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The zinc finger and BTB domain-containing 11 gene (zbtb11) is expressed in the Xenopus anterior neuroectoderm, but the molecular nature of the Zbtb11 protein during embryonic development remains to be elucidated. Here, we show the role of Zbtb11 in anterior patterning of the neuroectoderm and the cooperative action with the transcription factor Otx2. Both overexpression and knockdown of zbtb11 caused similar phenotypes: expanded expression of the posterior gene gbx2 in the neural plate, and later microcephaly with reduced eyes, suggesting that a proper level of zbtb11 expression is necessary for normal patterning of the neuroectoderm, including eye formation. Co-immunoprecipitation assays showed that Zbtb11 formed a complex with itself and with a phosphomimetic and repressive form of Otx2, suggesting that Zbtb11 forms a dimer or oligomer and interacts with Otx2 in a phosphorylation-dependent manner. Reporter analysis further showed that Zbtb11 enhanced the activity of the phosphomimetic Otx2 to repress a silencer element of the posterior gene meis3. These data suggest that Zbtb11 coordinates with phosphorylated Otx2 to specify the anterior neuroectoderm by repressing posterior genes., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Satou-Kobayashi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

This paper proposes multidimensional scaling (MDS) applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Currently, the mechanisms underlying the regulation of gene expression are poorly understood, and where and when DNA loops are formed remains undetermined. Previous studies have focused on reproducing the entire three-dimensional structure of chromatin; however, identifying DNA loops using these data is time-consuming and difficult. MDS is an unsupervised method for reconstructing the original coordinates from a distance matrix. Here, MDS was applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Hi-C data were converted to distances by taking the inverse to reproduce loops via MDS, and the missing values were set to zero. Using the converted data, MDS was applied to the log-transformed genomic coordinate distances and this process successfully reproduced the DNA loops in the given structure. Consequently, the reconstructed DNA loops revealed significantly more DNA-transcription factor interactions involved in DNA loop formation than those obtained from previously applied methods. Furthermore, the reconstructed DNA loops were significantly consistent with chromatin immunoprecipitation followed by sequencing (ChIP-seq) peak positions. In conclusion, the proposed method is an improvement over previous methods for identifying DNA loops., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Ryo Ishibashi. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Integrating gene expression, DNA methylation, and genomic variants simultaneously without location coincidence (i.e., irrespective of distance from each other) or pairwise coincidence (i.e., direct identification of triplets of gene expression, DNA methylation, and genomic variants, and not integration of pairwise coincidences) is difficult. In this study, we integrated gene expression, DNA methylation, and genome variants from the iMETHYL database using the recently proposed kernel tensor decomposition-based unsupervised feature extraction method with limited computational resources (i.e., short CPU time and small memory requirements). Our methods do not require prior knowledge of the subjects because they are fully unsupervised in that unsupervised tensor decomposition is used. The selected genes and genomic variants were significantly targeted by transcription factors that were biologically enriched in KEGG pathway terms as well as in the intra-related regulatory network. The proposed method is promising for integrated analyses of gene expression, methylation, and genomic variants with limited computational resources., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Taguchi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Scenic information plays an important role in face processing, whereas it has received limited attention in the field of developmental research. In the current study, we investigated whether infants, like adults, utilize scenic information for face processing by the preferential-looking method. In Experiment 1, we examined 4-5 and 6-7-month-olds' visual preferences for upright faces compared to inverted faces in two surrounding scene conditions: intact (in which a face occurs in an intact scene) and scrambled (in which a face occurs in a jumbled scene). We found that 6- to 7-month-olds preferred the upright face in the intact scene, but not in the scrambled scene. Meanwhile, 4- to 5-month-olds showed significant upright face preference in both scenes. The results of Experiment 2 ruled out the possibility that the lack of preference for upright faces in the scrambled scene in 6- to 7-month-olds resulted from more distraction by the scrambledness of the image than occurs with 4- to 5-month-olds, by showing no developmental changes in preference either for the scrambled images or the intact images when faces did not appear. Our results suggest that infants aged 6 months or more utilize scenic information for face processing., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Kobayashi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

