bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ada-WHIPS: Explaining AdaBoost Classification with Applications in the Health Sciences
Authors: Hatwell Julian , Gaber Mohamed Medhat , Azad R.M. Atif 
Published: September 2020

Abstract
Background Computer Aided Diagnostics (CAD) can support medical practitioners to make critical decisions about their patients' disease conditions. Practitioners require access to the chain of reasoning behind CAD to build trust in the CAD advice and to supplement their own expertise. Yet, CAD systems might be based on black box machine learning (ML) models and high dimensional data sources (electronic health records, MRI scans, cardiotocograms, etc). These foundations make interpretation and explanation of the CAD advice very challenging. This challenge is recognised throughout the machine learning research community. eXplainable Artificial Intelligence (XAI) is emerging as one of the most important research areas of recent years because it addresses the interpretability and trust concerns of critical decision makers, including those in clinical and medical practice. Methods In this work, we focus on AdaBoost, a black box ML model that has been widely adopted in the CAD literature. We address the challenge -- to explain AdaBoost classification -- with a novel algorithm that extracts simple, logical rules from AdaBoost models. Our algorithm, Adaptive-Weighted High Importance Path Snippets (Ada-WHIPS), makes use of AdaBoost's adaptive classifier weights. Using a novel formulation, Ada-WHIPS uniquely redistributes the weights among individual decision nodes of the internal decision trees (DT) of the AdaBoost model. Then, a simple heuristic search of the weighted nodes finds a single rule that dominated the model's decision. We compare the explanations generated by our novel approach with the state of the art in an experimental study. We evaluate the derived explanations with simple statistical tests of well-known quality measures, precision and coverage, and a novel measure stability that is better suited to the XAI setting.Results Experiments on 9 CAD-related data sets showed that Ada-WHIPS explanations consistently generalise better (mean coverage 15%-68%) than the state of the art while remaining competitive for speciﬁcity (mean precision 80%-99%). A very small trade-oﬀ in speciﬁcity is shown to guard againstover-ﬁtting which is a known problem in the state of the art methods.Conclusions The experimental results demonstrate the beneﬁts of using our novel algorithm for explaining CAD AdaBoost classiﬁers widely found in the literature. Our tightly coupled, AdaBoost-speciﬁc approach outperforms model-agnostic explanation methods and should be considered by practitioners looking for an XAI solution for this class of models.
Can virtual reality improve traditional anatomy educational programmes?A mixed-methods study on the use of a 3D skull model
Authors: Chen Shi , Zhu Jiawei , Cheng Cheng , Pan Zhouxian , Liu Lingshan , Du Jianhua , Shen Xinhua , Shen Zhen , Zhu Huijuan , Liu Jihai , Yang Hua , Ma Chao , Pan Hui 
Published: September 2020

Abstract
Background: Realistic, portable, and scalable lectures, cadaveric models, 2D atlases and computer simulations are being combined more frequently for teaching anatomy, which result in major increases in user satisfaction. However, although digital simulations may be more portable, interesting, or motivating than traditional teaching tools, whether they are superior in terms of student learning remain unclear. This paper presents a study in which the educational effectiveness of a virtual reality (VR) skull model is compared with that of cadaveric skulls and atlases. The aim of this study was to compare the results of teaching with VR to results of teaching with traditional teaching methods by administering objective questionnaires and perception surveys. Methods: A mixed-methods study with 73 medical students was conducted with three different groups, namely, the VR group (N=25), cadaver group (N=25) and atlas group (N=23). Anatomical structures were taught through an introductory lecture and model-based learning. All students completed the pre- and post-intervention tests, which comprised a theory test and an identification test. The theory test consisted of 18 multiple-choice questions, and the identification test consisted of 25 fill-in-the-blank questions.Results: The participants in all three groups had significantly higher total scores on the post-intervention test than on the pre-intervention test; the post-intervention test score in the VR group was not statistically significantly higher than the post-intervention test score of the other groups (VR: 30 [IQR: 22-33.5], cadaver: 26 [IQR: 20-31.5], atlas: 28[IQR: 20-33]; p>0.05). The participants in the VR and cadaver groups provided more positive feedback on their learning models than the atlas group (VR: 26 [IQR: 19-30], cadaver: 25 [IQR: 19.5-29.5], atlas: 12 [IQR: 9-20]; p<0.001).Conclusions: The skull virtual learning resource (VLR) was equally efficient as the cadaver skull and atlas in teaching anatomy structures. Such a model can aid individuals in understanding complex anatomical structures with a higher level of motivation and tolerable adverse effects.
Patterns and patient factors associated with loss to follow-up in the Muhimbili Sickle Cell Cohort, Tanzania
Authors: Masamu Upendo , Sangeda Raphael Zozimus , Kandoga Daniel , Ondego Jesca , Ndobho Florah , Mmbando Bruno , Nkya Siana , Msami Khadija , Makani Julie 
Published: September 2020

