Binding Sites Analyser (BiSA): Software for genomic binding sites archiving and overlap analysis

Genome-wide mapping of transcription factor binding and histone modification reveals complex patterns of interactions. Identifying overlaps in binding patterns by different factors is a major objective of genomic studies, but existing methods to archive large numbers of datasets in a personalised database lack sophistication and utility. Therefore we have developed transcription factor DNA binding site analyser software (BiSA), for archiving of binding regions and easy identification of overlap with or proximity to other regions of interest. Analysis results can be restricted by chromosome or base pair overlap between regions or maximum distance between binding peaks. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; and average region sizes. BiSA can identify genes located near binding regions of interest, genomic features near a gene or locus of interest and statistical significance of overlapping regions can also be reported. Overlapping results can be visualized as Venn diagrams. A major strength of BiSA is that it is supported by a comprehensive database of publicly available transcription factor binding sites and histone modifications, which can be directly compared to user data. The documentation and source code are available on http://bisa.sourceforge.net © 2014 Khushi et al

4-(4-Propoxybenzo­yloxy)benzoic acid

The title compound, C17H16O5, is an important inter­mediate for the synthesis of side-chain ligands for polymeric liquid crystals. The prop­oxy and benzoic acid groups subtend dihedral angles of 4.36 (6) and 55.35 (6)°, respectively, with the central benzo­yloxy unit. The crystal structure is stabilized by an inter­molecular O—H⋯O hydrogen bond

Feature learning for stock price prediction shows a significant role of analyst rating

Data Availability Statement: The code is available from https://mkhushi.github.io/ (accessed on 1 February 2021). Dataset License: License under which the dataset is made available (CC0).Efficient Market Hypothesis states that stock prices are a reflection of all the information present in the world and generating excess returns is not possible by merely analysing trade data which is already available to all public. Yet to further the research rejecting this idea, a rigorous literature review was conducted and a set of five technical indicators and 23 fundamental indicators was identified to establish the possibility of generating excess returns on the stock market. Leveraging these data points and various classification machine learning models, trading data of the 505 equities on the US S&P500 over the past 20 years was analysed to develop a classifier effective for our cause. From any given day, we were able to predict the direction of change in price by 1% up to 10 days in the future. The predictions had an overall accuracy of 83.62% with a precision of 85% for buy signals and a recall of 100% for sell signals. Moreover, we grouped equities by their sector and repeated the experiment to see if grouping similar assets together positively effected the results but concluded that it showed no significant improvements in the performance—rejecting the idea of sector-based analysis. Also, using feature ranking we could identify an even smaller set of 6 indicators while maintaining similar accuracies as that from the original 28 features and also uncovered the importance of buy, hold and sell analyst ratings as they came out to be the top contributors in the model. Finally, to evaluate the effectiveness of the classifier in real-life situations, it was backtested on FAANG (Facebook, Amazon, Apple, Netflix & Google) equities using a modest trading strategy where it generated high returns of above 60% over the term of the testing dataset. In conclusion, our proposed methodology with the combination of purposefully picked features shows an improvement over the previous studies, and our model predicts the direction of 1% price changes on the 10th day with high confidence and with enough buffer to even build a robotic trading system.This research received no external funding

Bioinformatic analysis of cis-regulatory interactions between progesterone and estrogen receptors in breast cancer

Supplemental Information: Enrichment analysis of ERα-PR common regions using GREAT, doi: 10.7717/peerj.654/supp-1.Copyright © 2014 Khushi et al. Chromatin factors interact with each other in a cell and sequence-specific manner in order to regulate transcription and a wealth of publically available datasets exists describing the genomic locations of these interactions. Our recently published BiSA (Binding Sites Analyser) database contains transcription factor binding locations and epigenetic modifications collected from published studies and provides tools to analyse stored and imported data. Using BiSA we investigated the overlapping cis-regulatory role of estrogen receptor alpha (ERα) and progesterone receptor (PR) in the T-47D breast cancer cell line. We found that ERα binding sites overlap with a subset of PR binding sites. To investigate further, we re-analysed raw data to remove any biases introduced by the use of distinct tools in the original publications. We identified 22,152 PR and 18,560 ERα binding sites (<5% false discovery rate) with 4,358 overlapping regions among the two datasets. BiSA statistical analysis revealed a non-significant overall overlap correlation between the two factors, suggesting that ERα and PR are not partner factors and do not require each other for binding to occur. However, Monte Carlo simulation by Binary Interval Search (BITS), Relevant Distance, Absolute Distance, Jaccard and Projection tests by Genometricorr revealed a statistically significant spatial correlation of binding regions on chromosome between the two factors. Motif analysis revealed that the shared binding regions were enriched with binding motifs for ERα, PR and a number of other transcription and pioneer factors. Some of these factors are known to co-locate with ERα and PR binding. Therefore spatially close proximity of ERα binding sites with PR binding sites suggests that ERα and PR, in general function independently at the molecular level, but that their activities converge on a specific subset of transcriptional targets.Australian Postgraduate Award (APA); Westmead Medical Research Foundation (WMRF) Top-Up scholarship