High-throughput omics technologies have enabled the profiling of entire biological systems. For the biological interpretation of such omics data, two analyses, hypothesis- and data-driven analyses including tensor decomposition, have been used. Both analyses have their own advantages and disadvantages and are mutually complementary; however, a direct comparison of these two analyses for omics data is poorly examined.We applied tensor decomposition (TD) to a dataset representing changes in the concentrations of 562 blood molecules at 14 time points in 20 healthy human subjects after ingestion of 75 g oral glucose. We characterized each molecule by individual dependence (constant or variable) and time dependence (later peak or early peak). Three of the four features extracted by TD were characterized by our previous hypothesis-driven study, indicating that TD can extract some of the same features obtained by hypothesis-driven analysis in a non-biased manner. In contrast to the years taken for our previous hypothesis-driven analysis, the data-driven analysis in this study took days, indicating that TD can extract biological features in a non-biased manner without the time-consuming process of hypothesis generation., Competing Interests: The authors have no competing interests to declare., (Copyright: © 2023 Fujita et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In innovation strategy, a type of Schumpeterian competitive strategy in business administration, "intra-individual diversity" has attracted attention as one factor for creating innovation. In this study, we redefine "framework for identifying researchers' areas of expertise" as "a framework for quantifying intra-individual diversity among researchers. Note that diversity here refers to authorship of articles in multiple research fields. The application of this framework then made it possible to visualize organizational diversity by accumulating the intra-individual diversity of researchers and to discuss the innovation strategy of the organization. The analysis in this study discusses how countries are promoting research on the topics of artificial intelligence (AI), big data, and Internet of Things (IoT) technologies, which are at the core of Industry 4.0, from an innovation perspective. Note that Industry 4.0 is a technological framework that aims to "improve the efficiency of all social systems," "create new industries," and "increase intellectual productivity." For the analysis, we used 19-year bibliographic data (2000-2018) from the top 20 countries in terms of the number of papers in AI, big data, and IoT technologies. As the results, this study classified the styles of cross-disciplinary fusion into four patterns in AI and three patterns in big data. This study did not consider the results in IoT because of only small differences between countries. Furthermore, regional differences in the style of cross-disciplinary fusion were also observed, and the global innovation patterns in Industry 4.0 were classified into seven categories. In Europe and North America, the cross-disciplinary integration style was similar to that between the United States, Germany, the Netherlands, Spain, England, Italy, Canada, and France. In Asia, the cross-disciplinary fusion style was similar between China, Japan, and South Korea., Competing Interests: The authors have declared that no competing interests exist.

Identifying differentially expressed genes is difficult because of the small number of available samples compared with the large number of genes. Conventional gene selection methods employing statistical tests have the critical problem of heavy dependence of P-values on sample size. Although the recently proposed principal component analysis (PCA) and tensor decomposition (TD)-based unsupervised feature extraction (FE) has often outperformed these statistical test-based methods, the reason why they worked so well is unclear. In this study, we aim to understand this reason in the context of projection pursuit (PP) that was proposed a long time ago to solve the problem of dimensions; we can relate the space spanned by singular value vectors with that spanned by the optimal cluster centroids obtained from K-means. Thus, the success of PCA- and TD-based unsupervised FE can be understood by this equivalence. In addition to this, empirical threshold adjusted P-values of 0.01 assuming the null hypothesis that singular value vectors attributed to genes obey the Gaussian distribution empirically corresponds to threshold-adjusted P-values of 0.1 when the null distribution is generated by gene order shuffling. For this purpose, we newly applied PP to the three data sets to which PCA and TD based unsupervised FE were previously applied; these data sets treated two topics, biomarker identification for kidney cancers (the first two) and the drug discovery for COVID-19 (the thrid one). Then we found the coincidence between PP and PCA or TD based unsupervised FE is pretty well. Shuffling procedures described above are also successfully applied to these three data sets. These findings thus rationalize the success of PCA- and TD-based unsupervised FE for the first time., Competing Interests: The authors have declared that no competing interests exist.

We propose a stochastic generative model to represent a directed graph constructed by citations among academic papers, where nodes and directed edges represent papers with discrete publication time and citations respectively. The proposed model assumes that a citation between two papers occurs with a probability based on the type of the citing paper, the importance of cited paper, and the difference between their publication times, like the existing models. We consider the out-degrees of citing paper as its type, because, for example, survey paper cites many papers. We approximate the importance of a cited paper by its in-degrees. In our model, we adopt three functions: a logistic function for illustrating the numbers of papers published in discrete time, an inverse Gaussian probability distribution function to express the aging effect based on the difference between publication times, and an exponential distribution (or a generalized Pareto distribution) for describing the out-degree distribution. We consider that our model is a more reasonable and appropriate stochastic model than other existing models and can perform complete simulations without using original data. In this paper, we first use the Web of Science database and see the features used in our model. By using the proposed model, we can generate simulated graphs and demonstrate that they are similar to the original data concerning the in- and out-degree distributions, and node triangle participation. In addition, we analyze two other citation networks derived from physics papers in the arXiv database and verify the effectiveness of the model., Competing Interests: The authors have declared that no competing interests exist.

In this study, to investigate whether infants showed face-specific brain activity to a cartoon human face, we conducted a functional near-infrared spectroscopy (fNIRS) experiment and a behavioral experiment. In the fNIRS experiment, we measured the hemodynamic responses of 5- and 6-month-old infants to cartoon female and cartoon character faces using fNIRS. The results showed that the concentration of oxy-Hb increased for cartoon female faces but not for cartoon character faces. This indicates that face-specific brain activity occurred for cartoon female faces but not cartoon character faces, despite the fact that both are faces. In the behavioral experiment, we examined whether the 5- and 6-month-old infants preferred cartoon female faces to cartoon character faces in the upright and inverted conditions. The results showed a preference for cartoon female faces in the upright but not in the inverted condition. This indicates that 5- and 6-month-old infants can perceive cartoon female faces, but not cartoon character faces, as faces. The results of the two experiments indicated that face-specific brain activity occurred for cartoon female faces. This indicates that infants can perceive cartoon female faces as faces., Competing Interests: The authors have declared that no competing interests exist.

