Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder

Objective Cohort selection is challenging for large-scale electronic health record (EHR) analyses, as International Classification of Diseases 9th edition (ICD-9) diagnostic codes are notoriously unreliable disease predictors. Our objective was to develop, evaluate, and validate an automated algorithm for determining an Autism Spectrum Disorder (ASD) patient cohort from EHR. We demonstrate its utility via the largest investigation to date of the co-occurrence patterns of medical comorbidities in ASD. Methods We extracted ICD-9 codes and concepts derived from the clinical notes. A gold standard patient set was labeled by clinicians at Boston Children’s Hospital (BCH) (N = 150) and Cincinnati Children’s Hospital and Medical Center (CCHMC) (N = 152). Two algorithms were created: (1) rule-based implementing the ASD criteria from Diagnostic and Statistical Manual of Mental Diseases 4th edition, (2) predictive classifier. The positive predictive values (PPV) achieved by these algorithms were compared to an ICD-9 code baseline. We clustered the patients based on grouped ICD-9 codes and evaluated subgroups. Results The rule-based algorithm produced the best PPV: (a) BCH: 0.885 vs. 0.273 (baseline); (b) CCHMC: 0.840 vs. 0.645 (baseline); (c) combined: 0.864 vs. 0.460 (baseline). A validation at Children’s Hospital of Philadelphia yielded 0.848 (PPV). Clustering analyses of comorbidities on the three-site large cohort (N = 20,658 ASD patients) identified psychiatric, developmental, and seizure disorder clusters. Conclusions In a large cross-institutional cohort, co-occurrence patterns of comorbidities in ASDs provide further hypothetical evidence for distinct courses in ASD. The proposed automated algorithms for cohort selection open avenues for other large-scale EHR studies and individualized treatment of ASD.
Characterizing land cover from X-band COSMO-SkyMed images by neural networks

The launch of last-generation satellites (COSMO-SkyMed and TerraSAR-X), equipped with X-band sensors acquiring images with a very high spatial resolution, has opened up new challenges in the field of SAR image processing for remote sensing applications. In this work, a set of Spotlight and Stripmap COSMO-Skymed images taken the Tor Vergata-Frascati test site was considered to investigate on the potential of this type of data in characterizing sub-urban areas by exploiting both amplitude and phase information contained in the radar return. In particular, this contribution deals with the development of a pixel based classification technique based on Multi-Layer Perceptron (MLP) Neural Networks (NN). The results have been compared with a land cover map of the same area, achieved by means of a different neural network algorithm exploiting the information carried by the eight bands of WorldView-2 satellite.
Role of VEGF in Kidney Development, Microvascular Maintenance and Pathophysiology of Renal Disease

Vascular endothelial growth factor, VEGF, is essential for endothelial cell differentiation (vasculogenesis) and for the sprouting of new capillaries from preexisting vessels (angiogenesis). In addition, there is strong evidence that VEGF is a survival factor allowing the cells to survive and proliferate under conditions of extreme stress. Hypoxia is a key regulator of VEGF gene expression. Besides hypoxia, many cytokines, hormones and growth factors can up-regulate VEGF mRNA expression in various cell types. VEGF is present in the glomerulus of both the fetal and adult kidney. The VEGF produced by glomerular epithelial cell may be responsible for maintenance of the fenestrated phenotype of glomerular epithelial cells, thus facilitating the high rate of glomerular ultrafiltration. But there is little known about the role of VEGF in the tubule. VEGF is thought to be involved in many kinds of kidney diseases. Whereas VEGF has a beneficial role in the pathogenesis in some diseases, it does harmful action in others. Because VEGF is known to be associated with the pathogenesis of some diseases, such as diabetic nephropathy, renal tumor and polycystic kidney disease, the study about the role of VEGF is going to be a target for disease control. On the other hand, an attempt at enhancing the role of VEGF has to be made at diseases like several ARF models and experimental glomerulonephritis.
Conscious Intelligent Systems - Part II - Mind, Thought, Language and Understanding

