Ultrafast RNA extraction-free SARS-CoV-2 detection by direct RT-PCR using a rapid thermal cycling approach

The surging COVID19 pandemic has underlined the need for quick, sensitive, and high-throughput SARS-CoV-2 detection assays. Although many different methods to detect SARS-CoV-2 particles in clinical material have been developed, none of these assays are successful in combining all three of the above characteristics into a single, easy-to-use method that is suitable for large-scale use. Here we report the development of a direct RT-PCR SARS-CoV-2 detection method that can reliably detect minute quantities of SARS-CoV-2 gRNA in nasopharyngeal swab samples as well as the presence of human genomic DNA. An extraction-less validation protocol was carried out to determine performance characteristics of the assay in both synthetic SARS-CoV-2 RNA as well as clinical specimens. Feasibility of the assay and analytical sensitivity was first determined by testing a dilution series of synthetic SARS-CoV-2 RNA in two different solvents (water and AMIES VTM), revealing a high degree of linearity and robustness in fluorescence readouts. Following analytical performance using synthetic RNA, the limit of detection was determined at equal to or less than 1 SARS-CoV-2 copy/ul of sample in a commercially available sample panel that contains surrogate clinical samples with varying SARS-CoV-2 viral load. Lastly, we benchmarked our method against a reference qPCR method by testing 87 nasopharyngeal swab samples. The direct endpoint ultra-fast RT-PCR method exhibited a positive percent agreement score of 98.5% and a negative percent agreement score of 100% as compared to the reference method, while RT-PCR cycling was completed in 27 minutes/sample as opposed to 60 minutes/sample in the reference qPCR method. In summary, we describe a rapid direct RT-PCR method to detect SARS-CoV-2 material in clinical specimens which can be completed in significantly less time as compared to conventional RT-PCR methods, making it an attractive option for large-scale SARS-CoV-2 screening applications.

User-Defined Gestures with Physical Props in Virtual Reality

When interacting with virtual reality (VR) applications like CAD and open-world games, people may want to use gestures as a means of leveraging their knowledge from the physical world. However, people may prefer physical props over handheld controllers to input gestures in VR. We present an elicitation study where 21 participants chose from 95 props to perform manipulative gestures for 20 CAD-like and open-world game-like referents. When analyzing this data, we found existing methods for elicitation studies were insufficient to describe gestures with props, or to measure agreement with prop selection (i.e., agreement between sets of items). We proceeded by describing gestures as context-free grammars, capturing how different props were used in similar roles in a given gesture. We present gesture and prop agreement scores using a generalized agreement score that we developed to compare multiple selections rather than a single selection. We found that props were selected based on their resemblance to virtual objects and the actions they afforded; that gesture and prop agreement depended on the referent, with some referents leading to similar gesture choices, while others led to similar prop choices; and that a small set of carefully chosen props can support multiple gestures.

P020 ESTABLISHING PEER-CONSENSUS ABOUT THE USE OF LONG-TERM BIOSYNTHETIC ABSORBABLE MESH FOR VENTRAL HERNIA (GRADE 2-3) AS THE STANDARD OF CARE

Aim “This consensus project was initiated to provide insight into those situations where a long-term biosynthetic absorbable mesh (LTBA) might be considered the standard of care in repair of ventral hernia grades 2 and 3 (original Ventral Hernia Working Group Classification, 2010).” Material and Methods “A steering group of surgical experts developed 35 initial statements formed from six domains. These statements were used to develop an online survey which was sent to surgeons involved in hernia repair surgery within Europe. Agreement (consensus) with the statements was defined as high if ≥ 70% and very high if ≥ 90% of respondents agreed with a statement. After the initial survey round, some statements were revised and these were then reissued, 34 statements were included in the final analysis” Results “A total of 255 responses were received over the two rounds of survey. Respondents (n = 255) were all surgeons involved in hernia repair in Europe. Fourteen statements (41%) achieved very high consensus (≥ 90%), 24 statements achieved consensus (≥70% to < 90%) while one statement (3%) fell short of consensus with an agreement score of 69%.” Conclusions “Expert consensus opinion about the use of LTBA for hernia (Grades 2-3) as the standard of care was achieved. Based on the consensus scores, the steering group derived eleven key recommendations which, if implemented, should result in a clearer understanding of how and when a LTBA might be used in hernia repair, aiming for improvement in surgical and patient related outcomes”

Listen, look, link and learn: a stepwise approach to use narrative quality data within resident-family-nursing staff triads in nursing homes for quality improvements