The histone group added to a gene sequence must be removed during mitosis to halt transcription during the DNA replication stage of the cell cycle. However, the detailed mechanism of this transcription regulation remains unclear. In particular, it is not realistic to reconstruct all appropriate histone modifications throughout the genome from scratch after mitosis. Thus, it is reasonable to assume that there might be a type of "bookmark" that retains the positions of histone modifications, which can be readily restored after mitosis. We developed a novel computational approach comprising tensor decomposition (TD)-based unsupervised feature extraction (FE) to identify transcription factors (TFs) that bind to genes associated with reactivated histone modifications as candidate histone bookmarks. To the best of our knowledge, this is the first application of TD-based unsupervised FE to the cell division context and phases pertaining to the cell cycle in general. The candidate TFs identified with this approach were functionally related to cell division, suggesting the suitability of this method and the potential of the identified TFs as bookmarks for histone modification during mitosis., Competing Interests: The authors have declared that no competing interests exist.

The single-cell green alga Chlamydomonas reinhardtii possesses two α-tubulin genes (tua1 and tua2) and two β-tubulin genes (tub1 and tub2), with the two genes in each pair encoding identical amino acid sequences. Here, we screened an insertional library to establish eight disruptants with defective tua2, tub1, or tub2 expression. Most of the disruptants did not exhibit major defects in cell growth, flagellar length, or flagellar regeneration after amputation. Because few tubulin mutants of C. reinhardtii have been reported to date, we then used our disruptants, together with a tua1 disruptant obtained from the Chlamydomonas Library Project (CLiP), to isolate tubulin-mutants resistant to the anti-tubulin agents propyzamide (pronamide) or oryzalin. As a result of several trials, we obtained 8 strains bearing 7 different α-tubulin mutations and 12 strains bearing 7 different β-tubulin mutations. One of the mutations is at a residue similar to that of a mutation site known to confer drug resistance in human cancer cells. Some strains had the same amino acid substitutions as those reported previously in C. reinhardtii; however, the mutants with single tubulin genes showed slightly stronger drug-resistance than the previous mutants that express the mutated tubulin in addition to the wild-type tubulin. Such increased drug-resistance may have facilitated sensitive detection of tubulin mutation. Single-tubulin-gene disruptants are thus an efficient background of generating tubulin mutants for the study of the structure-function relationship of tubulin., Competing Interests: The authors have declared that no competing interests exist.

Background: COVID-19 is a critical pandemic that has affected human communities worldwide, and there is an urgent need to develop effective drugs. Although there are a large number of candidate drug compounds that may be useful for treating COVID-19, the evaluation of these drugs is time-consuming and costly. Thus, screening to identify potentially effective drugs prior to experimental validation is necessary., Method: In this study, we applied the recently proposed method tensor decomposition (TD)-based unsupervised feature extraction (FE) to gene expression profiles of multiple lung cancer cell lines infected with severe acute respiratory syndrome coronavirus 2. We identified drug candidate compounds that significantly altered the expression of the 163 genes selected by TD-based unsupervised FE., Results: Numerous drugs were successfully screened, including many known antiviral drug compounds such as C646, chelerythrine chloride, canertinib, BX-795, sorafenib, sorafenib, QL-X-138, radicicol, A-443654, CGP-60474, alvocidib, mitoxantrone, QL-XII-47, geldanamycin, fluticasone, atorvastatin, quercetin, motexafin gadolinium, trovafloxacin, doxycycline, meloxicam, gentamicin, and dibromochloromethane. The screen also identified ivermectin, which was first identified as an anti-parasite drug and recently the drug was included in clinical trials for SARS-CoV-2., Conclusions: The drugs screened using our strategy may be effective candidates for treating patients with COVID-19., Competing Interests: The authors have declared that no competing interests exist.

Purpose: Many breast cancer patients suffer from chemotherapy-induced hair loss. Accurate information about temporal changes in chemotherapy-induced hair loss is important for supporting patients scheduled to receive chemotherapy, because it helps them to prepare. However, accurate information, on issues such as the frequency of hair loss after chemotherapy, when regrowth starts, the condition of regrown hair, and the frequency of incomplete hair regrowth, is lacking. This study aimed to clarify the long-term temporal changes in chemotherapy-induced hair loss using patient-reported outcomes for chemotherapy-induced hair loss., Methods: We conducted a multicenter, cross-sectional questionnaire survey. Disease-free patients who had completed adjuvant chemotherapy consisting of anthracycline and/or taxanes for breast cancer within the prior 5 years were enrolled from 47 hospitals and clinics in Japan. Descriptive statistics were obtained in this study. The study is reported according to the STROBE criteria., Results: The response rate was 81.5% (1511/1853), yielding 1478 questionnaires. Hair loss occurred in 99.9% of patients. The mean time from chemotherapy until hair loss was 18.0 days. Regrowth of scalp hair occurred in 98% of patients. The mean time from the completion of chemotherapy to the beginning of regrowth was 3.3 months. Two years after chemotherapy completion, the scalp-hair recovery rate was <30% in approximately 4% of patients, and this rate showed no improvement 5 years after chemotherapy. Eighty-four percent of the patients initially used wigs, decreasing to 47% by 1 year after chemotherapy and 15.2% after 2 years. The mean period of wig use was 12.5 months. However, a few patients were still using wigs 5 years after completing chemotherapy., Conclusions: Our survey focused on chemotherapy-induced hair loss in breast cancer patients. We believe these results to be useful for patients scheduled to receive chemotherapy., Competing Interests: The authors have declared that no competing interests exist.

