Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Learning versus Conventional Machine Learning for Detection of Healthcare-Associated Infections in French Clinical Narratives

Abstract Objective The objective of this article was to compare the performances of health care-associated infection (HAI) detection between deep learning and conventional machine learning (ML) methods in French medical reports. Methods The corpus consisted in different types of medical reports (discharge summaries, surgery reports, consultation reports, etc.). A total of 1,531 medical text documents were extracted and deidentified in three French university hospitals. Each of them was labeled as presence (1) or absence (0) of HAI. We started by normalizing the records using a list of preprocessing techniques. We calculated an overall performance metric, the F1 Score, to compare a deep learning method (convolutional neural network [CNN]) with the most popular conventional ML models (Bernoulli and multi-naïve Bayes, k-nearest neighbors, logistic regression, random forests, extra-trees, gradient boosting, support vector machines). We applied the hyperparameter Bayesian optimization for each model based on its HAI identification performances. We included the set of text representation as an additional hyperparameter for each model, using four different text representations (bag of words, term frequency–inverse document frequency, word2vec, and Glove). Results CNN outperforms all other conventional ML algorithms for HAI classification. The best F1 Score of 97.7% ± 3.6% and best area under the curve score of 99.8% ± 0.41% were achieved when CNN was directly applied to the processed clinical notes without a pretrained word2vec embedding. Through receiver operating characteristic curve analysis, we could achieve a good balance between false notifications (with a specificity equal to 0.937) and system detection capability (with a sensitivity equal to 0.962) using the Youden's index reference. Conclusions The main drawback of CNNs is their opacity. To address this issue, we investigated CNN inner layers' activation values to visualize the most meaningful phrases in a document. This method could be used to build a phrase-based medical assistant algorithm to help the infection control practitioner to select relevant medical records. Our study demonstrated that deep learning approach outperforms other classification learning algorithms for automatically identifying HAIs in medical reports.
Exploring barriers to reproductive, maternal, child and neonatal (RMNCH) health-seeking behaviors in Somali region, Ethiopia

Introduction Health-seeking behaviours are influenced by internal and external contributing factors. Internal factors include attitudes, beliefs and core values, life adaptation skills, psychological disposition whereas external factors include social support, media, socio-cultural, political, economic and biological aspects, health care systems, environmental stressors and societal laws and regulations. This study was meant to explore factors affecting health-seeking behaviors in the Somali regional state of Ethiopia. The study employed a cross-sectional study design using qualitative data collection tools. Data were collected from 50 individual interviews and 17 focused group discussions (FGD) on women of reproductive age and their partners, health extension workers (HEWs), health care providers and health administrators. To ensure representativeness, the region was categorized into three zones based on their settlement characteristics as agrarian, pastoralist and semi-pastoralist. Two districts (one from high and the other from low performance areas) were selected from each category. The data were entered, coded, categorized and analyzed using NVIVO version 11 software. The Socio-ecologic Model (SEM) was used for categorization. Results Using the social ecological model, the following major barriers for health seeking behaviors were identified. Low socio-demographic and economic status, poor exposure to health information or mass media, detrimental preferences of breast feeding methods and short acting family planning (FP) methods were identified barriers at the individual level; male dominance in decision making, the influence of the husband and society and the role of word of mouth were identified barriers at the interpersonal level and lack of acceptance, fear of modern health practices, unclean health facility environment, lack of well-equipped facilities shortage of trained staffs and barriers relating to distance and transportation were barriers identified at organizational and policy level. Conclusion Overall, factors at various level affected health seeking behaviors of the Somali community. Socio-demographic and economic factors, non-responsive bureaucratic system, shortages or absence of medical supplies and human resources, lack of supportive supervision, a shortage of water and electricity at the health facility and an unclean service delivery environment are significant barriers to health-seeking behaviors for the community.
Environmental Factors Influence Plant Vascular System and Water Regulation

Developmental initiation of plant vascular tissue, including xylem and phloem, from the vascular cambium depends on environmental factors, such as temperature and precipitation. Proper formation of vascular tissue is critical for the transpiration stream, along with photosynthesis as a whole. While effects of individual environmental factors on the transpiration stream are well studied, interactive effects of multiple stress factors are underrepresented. As expected, climate change will result in plants experiencing multiple co-occurring environmental stress factors, which require further studies. Also, the effects of the main climate change components (carbon dioxide, temperature, and drought) on vascular cambium are not well understood. This review aims at synthesizing current knowledge regarding the effects of the main climate change components on the initiation and differentiation of vascular cambium, the transpiration stream, and photosynthesis. We predict that combined environmental factors will result in increased diameter and density of xylem vessels or tracheids in the absence of water stress. However, drought may decrease the density of xylem vessels or tracheids. All interactive combinations are expected to increase vascular cell wall thickness, and therefore increase carbon allocation to these tissues. A comprehensive study of the effects of multiple environmental factors on plant vascular tissue and water regulation should help us understand plant responses to climate change.
Dialogic Model of Prevention and Resolution of Conflicts: Evidence of the Success of Cyberbullying Prevention in a Primary School in Catalonia