Vision-Language Transformer for Interpretable Pathology Visual Question Answering

Pathology visual question answering (PathVQA) attempts to answer a medical question posed by pathology images. Despite its great potential in healthcare, it is not widely adopted because it requires interactions on both the image (vision) and question (language) to generate an answer. Existing methods focused on treating vision and language features independently, which were unable to capture the high and low-level interactions that are required for VQA. Further, these methods failed to offer capabilities to interpret the retrieved answers, which are obscure to humans where the models’ interpretability to justify the retrieved answers has remained largely unexplored. Motivated by these limitations, we introduce a vision-language transformer that embeds vision (images) and language (questions) features for an interpretable PathVQA. We present an interpretable tra nsformer-based P ath- VQA (TraP-VQA), where we embed transformers’ encoder layers with vision and language features extracted using pre-trained CNN and domain-specific language model (LM), respectively. A decoder layer is then embedded to upsample the encoded features for the final prediction for PathVQA. Our experiments showed that our TraP-VQA outperformed the state-of-the-art comparative methods with public PathVQA dataset. Our experiments validated the robustness of our model on another medical VQA dataset, and the ablation study demonstrated the capability of our integrated transformer-based vision-language model for PathVQA. Finally, we present the visualization results of both text and images, which explain the reason for a retrieved answer in PathVQA.ARC (Grant Number: DP200103748)

Regime-Specific Quant Generative Adversarial Network: A Conditional Generative Adversarial Network for Regime-Specific Deepfakes of Financial Time Series

Data Availability Statement: The data that support the findings of this study are available from Bloomberg LLP but restrictions apply to the availability of this data, which were used under license for the current study, and so are not publicly available. Data are however available from the authors upon reasonable request and with permission of Bloomberg LLP.Simulating financial time series (FTS) data consistent with non-stationary, empirical market behaviour is difficult, but it has valuable applications for financial risk management. A better risk estimation can improve returns on capital and capital efficiency in investment decision making. Challenges to modelling financial risk in market crisis environments are anomalous asset price behaviour and a lack of historical data to learn from. This paper proposes a novel semi-supervised approach for generating regime-specific ‘deep fakes’ of FTS data using generative adversarial networks (GANs). The proposed architecture, a regime-specific Quant GAN (RSQGAN), is a conditional GAN (cGAN) that generates class-conditional synthetic asset return data. Conditional class labels correspond to distinct market regimes that have been detected using a structural breakpoint algorithm to segment FTS into regime classes for simulation. Our RSQGAN approach accurately simulated univariate time series behaviour consistent with specific empirical regimes, outperforming equivalently configured unconditional GANs trained only on crisis regime data. To evaluate the RSQGAN performance for simulating asset return behaviour during crisis environments, we also propose four test metrics that are sensitive to path-dependent behaviour and are also actionable during a crisis environment. Our RSQGAN model design borrows from innovation in the image GAN domain by enabling a user-controlled hyperparameter for adjusting the fit of synthetic data fidelity to real-world data; however, this is at the cost of synthetic data variety. These model features suggest that RSQGAN could be a useful new tool for understanding risk and making investment decisions during a time of market crisis.This research received no external funding

Effect of early maternal newborn skin to skin contact in labour room on third stage of labour and success at breastfeeding

Background: Immediate postpartum period and birth pose many challenges for the mother and the new-born. Initiation of early skin to skin contact in the labour room can be beneficial to both of them.Methods: Randomized control trial conducted over a period of 7 months in a tertiary care centre enrolling 400 laboring women.200 in the control group were given routine care. In the 200women in the study group, the newborn was given immediate skin to skin contact by placing him/her on the mother’s chest.Results: Duration of third stage of labour was less than 10 minutes in 95%women of study group compared to 56% women in the control group(p<0.01). Placenta was expulsed as a whole in 98% cases in the study group compared to 81% in the control group. Successful breastfeeding was observed in 88% women in study group compared to 54%in the control group(p<0.01). Breastfeeding was initiated within 30 minutes of birth in 96%women in the study group compared to 41% in the control group.Conclusions: Uterus could contract faster with the complete expulsion of placenta and shortening of the third stage of labour with early skin to skin contact. The newborn showed early initiation, success at breastfeeding and longer first breastfeeding with early skin to skin contact

K-PathVQA: Knowledge-Aware Multimodal Representation for Pathology Visual Question Answering

ARC (Grant Number: DP200103748