Abstract
Background: Monitoring patient's clinical attendance is a crucial means of improving retention in care and treatment programmes. Sickle cell patients' outcomes are improved by participation in comprehensive care programmes, but these benefits cannot be achieved when patients are lost from clinical care. In this study, patients are defined as loss to follow-up when they did not attend clinic for more than nine months. Precise information on the retention rate and characteristics of those who are not following their clinic appointments is needed to enable the implementation of interventions that will be effective in increasing the retention to care. Method: This was a retrospective study involving sickle cell patients registered in the Muhimbili Sickle Cohort in Tanzania. Descriptive and survival analysis techniques both non-parametric methods (Kaplan-Meier estimator and Log-rank test) and semi-parametric method (Cox’s proportional hazard model), were used. A p-value of 0.05 was considered significant to make an inference from the analysis.Results: A total of 5476 patients were registered in the cohort from 2004 to 2016. Of these, 3350 (58.13%) were actively participating in clinics, while 2126 (41.87%) were inactive, of which 1927 (35.19%) were loss to follow-up. We used data from 2004-2014 because between 2015-2016, patients were referred to other government hospitals. From the survival analysis results, pediatric (HR: 14.29,95% CI: 11.0071-18.5768, p <0.001) and children between 5-17 years [HR:2.61,95% CI:2.2324 - 3.0705, p< 0.001] patients were more likely to be loss to follow-up than the adult (18 and above years) patients. It was found that patients with above averages for hematocrit (HR: 2.38, 95% CI: 1.0076 - 1.0404, p=0.0039) or mean cell volume (HR: 4.28, (95% CI: 1.0260 - 1.0598, p<0.001) were more likely to be loss to follow-up than their counterparts. Conclusion: Loss to follow-up is evident in the cohort of patients in long term comprehensive care. It is, therefore, necessary to design interventions that improve patients’ retention. Suggested solutions include refresher training for health care workers and those responsible for patient follow-up on techniques for retaining patients and comprehensive transition programs to prepare patients who are moving from pediatric to adult clinics
Differential susceptibility of Onchocerca volvulus microfilaria to ivermectin in two areas of contrasting history of mass drug administration in Cameroon: Relevance of microscopy and molecular techniques for the monitoring of skin microfilarial repopulation within six months of direct observed treatment
Authors: Abong Raphael Awah , Amambo Glory Ngongeh , Ndongmo Patrick Chounna , Njouendou Abdel Jelil , Manuel Ritter , Beng Amuam Andrew , Esum Mathias Eyong , Deribe Kebede , Cho Jerome Fru , Fombad Fanny Fri , Nji Theobald Mue , Enyong Peter Ivo , Poole Catherine , Pfarr Kenneth , Hoerauf Achim , Carlow Clotilde , Wanji Samuel 
Published: September 2020

