Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔG(min)). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔG(min). This effectively excludes inappropriate sequences before ΔG(min) is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔG(exp)) of 126 sequences correlated well with ΔG(min) (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java

What shapes the loss landscape of self-supervised learning?

Prevention of complete and dimensional collapse of representations has recently become a design principle for self-supervised learning (SSL). However, questions remain in our theoretical understanding: When do those collapses occur? What are the mechanisms and causes? We answer these questions by deriving and thoroughly analyzing an analytically tractable theory of SSL loss landscapes. In this theory, we identify the causes of the dimensional collapse and study the effect of normalization and bias. Finally, we leverage the interpretability afforded by the analytical theory to understand how dimensional collapse can be beneficial and what affects the robustness of SSL against data imbalance.Comment: Published at ICLR 202

Practical Evaluation of Security for Quantum Key Distribution

Many papers proved the security of quantum key distribution (QKD) system, in the asymptotic framework. The degree of the security has not been discussed in the finite coding-length framework, sufficiently. However, to guarantee any implemented QKD system requires, it is needed to evaluate a protocol with a finite coding-length. For this purpose, we derive a tight upper bound of the eavesdropper's information. This bound is better than existing bounds. We also obtain the exponential rate of the eavesdropper's information. Further, we approximate our bound by using the normal distribution.Comment: The manuscript has been modfie

MARCKSL1 Regulates Spine Formation in the Amygdala and Controls the Hypothalamic-Pituitary-Adrenal Axis and Anxiety-Like Behaviors

Takashi Tanaka, Shoko Shimizu, Masaki Ueno, Yoshitaka Fujihara, Masahito Ikawa, Shingo Miyata, MARCKSL1 Regulates Spine Formation in the Amygdala and Controls the Hypothalamic-Pituitary-Adrenal Axis and Anxiety-Like Behaviors, EBioMedicine, Volume 30, 2018, Pages 62-73, ISSN 2352-3964, https://doi.org/10.1016/j.ebiom.2018.03.018

Changes in cellular ultrastructure induced by gamma-interferon in K562 cells may be prerequisite for apoptosis.

We report here the time-course of electron microscopic changes induced by gamma-interferon (IFN-gamma) in the human erythromyeloid leukemia cell line K562. In K562 cells treated with IFN-gamma for 6h, the nuclei were polygonal in shape and microvilli were far more abundant on cell membranes compared with control K562 cells, and invaginations were often seen in the cell membranes. There was a reduction in the number of cell-membrane microvilli and an increase in the number of lysosomal bodies in the cytoplasm of K562 cells treated with IFN-gamma for 12h. After treatment with IFN-gamma for 24h, the cell membrane microvilli disappeared, large numbers of cellular organelles were observed, such as mitochondria and lysosomes, and the cytoplasm became electron-dense. Cytoplasmic vesicles and vacuoles were also observed. These vesicles may correspond to an intermediate step in the ultimate cellular disintegration associated with apoptosis caused by IFN-gamma.</p

Social and cognitive functions in schizophrenia

Purpose: The purpose of the present study was to examine clinical factors related to social function in people with schizophrenia. Patients and methods: The participants were 55 stabilized outpatients with schizophrenia. Their mean age was 39.36 (SD =10.65) years. Social function was assessed using the Quality of Life Scale (QLS). Cognitive function was evaluated with the Measurement and Treatment Research to Improve Cognition in Schizophrenia Consensus Cognitive Battery (MCCB). Clinical symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS), the Calgary Depression Scale for Schizophrenia, and the Drug-Induced Extrapyramidal Symptoms Scale. Results: Neither the MCCB cognitive domain score nor composite score was correlated with the QLS scores. However, of the 10 MCCB subtests, the Trail Making Test Part A and the Brief Assessment of Cognition in Schizophrenia-Symbol Coding (BACS-SC) scores were positively correlated with the QLS scores. Among clinical variables, especially the PANSS negative syndrome scale score had a strong negative correlation with the QLS scores. Stepwise regression analyses showed that the PANSS negative syndrome scale score was an independent predictor of the QLS scores, and although the BACS-SC score predicted the QLS common objects and activities subscale score, the association was not so strong compared to the PANSS negative syndrome scale score. Conclusion: These results indicate that speed of processing evaluated by BACS-SC could predict some aspect of social function but negative symptoms have a much stronger impact on global social function in people with schizophrenia