This is the second part of a paper on Conscious Intelligent Systems. We use the understanding gained in the first part (Conscious Intelligent Systems Part 1: IXI (arxiv id cs.AI/0612056)) to look at understanding. We see how the presence of mind affects understanding and intelligent systems; we see that the presence of mind necessitates language. The rise of language in turn has important effects on understanding. We discuss the humanoid question and how the question of self-consciousness (and by association mind/thought/language) would affect humanoids too.
Ethics and Politics in Early Childhood Education

1. Opening Narrative 2. Technology as First Practice 3. What Ethics? 4. Preschools as a Loci of Ethical Practice 5. Towards a Pedagogy of Listening 6. Major and Minor Politics 7. The Preschool as a Site for Democratic Politics 8. In Search of Utopia
Transfer learning for sEMG hand gestures recognition using convolutional neural networks

In the realm of surface electromyography (sEMG) gesture recognition, deep learning algorithms are seldom employed. This is due in part to the large quantity of data required for them to train on. Consequently, it would be prohibitively time consuming for a single user to generate a sufficient amount of data for training such algorithms. In this paper, two datasets of 18 and 17 able-bodied participants respectively are recorded using a low-cost, low-sampling rate (200Hz), 8-channel, consumer-grade, dry electrode sEMG device named Myo armband (Thalmic Labs). A convolutional neural network (CNN) is augmented using transfer learning techniques to leverage inter-user data from the first dataset and alleviate the data generation burden imposed on a single individual. The results show that the proposed classifier is robust and precise enough to guide a 6DoF robotic arm (in conjunction with orientation data) with the same speed and precision as with a joystick. Furthermore, the proposed CNN achieves an average accuracy of 97.81% on seven hand/wrist gestures on the 17 participants of the second dataset.
Wide-band slow light in compact photonic crystal coupled-cavity waveguides

Slow light has a variety of applications, in particular for enhanced nonlinear effects like four-wave mixing and high-harmonic generation. Here, we propose a photonic crystal coupled-cavity waveguide with an ultracompact arrangement of the constituent cavities in the propagation direction, and use an optimization algorithm to tune several structural parameters to engineer slow light with a constant group index ng over a wide bandwidth. We propose several specific silicon designs, including one with ng≈37 over a 20 nm wavelength range and another one with ng≈116 over an 8.8 nm band, which yields a group index–bandwidth product of 0.66—a record value among all slow-light devices. The design is experimentally beneficial because of its small footprint and straightforward fabrication and could find applications in optical storage or switching, and in generating quantum states of light.
IQGAP1 and IGFBP2: Valuable Biomarkers for Determining Prognosis in Glioma Patients

Abstract Clinical treatment decisions and the survival outcomes of patients with gliomas are directly impacted by accurate tumor classification. New and more reliable prognostic markers are needed to better identify the variable duration of survival among histologically defined glioma grades. Microarray expression analysis and immunohistochemistry were used to identify biomarkers associated with gliomas with more aggressive biologic behaviors. The protein expression of IQGAP1 and IGFBP2, when used in conjunction with the World Health Organization grading system, readily identified and defined a subgroup of patients with grade III gliomas whose prognosis was poor. In addition, in patients with glioblastoma multiforme, in whom IQGAP1 and IGFBP2 were absent, long-term survival of more than 3 years was observed. The use of these markers confirmed a nonuniform distribution of survival in those with World Health Organization grade III and IV tumors. Thus, IQGAP1 and IGFBP2 immunostaining supplements current histologic grading by offering additional prognostic and predictive information.
Type 3 ryanodine receptors of skeletal muscle are segregated in a parajunctional position

