Miracle-dz/UniFAR-FTUs huggingface dataset:
A Deep Learning Approach for Rapid Mutational Screening in Melanoma

Image-based analysis as a rapid method for mutation detection can be advantageous in research or clinical settings when tumor tissue is limited or unavailable for direct testing. Here, we applied a deep convolutional neural network (CNN) to whole slide images of melanomas from 256 patients and developed a fully automated model that first selects for tumor-rich areas (Area Under the Curve AUC=0.96) then predicts for the presence of mutated BRAF in our test set (AUC=0.72) Model performance was cross-validated on melanoma images from The Cancer Genome Atlas (AUC=0.75). We confirm that the mutated BRAF genotype is linked to phenotypic alterations at the level of the nucleus through saliency mapping and pathomics analysis, which reveal that cells with mutated BRAF exhibit larger and rounder nuclei. Not only do these findings provide additional insights on how BRAF mutations affects tumor structural characteristics, deep learning-based analysis of histopathology images have the potential to be integrated into higher order models for understanding tumor biology, developing biomarkers, and predicting clinical outcomes.
Deciding and Interpolating Algebraic Data Types by Reduction

Recursive algebraic data types (term algebras, ADTs) are one of the most well-studied theories in logic, and find application in contexts including functional programming, modelling languages, proof assistants, and verification. At this point, several state-of-the-art theorem provers and SMT solvers include tailor-made decision procedures for ADTs, and version~2.6 of the SMT-LIB standard includes support for ADTs. We study an extremely simple approach to decide satisfiability of ADT constraints, the reduction of ADT constraints to equisatisfiable constraints over uninterpreted functions (EUF) and linear integer arithmetic (LIA). We show that the reduction approach gives rise to both decision and Craig interpolation procedures in (extensions of) ADTs.
Toward Prosodic Contrast : Suai and Pattani Malay

We may have an early stage of tonogenesis in two minority languages of Thailand. In one of them, Suai, its old voiceregister distinction is apparently giving way to one of pitch accent. In the other, Pattani Malay, an existing distinction of word-initial consonant length is giving way to one of relative salience on the first syllable of disyllabic words. The role of pitch in both may foretell the ultimate emergence of tones.
Histopathological Analysis of Testis: Effects of Astaxanthin Treatment against Nicotine Toxicity

Background: Nicotine is a toxic compound in the cigarette smoke and has destructive effects on various human organs. Astaxanthin is a carotenoid with high antioxidant property. In this study, we investigated the protective effects of astaxanthin against nicotine-induced toxicity in mice testes. Methods: Forty-two inbred balb/c male mice were divided into six groups:Group 1, received 1 ml normal saline daily; Group 2, received nicotine (1.5mg/kg); Group 3, received astaxanthin (25mg/kg); Group 4, received astaxanthin (50mg/kg); Group 5, received astaxanthin (25mg/kg) plus nicotine (1.5mg/kg); and group 6, received astaxanthin (50mg/kg) plus nicotine (1.5mg/kg). After collecting testes samples, microscopic slides were prepared at the School of Veterinary Medicine, University of Mashhad, and the prepared slides were examined under light microscopy. Results: The histological structures of the testes were normal in the control group and those receiving astaxanthin, regardless of nicotine (groups 3, 4, 5 & 6). However, group 2 that received only nicotine, showed transformed testicular histology with severe hemorrhage. Conclusion: Based on the results, nicotine caused harmful effects on the mice testes and astaxanthin appeared to protect the organs against the toxic effects of nicotine. Keyword: Astaxanthin, Balb/c mice, Nicotine toxicity, Testicular Hemorrhage.
Generic content-based audio indexing and retrieval framework

Rapid increase in the amount of the digital audio collections presenting various formats, types, durations and other parameters that the digital multimedia world refers demands a generic framework for robust and efficient indexing and retrieval based on the aural content. Moreover, from the content-based multimedia retrieval point of view, the audio information can be even more important than the visual part as it is mostly unique and significantly stable within the entire duration of the content. A generic and robust audio-based multimedia indexing and retrieval framework, which has been developed and tested under the MUVIS system, is presented. This framework supports the dynamic integration of the audio feature extraction modules during the indexing and retrieval phases and therefore provides a test-bed platform for developing robust and efficient aural feature extraction techniques. Furthermore, the proposed framework is designed based on the high-level content classification and segmentation in order to improve the speed and accuracy of the aural retrievals. Both theoretical and experimental results are finally presented, including the comparative measures of retrieval performance with respect to the visual counterpart.
Contemporary interspecific hybridization between Dracocephalum kotschyi and Dracocephalum oligadenium (Lamiaceae): Evidence from morphological, anatomical and molecular data

Dracocephalum is the second largest genus in the family Lamiaceae with about 186 species. These species are native in temperate regions of the Northern Hemisphere and occur in the territory of the extra-tropical Asia and Europe. Eight Dracocephalum species reported in Iran; these are mainly growing in the northern and central parts of the country belonging to the Irano-Turanian phytogeographical region. Dracocephalum kotschyi is an important medicinal plant . in the country. At the same time, taxonomic position of Dracocephalum oligadenium is a challenging issue. In this work morphological, anatomical and Inter Simple Sequence Repeat (ISSR) markers were used to identify these species in Iran. MDS plot based on morphological and anatomical characters, furthermore, PCoA and MST plot based on ISSR data of species revealed hybridization between D. oligadenium and D. kotschyi.
Reaching a Consensus through Participatory Design with Children: The Two-Way Approach

In this paper, we present a case study which investigates the process of reaching a consensus in a mobile game design project for children, carried on with the participatory design approach. Making consensus, here, is a matter of making group decision on one of the narrative designs produced in different themes with various techniques throughout the early stage of co-design process. We need a new methodology because neither of the methods in the relevant literature is perfectly fit to our case. Therefore we developed “Two-way design selection technique” that consisted of separate debriefing sessions with children and adults. Results showed that the new technique was successful in terms of children’s and adults’ effective participation, contribution to the co-design process as well as reaching a consensus. On the other hand, it has some limitations regarding interaction. In this sense, future studies should focus on enabling more interactive discussion opportunities.
Advanced Verification Techniques Based on Learning

Design verification poses a very practical problem during circuit synthesis. Learning based verification techniques prove to be an attractive option for verifying two circuits with internal gates having simple functional relationships. We present a verification method which employs a learning technique based on symbolic manipulation and which can more efficiently learn indirect implications. The method can also learn some useful functional implications. We also present a framework in which an indirect implication technique is integrated with an OBDD based verification tool. We present highly efficient verification results on some ISCAS circuits as well as on some very hard industrial circuits.
The Effect of the Hall Term on the Nonlinear Evolution of the Magnetorotational Instability. II. Saturation Level and Critical Magnetic Reynolds Number

The nonlinear evolution of the magnetorotational instability (MRI) in weakly ionized accretion disks, including the effect of the Hall term and ohmic dissipation, is investigated using local three-dimensional MHD simulations and various initial magnetic field geometries. When the magnetic Reynolds number, ReM ≡ v/ηΩ (where vA is the Alfvén speed, η is the magnetic diffusivity, and Ω is the angular frequency), is initially larger than a critical value ReM,crit, the MRI evolves into MHD turbulence in which angular momentum is transported efficiently by the Maxwell stress. If ReM < ReM,crit, however, ohmic dissipation suppresses the MRI, and the stress is reduced by several orders of magnitude. The critical value is in the range of 1-30 depending on the initial field configuration. The Hall effect does not modify the critical magnetic Reynolds number by much but enhances the saturation level of the Maxwell stress by a factor of a few. We show that the saturation level of the MRI is characterized by v/ηΩ, where vAz is the Alfvén speed in the nonlinear regime along the vertical component of the field. The condition for turbulence and significant transport is given by v/ηΩ ≳ 1, and this critical value is independent of the strength and geometry of the magnetic field or the size of the Hall term. If the magnetic field strength in an accretion disk can be estimated observationally and the magnetic Reynolds number v/ηΩ is larger than about 30, this would imply that the MRI is operating in the disk.
Design of a surface EMG based human-machine interface for an intelligent wheelchair

This paper presents a novel human-machine interface to control an intelligent wheelchair based on surface electromyography (sEMG) signals. Forehead sEMG signals generated by the facial movements are obtained and analysed by using a CyberLink sensing device. The autoregressive (AR) model is used to extract sEMG features. Then, the BP artificial neural network (BPANN) improved by Levenberg-Marquardt algorithm is proposed to recognize different facial movement patterns. A human-machine interface (HMI) is designed to map facial movement patterns into corresponding control commands. The experiment results show that the method is simple, real-time and at a high recognition rate. It lays the foundation for us to use forehead sEMG signals based control of wheelchairs in real world applications.
A New Mind of Wavelet Transform for Handwritten Chinese Character Recognition

Featureextraction and classification recognition are the most important parts in the process of off-line handwritten Chinese character recognition. Wavelet transform is put forward by predecessors and is a kind of feature extractional gorithm. It is said that we can use separately one dimensional wavelet transform along the rows and columns two directions and get the result. This paper presents a new direction, Wavelet transform along diagonal direction. It can solve the problem that left falling and right falling can not be directly separated. In addition this paper also proposes a new mind, that is radial Wavelet transform. Used to extract the outer border of the Chinese characters.
Longitudinal changes in recalled perceived life threat after a natural disaster

Background Post-traumatic stress disorder (PTSD) diagnosis often depends on a retrospective, self-report of exposure to a life-threatening event. Aims To examine the stability of recalled perceived life threat in a community sample exposed to a distinct stressful event. Method Five hundred and thirty-two Norwegian citizens who experienced the 2004 South-East Asia tsunami completed a self-report questionnaire 6 and 24 months post-disaster. The questionnaire measured perceived life-threat intensity, exposure, immediate stress response, psychopathology, personality dimensions, self-efficacy and social support. Results Recalled threat intensity increased from 6 to 24 months (P <0.001). Recall amplification was associated with lack of PTSD symptom improvement (P < 0.05), but not with degree of exposure, immediate stress response, mood or stress symptoms, personality, self-efficacy or social support. Conclusions Recall amplification of perceived life threat from a single stressful event occurs in the general population, it may hinder PTSD symptom improvement and it questions the diagnostic validity of PTSD.
Detecting and Classifying Rail Corrugation Based on Axle Bearing Vibration

Vienna’s tram network is regularly surveyed by an inspection tram that uses a laser light section method to measures wear of the rail head and a microphone to detect curve squeal. In order to expand the vehicle’s inspection capabilities and encompass more condition indicators for maintenance purposes, the vehicle’s accelerometers which were hitherto only employed as an inertial measurement unit are now used to monitor the vibration of the axle bearings as the tram travels across the network. The inspection tram is equipped with four triaxial accelerometers on the axle bearings of the middle bogie and another one on the bogie itself. In the first stage of the current research project, the aim is to automatically detect and classify periodic unevenness of the rail head, known as corrugation, by training a classifier on a range of vibration features. Applying this machine learning algorithm during post-processing allows the condition state of the rail head to be compared across the network.
Complete Longitudinal Analyses of the Randomized, Placebo-Controlled, Phase III Trial of Sunitinib in Patients with Gastrointestinal Stromal Tumor following Imatinib Failure

Purpose: To analyze final long-term survival and clinical outcomes from the randomized phase III study of sunitinib in gastrointestinal stromal tumor patients after imatinib failure; to assess correlative angiogenesis biomarkers with patient outcomes. Experimental Design: Blinded sunitinib or placebo was given daily on a 4-week-on/2-week-off treatment schedule. Placebo-assigned patients could cross over to sunitinib at disease progression/study unblinding. Overall survival (OS) was analyzed using conventional statistical methods and the rank-preserving structural failure time (RPSFT) method to explore cross-over impact. Circulating levels of angiogenesis biomarkers were analyzed. Results: In total, 243 patients were randomized to receive sunitinib and 118 to placebo, 103 of whom crossed over to open-label sunitinib. