Decoding Single Molecule Time Traces with Dynamic Disorder

Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm - Variational Bayes-double chain Markov model (VB-DCMM) - to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na$^+$ solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA

Quaternary semiconductor Cu2FeSnS4 nanoparticles as an alternative to Pt catalysts

We demonstrate an N719 dye sensitized solar cell based on Cu 2FeSnS4 (CFTS) as a counter electrode. The elements for the material are all earth abundant and environmentally benign. The power conversion efficiency of a DSSC using CFTS was comparable to that of a DSSC using Pt under A.M. 1.5G (100 mW cm-2).close3

MOMENT RESISTANCE PERFORMANCE OF LARCH LAMINATED TIMBER BEAM-COLUMN JOINTS REINFORCED WITH CFRP

This study evaluates the moment resisting capacity of the drift pin larch beam-column joint with slotted-in steel plates of larch laminated timber. It is reinforced with carbon fiber reinforced plastic (CFRP) to suppress the brittle fracture of the beam-column joint and improve the joint capacity using larch laminated timber, a wood material manufactured by multi-layering of timber as a structural member of heavy timber.The average maximum moment capacity of the control specimen was 16.9 kN·m and the average maximum moments of the Type-A (volume ratio of joint reinforced with CFRP: 3.6%) and Type-B (volume ratio of joint reinforced with CFRP: 5.4%) were increased by 46% and 62%, respectively, compared to that of the control specimen. The capacity of the joint, such as the average yield capacity, ultimate moment capacity, and ductility ratio, of the control, Type-A, and Type-B specimens increased as the reinforcement ratio of the CFRP increased. For the failure mode of the control specimen, splitting failure occurred in both the column and beam members in the end distance direction. However, the splitting failure did not occur in the beam member due to the improvement of the joint and ductility of the specimens reinforced with the CFRP. The Type-A specimen had improved joint capacity and ductility compared to the control specimen; however, brittle failure occurred owing to the external force exceeding the joint capacity. However, in some of the Type-B specimens, the splitting failure did not occur in the column and beam members due to the CFRP reinforcement. Particularly, the Type-B3 specimen exhibited ductility

LINE FUSION GENES: a database of LINE expression in human genes

BACKGROUND: Long Interspersed Nuclear Elements (LINEs) are the most abundant retrotransposons in humans. About 79% of human genes are estimated to contain at least one segment of LINE per transcription unit. Recent studies have shown that LINE elements can affect protein sequences, splicing patterns and expression of human genes. DESCRIPTION: We have developed a database, LINE FUSION GENES, for elucidating LINE expression throughout the human gene database. We searched the 28,171 genes listed in the NCBI database for LINE elements and analyzed their structures and expression patterns. The results show that the mRNA sequences of 1,329 genes were affected by LINE expression. The LINE expression types were classified on the basis of LINEs in the 5' UTR, exon or 3' UTR sequences of the mRNAs. Our database provides further information, such as the tissue distribution and chromosomal location of the genes, and the domain structure that is changed by LINE integration. We have linked all the accession numbers to the NCBI data bank to provide mRNA sequences for subsequent users. CONCLUSION: We believe that our work will interest genome scientists and might help them to gain insight into the implications of LINE expression for human evolution and disease. AVAILABILITY

The Feasibility of Endoscopy-Assisted Breast Conservation Surgery for Patients with Early Breast Cancer

PURPOSE: Breast conservation surgery (BCS) has become a standard treatment method for patients with early breast cancer. Endoscopy-assisted BCS (EABCS) can be performed through an inconspicuous periareolar and a small axillary incision for sentinel node biopsy, which may give better cosmetic outcomes than conventional BCS skin incisions. This study was designed to evaluate the feasibility of EABCS for patients with early breast cancer. METHODS: Forty-three patients were candidates for EABCS, and EABCS was performed in 40 patients with breast cancer between January 2008 and July 2010. Their clinicopathological features were retrospectively analyzed. Operative time, margin status, complications, and relapse-free survival were compared with those of patients treated by conventional BCS and who were treated at the same institute during the same period. RESULTS: The most common lesion site of the EABCS and conventional BCS groups was the upper area of the breast. Tumor size in all patients was less than 4 cm (range, 0.4-3.7 cm), and nodal involvement was found in eight (20%) patients in the BCS group. The mean operative time was 110 minutes for the EABCS group and 107 minutes for the conventional BCS group, and those were not significantly different. No significant difference in frozen or final margin status was observed between the EABCS and conventional BCS groups. Relapse-free survival was statistically equivalent between the groups with a median follow-up of 12 months. Postoperative complications occurred in five cases in four patients with EABCS, which was not significantly different from conventional BCS. CONCLUSION: Performing EABCS in patients with early breast cancer seems to be feasible and safe. Further study with a longer-term follow-up may be needed to confirm the clinical value of EABCS.ope

Uncovering transcriptional reprogramming during callus development in soybean: insights and implications

Callus, a valuable tool in plant genetic engineering, originates from dedifferentiated cells. While transcriptional reprogramming during callus formation has been extensively studied in Arabidopsis thaliana, our knowledge of this process in other species, such as Glycine max, remains limited. To bridge this gap, our study focused on conducting a time-series transcriptome analysis of soybean callus cultured for various durations (0, 1, 7, 14, 28, and 42 days) on a callus induction medium following wounding with the attempt of identifying genes that play key roles during callus formation. As the result, we detected a total of 27,639 alterations in gene expression during callus formation, which could be categorized into eight distinct clusters. Gene ontology analysis revealed that genes associated with hormones, cell wall modification, and cell cycle underwent transcriptional reprogramming throughout callus formation. Furthermore, by scrutinizing the expression patterns of genes related to hormones, cell cycle, cell wall, and transcription factors, we discovered that auxin, cytokinin, and brassinosteroid signaling pathways activate genes involved in both root and shoot meristem development during callus formation. In summary, our transcriptome analysis provides significant insights into the molecular mechanisms governing callus formation in soybean. The information obtained from this study contributes to a deeper understanding of this intricate process and paves the way for further investigation in the field