Towards a unified language in experimental designs propagated by a software framework

Experiments require human decisions in the design process, which in turn are reformulated and summarized as inputs into a system (computational or otherwise) to generate the experimental design. I leverage this system to promote a language of experimental designs by proposing a novel computational framework, called "the grammar of experimental designs", to specify experimental designs based on an object-oriented programming system that declaratively encapsulates the experimental structure. The framework aims to engage human cognition by building experimental designs with modular functions that modify a targeted singular element of the experimental design object. The syntax and semantics of the framework are built upon consideration from multiple perspectives. While the core framework is language-agnostic, the framework is implemented in the `edibble` R-package. A range of examples is shown to demonstrate the utility of the framework

Current state and prospects of R-packages for the design of experiments

Re-running an experiment is generally costly and, in some cases, impossible due to limited resources; therefore, the design of an experiment plays a critical role in increasing the quality of experimental data. In this paper, we describe the current state of R-packages for the design of experiments through an exploratory data analysis of package downloads, package metadata, and a comparison of characteristics with other topics. We observed that experimental designs in practice appear to be sufficiently manufactured by a small number of packages, and the development of experimental designs often occurs in silos. We also discuss the interface designs of widely utilized R packages in the field of experimental design and discuss their future prospects for advancing the field in practice.Comment: 14 pages, 8 figures, 1 supplementary materia

Linear mixed models for genomic selection

We commence by considering the analysis of a single trial. Let y denote the n x 1 vector of (phenotypic) data, where n is the number of plots in the trial

Placas estabilizadoras: avaliação de sua eficácia no tratamento das disfunções temporomandibulares

A placa estabilizadora é o mais difundido método de tratamento das disfunções têmporo-mandibulares. A Ressonância Magnética (RM) é o exame mais indicado para a visualização dos componentes da Articulação têmporo-mandibular (ATM). Quarenta pacientes com sinais e sintomas de disfunções têmporo-mandibulares foram tratados com as placas estabilizadoras por um período médio de 12 meses, com controles periódicos quinzenais. Após a estabilização do quadro clínico foram realizados ajustes oclusais e a avaliação por meio da RM. Concluímos que os melhores resultados dessa modalidade de tratamento são relacionados à melhora total (70%) ou parcial (22,5%) da sintomatologia dolorosa e ao restabelecimento da função do complexo crânio-mandibular. A RM permitiu avaliar e concluir que as placas possibilitam condições para que o organismo possa criar meios resistentes às disfunções da articulação têmporo-mandibular por meio da eliminação de vários fatores etiológicos. E que após o tratamento, os pacientes podem conviver com os deslocamentos do disco, alguns com maior, outros com menor tolerância.Occlusal stabilization appliances or splints are the most widely employed method for treatment of temporomandibular disorders (TMD). Magnetic Resonance Imaging (MRI) is the most indicated imaging modality to evaluate the components of the temporomandibular joint (TMJ). Forty patients with signs and symptoms of temporomandibular disorders were treated with splints for a mean period of 12 months, comprising regular semimonthly follow-ups. After stabilization of the clinical status, occlusal adjustments and MRI evaluation were performed. It was concluded that the success of this kind of treatment are related to the total (70%) or partial improvement (22.5%) of painful symptomatology and to the functional reestablishment of the craniomandibular complex. The MRI allowed evaluation and also the conclusion that the splints provide conditions for the organism to develop means to resist to the temporomandibular disorders by means of elimination of several etiologic factors. Moreover, after treatment the patients are able to cope with disc displacements with larger or smaller tolerance

Proton Irradiation Experiment for the X-ray Charge-Coupled Devices of the Monitor of All-sky X-ray Image mission onboard the International Space Station: I. Experimental Setup and Measurement of the Charge Transfer Inefficiency