Abstract
Background. Ivermectin is an excellent microfilaricide against Onchocerca volvulus. However, in some regions, long term use of ivermectin has resulted in sub-optimal responses to the treatment. More data to properly document the phenomenon in various contexts of ivermectin mass drug administration (IVM-MDA) is needed. Also, there is a need to accurately monitor a possible repopulation of skin by microfilariae following treatment. Skin snip microscopy is known to have a low sensitivity in individuals with light infections, which can be the case following treatment. This study was designed with two complementary objectives: (i) to assess the susceptibility of O. volvulus microfilariae to ivermectin in two areas undergoing IVM-MDA for different lengths of time, and (ii) to document the repopulation of skin by the O. volvulus microfilariae following treatment, using 3 independent diagnostic techniques.Method. Identified microfilaridermic individuals were treated with ivermectin and re-examined after 1, 3, and 6 months using microscopy, actin real-time PCR (actin-qPCR) and O-150 LAMP assays. Susceptibility to ivermectin and trends in detecting reappearance of skin microfilariae were determined using three techniques. Microscopy was used as an imperfect gold standard to determine the performance of actin-qPCR and LAMP.Results. In Bafia with over 20 years of IVM-MDA, 11/51 (21.6%) direct observe treated microfilaridemic participants were still positive for skin microfilariae after 1 month. In Melong, with 10 years of IVM-MDA, 2/29 (6.9%) treated participants were still positive. The microfilarial density reduction per skin biopsy within one month following treatment was significantly lower in participants from Bafia.In both study sites, the molecular techniques detected higher proportions of infected individuals than microscopy at all monitoring time points. LAMP demonstrated the highest levels of sensitivity and real-time PCR was found to have the highest specificity.Conclusion. Patterns in skin mirofilariae clearance and repopulation were established. O. volvulus worms from Bafia with higher number of annual MDA displayed a lower clearance and higher repopulation rate after treatment with ivermectin. Molecular assays displayed higher sensitivity in monitoring O. volvulus microfilaridemia within six months following treatment.
Incidence of Idiopathic Cardiomyopathy in Patients with Type 2 Diabetes in Taiwan: Age, Sex, and Urbanization Status-stratified Analysis
Authors: Chen Hua-Fen Chen , Chang Ya-Hui , Lo Hsien-Jung Lo , Isfandiari Atoillah , Martini Santi , Hou Wen-Hsuan , Li Chung-Yi 
Published: September 2020

Abstract
Background: The epidemiology of diabetes and idiopathic cardiomyopathy have limited data. We investigated the overall and the age-, sex-, and urbanization-specific incidence and relative hazard of idiopathic cardiomyopathy in association with type 2 diabetes and various anti-diabetic medications used in Taiwan.Methods: A total of 474,268 patients with type 2 diabetes were identified from ambulatory care and inpatient claims in 2007-2009 from Taiwan’s National Health Insurance (NHI) database. We randomly selected 474,266 age-, sex-, and diagnosis date-matched controls from the registry of NHI beneficiaries. All study subjects were linked to ambulatory care and inpatient claims (up to the end of 2016) to identify the possible diagnosis of idiopathic cardiomyopathy. The person-year approach with Poisson assumption was used to estimate the incidence, and Cox proportional hazard regression model with Fine and Gray’s method was used to estimate the relative hazards of idiopathic cardiomyopathy in relation to type 2 diabetes.Results: The overall incidence of idiopathic cardiomyopathy for men and women patients, respectively, was 3.83 and 2.94 per 10,000 person-years, which were higher than the corresponding men and women controls (2.00 and 1.34 per 10,000 person-years). Compared with the control group, patients with type 2 diabetes were significantly associated with an increased hazard of idiopathic cardiomyopathy (adjusted hazard ratio [aHR]: 1.60, 95% confidence interval [CI]: 1.45-1.77] in all age and sex stratifications except in those men aged >64 years. Patients with type 2 diabetes aged <45 years confronted the greatest increase in the hazard of idiopathic cardiomyopathy, with an aHR of 3.35 (95% CI: 2.21-5.06) and 3.48 (95% CI: 1.60-7.56) for men and women, respectively. The usage of some anti-diabetic medications revealed lower risks of idiopathic cardiomyopathy.Conclusions: In Taiwan, diabetes increased the risk of idiopathic cardiomyopathy in both sexes and in all age groups, except in men aged >64 years. Younger patients were vulnerable to have higher HRs of idiopathic cardiomyopathy. Some anti-diabetic medications may reduce the risks of cardiomyopathy.
125 I seeds irradiation inhibits tumor growth and induces apoptosis by Ki-67, P21, Survivin，Livin and Caspase-9 expression in lung carcinoma xenografts
Authors: Jin Qing , Lin Cunzhi , Zhu Xinhong , Cao Yiwei , Guo Caihong , Wang Lijun 
Published: September 2020

