BCR-ABL1 (p210) Transcript Kinetics

Context.— Delta checks are a powerful technique for monitoring clinical assays in many disciplines but have not been routinely used in molecular testing. Objective.— To determine if the biologically determined kinetics of BCR-ABL1's rise and fall could allow the development of a delta check in BCR-ABL1 testing. Design.— Nine years of BCR-ABL1 p210 results were evaluated and patients with 3 or more results were selected for inclusion. The kinetics of these percentages of international standard values were plotted against time along with the median and the 90th and 95th percentile lines. A Monte Carlo simulation of a batch mix-up was performed for 6 months of data to determine the efficacy of the proposed cutoff. Results.— The median kinetics showed a 1-log drop of the percentage of international standard in 90 days, with less than 5% of cases showing faster than a 2-log drop in 90 days, and less than 2.5% showing a faster than 3-log drop in 90 days (extrapolated to 1 log in 30 days). The Monte Carlo simulation of a batch mix-up showed that an average batch mix-up of 23 samples could routinely be flagged by this cutoff, albeit with wide variance. Conclusions.— These results suggest that using a drop in the percentage of international standard of greater than 1 log in 30 days can be a useful trigger in implementing a delta-check system for this molecular test.

Low-Energy Coulomb Excitation for the Shell Model

Low-energy Coulomb excitation is capable of providing unique information on static electromagnetic moments of short-lived excited nuclear states, including non-yrast states. The process selectively populates low-lying collective states and is, therefore, ideally suited to study phenomena such as shape coexistence and the development of exotic deformation (triaxial or octupole shapes). Historically, these experiments were restricted to stable isotopes. However, the advent of new facilities providing intense beams of short-lived radioactive species has opened the possibility to apply this powerful technique to a much wider range of nuclei. The paper discusses the observables that can be measured in a Coulomb-excitation experiment and their relation to the nuclear structure parameters with an emphasis on the nuclear shape. Recent examples of Coulomb-excitation studies that provided outcomes relevant for the Shell Model are also presented.

Polarization Tomography with Stokes Parameters

We present a simple but powerful technique for the analysis of polarized emission from radio galaxies and other objects. It is based on the fact that images of Stokes parameters often contain considerably more information than is available in polarized intensity and angle maps. In general, however, the orientation of the Stokes parameters will not be matched to the position angles of structures in the source. Polarization tomography, the technique presented in this paper, consists of making a series of single linear Stokes parameter images, S(ρ), where each image is rotated by an angle ρ from the initial orientation of Q and U. Examination of these images, in a series of still frames or a movie, reveals often hidden patterns of polarization angles, as well as structures that were obscured by the presence of overlapping polarized emission. We provide both cartoon examples and a quick look at the complex polarized structure in Cygnus A.

Comparative Analysis and Enhancement of CFG-based Hardware-Assisted CFI Schemes

Subverting the flow of instructions (e.g., by use of code-reuse attacks) still poses a serious threat to the security of today’s systems. Various control flow integrity (CFI) schemes have been proposed as a powerful technique to detect and mitigate such attacks. In recent years, many hardware-assisted implementations of CFI enforcement based on control flow graphs (CFGs) have been presented by academia. Such approaches check whether control flow transfers follow the intended CFG by limiting the valid target addresses. However, these papers all target different platforms and were evaluated with different sets of benchmark applications, which makes quantitative comparisons hardly possible. For this paper, we have implemented multiple promising CFG-based CFI schemes on a common platform comprising a RISC-V within FPGA. By porting almost 40 benchmark applications to this system we can present a meaningful comparison of the various techniques in terms of run-time performance, hardware utilization, and binary size. In addition, we present an enhanced CFI approach that is inspired by what we consider the best concepts and ideas of previously proposed mechanisms. We have made this approach more practical and feature-complete by tackling some problems largely ignored previously. We show with this fine-grained scheme that CFI can be achieved with even less overheads than previously demonstrated.

STUDENTS’ ATTITUDE TOWARD THE IMPLEMENTATION OF ROLE-PLAYING ACTIVITY IN ENGLISH FOR BUSINESS CLASS AT MANAGEMENT DEPARTMENT

This research is about the students’ attitude toward the implementation of role-playing activities in English for business class of Management Department. English for Business is a compulsory subject for Management Department at Bina Bangsa University. The aim of this research was to describe students' attitudes towards the implementation of role-playing activities in the classroom. Role-playing activities is a very effective and powerful technique that can help students enhance their creativity and ability at speaking, it can create a favorable learning environment as well, and classes became more interactive and student-oriented. 40 students of the management study program who took English for Business subject took a part in this research. Data were collected through questionnaires, interviews and observations which were then analyzed and tabulated. The results of this study showed that 80% of students had a positive attitude towards role playing activities during learning process. Recognizing their role in certain situations based on the topics studied in the class and playing the role made them easier to practice speaking English and enhance their English ability. Students were enthusiastic as well to learn English because it was fun for them. students are contented with their performance in role-playing activities