This article analyses the evidence obtained from the application of the dialogic model of prevention and resolution of conflicts to eradicate cyberbullying behaviour in a primary school in Catalonia. The Dialogic Prevention Model is one of the successful educational actions identified by INCLUD-ED (FP6 research project). This case study, based on communicative methodology, includes the results obtained from documentary analysis, communicative observations and in-depth interviews. The evidence collected indicates that the implementation of this type of model can help to overcome cyberbullying; children are more confident to reject violence, students support the victims more and the whole community is involved in Zero Tolerance to violence.
Signals Among Signals: Prioritizing Nongenetic Associations in Massive Data Sets

Abstract Massive data sets are often regarded as a panacea to the underpowered studies of the past. At the same time, it is becoming clear that in many of these data sets in which thousands of variables are measured across hundreds of thousands or millions of individuals, almost any desired relationship can be inferred with a suitable combination of covariates or analytic choices. Inspired by the genome-wide association study analysis paradigm that has transformed human genetics, X-wide association studies or “XWAS” have emerged as a popular approach to systematically analyzing nongenetic data sets and guarding against false positives. However, these studies often yield hundreds or thousands of associations characterized by modest effect sizes and miniscule P values. Many of these associations will be spurious and emerge due to confounding and other biases. One way of characterizing confounding in the genomics paradigm is the genomic inflation factor. An analogous “X-wide inflation factor,” denoted λX, can be defined and applied to published XWAS. Effects that arise in XWAS may be prioritized using replication, triangulation, quantification of measurement error, contextualization of each effect in the distribution of all effect sizes within a field, and pre-registration. Criteria like those of Bradford Hill need to be reconsidered in light of exposure-wide epidemiology to prioritize signals among signals.
Proteomics Analysis to Identify Proteins and Pathways Associated with the Novel Lesion Mimic Mutant E40 in Rice Using iTRAQ-Based Strategy

A novel rice lesion mimic mutant (LMM) was isolated from the mutant population of Japonica rice cultivar Hitomebore generated by ethyl methane sulfonate (EMS) treatment. Compared with the wild-type (WT), the mutant, tentatively designated E40, developed necrotic lesions over the whole growth period along with detectable changes in several important agronomic traits including lower height, fewer tillers, lower yield, and premature death. To understand the molecular mechanism of mutation-induced phenotypic differences in E40, a proteomics-based approach was used to identify differentially accumulated proteins between E40 and WT. Proteomic data from isobaric tags for relative and absolute quantitation (iTRAQ) showed that 233 proteins were significantly up- or down-regulated in E40 compared with WT. These proteins are involved in diverse biological processes, but phenylpropanoid biosynthesis was the only up-regulated pathway. Differential expression of the genes encoding some candidate proteins with significant up- or down-regulation in E40 were further verified by qPCR. Consistent with the proteomic results, substance and energy flow in E40 shifted from basic metabolism to secondary metabolism, mainly phenylpropanoid biosynthesis, which is likely involved in the formation of leaf spots.
Mesenteric manifestations in Crohn’s disease

publications . 13 Presentations from this thesis . 15 Awards from this thesis . 18 List of tables. 19 List of abbreviations . 21 Chapter one: Mesenteric manifestations in Crohn’s disease represent novel opportunities for research . 23 Crohn’s disease . 24 Management . 26 Pathobiology . 26 Disease classification . 27 Assessment of disease activity . 30 Biomarkers . 33 Surgery for Crohn’s disease . 33 Mesenteric manifestations in Crohn’s disease . 34 Recent advances in anatomy and histology of the mesentery . 36 Opportunities presented . 39 Objectives of thesis . 41
Diabetic Foot Awareness among Diabetic Patients in Saudi Arabia