Abstract
Background: Lung cancer is a fatal disease and a serious health problem worldwide. Patients are usually diagnosed at an advanced stage, and the effectiveness of chemotherapy for such patients is very limited. Iodine 125 seed(125I) irradiation can be used as an important adjuvant treatment for lung carcinoma. The purpose of this study was to examine the role of irradiation by 125I seeds in human lung cancer xenograft model and to determine the underlying mechanisms involved, with a focus on apoptosis. Methods: 40 mice with A549 lung adenocarcinoma xenografts were randomly divided into 4 groups: control group (n=10), sham seed (0 mCi) implant group (n=10), 125I seed (0.6 mCi) implant group (n=10) and 125I seed (0.8 mCi) implant group (n=10), respectively. The body weight and tumor volume, were recorded every four days until the end of the study. Apoptotic cells were checked by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay and activities of caspase-3 and caspase-8 enzyme were tested. Expression of P21, survivin, livin, caspase-9 and proliferating cell nuclear antigen (Ki-67) was detected with immunohistochemical staining. Results: The results of TUNEL staining assays showed that 125I seed irradiation suppresses the growth of lung cancer xenografts in nude mice and induced apoptosis. The activity of caspase-3 and caspase-8 was significantly higher. The expression levels Ki67, survivin and livin were substantially downregulated, while P21 and caspase-9 protein expression were significantly increased following 125I seed irradiation. This study revealed that 125I seed irradiation could significantly change apoptosis-related protein in human lung cancer xenografts. Conclusions: Overall, our study demonstrates that radiation exposure by 125I seedscould be a new treatment option for lung cancer.
Slow radiological improvement and persistent low-grade inflammation after chemotherapy in tuberculosis patients with type 2 diabetes
Authors: Mily Akhirunnesa , Sarker Protim , Taznin Inin , Hossain Md. Delwar , Haq Md. Ahsanul , Kamal SM. Mostofa , Agerberth Birgitta , Brighenti Susanna , Raqib Rubhana 
Published: September 2020

Abstract
Background: Diabetes mellitus type 2 (DM) may impede immune responses in tuberculosis (TB) and thus contribute to enhanced disease severity. In this study, we aimed to evaluate DM-mediated alterations in clinical, radiological and immunological outcomes in TB disease.Methods: Newly diagnosed pulmonary TB patients with or without DM (TB n=40; TB-DM n=40) were recruited in Dhaka, Bangladesh. Clinical symptoms, sputum smear and culture conversion as well as chest radiography were assessed. Peripheral blood and sputum samples were collected at the time of diagnosis (baseline) and after 1, 2 and 6 months of standard anti-TB treatment. Blood samples were also obtained from healthy controls (n=20). mRNA expression of inflammatory markers in blood and sputum samples were quantified using real-time PCR.Results: The majority of TB-DM patients had poor glycemic control (HbA1c>8%) and displayed elevated pulmonary pathology (P=0.039) particularly in the middle (P<0.004) and lower lung zones (P<0.02) throughout the treatment period. However, reduction of clinical symptoms and time to sputum smear and culture conversion did not differ between the groups. Transcripts levels of the pro-inflammatory cytokines IL-1β (P=0.003 at month-1 and P=0.045 at month-2) and TNF-α (P=0.005 at month-1) and the anti-inflammatory cytokine IL-10 (P=0.005 at month-2) were higher in peripheral blood after anti-TB treatment in TB-DM compared to TB patients. Conversely in sputum, TB-DM patients had reduced CD4 (P<0.009 at month-1) and IL-10 (P=0.005 at month-1 and P=0.006 at month-2) transcripts, whereas CD8 was elevated (P=0.016 at month-2). At 1- and 2-months post-treatment, sputum IL-10 transcripts were inversely correlated with fasting blood glucose and HbA1C levels in all patients. Conclusion: Insufficient up-regulation of IL-10 in the lung may fuel persistent local inflammation thereby promoting lung pathology in TB-DM patients with poorly controlled DM.
Barriers and Facilitators to Colorectal Cancer Diagnosis in New Zealand: A Qualitative Study
Authors: Blackmore Tania , Norman Kimberley , Kidd Jacquie , Cassim Shemana , Chepulis Lynne , Keenan Rawiri , Firth Melissa , Jackson Christopher , Stokes Tim , Weller David , Emery Jon , Lawrenson Ross 
Published: September 2020