We have investigated the radiation damage effects on a CCD to be employed in the Japanese X-ray astronomy mission including the Monitor of All-sky X-ray Image (MAXI) onboard the International Space Station (ISS). Since low energy protons release their energy mainly at the charge transfer channel, resulting a decrease of the charge transfer efficiency, we thus focused on the low energy protons in our experiments. A 171 keV to 3.91 MeV proton beam was irradiated to a given device. We measured the degradation of the charge transfer inefficiency (CTI) as a function of incremental fluence. A 292 keV proton beam degraded the CTI most seriously. Taking into account the proton energy dependence of the CTI, we confirmed that the transfer channel has the lowest radiation tolerance. We have also developed the different device architectures to reduce the radiation damage in orbit. Among them, the ``notch'' CCD, in which the buried channel implant concentration is increased, resulting in a deeper potential well than outside, has three times higher radiation tolerance than that of the normal CCD. We then estimated the charge transfer inefficiency of the CCD in the orbit of ISS, considering the proton energy spectrum. The CTI value is estimated to be 1.1e-5 per each transfer after two years of mission life in the worse case analysis if the highest radiation-tolerant device is employed. This value is well within the acceptable limit and we have confirmed the high radiation-tolerance of CCDs for the MAXI mission.Comment: 17 pages, 2 table, 12 figures. Accepted for publication of Japanese Journal of Applied Physics. High resolution file is available from http://wwwxray.ess.sci.osaka-u.ac.jp/~miyata/paper/proton_cti.pd

family members and health-related behaviors

The aim of this study was to clarify the associations of family members living together with health-related behaviors in Japanese young workers. The participants were 300 men and women aged 20-39 years in 2015 who had a job. A web-based self-administered questionnaire on status of partnering and parenting, number of family members living together, dietary habits, drinking habit, smoking habit, self-rated health, employment status, working time and commuting time was conducted through Internet. Multiple logistic regression analysis and general linear models were used to assess the association of family members living together with health-related behaviors. The multivariate-adjusted odds ratio (95% confidence interval, p-value) for current drinking in unmarried participants living with their parents compared to unmarried participants living alone was 0.35 (0.13-0.93, p=0.036). The adjusted means of frequency of breakfast skipping and frequency of eating out showed a trend for inverse associations with the presence of a partner and children. However, those associations disappeared after adjustment for age of youngest child. The findings suggest that the presence of parents might affect drinking behavior and that age of youngest child living together might affect the frequency of breakfast skipping in young Japanese workers

Theobromine enhances the conversion of white adipocytes into beige adipocytes in a PPARγ activation-dependent manner

The adipocytes play an important role in driving the obese-state—white adipose tissue (WAT) stores the excess energy as fat, wherein brown adipose tissue (BAT) is responsible for energy expenditure via the thermoregulatory function of uncoupling protein 1 (UCP1)—the imbalance between these two onsets obesity. Moreover, the anti-obesity effects of brown-like-adipocytes (beige) in WAT are well documented. Browning, the process of transformation of energy-storing into energy-dissipating adipocytes, is a potential preventive strategy against obesity and its related diseases. In the present study, to explore an alternative source of natural products in the regulation of adipocyte transformation, we assessed the potential of theobromine (TB), a bitter alkaloid of the cacao plant, inducing browning in mice (in vivo) and primary adipocytes (in vitro). Dietary supplementation of TB significantly increased skin temperature of the inguinal region in mice and induced the expression of UCP1 protein. It also increased the expression levels of mitochondrial marker proteins in subcutaneous adipose tissues but not in visceral adipose tissues. The microarray analysis showed that TB supplementation upregulated multiple thermogenic and beige adipocyte marker genes in subcutaneous adipose tissue. Furthermore, in mouse-derived primary adipocytes, TB upregulated the expression of the UCP1 protein and mitochondrial mass in a PPARγ ligand-dependent manner. It also increased the phosphorylation levels of PPARγ coactivator 1α without affecting its protein expression. These results indicate that dietary supplementation of TB induces browning in subcutaneous WAT and enhances PPARγ-induced UCP1 expression in vitro, suggesting its potential to treat obesity.ArticleThe Journal of Nutritional Biochemistry. 100: 108898 (2021)journal articl

生体医用応用を目的としたTi合金中のα相とβ相の体積磁化率の評価

Metallic medical devices in the human body cause serious artifacts in magnetic resonance imaging owing to the volume magnetic susceptibility (χν) mismatch between the device and tissue around the device. To reduce artifacts, medical devices produced from alloys with χν values of approximately −9 × 10−6 are required. Controlling the phase constitution is a basic technique used to control the χν value of an alloy, and the χν value of each phase is a fundamental property. In this study, an α+β-type Ti alloy and two β-type Ti alloys were investigated. The estimated χν values of the α-phase of the alloys were similar to or smaller than that of pure Ti. In contrast, the estimated χν values of the β-phase of the alloys were larger than that of pure Ti. Since the χν value of pure Ti is much larger than −9 × 10−6, the χν values of the β-phases suggested that increasing the volume fraction of the β-phase was not appropriate for producing a Ti alloy with a lower χν value