Aim of the work: diabetic foot disease(DFD) is diabetic patient's foot affection by ulcers which are accompanied by peripheral vascular disease and/or diabetic neuropathy of the lower limb. Prevalence of diabetic ulcer is ranging from 2%-10%. High rate of lower limb amputation in DFD (More than 15%) and survival rate for undertaken amputation patient are short. Ninety diabetic amputations are performed monthly in Saudi Arabia capital of Riyadh. Identification of DFD and diabetic patient's awareness of DFD and how to take care of it will reduce the incidence of more complications like amputation. This study aimed to evaluate knowledge, education, attitude and practice with diabetic foot among diabetic patients all over Saudi Arabia. Patients and Method: cross-sectional study directed among the diabetic clinic visitors in Primary Health Care Centers (PHCs s). Selection of 55 PHCs was done by random sampling. Ten diabetic patients were randomly selected from each PHCs and collecting of data was done by interviews. Research questionnaire contains three parts; first part is asking about demographic data; second part is about data that are focusing on diabetes and its related questions and last part is the main part which asking about diabetic foot. Results: 519 diabetic patients were participated in this study. Only 180 participants were complaining of diabetic complications (34.7%). Most of participants (55.1%) get high score 7-8 out of 8 questions in Knowledge. Although, there were 166 persons (32%) who couldn’t reach full score in attitude evaluation. There was a large percentage of our participants (69%) had very low score 0-2 out of 6 in assessment of previous education of diabetic foot. More than half of participants (56.5%) had score 6-10 out of 15 in evaluation of practice with diabetic foot. Conclusion: diabetic foot in Saudi Arabia is existing, even amputations and other diabetic foot complications were also present. Diabetic patients have good knowledge and attitude toward diabetic foot. Education about diabetic foot and practice is still weak.
Early experience of laparoscopic cholecystectomy in acutely inflamed gallbladder

Gallstones are now among the most important disease in the era of surgery. Definitive treatment of gall stone disease remains cholecystectomy. One of the common causes of emergency surgical referral is acute cholecystitis of which 50-70% cases are seen in the elderly patients.50 patients were treated with laparoscopic cholecystectomy from October 2013 to October 2015. The patient’s age was from 20 to 65 years old with a mean age of 34 ±3 years old. The patients received in the emergency unit and their attack not more than 72 hrs of acute gall stone inflammation were included in this study.From the 50 patients,15 were males (34%) and females were 35 (74%) so the ratio of 1:2of male to female. Problems and complications that facing in this study at time of laparoscopy were mainly adhesions to the adjacent structures like stomach, colon, and omentum. Adhesion into CBD also considered.Early intervention for acute cholecystitis of calculus type by laparoscopy now regarding safe and gold standard approach that should be kept in mind when dealing with such cases.
Donepezil's Effects on Brain Functions of Patients With Alzheimer Disease: A Regional Homogeneity Study Based on Resting-State Functional Magnetic Resonance Imaging

Purpose Donepezil is known to increase cholinergic synaptic transmission in Alzheimer disease (AD), although how it affects cortical brain activity and how it consequently affects brain functions need further clarification. To investigate the therapeutic mechanism of donepezil underlying its effect on brain function, regional homogeneity (ReHo) technology was used in this study. Patients and methods This study included 11 mild-to-moderate AD patients who completed 24 weeks of donepezil treatment and 11 matched healthy controls. All participants finished neuropsychological assessment and resting-state functional magnetic resonance imaging scanning to compare whole-brain ReHo before and after donepezil treatment. Results Significantly decreased Alzheimer's Disease Assessment Scale–Cognitive Subscale scores (P = 0.010) and increased Mini-Mental State Examination scores (P = 0.043) were observed in the AD patients. In addition, in the right gyrus rectus (P = 0.021), right precentral gyrus (P = 0.026), and left superior temporal gyrus (P = 0.043) of the AD patients, decreased ReHo was exhibited. Conclusion Donepezil-mediated improvement of cognitive function in AD patients is linked to spontaneous brain activities of the right gyrus rectus, right precentral gyrus, and left superior temporal gyrus, which could be used as potential biomarkers for monitoring the therapeutic effect of donepezil.
Bottom-level motion control for robotic fish to swim in groups: modeling and experiments

Moving in groups is an amazing spectacle of collective behaviour in fish and has attracted considerable interest from many fields, including biology, physics and engineering. Although robotic fish have been well studied, including algorithms to simulate group swimming, experiments that demonstrate multiple robotic fish as a stable group are yet to be achieved. One of the challenges is the lack of a robust bottom-level motion control system for robotic fish platforms. Here we seek to overcome this challenge by focusing on the design and implementation of a motion controller for robotic fish that allows multiple individuals to swim in groups. As direction control is essential in motion control, we first propose a high-accuracy controller which can control a sub-carangiform robotic fish from one arbitrary position/pose (position and direction) to another. We then develop a hydrodynamic-model-based simulation platform to expedite the process of the parameter tuning of the controller. The accuracy of the simulation platform was assessed by comparing the results from experiments on a robotic fish using speeding and turning tests. Subsequently, extensive simulations and experiments with robotic fish were used to verify the accuracy and robustness of the bottom-level motion control. Finally, we demonstrate the efficacy of our controller by implementing group swimming using three robotic fish swimming freely in prescribed trajectories. Although the fluid environment can be complex during group swimming, our bottom-level motion control remained nominally accurate and robust. This motion control strategy lays a solid foundation for further studies of group swimming with multiple robotic fish.
Attenuating the nonresponse bias in hunting bag surveys: The multiphase sampling strategy

