Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Genetic Alterations in Tunisian Patients with Lung Adenocarcinoma

The identification of the mutations that drive lung cancer have furnished new targets for the treatment of non-small cell lung cancer (NSCLC) and led to the development of targeted therapies such as tyrosine kinase inhibitors that are used to combat the molecular changes promoting cancer progression. Furthermore, biomarkers identified from gene analysis can be used to detect early lung cancer, determine patient prognosis, and monitor response to therapy. In the present study we analyzed the molecular profile of seventy-three Tunisian patients with lung adenocarcinoma (LAD). Mutational analyses for EGFR and KRAS were performed using direct sequencing, immunohistochemistry or MassARRAY. Anaplastic lymphoma kinase (ALK) rearrangement was evaluated by immunohistochemistry using the D5F3 clone, and p53 expression was also assessed. The median age of patients at diagnosis was 61 years (range 23–82 years). Using different methodologies, EGFR mutations were found in 5.47% of patients and only exon 19 deletions “E746-A750 del” were detected. KRAS mutations were present in 9.58% of cases, while only one patient was ALK-positive. Moreover, abnormal immunostaining of p53 was detected in 56.16% of patients. In conclusion, the detected rates of EGFR and KRAS mutation and ALK rearrangement were lower than those found in European and Asian countries, whereas, abnormal p53 expression was slightly more frequent. Furthermore, given the small sample size of this study, a more comprehensive analysis of this patient set is warranted.
Parenting Stress and Broader Phenotype in Parents of Children with Attention Deficit Hyperactivity Disorder, Dyslexia or Typical Development

In the present study parenting stress and the broader phenotype are investigated in two highly common developmental disorders, namely Attention Deficit Hyperactivity Disorder (ADHD) and specific reading impairment (dyslexia). Within a total sample of 130 parents, 27 were parents of children with ADHD (P-ADHD), 38 were parents of children with a diagnosis of dyslexia (P-DYS) and the other 65 participants were parents of children with typical development (P-TD). A battery of cognitive tasks was administered which included verbal and non-verbal Intellectual Quotient (IQ), reading speed (passage and nonwords), verbal fluency and the Attention Network Task (ANT). Reading history, symptoms of ADHD in adults and parenting stress were measured through questionnaires. Group differences evidenced that the P-DYS group had lower scores in the reading tasks, in the verbal fluency task and in the reading history questionnaire. Conversely, the P-ADHD group had more transversal cognitive weaknesses (IQ, reading tasks, verbal fluency) and the highest scores in parenting stress and ADHD symptoms, together with poor reading history. The groups did not differ in the ANT task. Parenting stress was predicted, on the whole sample, by lower socioeconomic status (SES) and number of family members and higher ADHD symptoms. Implications for research and clinical settings are discussed.
Semiautomatic software for measurement of abdominal muscle and adipose areas using computed tomography

Abstract The aim of the study was to introduce our in-house software to measure the muscle and adipose area on axial computed tomography (CT) scans and to compare with various quantification methods. Our institutional review board approved this retrospective study and informed consent was waived. We developed in-house software to identify body composition analysis on CT scan, which semiautomatically operates 3 image processing steps. Abdominal images were obtained using multidetector row CT (MDCT). Two radiologists analyzed the same cross-sectional areas of subcutaneous fat, muscle, and visceral fat using the following techniques: manual measurements, Aquarius, ImageJ, and our newly developed software. We calculated an intraclass correlation coefficient (ICC) for comparison of muscle and fat areas quantified by various measurement methods using a 2-way random model. Interobserver agreement between the radiologists was also evaluated. Agreements in the measurement of subcutaneous fat and muscle areas were excellent among the methods (ICC = 0.962 and 0.897, respectively), and that of the visceral fat area was good (ICC = 0.822). In the subgroup analysis, ICC of the visceral fat area in the female group and in subjects with ascites was slightly lower than the other group (ICC = 0.742 and 0.787, respectively). The correlation coefficients between our software and other methods were relatively high (r = 0.854–0.996). Additionally, ICCs between both observers of our program for quantification of subcutaneous fat, muscle, and visceral fat areas were 0.999, 0.980, and 0.999, respectively. In conclusion, our method showed be reliable in quantifying muscle and adipose tissue using cross-sectional areas of MDCT with high reproducibility.
Towards Concept Map Based Free Student Answer Assessment

We propose a concept map based approach to assessing freely generated student responses. The proposed approach is based on a novel automated tuple extraction system, DT-OpenIE, for automatically extracting concept maps from student responses. The DT-OpenIE system is signiﬁcantly better, for assessment purposes, in terms of concept map quality than state-of-the-art open information extraction (IE) systems such as Ollie or Stanford as evidenced by our experimental results. The concept map based approach can not only generate a holistic score assessing the accuracy of a student response but also enable diagnostic feedback.
Validity of Instrumented Insoles for Step Counting, Posture and Activity Recognition: A Systematic Review

