bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learnings from conducting mental health research during 2004 tsunami in Tamil Nadu, India
Authors: Padmavati R. , Raghavan Vijaya , Rera Heather , Kearns Megan , Rao Kotteeswara , John Sujit , Thara R. 
Published: October 2020

Abstract

Background
The Indian Ocean tsunami experience in 2004 caused a major loss of life and subsequent emotional trauma for survivors. Psychosocial needs in the aftermath of this disaster were extensive, yet the cohesion and effectiveness of response were limited due to lack of preparedness and relevant policy. The Schizophrenia Research Foundation (SCARF) was one of the organizations that quickly responded to provide psychosocial assistance to people in the tsunami affected areas and recognized a need for relevant research on disaster response. Therefore, we undertook research on the challenges, success and limitations of psychosocial interventions in alleviating post-traumatic symptomology.

Discussion
Both community-level workers and researchers were limited in their preparedness to carry out tasks related to response. Language barriers, cultural differences, and a gap in long-term services limited the breadth and scope of research that was able to be completed. Lack of policy, poor co-ordination of services, lack of trained researchers and limited resources were challenges that emerged during this period and various strategies were adopted to meet these challenges.

Conclusions
Continued research and evaluation of data has brought crucial considerations to light, including the variance in symptomology, effective tools of measurement, and the nuanced response of survivors. Future research should take relevant factors into consideration including barriers to care. Understanding of the local language and religious beliefs are significant resources in understanding the nature of survivors’ trauma response and effective means of coping. Lastly, limitations regarding time frame and scope of research should be evaluated to provide more effective, comprehensive methods in future studies.
Evaluation of semi-quantitative compared to quantitative cultures of tracheal aspirates for the yield of culturable respiratory pathogens – a cross-sectional study
Authors: Rattani Salima , Farooqi Joveria , Jabeen Ghazala , Chandio Saeeda , Kash Qaiser , Khan Aijaz , Jabeen Kauser 
Published: October 2020

Abstract

Background
Diagnosis of lower respiratory tract infections (LRTI) depends on the presence of clinical, radiological and microbiological findings. Endotracheal suction aspirate (ETSA) is the commonest respiratory sample sent for culture from intubated patients. Very few studies have compared quantitative and semi-quantitative processing of ETSA cultures for LRTI diagnosis. We determined the diagnostic accuracy of quantitative and semi-quantitative ETSA culture for LRTI diagnosis, agreement between the quantitative and semi quantitative culture techniques and the yield of respiratory pathogens with both methods.

Methods
This was a cross-sectional study conducted at the Aga Khan University clinical laboratory, Karachi, Pakistan. One hundred and seventy-eight ETSA samples sent for routine bacteriological cultures were processed quantitatively as part of regular specimen processing method and semi-quantitatively. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic accuracy was calculated for both methods using clinical diagnosis of pneumonia as reference standard. Agreement between the quantitative and semi quantitative methods was assessed via the kappa statistic test. Pathogen yield between the two methods was compared using Pearson’s chi-square test.

Results
The quantitative and semi-quantitative methods yielded pathogens in 81 (45.5%) and 85 (47.8%) cases respectively. There was complete concordance of both techniques in 155 (87.1%) ETSA samples. No growth was observed in 45 (25.3%) ETSA specimens with quantitative culture and 37 (20.8%) cases by semi-quantitative culture. The diagnostic accuracy of both techniques were comparable; 64.6% for quantitative and 64.0% for semi-quantitative culture. The kappa agreement was found to be 0.84 (95% CI, 0.77–0.91) representing almost perfect agreement between the two methods. Although semi-quantitative cultures yielded more pathogens (47.8%) as compared to quantitative ETSA cultures (45.5%), the difference was only 2.3%. However, this difference achieved statistical (chi-square p-value < 0.001) favoring semi-quantitative culture methods over quantitative culture techniques for processing ETSA.