In the human retina, rod and cone cells detect incoming light with a molecule called rhodopsin. After rhodopsin molecules are activated (by photon impact), these molecules activate the rest of the signalling process for a brief period of time until they are deactivated by a multistage process. First, active rhodopsin is phosphorylated multiple times. Following this, they are further inhibited by the binding of molecules called arrestins. Finally, they decay into opsins. The time required for each of these stages becomes progressively longer, and each stage further reduces the activity of rhodopsin. However, while this deactivation process itself is well researched, the roles of the above stages in signal (and image) processing are poorly understood. In this paper, we will show that the activity of rhodopsin molecules during the deactivation process can be described as the fractional integration of an incoming signal. Furthermore, we show how this affects an image; specifically, the effect of fractional integration in video and signal processing and how it reduces noise and the improves adaptability under different lighting conditions. Our experimental results provide a better understanding of vertebrate and human vision, and why the rods and cones of the retina differ from the light detectors in cameras., Competing Interests: The authors have declared that no competing interests exist.

Recently, various studies have clarified that humans can immediately make social evaluations from facial appearance and that such judgment have an important role in several social contexts. However, the origins and early development of this skill have not been well investigated. To clarify the mechanisms for the acquisition of this skill, we examined whether 6- to 8-month-old infants show a preference for a more trustworthy-looking person. Results showed that infants preferred a trustworthy face to an untrustworthy one when both faces were high in dominance. This difference was not seen when both faces were low in dominance. Moreover, this preference disappeared when the faces were upside down. These findings suggest that the perception of trustworthiness based on facial appearance emerges in early development with little social experience. Further research is needed to verify whether infants also perceive other traits, such as competence., Competing Interests: The authors have declared that no competing interests exist.

Ossification of the posterior longitudinal ligament (OPLL), a spinal ligament, reduces the range of motion in limbs. No treatment is currently available for OPLL, which is why therapies are urgently needed. OPLL occurs in obesity, is more common in men, and has an onset after 40 years of age. The mechanisms underlying OPLL remain unclear. In this study, we performed a serum proteomic analysis in both OPLL patients and healthy subjects to identify factors potentially involved in the development of OPLL, and found reduced levels of a protein that might underlie the pathology of OPLL. We isolated the protein, determined its amino acid sequence, and identified it as chemokine (C-X-C motif) ligand 7 (CXCL7). Based on these proteomics findings, we generated a CXCL7 knockout mouse model to study the molecular mechanisms underlying OPLL. CXCL7-null mice presented with a phenotype of OPLL, showing motor impairment, heterotopic ossification in the posterior ligament tissue, and osteoporosis in vertebrate tissue. To identify the mechanisms of CXCL7 deficiency in OPLL, we searched for single nucleotide polymorphisms and altered DNA exons, but no abnormalities were found. Although miR-340 levels were found to be high in an miRNA array, they were insufficient to reduce CXCL7 levels. Ubiquitin C-terminal hydrolase1 (UCHL1) was found to be overexpressed in CXCL7-null mice and in the sera of patients with OPLL, and was correlated with OPLL severity. Post-translational modifications of proteins with ubiquitin and ubiquitin-like modifiers, orchestrated by a cascade of specialized ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2), and ubiquitin ligase (E3) enzymes, are thought to control a wide range of cellular processes, and alterations in the ubiquitin-proteasome system have been associated with several degenerative disorders. In addition, the OPLL tissue of CXCL7-null mouse and its primary cells expressed the antibody to ubiquitin (linkage-specific K48). Our data clearly show decreased CXCL7 levels in patients with OPLL, and that OPLL developed in mice lacking CXCL7. Tumor necrosis factor receptor-associated factor (TRAF)6 expression was decreased in CXCL7-null mouse primary cells. Furthermore, K48 polyubiquitination was found in posterior longitudinal ligament ossified tissue and primary cells from CXCL7-null mice. We performed a phosphoproteomics analysis in CXCL7-deficient mice and identified increased phosphorylation of mitogen-activated protein kinase kinase (ME3K)15, ubiquitin protein ligase E3C (UBE3C) and protein kinase C (PKC) alpha, suggesting that ubiquitin-dependent degradation is involved in CXCL7 deficiency. Future studies in the CXCL7-null mouse model are, therefore, warranted to investigate the role of ubiquitination in the onset of OPLL. In conclusion, CXCL7 levels may be useful as a serum marker for the progression of OPLL. This study also suggests that increasing CXCL7 levels in patients can serve as an effective therapeutic strategy for the treatment of OPLL., Competing Interests: The authors have declared that no competing interests exist.