With the growing interest in daily activity monitoring, several insole designs have been developed to identify postures, detect activities, and count steps. However, the validity of these devices is not clearly established. The aim of this systematic review was to synthesize the available information on the criterion validity of instrumented insoles in detecting postures activities and steps. The literature search through six databases led to 33 articles that met inclusion criteria. These studies evaluated 17 different insole models and involved 290 participants from 16 to 75 years old. Criterion validity was assessed using six statistical indicators. For posture and activity recognition, accuracy varied from 75.0% to 100%, precision from 65.8% to 100%, specificity from 98.1% to 100%, sensitivity from 73.0% to 100%, and identification rate from 66.2% to 100%. For step counting, accuracies were very high (94.8% to 100%). Across studies, different postures and activities were assessed using different criterion validity indicators, leading to heterogeneous results. Instrumented insoles appeared to be highly accurate for steps counting. However, measurement properties were variable for posture and activity recognition. These findings call for a standardized methodology to investigate the measurement properties of such devices.
A CRISPR Activation Screen Identifies Genes That Protect against Zika Virus Infection

Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barré syndrome, neuropathy, and myelitis. Vertical transmission of ZIKV can cause fetus demise, stillbirth, or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome-wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide a better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets. ABSTRACT Zika virus (ZIKV) is an arthropod-borne emerging pathogen causing febrile illness. ZIKV is associated Guillain-Barré syndrome and other neurological complications. Infection during pregnancy is associated with pregnancy complications and developmental and neurological abnormalities collectively defined as congenital Zika syndrome. There is still no vaccine or specific treatment for ZIKV infection. To identify host factors that can rescue cells from ZIKV infection, we used a genome-scale CRISPR activation screen. Our highly ranking hits included a short list of interferon-stimulated genes (ISGs) previously reported to have antiviral activity. Validation of the screen results highlighted interferon lambda 2 (IFN-λ2) and interferon alpha-inducible protein 6 (IFI6) as genes providing high levels of protection from ZIKV. Activation of these genes had an effect on an early stage in viral infection. In addition, infected cells expressing single guide RNAs (sgRNAs) for both of these genes displayed lower levels of cell death than did the controls. Furthermore, the identified genes were significantly induced in ZIKV-infected placenta explants. Thus, these results highlight a set of ISGs directly relevant for rescuing cells from ZIKV infection or its associated cell death and substantiate CRISPR activation screens as a tool to identify host factors impeding pathogen infection. IMPORTANCE Zika virus (ZIKV) is an emerging vector-borne pathogen causing a febrile disease. ZIKV infection might also trigger Guillain-Barré syndrome, neuropathy, and myelitis. Vertical transmission of ZIKV can cause fetus demise, stillbirth, or severe congenital abnormalities and neurological complications. There is no vaccine or specific antiviral treatment against ZIKV. We used a genome-wide CRISPR activation screen, where genes are activated from their native promoters to identify host cell factors that protect cells from ZIKV infection or associated cell death. The results provide a better understanding of key host factors that protect cells from ZIKV infection and might assist in identifying novel antiviral targets.
Study of symptoms and gene expression in four Pinus species after pinewood nematode infection

Pine wilt disease, caused by the pinewood nematode Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle, is originating severe infections in pine trees. The disease is detected when external symptoms appear (e.g. needle chlorosis), but trees could remain asymptomatic for long periods and serve as a long-term host. The primary goal of this study was to assess the effect of inoculation with an avirulent isolate of B. xylophilus (C14-5) on different Pinus spp. seedlings (P. sylvestris, P. nigra, P. pinea and P. pinaster). At the same time, seedlings were also inoculated with a virulent strain, HF, in order to compare the phenotypic and genomic results of the two types of inoculations. The effect of inoculation was determined in terms of expression of various Pinus genes potentially involved in the response to the disease.The results suggest that P. pinea and P. nigra are more resistant to infection by the nematode than P. sylvestris and P. pinaster. The phenotypic and genetic differences were more marked among P. pinea and P. pinaster.
Impact of automated response systems on in‐class cell phone use