PurposeThe use of qualitative data to assess quality of care in nursing homes from the resident’s perspective has shown to be valuable, yet more research is needed to determine how this data can be used to gain insight into the quality of care within nursing homes. Whereas it is crucial to stay close to the stories that are the strength of qualitative data, an intermittent step to classify this data can support the interpretation and use. Therefore, this study introduces an approach that enables the use of narrative quality of care data to learn from and improve with.DesignA cross-sectional mixed-methods study in which qualitative data were collected with the narrative quality assessment method Connecting Conversations and interpreted for analysis.MethodsConnecting Conversations was used to collect narrative data about experienced quality of care in nursing homes according to residents, their families and nursing staff (triads). Data analysis consisted of coding positive/negative valences in each transcript.FindingsA stepwise approach can support the use of narrative quality data consisting of four steps: (1) perform and transcribe the conversations (listen); (2) calculate a valence sore, defined as the mean %-positive within a triad (look); (3) calculate an agreement score, defined as the level of agreement between resident-family-nursing staff (link); and (4) plot scores into a graph for interpretation and learning purposes with agreement score (x-axis) and valence score (y-axis) (learn).ConclusionsNarrative quality data can be interpreted as a valence and agreement score. These scores need to be related to the raw qualitative data to gain a rich understanding of what is going well and what needs to be improved.

Creation of annotated country-level dialectal Arabic resources: An unsupervised approach

The wide usage of multiple spoken Arabic dialects on social networking sites stimulates increasing interest in Natural Language Processing (NLP) for dialectal Arabic (DA). Arabic dialects represent true linguistic diversity and differ from modern standard Arabic (MSA). In fact, the complexity and variety of these dialects make it insufficient to build one NLP system that is suitable for all of them. In comparison with MSA, the available datasets for various dialects are generally limited in terms of size, genre and scope. In this article, we present a novel approach that automatically develops an annotated country-level dialectal Arabic corpus and builds lists of words that encompass 15 Arabic dialects. The algorithm uses an iterative procedure consisting of two main components: automatic creation of lists for dialectal words and automatic creation of annotated Arabic dialect identification corpus. To our knowledge, our study is the first of its kind to examine and analyse the poor performance of the MSA part-of-speech tagger on dialectal Arabic contents and to exploit that in order to extract the dialectal words. The pointwise mutual information association measure and the geographical frequency of word occurrence online are used to classify dialectal words. The annotated dialectal Arabic corpus (Twt15DA), built using our algorithm, is collected from Twitter and consists of 311,785 tweets containing 3,858,459 words in total. We randomly selected a sample of 75 tweets per country, 1125 tweets in total, and conducted a manual dialect identification task by native speakers. The results show an average inter-annotator agreement score equal to 64%, which reflects satisfactory agreement considering the overlapping features of the 15 Arabic dialects.

Expert Opinion on COVID-19 Vaccination and the Use of Cladribine Tablets in Clinical Practice

Background: Gaps in current evidence and guidance leave clinicians with unanswered questions on the use of cladribine tablets for the treatment of multiple sclerosis (MS) in the era of the COVID 19 pandemic, in particular relating to COVID 19 vaccination. Objective: We describe a consensus-based programme led by international MS experts with the aim of supplementing current guidelines and treatment labels by providing timely recommendations relating to COVID 19 vaccination and the use of cladribine tablets in clinical practice. Methods: A steering committee (SC) of 10 international MS experts identified 7 clinical questions to answer concerning the use of cladribine tablets and COVID 19 vaccination, which addressed issues relating to patient selection, timing and efficacy, and safety. Clinical recommendations to address each question were drafted using available evidence combined with expert opinion from the SC. An extended faculty of 28 MS experts, representing 19 countries, in addition to the SC members, voted on the recommendations. Consensus on recommendations was achieved when more than or equal to 75% of respondents expressed an agreement score of 7 to 9, on a 9 point scale. Results: Consensus was achieved on all 13 recommendations. Clinical recommendations are provided on whether all patients with MS receiving cladribine tablets should be vaccinated against COVID 19, and whether they should be prioritized; the timing of vaccination around dosing of cladribine tablets (i.e., before and after a treatment course); and the safety of COVID 19 vaccination for these patients. Conclusions: These expert recommendations provide timely guidance on COVID 19 vaccination in patients receiving cladribine tablets, which is relevant to everyday clinical practice.

The Extent of Awareness of Intermediate Stage Mathematics Teachers about Digital Educational Technologies in Jeddah, Saudi Arabia: مدى وعي معلمات الرياضيات بالمرحلة المتوسطة في محافظة جدة بالتقنيات التعليمية الرقمية

The research aimed to examine the extent to which Teachers of Mathematics at the intermediate stage in Jeddah, Saudi Arabia, were aware of digital educational technologies. It used the descriptive method, and a questionnaire of (25) items divided into three areas and the research sample consisted of (230) Intermediate School Mathematics teachers in Jeddah. The results indicated that the mathematics teachers ’awareness of digital educational technologies was of a medium agreement score, with an arithmetic mean of (3.08) and a percentage of (61.6%). The awareness of the cognitive dimension of technologies obtained a medium agreement score, with an arithmetic mean of (3.36), and a percentage of (67.2%). Also, the awareness of the skill dimension of technologies obtained a medium agreement score, with an arithmetic mean of (2.80), and a percentage of (55.9%). The results also showed that the teachers face obstacles in using digital educational technologies to a very large extent, with an arithmetic mean of (4.23), and a percentage of (84.5%). The results did not reveal any statistically significant differences in the degree of awareness of mathematics teachers to digital educational technologies and the obstacles to their use due to years of experience. The research recommended the necessity of enhancing the knowledge and skill aspects of modern educational technologies among intermediate school teachers in Jeddah, as well as overcome obstacles to their use of these technologies.