The present study was performed to establish a novel ocular surgery simulator for training in peeling of the inner limited membrane (ILM). This simulator included a next-generation artificial ILM with mechanical properties similar to the natural ILM that could be peeled underwater in the same manner as in actual surgery. An artificial eye consisting of a fundus and eyeball parts was fabricated. The artificial eye was installed in the eye surgery simulator. The fundus part was mounted in the eyeball, which consisted of an artificial sclera, retina, and ILM. To measure the thickness of the fabricated ILM on the artificial retina, we calculated the distance of the step height as the thickness of the artificial ILM. Two experienced ophthalmologists then assessed the fabricated ILM by sensory evaluation. The minimum thickness of the artificial ILM was 1.9 ± 0.3 μm (n = 3). We were able to perform the peeling task with the ILM in water. Based on the sensory evaluation, an ILM with a minimum thickness and 1000 degrees of polymerization was suitable for training. We installed the eye model on an ocular surgery simulator, which allowed for the performance of a sequence of operations similar to ILM peeling. In conclusion, we developed a novel ocular surgery simulator for ILM peeling. The artificial ILM was peeled underwater in the same manner as in an actual operation.

Microelectromechanical systems (MEMS)-based high-performance accelerometers are ubiquitously used in various electronic devices. However, there is an existing need to detect physical impacts using low-cost devices with no electronic circuits or a battery. We designed and fabricated an impact sensor prototype using a commercial stereolithography apparatus that only consists of a plastic housing and working fluids. The sensor device responds to the instantaneous acceleration (impact) by deformation and pinch off of a water droplet that is suspended in oil in a sensor cavity. We tested the various geometrical and physical parameters of the impact sensor to identify their relations to threshold acceleration values. We show that the state diagram that is plotted against the dimensionless Archimedes and Bond numbers adequately describes the response of the proposed sensor.

In the current era of big data, the amount of data available is continuously increasing. Both the number and types of samples, or features, are on the rise. The mixing of distinct features often makes interpretation more difficult. However, separate analysis of individual types requires subsequent integration. A tensor is a useful framework to deal with distinct types of features in an integrated manner without mixing them. On the other hand, tensor data is not easy to obtain since it requires the measurements of huge numbers of combinations of distinct features; if there are m kinds of features, each of which has N dimensions, the number of measurements needed are as many as Nm, which is often too large to measure. In this paper, I propose a new method where a tensor is generated from individual features without combinatorial measurements, and the generated tensor was decomposed back to matrices, by which unsupervised feature extraction was performed. In order to demonstrate the usefulness of the proposed strategy, it was applied to synthetic data, as well as three omics datasets. It outperformed other matrix-based methodologies.

A hydroponic experiment was performed to investigate the stress responses and biochemical adaptations of four submerged macrophytes, Potamogeton crispus, Myriophyllum spicatum, Egeria densa, and Potamogeton oxyphyllus, to the combined exposure of hypoxia and hydrogen sulfide (H2S, provided by NaHS). The investigated plants were subjected to a control, hypoxia, 0.1mM NaHS, 0.5 mM NaHS, 0.1 mM NaHS+hypoxia and 0.5 mM NaHS+hypoxia conditions. All experimental plants grew optimally under control, hypoxic and NaHS conditions in comparison to that grown in the combined exposure of hypoxia and hydrogen sulfide. For P. crispus and M. spicatum, significant decreases of total chlorophyll and increases in oxidative stress (measured by hydrogen peroxide, H2O2, and malondialdehyde, MDA) were observed with exposure to both sulfide concentrations. However, the decrease in catalase (CAT) and ascorbate peroxidase (APX) from exposure to 0.5 mM NaHS suggests that the function of the protective enzymes reached their limit under these conditions. In contrast, for E. densa and P. oxyphyllus, the higher activities of the three antioxidative enzymes and their anaerobic respiration abilities (ADH activity) resulted in higher tolerance and susceptibility under high sulfide concentrations.

The authors present a method for extracting polygon data of endocranial surfaces from CT images of human crania. Based on the fact that the endocast is the largest empty space in the crania, we automate a procedure for endocast extraction by integrating several image processing techniques. Given CT images of human crania, the proposed method extracts endocranial surfaces by the following three steps. The first step is binarization in order to fill void structures, such as diploic space and cracks in the skull. We use a void detection method based on mathematical morphology. The second step is watershed-based segmentation of the endocranial part from the binary image of the CT image. Here, we introduce an automatic initial seed assignment method for the endocranial region using the distance field of the binary image. The final step is partial polygonization of the CT images using the segmentation results as mask images. The resulting polygons represent only the endocranial part, and the closed manifold surfaces are computed even though the endocast is not isolated in the cranium. Since only the isovalue threshold and the size of void structures are required, the procedure is not dependent on the experience of the user. The present paper also demonstrates that the proposed method can extract polygon data of endocasts from CT images of various crania.

When humans perceive the lightness of an object's surface in shadows there is an implicit assumption that cast shadows dim the surface. In two experiments, we investigated whether 5- to 8-month-old infants make this assumption about shadows. According to this shadow assumption, the apparent change in lightness produced by shadows on an object's surface are attributed to blocked light sources. If infants can use the shadow assumption to perceive the object's lightness in shadows, they will also be able to detect unnatural lightness changes in shadows. We compared the infants' looking times to the unnatural and the natural lightness changes in the shadow when an object (duck) goes through the cast shadow. In Experiment 1, we examined whether infants could detect the unnatural lightness changes of the object's surface in shadows. We created computer-graphic movies of unnatural and natural lightness changes to the duck's surface. Our results showed that 7- to 8-month-olds but not 5- to 6-month-olds significantly preferred the movie with the unnatural changes in lightness, indicating that only the older infants could detect these changes. In Experiment 2, we confirmed that the infants' preference was based on the detection of unnatural lightness changes according to the shadow assumption. The natural and the unnatural lightness changes of Experiment 1 were presented without cast shadows. Under these conditions, neither younger nor older infants showed a significant preference. Taken together, the experiments showed that 7- to 8-month-old infants could detect the unnaturalness of a surface's lightness changes produced by shadows. In conclusion, our findings suggest that 7- to 8-month-old infants can perceive an object's lightness in shadows by using an assumption that cast shadows dim the surface of an object.