A key event in skeletal muscle activation is the rapid release of Ca2+ from the sarcoplasmic reticulum (SR), the Ca2+ storage organelle in the muscle cell. The surface membrane/transverse tubules and the SR form functional units (calcium release units containing one or two couplons or junctions), where the voltage-sensing dihydropyridine receptor of the surface membrane interacts with the SR Ca2+ release channel [ryanodine receptor (RyR)] and depolarization of the cell membrane is converted into Ca2+ release from the SR. Although RyR1 is the most important isoform in skeletal muscle, some muscles also express high levels of RyR3, an isoform with a wide tissue distribution. The cytoplasmic domains of RyRs are visible in the electron microscope as periodically disposed feet. We find that, in muscles containing only RyR1, feet are exclusively located over the junctional SR surface facing the surface membrane/transverse tubule. In muscles containing RyR1 as well as RyR3, additional feet are located in lateral parajunctional regions immediately adjacent to junctional SR. Biochemical content of RyR3 and content of parajunctional feet are highly correlated in different muscles and the disposition of parajunctional versus junctional feet are notably different. On the basis of these two observations, we postulate that RyR3s are restricted to the parajunctional region, and thus their activation must be indirect and derivative during excitation–contraction coupling.
The Development of Physical-Education Institutions in Europe: A Short Introduction

Inspired by the ideas of the Enlightenment and Jean Jacques Rousseau, one of the important representatives of the period, as well as by international scholars and pedagogues such as the Swiss Johann Heinrich Pestalozzi, the German Johann Christoph Friedrich GutsMuths, the Swedish Per Henrik Ling, the Dutch Franz Nachtegall, and the Swiss Johann Heinrich Clias, physical education was introduced by and into the schools in many European countries during the nineteenth century. Education, including physical education, was seen as relevant for a better future for individuals as well as modern, enlightened societies. Relating to ancient traditions of the Western world, education should include body and mind, physical and mental fitness, health and well-being of individuals and communities. And moreover, education was no longer considered to be a privilege of a few upper-class children or offspring of the nobility. It was seen as a necessity for all at a time when Europe went through various nation-building processes. A main argument favoring the spread of German Turnen and Swedish gymnastics as didactical concepts of physical education in the nineteenth century was that they supported and strengthened male youth to become healthy citizens and strong soldiers. Step by step, physical education, Turnen, and gymnastics – known under various names – were included in the school curricula. Initially, physical education was mainly for boys of the upper or educated classes but soon it was opened to pupils of all social classes, and eventually also to girls. However, the original idea that new, modern societies needed education including body exercises for healthy and successful development had to be accepted among the educated classes in Europe. The early theorists of physical education were convinced that physical training or education could not be separated from mental or cognitive learning. Rousseau’s publications taught that physical experiences are closely connected to mental, personal, social, and even moral issues in the overall development of humans. Meanwhile, these essentials of physical education seem to have been accepted worldwide. However, critical discussions were held about the status of physical education among other educational fields, including its recognition as an academic field of teaching and research. In consequence, children were not only to be given opportunities to move and play at schools freely but also to be taught in exercises, health, and fitness in a systematic and well-prepared way. To guarantee this, teachers had to be educated at specific institutions, universities, or teacher-training colleges. These institutions grew up in numerous
Improving Minor Opinion Polarity Classification with Named Entity Analysis (L’apport des Entités Nommées pour la classification des opinions minoritaires) [in French]

RÉSUMÉ La majeure partie des travaux en fouille d’opinion et en analyse de sentiment concerne le classement des opinions majoritaires. Les méthodes d’apprentissage supervisé à base de ngrammes sont souvent employées. Elles ont l’inconvénient d’avoir un biais en faveur des opinions majoritaires si on les utilise de manière classique. En fait la présence d’un terme particulier, fortement associé à la cible de l’opinion dans un document peut parfois suffire à faire basculer le classement de ce document dans la classe de ceux qui expriment une opinion majoritaire sur la cible. C’est un phénomène positif pour l’exactitude globale du classifieur, mais les documents exprimant des opinions minoritaires sont souvent mal classés. Ce point est un problème dans le cas où l’on s’intéresse à la détection des signaux faibles (détection de rumeur) ou pour l’anticipation de renversement de tendance. Nous proposons dans cet article d’améliorer la classification des opinions minoritaires en prenant en compte les Entités Nommées dans le calcul de pondération destiné à corriger le biais en faveur des opinions majoritaires.
The effects of optic disc drusen on the latency of the pattern-reversal checkerboard and multifocal visual evoked potentials.

