Phase Structure of the Random-Plaquette Z_2 Gauge Model: Accuracy Threshold for a Toric Quantum Memory

We study the phase structure of the random-plaquette Z_2 lattice gauge model in three dimensions. In this model, the "gauge coupling" for each plaquette is a quenched random variable that takes the value \beta with the probability 1-p and -\beta with the probability p. This model is relevant for the recently proposed quantum memory of toric code. The parameter p is the concentration of the plaquettes with "wrong-sign" couplings -\beta, and interpreted as the error probability per qubit in quantum code. In the gauge system with p=0, i.e., with the uniform gauge couplings \beta, it is known that there exists a second-order phase transition at a certain critical "temperature", T(\equiv \beta^{-1}) = T_c =1.31, which separates an ordered(Higgs) phase at T<T_c and a disordered(confinement) phase at T>T_c. As p increases, the critical temperature T_c(p) decreases. In the p-T plane, the curve T_c(p) intersects with the Nishimori line T_{N}(p) at the certain point (p_c, T_{N}(p_c)). The value p_c is just the accuracy threshold for a fault-tolerant quantum memory and associated quantum computations. By the Monte-Carlo simulations, we calculate the specific heat and the expectation values of the Wilson loop to obtain the phase-transition line T_c(p) numerically. The accuracy threshold is estimated as p_c \simeq 0.033.Comment: 24 pages, 14 figures, some clarification

The L motifs of two moss pentatricopeptide repeat proteins are involved in RNA editing but predominantly not in RNA recognition.

Pentatricopeptide repeat (PPR) proteins, composed of PPR motifs repeated in tandem, are sequence-specific RNA binding proteins. Recent bioinformatic studies have shown that the combination of polar amino acids at positions 5 and last in each PPR motif recognizes RNA bases, and an RNA recognition code for PPR proteins has been proposed. Subsequent studies confirmed that the P (canonical length) and S (short) motifs bind to specific nucleotides according to this code. However, the contribution of L (long) motifs to RNA recognition is mostly controversial, owing to the presence of a nonpolar amino acid at position 5. The PLS-class PPR protein PpPPR_56 is a mitochondrial RNA editing factor in the moss Physcomitrella patens. Here, we performed in vitro RNA binding and in vivo complementation assays with PpPPR_56 and its variants containing mutated L motifs to investigate their contributions to RNA recognition. In vitro RNA binding assay showed that the original combination of amino acids at positions 5 and last in the L motifs of PpPPR_56 is not required for RNA recognition. In addition, an in vivo complementation assay with RNA editing factors PpPPR_56 and PpPPR_78 revealed the importance of nonpolar amino acids at position 5 of C-terminal L motifs for efficient RNA editing. Our findings suggest that L motifs function as non-binding spacers, not as RNA-binding motifs, to facilitate the formation of a complex between PLS-class PPR protein and RNA. As a result, the DYW domain, a putative catalytic deaminase responsible for C-to-U RNA editing, is correctly placed in proximity to C, which is to be edited

Spatial Geometries of Self-Assembled Chitohexaose Monolayers Regulate Myoblast Fusion

Myoblast fusion into functionally-distinct myotubes to form in vitro skeletal muscle constructs under differentiation serum-free conditions still remains a challenge. Herein, we report that our microtopographical carbohydrate substrates composed of bioactive hexa-N-acetyl-d-glucosamine (GlcNAc6) modulated the efficiency of myoblast fusion without requiring horse serum or any differentiation medium during cell culture. Promotion of the differentiation of dissociated mononucleated skeletal myoblasts (C2C12; a mouse myoblast cell line) into robust myotubes was found only on GlcNAc6 micropatterns, whereas the myoblasts on control, non-patterned GlcNAc6 substrates or GlcNAc6-free patterns exhibited an undifferentiated form. We also examined the possible role of GlcNAc6 micropatterns with various widths in the behavior of C2C12 cells in early and late stages of myogenesis through mRNA expression of myosin heavy chain (MyHC) isoforms. The spontaneous contraction of myotubes was investigated via the regulation of glucose transporter type 4 (GLUT4), which is involved in stimulating glucose uptake during cellular contraction. Narrow patterns demonstrated enhanced glucose uptake rate and generated a fast-twitch muscle fiber type, whereas the slow-twitch muscle fiber type was dominant on wider patterns. Our findings indicated that GlcNAc6-mediated integrin interactions are responsible for guiding myoblast fusion forward along with myotube formation