Reliable hunting bag statistics are a prerequisite for sustainable harvest management based on quantitative modeling. Estimating the total hunting bag for a given game species is faced with a multiplicity of error sources. Of particular concern is the nonresponse error. We consider that the major cause of nonresponse bias is when the reluctance to respond is related to a null harvest, which leads to a potentially important overestimation. For tackling the nonresponse bias issue, we advocate the repeated subsampling of nonrespondents, with a final phase of personal interview by phone, intended to be without nonresponse. When a 100% response rate is actually reached at the last phase, both total and sampling variance can be estimated without bias, whatever the response rates at the previous phases. The actual case of imperfect response at the last phase is studied using Monte Carlo simulations. For imperfect response at the last phase, we show that the estimators we advocate are biased downwards but that these bias remain very moderate if the response rate at the last phase is high enough, depending on the circumstances. Furthermore, we illustrate that increasing the number of phases improves the nonresponse bias attenuation. In case of a hunting bag collecting scheme prone to a high nonresponse rate, for obtaining a very satisfying nonresponse bias attenuation we advocate relying on the multiphase sampling strategy with two- or three-phases, and a response rate in the last phase of at least 90%.
An intra-population heterothermy continuum: notable repeatability of body temperature variation in food-deprived yellow-necked mice

ABSTRACT Theoretical modelling predicts that the thermoregulatory strategies of endothermic animals range from those represented by thermal generalists to those characteristic for thermal specialists. While the generalists tolerate wide variations in body temperature (Tb), the specialists maintain Tb at a more constant level. The model has gained support from inter-specific comparisons relating to species and population levels. However, little is known about consistent among-individual variation within populations that could be shaped by natural selection. We studied the consistency of individual heterothermic responses to environmental challenges in a single population of yellow-necked mice (Apodemus flavicollis), by verifying the hypothesis that Tb variation is a repeatable trait. To induce the heterothermic response, the same individuals were repeatedly food deprived for 24 h. We measured Tb with implanted miniaturised data loggers. Before each fasting experiment, we measured basal metabolic rate (BMR). Thus, we also tested whether individual variation of heterothermy correlates with individual self-maintenance costs, and the potential benefits arising from heterothermic responses that should correlate with body size/mass. We found that some individuals clearly entered torpor while others kept Tb stable, and that there were also individuals that showed intermediate thermoregulatory patterns. Heterothermy was found to correlate negatively with body mass and slightly positively with the BMR achieved 1–2 days before fasting. Nonetheless, heterothermy was shown to be highly repeatable, irrespective of whether we controlled for self-maintenance costs and body size. Our results indicate that specialist and generalist thermoregulatory phenotypes can co-exist in a single population, creating a heterothermy continuum. Summary: Intra-specific analysis of the heterothermic response in a wild mammal supports a novel specialist–generalist theoretical model for endothermic thermoregulation.
Rehabilitation of the Dysmorphic Lower Eyelid From Hyaluronic Acid Filler: What to Do After a Good Periocular Treatment Goes Bad.

BACKGROUND Chronic, long-lasting edema accompanied by the Tyndall effect as a delayed reaction to hyaluronic acid (HA) filler injection seems to occur exclusively in the eyelids. OBJECTIVES To present a treatment algorithm for management of patients with chronic lower eyelid edema as a delayed complication of HA filler injection. METHODS Retrospective study including 61 patients with delayed-onset chronic periocular edema following uneventful HA filler injection in the lower eyelids or cheeks. All patients underwent hyaluronidase enzyme dissolution followed by secondary treatment. Three retreatment options were presented: (1) observation; (2) secondary treatment with HA filler; and (3) lower eyelid blepharoplasty. RESULTS All patients underwent filler dissolution using hyaluronidase. The mean age was 48 years and 97% of the patients were female. Single treatment was effective in 92% of patients with 8% requiring another hyaluronidase injection to completely eradicate residual edema. Six patients (10%) were satisfied after hyaluronidase only and six patients (10%) underwent lower eyelid blepharoplasty. Secondary treatment with HA filler was performed in 48 patients (80%). All were satisfied with final results without further edema in the follow up period. CONCLUSIONS Delayed-onset chronic lower eyelid edema is a frequent HA-related complication and cause of patient and practitioner concern when considering periocular HA treatment. Previous treatment has been limited to either hyaluronidase only or blepharoplasty as a secondary solution after hyaluronidase, with only a minority of patients satisfied with this regimen; our results highlight the importance of an effective, non-invasive alternative after filler dissolution. Hyaluronidase, shortly followed by HA filler retreatment, is a safe and effective solution.