The Escherichia coli bacteriophage P1 encodes a site-specific recombinase called Cre and two 34-bp target sites of Cre recombinase called loxP. The Cre/loxP system has been used to achieve targeted insertion and precise deletion in many animal and plant genomes. The Cre/loxP system has particularly been used for the removal of selectable marker genes to create marker-free transgenic organisms. For the first time, we applied the Cre/loxP-mediated site-specific recombination system to Chlamydomonas reinhardtii to construct marker-free transgenic strains. Specifically, C. reinhardtii strains cc4350 and cc124 carrying an aphVIII expression cassette flanked by two direct repeats of loxP were constructed. Separately, a synthetic Cre recombinase gene (CrCRE), the codons of which were optimized for expression in C. reinhardtii, was synthesized, and a CrCRE expression cassette was introduced into strain cc4350 carrying a single copy of the loxP-flanked aphVIII expression cassette. Among 46 transformants carrying the CrCRE expression cassette stably, the excision of aphVIII by CrCre recombinase was observed only in one transformant. We then constructed an expression cassette of an in-frame fusion of ble to CrCRE via a short linker peptide. The product of ble (Ble) is a bleomycin-binding protein that confers resistance to bleomycin-related antibiotics such as Zeocin and localizes in the nucleus. Therefore, the ble-(linker)-CrCRE fusion protein is expected to localize in the nucleus. When the ble-(linker)-CrCRE expression cassette was integrated into the genome of strain cc4350 carrying a single copy of the loxP-flanked aphVIII expression cassette, CrCre recombinase-mediated excision of the aphVIII expression cassette was observed at a frequency higher than that in stable transformants of the CrCRE expression cassette. Similarly, from strain cc124 carrying a single loxP-flanked aphVIII expression cassette, the aphVIII expression cassette was successfully excised after introduction of the ble-(linker)-CrCRE expression cassette. The ble-(linker)-CrCRE expression cassette remained in the genome after excision of the aphVIII expression cassette, and it was subsequently removed by crossing with the wild-type strain. This precise Cre-mediated deletion method applicable to transgenic C. reinhardtii could further increase the potential of this organism for use in basic and applied research., Competing Interests: The authors have declared that no competing interests exist.

Recent advances in the use of summed probability distribution (SPD) of calibrated 14C dates have opened new possibilities for studying prehistoric demography. The degree of correlation between climate change and population dynamics can now be accurately quantified, and divergences in the demographic history of distinct geographic areas can be statistically assessed. Here we contribute to this research agenda by reconstructing the prehistoric population change of Jomon hunter-gatherers between 7,000 and 3,000 cal BP. We collected 1,433 14C dates from three different regions in Eastern Japan (Kanto, Aomori and Hokkaido) and established that the observed fluctuations in the SPDs were statistically significant. We also introduced a new non-parametric permutation test for comparing multiple sets of SPDs that highlights point of divergences in the population history of different geographic regions. Our analyses indicate a general rise-and-fall pattern shared by the three regions but also some key regional differences during the 6th millennium cal BP. The results confirm some of the patterns suggested by previous archaeological studies based on house and site counts but offer statistical significance and an absolute chronological framework that will enable future studies aiming to establish potential correlation with climatic changes.

A hemoglobin wrapped covalently by three human serum albumins, a Hb-HSA3 cluster, is an artificial O2-carrier with the potential to function as a red blood cell substitute. This paper describes the synthesis and O2-binding properties of new hemoglobin‒albumin clusters (i) bearing four HSA units at the periphery (Hb-HSA4, large-size variant) and (ii) containing an intramolecularly crosslinked Hb in the center (XLHb-HSA3, high O2-affinity variant). Dynamic light scattering measurements revealed that the Hb-HSA4 diameter is greater than that of either Hb-HSA3 or XLHb-HSA3. The XLHb-HSA3 showed moderately high O2-affinity compared to the others because of the chemical linkage between the Cys-93(β) residues in Hb. Furthermore, the blood circulation behavior of 125I-labeled clusters was investigated by assay of blood retention and tissue distribution after intravenous administration into anesthetized rats. The XLHb-HSA3 was metabolized faster than Hb-HSA3 and Hb-HSA4. Results suggest that the molecular structure of the protein cluster is a factor that can influence in vivo circulation behavior.