Abstract
Background: New Zealand (NZ) has high rates of colorectal cancer but low rates of early diagnosis. Due to a lack of understanding of the pre-diagnostic experience from the patient’s perspective, it is necessary to investigate potential patient and health system factors that contribute to longer diagnostic intervals. Previous qualitative studies have discussed delays using The Model of Pathways to Treatment, but this has not been explored in the NZ context. This study aimed to understand the patient experience and perception of their general practitioner (GP) through the diagnostic process in the Waikato region of NZ. In particular, we sought to investigate potential barriers and facilitators that contribute to longer diagnostic intervals. Methods: Ethical approval for this study was granted by the New Zealand Health and Disability Ethics Committee. Twenty-eight participants, diagnosed with colorectal cancer, were interviewed about their experience. Semi-structured interviews were audio recorded, transcribed verbatim and analysed thematically using The Model of Pathways to Treatment framework (intervals: appraisal, help-seeking, diagnostic). Results: Participant appraisal of symptoms was a barrier to prompt diagnosis, particularly if symptoms were normalised, intermittent, or isolated in occurrence. Successful self-management techniques also resulted in delayed help-seeking. However if symptoms worsened, disruption to work and daily routines were important facilitators to seeking a GP consultation. Participants positively appraised GPs if they showed good technical competence and were proactive in investigating symptoms. Negative GP appraisals were associated with a lack of physical examinations and misdiagnosis, and left participants feeling dehumanised during the diagnostic process. However high levels of GP interpersonal competence could override poor technical competence, resulting in an overall positive experience, even if the cancer was diagnosed at an advanced stage. Māori participants often appraised symptoms inclusive of their sociocultural environment and considered the impact of their symptoms in relation to family. Conclusions: The findings of this study highlight the importance of tailored colorectal cancer symptom communication in health campaigns, and indicate the significance of the interpersonal competence aspect of GP-patient interactions. These findings suggest that interpersonal competence be overtly displayed in all GP interactions to ensure a higher likelihood of a positive experience for the patient.
Predicting Target Profiles with Confidence as a Service using Docking Scores
Authors: Ahmed Laeeq , Alogheli Hiba , Arvidsson Staffan , Alvarsson Jonathan , Berg Arvid , Larsson Anders , Schaal Wesley , Laure Erwin , Spjuth Ola 
Published: September 2020

Abstract
Background: Identifying and assessing ligand-target binding is a core component in early drug discovery asone or more unwanted interactions may be associated with safety issues.Contributions: We present an open-source, extendable web service for predicting target profiles withconfidence using machine learning for a panel of 7 targets, where models are trained on molecular dockingscores from a large virtual library. The method uses conformal prediction to produce valid measures ofprediction efficiency for a particular confidence level. The service also offers the possibility to dock chemicalstructures to the panel of targets with QuickVina on individual compound basis.Results: The docking procedure and resulting models were validated by docking well-known inhibitors for eachof the 7 targets using QuickVina. The model predictions showed comparable performance to molecular dockingscores against an external validation set. The implementation as publicly available microservices on Kubernetesensures resilience, scalability, and extensibility
Malaria Risks Related to Poor Practices in the Use of Mosquito Bite Control Tools During The Cold and Hot Seasons
Authors: Sominahouin André , Dagnon Fortuné , Padonou Gil , Aikpon Rock , N'tcha Ludovic , Akinro Bruno , Salako Albert , Agossa Fiacre , Gbenou Dina , Odjo Esdras , Houssou Christophe , Akogbeto Martin 
Published: September 2020

Abstract
Background: It is generally accepted that one of the reasons for the declining effectiveness of vector control tools (LLINs, IRS) is the misuse of these tools. Some people sleep outside while the walls of houses are treated with insecticide to protect people from mosquito bites.Methods:To check whether communities that misuse these tools are more exposed to malaria, we used the technique of direct and participatory observation of sleeping habits and we clocked every 30 min, the activities and positions of the communities from 7pm to 7am. The survey was conducted in 3 departments Northern Benin. These were mainly treatments related to variance analysis and descriptive statistics. Softwares used included SPSS 21, SAS 9.2 and Arcgis 10.4.Results: The study shows that 95% of the villages population included in the study stay in their rooms from 7:00 pm to 7:00 am, and only 5% of household members are outdoors during same time intervals during the harmattan season. On the other hand, during hot weather, there are more households outdoors (37%). Less than 20% of household members are outside their rooms during the harmattan season. This number decreases gradually until 10:00 pm when all of them are inside their rooms.Student Newman Keuls test shows that the household members being inside or outside their rooms does not depend on the urbanization situation of the village, but rather on the period.65% exposed to mosquito bites gave irritation as the main reason for their behavior and 15% because of heat and lack of space. Overall, because of household member mobility and malaria vector behaviors, human exposure to An. gambiae was higher outside than inside, despite all the observed food preferences in the vectors.Conclusion:To curtail residual malaria transmission, it must be prioritized to raise awareness in the best use of the tools and provide other complementary control tools for use outside the home.