ARABIC QUESTION ANSWERING ON THE HOLY QUR'AN

In this dissertation,we address the need for an intelligent machine reading at scale (MRS) Question Answering (QA) system on the Holy Qur'an, given the permanent interest of inquisitors and knowledge seekers in this sacred and fertile knowledge resource. We adopt a pipelined Retriever-Reader architecture for our system to constitute (to the best of our knowledge) the first extractive MRS QA system on the Holy Qur'an. We also construct QRCD as the first extractive Qur'anic Reading Comprehension Dataset, composed of 1,337 question-passage-answer triplets for 1,093 question-passage pairs that comprise single-answer and multi-answer questions in modern standard Arabic (MSA). We then develop a sparse bag-of-words passage retriever over an index of Qur'anic passages expanded with Qur'an-related MSA resources to help in bridging the gap between questions posed in MSA and their answers in Qur'anic Classical Arabic (CA). Next, we introduce CLassical AraBERT (CL-AraBERT for short), a new AraBERT-based pre-trained model that is further pre-trained on about 1.05B-word Classical Arabic dataset (after being initially pre-trained on MSA datasets), to make it a better fit for NLP tasks on CA text such as the Holy Qur'an. We leverage cross-lingual transfer learning from MSA to CA, and fine-tune CL-AraBERT as a reader using a couple of MSA-based MRC datasets followed by fine-tuning it on our QRCD dataset, to bridge the above MSA-to-CA gap, and circumvent the lack of MRC datasets in CA. Finally, we integrate the retriever and reader components of the end-to-end QA system such that the top k retrieved answer-bearing passages to a given question are fed to the fine-tuned CL-AraBERT reader for answer extraction. We first evaluate the retriever and the reader components independently, before evaluating the end-to-end QA system using Partial Average Precision (pAP). We introduce pAP as an adapted version of the traditional rank-based Average Precision measure, which integrates partial matching in the evaluation over multi-answer and single-answer questions. Our experiments show that a passage retriever over a BM25 index of Qur'anic passages expanded with two MSA resources significantly outperformed a baseline retriever over an index of Qur'anic passages only. Moreover, we empirically show that the fine-tuned CL-AraBERT reader model significantly outperformed the similarly finetuned AraBERT model, which is the baseline. In general, the CL-AraBERT reader performed better on single-answer questions in comparison to multi-answer questions. Moreover, it has also outperformed the baseline over both types of questions. Furthermore, despite the integral contribution of fine-tuning with the MSA datasets in enhancing the performance of the readers, relying exclusively on those datasets (without MRC datasets in CA, e.g., QRCD) may not be sufficient for our reader models. This finding demonstrates the relatively high impact of the QRCD dataset (despite its modest size). As for the QA system, it consistently performed better on single-answer questions in comparison to multi-answer questions. However, our experiments provide enough evidence to suggest that a native BERT-based model architecture fine-tuned on the MRC task may not be intrinsically optimal for multi-answer questions

Evidence-Based Guideline on Laparoscopy in Pregnancy: Commissioned by the British Society for Gynaecological Endoscopy (BSGE) Endorsed by the Royal College of Obstetricians & Gynaecologists (RCOG).

Laparoscopy is widely utilised to diagnose and treat acute and chronic, gynaecological and general surgical conditions. It has only been in recent years that laparoscopy has become an acceptable surgical alternative to open surgery in pregnancy. To date there is little clinical guidance pertaining to laparoscopic surgery in pregnancy. This is why the BSGE commissioned this guideline. MEDLINE, EMBASE, CINAHL and the Cochrane library were searched up to February 2017 and evidence was collated and graded following the NICE-approved process. The conditions included in this guideline are laparoscopic management of acute appendicitis, acute gall bladder disease and symptomatic benign adnexal tumours in pregnancy. The intended audience for this guideline is obstetricians and gynaecologists in secondary and tertiary care, general surgeons and anaesthetists. However, only laparoscopists who have adequate laparoscopic skills and who perform complex laparoscopic surgery regularly should undertake laparoscopy in pregnant women, since much of the evidence stems from specialised centres

The E1A-Associated p400 Protein Modulates Cell Fate Decisions by the Regulation of ROS Homeostasis

The p400 E1A-associated protein, which mediates H2A.Z incorporation at specific promoters, plays a major role in cell fate decisions: it promotes cell cycle progression and inhibits induction of apoptosis or senescence. Here, we show that p400 expression is required for the correct control of ROS metabolism. Depletion of p400 indeed increases intracellular ROS levels and causes the appearance of DNA damage, indicating that p400 maintains oxidative stress below a threshold at which DNA damages occur. Suppression of the DNA damage response using a siRNA against ATM inhibits the effects of p400 on cell cycle progression, apoptosis, or senescence, demonstrating the importance of ATM–dependent DDR pathways in cell fates control by p400. Finally, we show that these effects of p400 are dependent on direct transcriptional regulation of specific promoters and may also involve a positive feedback loop between oxidative stress and DNA breaks since we found that persistent DNA breaks are sufficient to increase ROS levels. Altogether, our results uncover an unexpected link between p400 and ROS metabolism and allow deciphering the molecular mechanisms largely responsible for cell proliferation control by p400

The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome – NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome – NL interactions

Surgical simulation flexor tendon repair using Thiel cadavers:a comparison with formalin embalmed cadavers and porcine models

The aim of this study was to compare Thiel-embalmed cadavers with formalin-embalmed cadavers and porcine models in the surgical simulation repair of a Zone II flexor tendon division. Nine participants were recruited to the study. The models were assessed using a five-point scale. Assessment was divided into tissue quality, surgical approach and identification of structures. Thiel cadavers rated consistently higher compared with the formalin and porcine models (mean 37 SD 2, 22 SD 6 and 23 SD 5, respectively). Thiel cadavers recorded an average tendon glide of 21 mm SD 5, formalin cadavers 2 mm SD 2 and the porcine model 6 mm SD 2. We have demonstrated the benefit of Thiel embalming, with flexibility of tissues allowing testing of the repair of a flexor tendon in a realistic anatomical model. Level of evidence: Level V. </jats:p

Low-Grade Central Osteosarcoma: A Difficult Condition to Diagnose

Low-grade central osteosarcoma (LGCO) is a rare variant of osteosarcoma which is difficult to diagnose. If not treated appropriately, the tumour can recur with higher-grade disease. We reviewed our experience of this condition to try and identify factors that could improve both diagnosis and outcome. 18 patients out of 1540 osteosarcoma cases (over 25 years) had LGCO (1.2%). Only 11 patients (61%) were direct primary referrals. Almost 40% (7 of 18) cases were referred after treatment elsewhere when the diagnosis had not been made initially and all presented with local recurrence. Of the 11 who presented primarily, the first biopsy was diagnostic in only 6 (55%) cases. Of the remaining cases, up to three separate biopsies were required before a definitive diagnosis was made. Overall survivorship at 5 years was 90%. 17 patients were treated with limb salvage procedures, and one patient had an amputation. The diagnosis of LGCO remains challenging due to the relatively nonspecific radiological and histological findings. Since treatment of LGCO is so different to a benign lesion, accurate diagnosis is essential. Any difficult or nondiagnostic biopsies of solitary bone lesions should be referred to specialist tumour units for a second opinion