N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation

宿主がHIV-1感染を抑制する新たなメカニズムの解明 --N4BP1によるRNA分解とその調節がウイルス再活性化を調節する--. 京都大学プレスリリース. 2019-05-29.RNA-modulating factors not only regulate multiple steps of cellular RNA metabolism, but also emerge as key effectors of the immune response against invading viral pathogens including human immunodeficiency virus type-1 (HIV-1). However, the cellular RNA-binding proteins involved in the establishment and maintenance of latent HIV-1 reservoirs have not been extensively studied. Here, we screened a panel of 62 cellular RNA-binding proteins and identified NEDD4-binding protein 1 (N4BP1) as a potent interferon-inducible inhibitor of HIV-1 in primary T cells and macrophages. N4BP1 harbours a prototypical PilT N terminus-like RNase domain and inhibits HIV-1 replication by interacting with and degrading viral mRNA species. Following activation of CD4+ T cells, however, N4BP1 undergoes rapid cleavage at Arg 509 by the paracaspase named mucosa-associated lymphoid tissue lymphoma translocation 1 (MALT1). Mutational analyses and knockout studies revealed that MALT1-mediated inactivation of N4BP1 facilitates the reactivation of latent HIV-1 proviruses. Taken together, our findings demonstrate that the RNase N4BP1 is an efficient restriction factor of HIV-1 and suggest that inactivation of N4BP1 by induction of MALT1 activation might facilitate elimination of latent HIV-1 reservoirs

Crystallization of selenomethionyl exo-β-1,3-galactanase from the basidiomycete Phanerochaete chrysosporium

Selenomethionyl exo-β-1,3-galactanase from P. chrysosporium K-3 produced in Pichia pastoris was crystallized. The crystals diffracted to a resolution of 1.8 Å and belonged to space group P21

Validation of a COPD screening questionnaire and establishment of diagnostic cut-points in a Japanese general population: The Hisayama study

Background: Chronic obstructive pulmonary disease (COPD) is highly prevalent worldwide. COPD is a treatable disease and it is important to identify COPD subjects, highlighting the need for an efficient screening measure. Although the COPD screening questionnaire (COPD Population Screener, COPD-PS) was developed as a screening tool, its validity is not clear in population-based studies. This study determines the validity of the COPD-PS in the general Japanese population. Methods: All registered residents living in the town of Hisayama aged above 40 were solicited to participate in a health check-up in 2012. All subjects aged 40–79 without physician-diagnosed asthma or lung resection were recruited, and 2357 subjects with the COPD-PS recorded and valid spirometry measurements were analyzed. Persistent airflow obstruction (AO) was defined by post-bronchodilator FEV1/FVC < 0.7. The sensitivity and specificity of the COPD-PS score for identifying AO was assessed by logistic regression analysis. Results: The prevalence of AO in this population was 6.5%. The overall area under the receiver operating characteristic (ROC) curve for the continuous COPD-PS score was 0.748. A cut-point of 4-points is recommended, resulting in a sensitivity of 67.1% and specificity of 72.9% with an area under the ROC curve of 0.70. The positive predictive value was 14.6% and negative predictive value was 97.0%. Conclusions: The COPD-PS appears to be an adequate measure for large scale screening of possible airflow obstruction requiring further testing with spirometry

A Phase I clinical trial of EUS-guided intratumoral injection of the oncolytic virus, HF10 for unresectable locally advanced pancreatic cancer

Abstract Background Prognosis of pancreatic cancer is poor with a 5-year survival rate of only 7%. Although several new chemotherapy treatments have shown promising results, all patients will eventually progress, and we need to develop newer chemotherapy treatments to improve response rates and overall survival (OS). HF10 is a spontaneously mutated oncolytic virus derived from a herpes simplex virus-1, and it has potential to show strong antitumor effect against malignancies without damaging normal tissue. We aimed to evaluate the safety and anti-tumor effectiveness in phase I dose-escalation trial of direct injection of HF10 into unresectable locally advanced pancreatic cancer under endoscopic ultrasound (EUS)-guidance in combination with erlotinib and gemcitabine administration. The mid-term results have been previously reported and here we report the final results of our study. Methods This was a single arm, open-label Phase I trial. HF10 was injected once every 2 weeks and continued up to four times in total unless dose-limiting toxicity (DLT) appears. A total of nine subjects in three Cohorts with dose-escalation were planned to be enrolled in this trial. The primary endpoint was the safety assessment and the secondary endpoint was the efficacy assessment. Results Twelve patients enrolled in this clinical trial, and ten subjects received this therapy. Five patients showed Grade III myelosuppression and two patients developed serious adverse events (AEs) (perforation of duodenum, hepatic dysfunction). However, all of these events were judged as AEs unrelated to HF10. Tumor responses were three partial responses (PR), four stable diseases (SD), and two progressive diseases (PD) out of nine subjects who completed the treatment. Target lesion responses were three PRs and six SDs. The median progression free survival (PFS) was 6.3 months, whereas the median OS was 15.5 months. Two subjects from Cohort 1 and 2 showed downstaging and finally achieved surgical complete response (CR). Conclusions HF10 direct injection under EUS-guidance in combination with erlotinib and gemcitabine was a safe treatment for locally advanced pancreatic cancer. Combination therapy of HF10 and chemotherapy should be explored further in large prospective studies. Trial registration: This study was prospectively registered in UMIN-CTR (UMIN000010150) on March 4th, 2013