Cell phones have long been known as a potential distraction from attention intensive activities such as studying and driving. Many, however, are developing the cell phone as a powerful tool to augment some of these same activities. Audience response systems (ARSs) are a type of teaching tool that allows educators to poll audience members in real time. Increasingly, cell phones are being integrated into ARSs to make them more versatile and affordable. As cell phones and other personal electronic devices (tablets, laptops) are becoming more common classroom learning tools, we sought to explore how student cell phone use is impacted by this change. Additionally, we studied how a student's seat location and how the time during a term impacts students' cell phone use. To measure student cell phone use in lecture, we observed introductory biology classes at the University of Washington and recorded when students' cell phones were visible. We found that students sitting in the back of the room showed an increased likelihood of having a cell phone out. However contrary to our expectations, students using personal device (cell phone) based polling technology were no more likely to be using cell phones during lecture than their peers using traditional ARSs. Our results suggest that the downsides to using cell phones as teaching tools may be limited. © 2019 The International Union of Biochemistry and Molecular Biology, 47(5):538–546, 2019.
Improving the Dietary Vitamin A Content of Rural Communities in South Africa by Replacing Non-Biofortified White Maize and Sweet Potato with Biofortified Maize and Sweet Potato in Traditional Dishes

Biofortification of staple crops has a potential for addressing micronutrient deficiencies, such as vitamin A deficiency (VAD), which are prevalent in South Africa. The poor acceptability of provitamin A (PVA)-biofortified foods could be improved by combining them with other food items to produce modified traditional dishes. The nutritional composition of the dishes could also be improved by the modification. The study aimed to investigate the effect of replacing white maize and cream-fleshed sweet potato (CFSP)] with PVA-biofortified maize and orange-fleshed sweet potato (OFSP) on the nutritional composition of South African traditional dishes. The protein, fibre, total mineral (ash), lysine, and iron concentrations of the PVA maize phutu (traditional porridge) composite dishes (control), were not significantly different (P > 0.05) from those of white maize phutu composite dishes. However, the PVA concentration of PVA maize phutu composite dishes was higher than that of the white phutu composite dishes (P > 0.05). The OFSP had a significantly lower protein concentration, but a significantly higher (P > 0.05) fibre, ash, lysine, isoleucine, leucine, and PVA concentration, relative to the CFSP. The findings indicate that composite dishes in which white maize is replaced with PVA-biofortified maize, and switching over from CFSP to OFSP, would contribute to combating VAD in South Africa, and in other developing counties.
Satellite cell activation and apoptosis in skeletal muscle from severely burned children

Severe burns result in profound skeletal muscle atrophy that hampers recovery. The activity of skeletal muscle stem cells, satellite cells, acutely following a severe burn is unknown and may contribute to the recovery of lean muscle. Severe burn injury induces skeletal muscle regeneration and myonuclear apoptosis. Satellite cells undergo concurrent apoptosis and activation acutely following a burn, with a net reduction in satellite cell content compared to healthy controls. The activation and apoptosis of satellite cells probably impacts the recovery of lean tissue following a severe burn, contributing to prolonged frailty in burn survivors.
Examining the Impact of Victimization on Girls’ Delinquency: A Study of Direct and Indirect Effects

Previous research has acknowledged that there is a relationship between victimization and later delinquency, but the specific attributes of this relationship are unclear because measures of both direct and indirect victimization are rarely explored in a single study. We included both indirect and direct victimization to examine which form of victimization was a stronger predictor of substance use, fighting, running away, and sex work among girls committed to a juvenile justice facility. Findings indicated that direct victimization was typically a more salient predictor of delinquency than indirect forms of victimization. Further, running away and sex work appear to be unique outcomes that are particularly likely when girls experience direct rather than indirect victimization. Findings are summarized with implications for health and public policy.
Transanal Hemorrhoidal Dearterialization With Doppler Arterial Identification Versus Classic Hemorrhoidectomy: A Retrospective Analysis of 270 Patients

Purpose Despite the minimally invasive nature of transanal hemorrhoidal dearterialization (THD) with Doppler arterial identification procedures, hemorrhoidectomy is still considered the gold standard procedure for hemorrhoidal disease. However, the classical techniques of hemorrhoidectomy have a high rate of postoperative complications. The main purpose of this study is to demonstrate the efficacy and complications of these techniques used for grades II and III hemorrhoids. Methods A retrospective (case-control) study was carried out from January 2009 to May 2014, and all patients undergoing surgical procedures for hemorrhoidal disease in two French clinics were considered. Application of inclusion and exclusion criteria identified 270 eligible patients (163 undergoing Doppler THD and 107 treated with Milligan Morgan hemorrhoidectomy). Statistical analysis was calculated considering immediate postoperative complications, functional results, chronic complications, and recurrences. Results Analysis of primary outcomes showed a significant difference between the 2 groups concerning postoperative pain, which had a lower rate in THD (P = 0.0001) and in postoperative bleeding (P = 0.02) than hemorrhoidectomy. However, long-term follow-up at three years showed a superior rate of recurrence in the THD group (P = 0.009). Conclusion The THD technique is a safe and effective procedure for grades II and III hemorrhoids, has lower rates of post-operative pain and bleeding, and allows faster hospital discharge; however, it also shows a higher rate of recurrence at three years of follow-up.
Comparable glycaemic control and hypoglycaemia in adults with type 2 diabetes after initiating insulin glargine 300 units/mL or insulin degludec: The DELIVER Naïve D real‐world study