Transfer matrix in counting problems

The transfer matrix is a powerful technique that can be applied to statistical mechanics systems as, for example, in the calculus of the entropy of the ice model. One interesting way to study such systems is to map it onto a three-color problem. In this paper, we explicitly build the transfer matrix for the three-color problem in order to calculate the number of possible configurations for finite systems with free, periodic in one direction and toroidal boundary conditions (periodic in both directions)

Biologically relevant transfer learning improves transcription factor binding prediction

Background Deep learning has proven to be a powerful technique for transcription factor (TF) binding prediction but requires large training datasets. Transfer learning can reduce the amount of data required for deep learning, while improving overall model performance, compared to training a separate model for each new task. Results We assess a transfer learning strategy for TF binding prediction consisting of a pre-training step, wherein we train a multi-task model with multiple TFs, and a fine-tuning step, wherein we initialize single-task models for individual TFs with the weights learned by the multi-task model, after which the single-task models are trained at a lower learning rate. We corroborate that transfer learning improves model performance, especially if in the pre-training step the multi-task model is trained with biologically relevant TFs. We show the effectiveness of transfer learning for TFs with ~ 500 ChIP-seq peak regions. Using model interpretation techniques, we demonstrate that the features learned in the pre-training step are refined in the fine-tuning step to resemble the binding motif of the target TF (i.e., the recipient of transfer learning in the fine-tuning step). Moreover, pre-training with biologically relevant TFs allows single-task models in the fine-tuning step to learn useful features other than the motif of the target TF. Conclusions Our results confirm that transfer learning is a powerful technique for TF binding prediction.

The Short-Term Performances of Two Independent Gas Modulated Refractometers for Pressure Assessments

Refractometry is a powerful technique for pressure assessments that, due to the recent redefinition of the SI system, also offers a new route to realizing the SI unit of pressure, the Pascal. Gas modulation refractometry (GAMOR) is a methodology that has demonstrated an outstanding ability to mitigate the influences of drifts and fluctuations, leading to long-term precision in the 10−7 region. However, its short-term performance, which is of importance for a variety of applications, has not yet been scrutinized. To assess this, we investigated the short-term performance (in terms of precision) of two similar, but independent, dual Fabry–Perot cavity refractometers utilizing the GAMOR methodology. Both systems assessed the same pressure produced by a dead weight piston gauge. That way, their short-term responses were assessed without being compromised by any pressure fluctuations produced by the piston gauge or the gas delivery system. We found that the two refractometer systems have a significantly higher degree of concordance (in the 10−8 range at 1 s) than what either of them has with the piston gauge. This shows that the refractometry systems under scrutiny are capable of assessing rapidly varying pressures (with bandwidths up to 2 Hz) with precision in the 10−8 range.

Multifrequency STD NMR Unveils the Interactions of Antibiotics With Burkholderia multivorans Biofilm Exopolysaccharide

Biofilms confine bacterial cells within self-produced matrices, offering advantages such as protection from antibiotics and entrapment of nutrients. Polysaccharides are major components in these macromolecular assemblies, and their interactions with other chemicals are of high relevance for the benefits provided by the biofilm 3D molecular matrix. NMR is a powerful technique for the study and characterization of the interactions between molecules of biological relevance. In this study, we have applied multifrequency saturation transfer difference (STD) NMR and DOSY NMR approaches to elucidate the interactions between the exopolysaccharide produced by Burkholderia multivorans C1576 (EpolC1576) and the antibiotics kanamycin and ceftadizime. The NMR strategies presented here allowed for an extensive characterization at an atomic level of the mechanisms behind the implication of the EpolC1576 in the recalcitrance phenomena, which is the ability of bacteria in biofilms to survive in the presence of antibiotics. Our results suggest an active role for EpolC1576 in the recalcitrance mechanisms toward kanamycin and ceftadizime, though through two different mechanisms.

An improved iCLIP protocol

Crosslinking and Immunoprecipitation (CLIP) is a powerful technique to obtain transcriptome-wide maps of in vivo protein-RNA interactions, which are important to understand the post-transcriptional mechanisms mediated by RNA binding proteins (RBPs). Many variant CLIP protocols have been developed to improve the efficiency and convenience of cDNA library preparation. Here we describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions, and with public eCLIP and iCLIP PTBP1 data. We visualised enriched motifs surrounding the identified crosslink positions and RNA maps of these crosslinks around the alternative exons regulated by PTBP1. Notably, motif enrichment was higher in iiCLIP and iCLIP2 in comparison to public eCLIP and iCLIP, and we show how this impacts the specificity of RNA maps. In conclusion, iiCLIP is technically convenient and efficient, and enables production of highly specific datasets for identifying RBP binding sites.