Conclusion
In conclusion, there is a strong agreement between the performances of both methods of processing ETSA cultures in terms of accuracy of LRTI diagnosis. Semi-quantitative cultures of ETSA yielded more pathogens as compared to quantitative cultures. Although both techniques were comparable, we recommend processing of ETSA using semi-quantitative technique due to its ease and reduced processing time.
8q24 clear cell renal cell carcinoma germline variant is associated with VHL mutation status and clinical aggressiveness
Authors: Eckel-Passow Jeanette E. , Yan Huihuang , Kosel Matthew L. , Serie Daniel , Decker Paul A. , Jenkins Robert B. , Costello Brian , Leibovich Bradley , Ho Thai H. , Parker Alexander 
Published: October 2020

Abstract

Background
The four most commonly-mutated genes in clear cell renal cell carcinoma (ccRCC) tumors are BAP1, PBRM1, SETD2 and VHL. And, there are currently 14 known RCC germline variants that have been reproducibly shown to be associated with RCC risk. However, the association of germline genetics with tumor genetics and clinical aggressiveness are unknown.

Methods
We analyzed 420 ccRCC patients from The Cancer Genome Atlas. Molecular subtype was determined based on acquired mutations in BAP1, PBRM1, SETD2 and VHL. Aggressive subtype was defined clinically using Mayo SSIGN score and molecularly using the ccA/ccB gene expression subtype. Publically-available Hi-C data were used to link germline risk variants with candidate target genes.

Results
The 8q24 variant rs35252396 was significantly associated with VHL mutation status (OR = 1.6, p = 0.0037) and SSIGN score (OR = 1.9, p = 0.00094), after adjusting for multiple comparisons. We observed that, while some germline variants have interactions with nearby genes, some variants demonstrate long-range interactions with target genes.

Conclusions
These data further demonstrate the link between rs35252396, HIF pathway and ccRCC clinical aggressiveness, providing a more comprehensive picture of how germline genetics and tumor genetics interact with respect to tumor development and progression.
Student perspective of classroom and distance learning during COVID-19 pandemic in the undergraduate dental study program Universitas Indonesia
Authors: Amir Lisa R. , Tanti Ira , Maharani Diah Ayu , Wimardhani Yuniardini Septorini , Julia Vera , Sulijaya Benso , Puspitawati Ria 
Published: October 2020

Abstract

Background
The COVID-19 pandemic has become a global health issue and has had a major impact on education. Consequently, half way through the second semester of the academic year 2019/2020, learning methods were delivered through distance learning (DL). We aimed to evaluate the student perspective of DL compared to classroom learning (CL) in the undergraduate dentistry study program at the Faculty of Dentistry Universitas Indonesia.

Methods
An online questionnaire was sent at the end of the semester. A total of 301 students participated in the study.

Results
Duration of study influenced student preference. Higher number of first-year students preferred DL compared to their seniors (p < 0.001). Students preferred CL for group discussion, as DL resulted in more difficult communication and gave less learning satisfaction. Only 44.2% students preferred DL over CL, although they agreed that DL gave a more efficient learning method (52.6%), it provided more time to study (87.9%) and to review study materials (87.3%). Challenges during DL included external factors such as unstable internet connection, extra financial burden for the internet quota and internal factors such as time management and difficulty to focus while learning online for a longer period of time.

Conclusion
Despite some challenges, dental students could adapt to the new learning methods of full DL and the majorities agreed blended learning that combined classroom and distance learning can be implemented henceforth. This current COVID-19 pandemic, changes not only the utilization of technology in education but the pedagogy strategies in the future.
Communication skills teaching and learning in Nepal; what are medical students’ perceptions and experiences? A qualitative study
Authors: Douglas Amanda Helen , Acharya Samita Pant , Allery Lynne A. 
Published: October 2020

Abstract

Background
Communication skills (CS) are vital for doctors. Indeed, as the most important element of consultations, are highly valued by patients. CS are core, teachable skills, however, have not been widely taught in South Asian medical schools, unlike their western counterparts.
Patan Academy of Health Sciences, is one of the first in Nepal to have CS central to its’ aims and curriculum. CS are taught from the first weeks of medical school and re-enforced during preclinical study (first 2 years). Our study seeks to explore students’ perceptions and experiences of CS teaching in this South Asian, Nepal context.