PURPOSE To determine the effect of optic disc drusen on the latency of the pattern-reversal checkerboard visual evoked potentials (VEPs) and multifocal (mf)VEPs and to better understand the pathophysiology of the condition. METHODS Eighteen eyes with optic disc drusen (10 patients) and 38 control eyes (19 subjects) underwent VEP, mfVEP, and visual field testing. Only one eye of each individual, the one with the more affected visual field, was used in the analyses. The VEPs were recorded with a 15' and 60' reversing checkerboard pattern, and the mfVEPs were elicited by a 60-sector dartboard display. RESULTS Unlike the VEP results, the mfVEP revealed a significant increase in the average monocular latency of the optic disc drusen group compared with that of the control group. The average mfVEP relative latency for the optic disc drusen group (4.1 ms) was greater than that (0.8 ms) in the control group. For monocular and interocular analyses, the average percentage of points delayed in the drusen group was significantly greater than that in the control group. CONCLUSIONS Optic disc drusen produced significant latency delays on the mfVEP test but not on the VEP test, presumably due to the mfVEP's ability to detect the effects of local changes. The results are consistent with the hypothesis that local mechanical compression by optic disc drusen leads to abnormal retinal ganglion cell activity.
Signaling Over Two-User Parallel Gaussian Interference Channels: Outage Analysis

This paper presents an outage analysis for a two-user parallel Gaussian interference channel consisting of two sub-channels. Each sub-channel is modeled as a two-user Gaussian interference channel with quasi-static and flat fading. Both users employ single-layer Gaussian code-books and maintain a statistical correlation ρ between the signals transmitted over the underlying sub-channels. When joint decoding (JD) is performed at the receivers, setting ρ = 0 minimizes the outage probability, regardless of the value of the signal-to-noise ratio (SNR). It is shown, however, that if the receivers treat interference as noise (TIN) or cancel interference (CI), the value of optimum ρ approaches 1 as SNR goes to infinity. Motivated by these observations, we let ρ = 0 under JD and ρ = 1 under TIN and CI and compute the outage probability in finite SNR, assuming that the direct and crossover channel coefficients are independent zero-mean complex Gaussian random variables with possibly different variances. In the asymptote of large SNR and assuming the transmission rate per user is r log snr, it is shown that the outage probability scales like snr-(1-r) under both TIN and CI, while it vanishes at least as fast as snr-min{2-r,4(1-r)} log snr under JD. This paper is concluded by extending some of the results to a two-user parallel Gaussian interference channel with an arbitrary number of sub-channels.
Novel Mycobacteria Antigen 85 Complex Binding Motif on Fibronectin*

Background: The Ag85 proteins are fibronectin-binding proteins of mycobacteria. Results: The binding site is mapped in the C terminus of fibronectin, Fn14. Conclusion: Mycobacterial Ag85 proteins interact with the C terminus of fibronectin. Significance: This was the first evidence that Ag85 proteins bind to the C terminus of fibronectin (Fn14). The members of the antigen 85 protein family (Ag85), consisting of members Ag85A, Ag85B, and Ag85C, are the predominantly secreted proteins of mycobacteria and possess the ability to specifically interact with fibronectin (Fn). Because Fn-binding proteins are likely to be important virulence factors of Mycobacterium spp. , Ag85 may contribute to the adherence, invasion, and dissemination of organisms in host tissue. In this study, we reported the Fn binding affinity of Ag85A, Ag85B, and Ag85C from Mycobacterium avium subsp. paratuberculosis (MAP) (KD values were determined from 33.6 to 68.4 nm) and mapped the Ag85-binding motifs of Fn. Fn14, a type III module located on the heparin-binding domain II (Hep-2) of Fn, was discovered to interact with Ag85 from MAP. The peptide inhibition assay subsequently demonstrated that a peptide consisting of residues 17–26 from Fn14 (17SLLVSWQPPR26, termed P17–26) could interfere with Ag85B binding to Fn (73.3% reduction). In addition, single alanine substitutions along the sequence of P17–26 revealed that the key residues involved in Ag85-Fn binding likely contribute through hydrophobic and charge interactions. Moreover, binding of Ag85 on Fn siRNA-transfected Caco2 cells was dramatically reduced (44.6%), implying the physiological significance of the Ag85-Fn interaction between mycobacteria and host cells during infection. Our results indicate that Ag85 binds to Fn at a novel motif and plays a critical role in mycobacteria adherence to host cells by initiating infection. Ag85 might serve as an important colonization factor potentially contributing to mycobacterial virulence.
Laryngeal Findings in Advanced Parkinson's Disease