Standardization of Evaluation Method and Prognostic Significance of Histological Response to Preoperative Chemotherapy in High-grade Non-round Cell Soft Tissue Sarcomas: a Report From the Central Pathology Review for the Japan Clinical Oncology Group Study JCOG0304

PurposePreoperative chemotherapy is widely applied to high-grade localized soft tissue sarcomas (STSs); however, the prognostic significance of histological response to chemotherapy remains controversial. This study aimed to standardize evaluation method of histological response to chemotherapy with high agreement score among pathologists, and to establish a cut-off value closely related to prognosis. MethodsUsing data and specimens from the patients who had registered in the Japan Clinical Oncology Group study, JCOG0304, a phase II trial evaluating the efficacy of perioperative chemotherapy with doxorubicin (DOX) and ifosfamide (IFO), we evaluated histological response to preoperative chemotherapy at the central review board.ResultsA total of 64 patients were eligible for this study. The percentage of viable tumor area ranged from 0.1% to 97.0%, with median value of 35.7%. Regarding concordance proportion between pathologists, the weighted kappa coefficient (κ) score in all patients was 0.71, indicating that the established evaluation method achieved substantial agreement score. When the cut-off value of the percentage of the residual tumor area was set as 25%, the p-value for the difference in overall survival showed the minimum value. Hazard ratio of the non-responder with percentage of the residual tumor < 25%, to the responder was 4.029 (95% confidence interval 0.893–18.188, p = 0.070). ConclusionThe standardized evaluation method of pathological response to preoperative chemotherapy showed a substantial agreement in the weighted κ score. The evaluation method established here was useful for estimating of the prognosis in STS patients who were administered perioperative chemotherapy with DOX and IFO.Trial registrationUMIN Clinical Trials Registry C000000096. Registered 30 August, 2005 (retrospectively registered).

Level of Effectiveness for ERP System in Improving the Educational Process in Higher Education Institutions in Yemen: A Case Study of the University of Science and Technology

This study aimed to identify the level of effectiveness of the Enterprises Resource Planning (ERP) in improving the educational process in higher education institutions in Yemen. The case study was carried out in the University of Science and Technology (UST). The study adopted the analytical descriptive method, using a questionnaire, which was distributed to the whole population (90 employees), who deal with the ERP system at the university, and who were selected by the complete census method. Only 74 questionnaires were returned and were subject to statistical analysis. Major findings revealed that there was a statistically significant correlation between the dimensions of the questionnaire and the overall effectiveness of the ERP system at the university. Therefore, this result indicates that there is a high degree of effectiveness of the ERP system in improving the educational process with a high agreement score on the dimensions of the questionnaire. It was found that the highest effectiveness degree was in the dimension of admission and registration support, followed by academic support and student affairs, and the lowest degree was in the dimension of technical support. Overall, the level of application of the ERP system at the university was high. Based on these findings, it was recommended that this system should be applied so as to cover all departments that do not use the ERP system, which would lead to effective and efficient performance of such departments. Keywords: ERP system effectiveness, educational process, higher education institutions

Expert opinion on COVID-19 vaccination and the use of cladribine tablets in clinical practice

Background: Gaps in current evidence and guidance leave clinicians with unanswered questions on the use of cladribine tablets for the treatment of multiple sclerosis (MS) in the era of the COVID-19 pandemic, in particular relating to COVID-19 vaccination. Objective: We describe a consensus-based program led by international MS experts with the aim of supplementing current guidelines and treatment labels by providing timely recommendations relating to COVID-19 vaccination and the use of cladribine tablets in clinical practice. Methods: A steering committee (SC) of 10 international MS experts identified 7 clinical questions to answer concerning the use of cladribine tablets and COVID-19 vaccination, which addressed issues relating to patient selection, timing and efficacy, and safety. Clinical recommendations to address each question were drafted using available evidence combined with expert opinion from the SC. An extended faculty of 28 MS experts, representing 19 countries, in addition to the 10 SC members, voted on the recommendations. Consensus on recommendations was achieved when ⩾75% of respondents expressed an agreement score of 7–9, on a 9-point scale. Results: Consensus was achieved on all 13 recommendations. Clinical recommendations are provided on whether all patients with MS receiving cladribine tablets should be vaccinated against COVID-19, and whether they should be prioritized; the timing of vaccination around dosing of cladribine tablets (i.e. before and after a treatment course); and the safety of COVID-19 vaccination for these patients. Conclusion: These expert recommendations provide timely guidance on COVID-19 vaccination in patients receiving cladribine tablets, which is relevant to everyday clinical practice.