Methods
This study is a qualitative evaluation of a CS course in Nepal, exploring the experiences and perceptions of participants. The study aims to also identify aspects that were helpful or not for student learning and areas for potential development.
A purposive sample of twenty: second, fourth and Intern year students was selected for interview. Data were collected through audio recorded semi-structured interviews following a piloted schedule. Interview transcripts were manually coded and thematically analysed. Codes were arranged into themes and subthemes.

Results
The two main themes:

Positivity

Experiential learning.

Results demonstrate participants’ positive perceptions of CS teaching: believing it is important, effective, relevant and valuable for personal development. Participants identified experiential learning features as valuable for CS acquisition. Intern students recognised CS relevance and requested expanding teaching to clinical years,incorporating challenging communication scenarios.

Discussion
This study shows that PAHS’ CS course is well perceived and valuable to learners. Experiential learning is powerful for CS development. Expansion of formal, structured CS teaching through all years in a spiral curriculum, should be considered. Violence towards doctors in South Asia is increasing. Students recognised CS teaching’s significance in addressing this.

Conclusion
CS teaching,still in its’ infancy in South Asia, is a pressing issue for medical educators here. Our study provides evidence it is well perceived with positive impacts in this context, particularly when employing experiential learning. Medical schools in south Asia should be encouraged to incorporate and strengthen their CS teaching curriculum. .
Combining structured and unstructured data for predictive models: a deep learning approach
Authors: Zhang Dongdong , Yin Changchang , Zeng Jucheng , Yuan Xiaohui , Zhang Ping 
Published: October 2020

Abstract

Background
The broad adoption of electronic health records (EHRs) provides great opportunities to conduct health care research and solve various clinical problems in medicine. With recent advances and success, methods based on machine learning and deep learning have become increasingly popular in medical informatics. However, while many research studies utilize temporal structured data on predictive modeling, they typically neglect potentially valuable information in unstructured clinical notes. Integrating heterogeneous data types across EHRs through deep learning techniques may help improve the performance of prediction models.

Methods
In this research, we proposed 2 general-purpose multi-modal neural network architectures to enhance patient representation learning by combining sequential unstructured notes with structured data. The proposed fusion models leverage document embeddings for the representation of long clinical note documents and either convolutional neural network or long short-term memory networks to model the sequential clinical notes and temporal signals, and one-hot encoding for static information representation. The concatenated representation is the final patient representation which is used to make predictions.

Results
We evaluate the performance of proposed models on 3 risk prediction tasks (i.e. in-hospital mortality, 30-day hospital readmission, and long length of stay prediction) using derived data from the publicly available Medical Information Mart for Intensive Care III dataset. Our results show that by combining unstructured clinical notes with structured data, the proposed models outperform other models that utilize either unstructured notes or structured data only.

Conclusions
The proposed fusion models learn better patient representation by combining structured and unstructured data. Integrating heterogeneous data types across EHRs helps improve the performance of prediction models and reduce errors.
Measuring the quality of nursing clinical placements and the development of the Placement Evaluation Tool (PET) in a mixed methods co-design project
Authors: Cooper Simon , Cant Robyn , Waters Donna , Luders Elise , Henderson Amanda , Willetts Georgina , Tower Marion , Reid-Searl Kerry , Ryan Colleen , Hood Kerry 
Published: October 2020

Abstract

Background
The quality of nursing clinical placements has been found to vary. Placement evaluation tools for nursing students are available but lack contemporary reviews of clinical settings. Therefore, the aim of this study was to develop a feasible, valid and reliable clinical placement evaluation tool applicable to nursing student placements in Australia.