To compare glycaemic control, hypoglycaemia and treatment discontinuation of insulin glargine 300 units/mL (Gla‐300) and insulin degludec (IDeg) in a real‐world study of insulin‐naïve adults with type 2 diabetes (T2D).
Predicting Learners' Performance Using EEG and Eye Tracking Features

In this paper, we aim to predict students’ learning performance by combining two-modality sensing variables, namely eye tracking that monitors learners’ eye movements and electroencephalography (EEG) that measures learners’ cerebral activity. Our long-term goal is to use both data to provide appropriate adaptive assistance for students to enhance their learning experience and optimize their performance. An experimental study was conducted in order to collet gaze data and brainwave signals of fifteen students during an interaction with a virtual learning environment. Different classification algorithms were used to discriminate between two groups of learners: students who successfully resolve the problem-solving tasks and students who do not. Experimental results demonstrated that the K-Nearest Neighbor classifier achieved good accuracy when combining both eye movement and EEG features compared to using solely eye movement or EEG.
Using EEG Features and Machine Learning to Predict Gifted Children

Gifted students have a higher capability of understanding and learning. They are characterized by a high level of attention and a high performance in the classroom. Gifted children are defined in this paper as children who have a performance higher than the average group (59.64%). In order to predict gifted students from normal students, we conducted an experiment where 17 pupils have voluntarily participated in this study. We collected different types of data (gender, age, performance, initial average in math and EEG mental states) in a web platform to learn mathematics called NetMath. Participants were invited to respond to top-level exercises on the four basic operations in decimals. We trained different machine learning algorithms to predict gifted students. Our first results show that the decision tree could predict gifted students with an accuracy of 76.88%. Using J48 trees, we noticed also that two relevant features could determine gifted children: the relaxation extracted from EEG headset and the characteristic of strong student. A strong student is defined as a student who obtained a mean higher than the group’s mean in the first step evaluation in class.
Characterizing joint attention behavior during real world interactions using automated object and gaze detection

Joint attention is an essential part of the development process of children, and impairments in joint attention are considered as one of the first symptoms of autism. In this paper, we develop a novel technique to characterize joint attention in real time, by studying the interaction of two human subjects with each other and with multiple objects present in the room. This is done by capturing the subjects' gaze through eye-tracking glasses and detecting their looks on predefined indicator objects. A deep learning network is trained and deployed to detect the objects in the field of vision of the subject by processing the video feed of the world view camera mounted on the eye-tracking glasses. The looking patterns of the subjects are determined and a real-time audio response is provided when a joint attention is detected, i.e., when their looks coincide. Our findings suggest a trade-off between the accuracy measure (Look Positive Predictive Value) and the latency of joint look detection for various system parameters. For more accurate joint look detection, the system has higher latency, and for faster detection, the detection accuracy goes down.
Price Effects in Online Product Reviews: An Analytical Model and Empirical Analysis

Consumer reviews may reflect not only perceived quality but also the difference between quality and price (perceived value). In markets where product prices change frequently, these price-influenced reviews may be biased as a signal of product quality when used by consumers possessing no knowledge of historical prices. In this paper, we develop an analytical model that examines the impact of price-influenced reviews on firm optimal pricing and consumer welfare. We quantify the price effects in consumer reviews for different formats of review systems using actual market prices and online consumer ratings data collected for the digital camera market. Our empirical results suggest that unidimensional ratings, commonly used in most review systems, can be substantially biased by price effects. In fact, unidimensional ratings are more closely correlated with ratings of product value than ratings of product quality. Our findings suggest the importance for firms to account for these price effects in their overall marketing strategy and suggest that review systems could better serve consumers by explicitly expanding review dimensions to separate perceived value and perceived quality.
Paternal heritage in Jujuy province (Northwest Argentina): Evidence for sex‐biased gene flow and genetic drift effects

This study aimed to explore the diversity of paternal lineages in Jujuy province (Argentina) by analyzing Y chromosome markers. Furthermore, we examined among‐population genetic variability based both on paternally (NRY haplotypes) and maternally (mtDNA haplogroups) inherited markers. We sought to evaluate the impact of sex‐biased gene flow on genetic background in Jujuy, and contribute data on the microevolutionary forces acting in this zone.