Orienting visual attention allows us to properly select relevant visual information from a noisy environment. Despite extensive investigation of the orienting of visual attention in infancy, it is unknown whether and how stimulus characteristics modulate the deployment of attention from birth to 4 months of age, a period in which the efficiency in orienting of attention improves dramatically. The aim of the present study was to compare 4-month-old infants' and newborns' ability to orient attention from central to peripheral stimuli that have the same or different attributes. In Experiment 1, all the stimuli were dynamic and the only attribute of the central and peripheral stimuli to be manipulated was face orientation. In Experiment 2, both face orientation and motion of the central and peripheral stimuli were contrasted. The number of valid trials and saccadic latency were measured at both ages. Our results demonstrated that the deployment of attention is mainly influenced by motion at birth, while it is also influenced by face orientation at 4-month of age. These findings provide insight into the development of the orienting visual attention in the first few months of life and suggest that maturation may be not the only factor that determines the developmental change in orienting visual attention from birth to 4 months.

There have been no reports concerning the self-face perception in patients with anorexia nervosa (AN). The purpose of this study was to compare the neuronal correlates of viewing self-face images (i.e. images of familiar face) and stranger-face images (i.e. images of an unfamiliar face) in female adolescents with and without AN. We used near-infrared spectroscopy (NIRS) to measure hemodynamic responses while the participants viewed full-color photographs of self-face and stranger-face. Fifteen females with AN (mean age, 13.8 years) and 15 age- and intelligence quotient (IQ)-matched female controls without AN (mean age, 13.1 years) participated in the study. The responses to photographs were compared with the baseline activation (response to white uniform blank). In the AN group, the concentration of oxygenated hemoglobin (oxy-Hb) significantly increased in the right temporal area during the presentation of both the self-face and stranger-face images compared with the baseline level. In contrast, in the control group, the concentration of oxy-Hb significantly increased in the right temporal area only during the presentation of the self-face image. To our knowledge the present study is the first report to assess brain activities during self-face and stranger-face perception among female adolescents with AN. There were different patterns of brain activation in response to the sight of the self-face and stranger-face images in female adolescents with AN and controls.

A covalent core-shell structured protein cluster composed of hemoglobin (Hb) at the center and human serum albumins (HSA) at the periphery, Hb-HSAm, is an artificial O2 carrier that can function as a red blood cell substitute. Here we described the preparation of a novel Hb-HSA3 cluster with antioxidant activities and its O2 complex stable in aqueous H2O2 solution. We used an approach of incorporating a Pt nanoparticle (PtNP) into the exterior HSA unit of the cluster. A citrate reduced PtNP (1.8 nm diameter) was bound tightly within the cleft of free HSA with a binding constant (K) of 1.1×10(7) M(-1), generating a stable HSA-PtNP complex. This platinated protein showed high catalytic activities for dismutations of superoxide radical anions (O2•-) and hydrogen peroxide (H2O2), i.e., superoxide dismutase and catalase activities. Also, Hb-HSA3 captured PtNP into the external albumin unit (K = 1.1×10(7) M(-1)), yielding an Hb-HSA3(PtNP) cluster. The association of PtNP caused no alteration of the protein surface net charge and O2 binding affinity. The peripheral HSA-PtNP shell prevents oxidation of the core Hb, which enables the formation of an extremely stable O2 complex, even in H2O2 solution.

Background: Although lifestyle factors such as cigarette smoking, excessive drinking, obesity, low or no exercise, and unhealthy dietary habits have each been associated with inadequate sleep, little is known about their combined effect. The aim of this study was to quantify the overall impact of lifestyle-related factors on non-restorative sleep in the general Japanese population., Methods and Findings: A cross-sectional study of 243,767 participants (men, 39.8%) was performed using the Specific Health Check and Guidance System in Japan. A healthy lifestyle score was calculated by adding up the number of low-risk lifestyle factors for each participant. Low risk was defined as (1) not smoking, (2) body mass index<25 kg/m², (3) moderate or less alcohol consumption, (4) regular exercise, and (5) better eating patterns. Logistic regression analysis was used to examine the relationship between the score and the prevalence of non-restorative sleep, which was determined from questionnaire responses. Among 97,062 men (mean age, 63.9 years) and 146,705 women (mean age, 63.7 years), 18,678 (19.2%) and 38,539 (26.3%) reported non-restorative sleep, respectively. The prevalence of non-restorative sleep decreased with age for both sexes. Compared to participants with a healthy lifestyle score of 5 (most healthy), those with a score of 0 (least healthy) had a higher prevalence of non-restorative sleep (odds ratio, 1.59 [95% confidence interval, 1.29-1.97] for men and 2.88 [1.74-4.76] for women), independently of hypertension, hypercholesterolemia, diabetes, and chronic kidney disease. The main limitation of the study was the cross-sectional design, which limited causal inferences for the identified associations., Conclusions: A combination of several unhealthy lifestyle factors was associated with non-restorative sleep among the general Japanese population. Further studies are needed to establish whether general lifestyle modification improves restorative sleep.