Parkinson's disease is a major source of neurologic morbidity. A majority of patients with Parkinson's disease complain of problems with voice, speech, and swallowing. Treatments for these problems center on the improvement of vocal fold adduction through either speech therapy or vocal fold augmentation. No prior study has looked at laryngeal improvement after neurologic surgery, specifically deep brain stimulation, performed to treat Parkinson's disease. The goal of this study was to establish a baseline of laryngeal findings in patients who are considering deep brain stimulation. Fifteen patients underwent physical examination with videostroboscopy and fiberoptic endoscopic evaluation of swallowing before deep brain stimulation. In addition, they were asked to self-report voice handicap. Eighty-seven percent of patients demonstrated significant vocal fold bowing. All patients had some degree of pharyngeal residue of solids noted on evaluation of swallowing. All but one patient had a significant self-reported voice handicap. These findings are reviewed and established as a baseline for further study.
Environmental Ethics in Islam

Tawhid The fundamental belief in Islam is tawhid, which affects every component of Islam, including environmental ethics. Tawhid is God’s Unity and Oneness and includes not ascribing any form of partnership with God. Tawhid, means that God is the Owner and Creator of everything in the universe. “To God belongs all that is in the heavens and on earth” (Qur'an, 4:126). This includes the human being, which is part of this interdependent universe as all is created by God.
CPEB1, a novel gene silenced in gastric cancer: a Drosophila approach

Background Gastric cancer (GC) is a highly prevalent disease, being the fourth most common cancer and the second leading cause of cancer-associated deaths worldwide. Although many genes have been implicated in its development, many cases remain genetically unexplained. Hence, there is an urgent need to find new disease-related genes. Methods A transgenic Drosophila model was used to screen for novel genes putatively involved in GC. The authors evaluated the expression of the most interesting candidates in GC cell lines and primary tumours by semi-quantitative reverse transcription PCR, dissected the molecular mechanisms responsible for the deregulation of the most relevant one, and analysed its functional role in vitro and in a chicken embryo model. Results Six candidate genes were identified, of which cytoplasmic polyadenylation element binding protein 1 (CPEB1) was downregulated in all GC cell lines and in 11 of 12 primary GC tumours. The pivotal CPEB1 promoter CpG site was determined, and it was found that methylation at this 79th CpG site was associated with CPEB1 silencing in GC cell lines and primary tumours. It was also discovered that methylation of this site was significantly more prevalent in diffuse type GC (p=0.007) and in cases with lymph node metastases (p=0.042). In vitro, CPEB1 impaired invasion. Its antiangiogenic role was also discovered, which was associated with downregulation of MMP14 and VEGFA. Conclusions The first evidence of CPEB1 involvement in GC is presented, along with the molecular mechanism underlying the regulation of its expression and its potential role in invasion and angiogenesis.
Variability in architectural simulations of multi-threaded workloads

Multi-threaded commercial workloads implement many important Internet services. Consequently, these workloads are increasingly used to evaluate the performance of uniprocessor and multiprocessor system designs. This paper identifies performance variability as a potentially major challenge for architectural simulation studies using these workloads. Variability refers to the differences between multiple estimates of a workload's performance. Time variability occurs when a workload exhibits different characteristics during different phases of a single run. Space variability occurs when small variations in timing cause runs starting from the same initial condition to follow widely different execution paths. Variability is a well-known phenomenon in real systems, but is nearly universally ignored in simulation experiments. In a central result of this paper we show that variability in multi-threaded commercial workloads can lead to incorrect architectural conclusions (e.g., 31% of the time in one experiment). We propose a methodology, based on multiple simulations and standard statistical techniques, to compensate for variability. Our methodology greatly reduces the probability of reaching incorrect conclusions, while enabling simulations to finish within reasonable time limits.