Methods
An exploratory mixed methods co-design project. Phase 1 included a literature review; expert rating of potential question items and Nominal Group Technique meetings with a range of stakeholders for item development. Phase 2 included on-line pilot testing of the Placement Evaluation Tool (PET) with 1263 nursing students, across all year levels at six Australian Universities and one further education college in 2019–20, to confirm validity, reliability and feasibility.

Results
The PET included 19-items (rated on a 5-point agreement scale) and one global satisfaction rating (a 10-point scale). Placements were generally positively rated. The total scale score (19 items) revealed a median student rating of 81 points from a maximum of 95 and a median global satisfaction rating of 9/10. Criterion validity was confirmed by item correlation: Intra-class Correlation Co-efficient ICC = .709; scale total to global score r = .722; and items to total score ranging from .609 to .832. Strong concurrent validity was demonstrated with the Clinical Learning Environment and Supervision Scale (r = .834). Internal reliability was identified and confirmed in two subscale factors: Clinical Environment (Cronbach’s alpha = .94) and Learning Support (alpha = .96). Based on the short time taken to complete the survey (median 3.5 min) and students’ comments, the tool was deemed applicable and feasible.

Conclusions
The PET was found to be valid, reliable and feasible. Use of the tool as a quality assurance measure is likely to improve education and practice in clinical environments. Further international evaluation of the instrument is required to fully determine its psychometric properties.
Perception of the healthcare professionals towards the current trauma and emergency care system in Kabul, Afghanistan: a mixed method study
Authors: Khudadad Umerdad , Aftab Wafa , Ali Asrar , Khan Nadeem Ullah , Razzak Junaid , Siddiqi Sameen 
Published: October 2020

Abstract

Background
Trauma and injury contribute to 11% of the all-cause mortality in Afghanistan. The study aimed to explore the perceptions of the healthcare providers (pre and in-hospital), hospital managers and policy makers of the public and private health sectors to identify the challenges in the provision of an effective trauma care in Kabul, Afghanistan.

Methods
A concurrent mixed method design was used, including key-informant interviews (healthcare providers, hospital managers and policy makers) of the trauma care system (N = 18) and simultaneous structured emergency care system assessment questionnaire (N = 35) from July 15 to September 25, 2019. Interviews were analyzed using content analysis approach and structured questionnaire data were descriptively analyzed.

Results
Four themes were identified that describe the challenges: 1) pre-hospital care, 2) cohesive trauma management system, 3) physical and human resources and 4) stewardship. Some key challenges were found related to scene and transportation care, in-hospital care and emergency preparedness within the wider trauma care system. Less than 25% of the population is covered by the pre-hospital ambulance system (n = 23, 65.7%) and there is no communication process between health care facilities to facilitate transfer (n = 28, 80%). Less than 25% of patients with an injury requiring emergent surgery have access to surgical care in a staffed operating theatre within 2 h of injury (n = 19, 54.2%) and there is no regular assessment of the ability of the emergency care system to mobilize resources (human and physical) to respond to disasters, and other large-scale emergencies (n = 28, 80%).

Conclusion
This study highlighted major challenges in the delivery of trauma care services across Kabul, Afghanistan. Systematic improvement in the workforce training, structural organization of the trauma care system and implementing externally validated clinical guidelines for trauma management could possibly enhance the functions of the existing trauma care services. However, an integrated state-run trauma care system will address the current burden of traumatic injury more effectively within the wider healthcare system of Afghanistan.
Postpartum vertebral artery dissection: case report and review of the literature
Authors: Manasewitsch Nicholas T. , Hanfy Ahmed A. , Beutler Bryce D. , Antwi-Amoabeng Daniel , Taha Moutaz , Elnaggar Mohamed , Chahal Gurpreet S. 
Published: October 2020