MicroRNA (miRNA) expression profiling has proven useful in diagnosing and understanding the development and progression of several diseases. Microarray is the standard method for analyzing miRNA expression profiles; however, it has several disadvantages, including its limited detection of miRNAs. In recent years, advances in genome sequencing have led to the development of next-generation sequencing (NGS) technologies, which significantly advance genome sequencing speed and discovery. In this study, we compared the expression profiles obtained by next generation sequencing (NGS) with the profiles created using microarray to assess if NGS could produce a more accurate and complete miRNA profile. Total RNA from 14 hepatocellular carcinoma tumors (HCC) and 6 matched non-tumor control tissues were sequenced with Illumina MiSeq 50-bp single-end reads. Micro RNA expression profiles were estimated using miRDeep2 software. As a comparison, miRNA expression profiles for 11 out of 14 HCCs were also established by microarray (Agilent human microRNA microarray). The average total sequencing exceeded 2.2 million reads per sample and of those reads, approximately 57% mapped to the human genome. The average correlation for miRNA expression between microarray and NGS and subtraction were 0.613 and 0.587, respectively, while miRNA expression between technical replicates was 0.976. The diagnostic accuracy of HCC, p-value, and AUC were 90.0%, 7.22×10(-4), and 0.92, respectively. In summary, NGS created an miRNA expression profile that was reproducible and comparable to that produced by microarray. Moreover, NGS discovered novel miRNAs that were otherwise undetectable by microarray. We believe that miRNA expression profiling by NGS can be a useful diagnostic tool applicable to multiple fields of medicine.

This paper describes the utilization of giant unilamellar vesicles (GUVs) as a platform for handling chemical and biochemical reagents. GUVs with diameters of 5 to 10 µm and containing chemical/biochemical reagents together with inert polymers were fused with electric pulses (electrofusion). After reagent mixing, the fused GUVs spontaneously deformed to a budding shape, separating the mixed solution into sub-volumes. We utilized a microfluidic channel and optical tweezers to select GUVs of interest, bring them into contact, and fuse them together to mix and aliquot the reaction product. We also show that, by lowering the ambient temperature close to the phase transition temperature Tm of the lipid used, daughter GUVs completely detached (fission). This process performs all the liquid-handing features used in bench-top biochemistry using the GUV, which could be advantageous for the membrane-related biochemical assays.

Many social animals can discriminate between familiar and unfamiliar faces. Orangutans, however, lead a semi-solitary life and spend much of the day alone. As such, they may be less adept at recognizing conspecifics and are a good model for determining how social structure influences the evolution of social cognition such as facial recognition. The present study is the first report of whether orangutans can distinguish among individual faces. We adopted a preferential looking method and found that orangutans used facial discrimination to identify known conspecifics. This suggests that frequent and intense social interaction is not necessary for facial discrimination, although our findings were limited by the small number of stimuli and the unequal numbers of male and female orangutans depicted in the stimuli.

Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

There is a large literature focused on the color perception of matte surface. However, recent research showed that the component of surface specular reflection, such as glossiness, also affects categorical color perception. For instance, the color term "gold" was used to name high specular stimuli within a specific range of chromaticity, which overlaps with those of yellow and orange for low specular stimuli. In the present study, we investigated whether the component of surface specular reflectance affects the color perception of 5- to 8-month-old infants by using the preferential looking technique. In the first experiment, we conducted a simple test to determine whether infants perceive yellow and gold as the same color by comparing their preference for these colors over green. If the infants perceive yellow and gold as the same color, they would show similar preference scores over green. On the other hand, if infants show different preference scores over green, it indicates that infants do not perceive yellow and gold as the same color. Only the 7-8 month-old infants showed different preference scores for gold and yellow over green. This result indicates that the 7-8 month-old infants perceive gold and yellow as different colors. In Experiment 2, we eliminated the component of specular reflectance on the gold surface and presented it against green to infants. A similar preference score of yellow over green was obtained. This result suggests that the difference between the preference scores for gold and yellow over green in Experiment 1 was based on representations of glossiness.

The discovery and characterization of blood-based disease biomarkers are clinically important because blood collection is easy and involves relatively little stress for the patient. However, blood generally reflects not only targeted diseases, but also the whole body status of patients. Thus, the selection of biomarkers may be difficult. In this study, we considered miRNAs as biomarker candidates for several reasons. First, since miRNAs were discovered relatively recently, they have not yet been tested extensively. Second, since the number of miRNAs is relatively limited, selection is expected to be easy. Third, since they are known to play critical roles in a wide range of biological processes, their expression may be disease specific. We applied a newly proposed method to select combinations of miRNAs that discriminate between healthy controls and each of 14 diseases that include 5 cancers. A new feature selection method is based on principal component analysis. Namely this method does not require knowledge of whether each sample was derived from a disease patient or a healthy control. Using this method, we found that hsa-miR-425, hsa-miR-15b, hsa-miR-185, hsa-miR-92a, hsa-miR-140-3p, hsa-miR-320a, hsa-miR-486-5p, hsa-miR-16, hsa-miR-191, hsa-miR-106b, hsa-miR-19b, and hsa-miR-30d were potential biomarkers; combinations of 10 of these miRNAs allowed us to discriminate each disease included in this study from healthy controls. These 12 miRNAs are significantly up- or downregulated in most cancers and other diseases, albeit in a cancer- or disease-specific combinatory manner. Therefore, these 12 miRNAs were also previously reported to be cancer- and disease-related miRNAs. Many disease-specific KEGG pathways were also significantly enriched by target genes of up-/downregulated miRNAs within several combinations of 10 miRNAs among these 12 miRNAs. We also selected miRNAs that could discriminate one disease from another or from healthy controls. These miRNAs were found to be largely overlapped with miRNAs that discriminate each disease from healthy controls.