLT) and cadaveric lung transplantation (CLT) remain unclear. We conducted this study to compare the impact of CLAD on the outcomes after LDLLT vs. CLT. METHODS: We conducted a retrospective review of the data of 97 recipients of bilateral lung transplantation, including 51 recipients of LDLLT and 46 recipients of CLT. RESULTS: The CLAD-free survival and overall survival after LDLLT were similar to those after CLT. CLAD and restrictive allograft syndrome (RAS), but not bronchiolitis obliterans syndrome (BOS), developed significantly later after LDLLT than after CLT (p = 0.015 and p = 0.035). Consequently, patients with CLAD and RAS, but not those with BOS, after LDLLT had a significantly better overall survival than those after CLT (p = 0.037 and p = 0.0006). Furthermore, after the diagnosis of CLAD, the survival of patients with RAS after LDLLT tended to be better than that after CLT (p = 0.083). CONCLUSION: CLAD, especially RAS, appears to develop later after LDLLT than after CLT and seems to have a lower impact on the overall survival after LDLLT than that after CLT

Quantitative evaluation of protocorm growth and fungal colonization in Bletilla striata (Orchidaceae) reveals less-productive symbiosis with a non-native symbiotic fungus

Quantitative evaluation of symbiotic cells in Pecteilis radiata protocorm. (a) Symbiotic cells with hyphal coils in P. radiata protocorm. Scale bars, 50 Οm. (b) Ratio of the number of symbiotic cells at each stage in a symbiotic protocorm. Each value represents the average number of symbiotic cells in ten protocorms. The experiments were repeated six times with similar results. (PDF 959 kb

Lung perfusion scintigraphy to detect chronic lung allograft dysfunction after living-donor lobar lung transplantation

Because chronic lung allograft dysfunction (CLAD) develops predominantly on one side after bilateral living-donor lobar lung transplantation (LDLLT), lung perfusion scintigraphy (Q-scinti) was expected to show a perfusion shift to the contralateral unaffected lung with the development of CLAD. Our study examined the potential usefulness of Q-scinti in the diagnosis of CLAD after bilateral LDLLT. We conducted a single-center retrospective cohort study of 58 recipients of bilateral LDLLT. The unilateral shift values on Q-scinti were calculated and compared between the CLAD group (N=27) and the non-CLAD group (N=31) from 5 years before to 5 years after the diagnosis of CLAD. The unilateral shift values in Q-scinti were significantly higher in the CLAD group than in the non-CLAD group from 5 years before the diagnosis of CLAD to 5 years after the diagnosis (P<0.05). The unilateral shift values in Q-scinti were significantly correlated with the percent baseline values of the forced expiratory volume in 1 s (P=0.0037), the total lung capacity (P=0.0028), and the forced vital capacity (P=0.00024) at the diagnosis of CLAD. In patients developing unilateral CLAD after bilateral LDLLT, Q-scinti showed a unilateral perfusion shift to the contralateral unaffected lung. Thus, Q-scinti appears to have the potential to predict unilateral CLAD after bilateral LDLLT