AbstractBackgroundHypertensive disorders of pregnancy are associated with vascular complications, including ischemic stroke and cervical artery dissection. Vertebral artery dissection (VAD), however, is rare. We describe a 31-year-old female who presented with vertigo, nausea, and vomiting and was found to have a VAD. In addition, we discuss the presentation, differential diagnosis, and pathogenesis of this uncommon but clinically significant vascular event and summarize other cases of vertebral artery dissection described in the medical literature.Case presentationA 31-year-old Hispanic woman presented 10 days postpartum with a one-day history of vertigo, nausea, vomiting, and frontal headache. The patient’s pregnancy course had been complicated by preeclampsia, chorioamnionitis, and iron-deficiency anemia, and her delivery was complicated by acute hemorrhage. Physical examination was significant for left leg ataxia. Laboratory studies showed marked thrombocytosis. Emergent computed tomography (CT) scan of the head was obtained and revealed a left cerebellar ischemic large vessel stroke. Subsequent CT angiography of the head and neck showed a left VAD. Based on correlation of the clinical history and laboratory and imaging findings, a diagnosis of vertebral artery dissection secondary to reactive (secondary) thrombocytosis from overlapping iron-deficiency anemia and acute hemorrhage was established. The patient was started on a heparin infusion and experienced significant improvement after a four-day hospitalization.ConclusionVAD is a rare but important cause of neurologic symptoms in the postpartum period and should be considered in the differential diagnosis for women who present with headache and/or vertigo. Women aged 30 years or older and those with a history of a hypertensive disorder of pregnancy are at particularly high risk. Prompt diagnosis and management of VAD is essential to ensure favorable outcomes.
Chronic active Epstein–Barr virus infection manifesting as coronary artery aneurysm and uveitis
Authors: Xiao Haijuan , Hu Bing , Luo Rongmu , Hu Huili , Zhang Junmei , Kuang Weiying , Zhang Rui , Li Li , Liu Gang 
Published: October 2020

Abstract

Background
Chronic active Epstein–Barr virus (CAEBV) infection is a type of lymphoproliferative disorder characterized by chronic or recurrent infectious mononucleosis (IM)-like symptoms, which can have less-frequent clinical presentations. The prognosis of CAEBV is poor, and hematopoietic stem cell transplantation (HSCT) has been shown to be the only potentially effective treatment. In this article, we present a special CAEBV case of a patient who had no typical IM-like symptoms at the early stage, but manifested with severe and progressive coronary artery aneurysm (CAA), abdominal aortic lesions, and severe uveitis. These manifestations were uncommon features and could only be blocked by HSCT.

Case presentation
A 4-year-old girl with no special medical history complained of decreased vision for 10 months and cough after physical activities for three months. The blurred vision grew rapidly worse within one month, until only light perception remained. She was diagnosed with uveitis and cataract, and received prednisone and ciclosporin A treatment. However, her vision did not improve. Physical examination showed slight hepatosplenomegaly. Ultrasonic cardiogram showed bilateral CAA (5.0 mm and 5.7 mm for inner diameters), and abdominal CT scan revealed a thickened aortic wall, as well as stenosis and dilation of the segmental abdominal aorta. Other significant findings were increased EBV-DNA (3.29 × 104 copies/mL) from peripheral blood, positive EBV antibodies (EBV-CA-IgG, EBV-EA-IgA, and EBV-NA-IgG), and positive EBV-encoded small RNAs found by bone marrow biopsy. Based on her clinical manifestations and evidence for EBV infection, we diagnosed CAEBV. She received allogeneic HSCT, and the cataract operation was performed after HSCT. EBV-DNA could not be detected in peripheral blood after HSCT. Her CAAs did not progress, and uveitis was well controlled. Her vision recovered gradually over the 3 years after HSCT.

Conclusions
We present a rare CAEBV case of a patient who suffered from uncommon and severe cardiovascular and ocular involvement that was relieved by HSCT. Therefore, early recognition and diagnosis of CAEBV are of vital importance to improve its prognosis. In summary, this atypical CAEBV case could help us recognize similar cases more easily, make the right diagnosis as early as possible, and deliver proper and timely treatment.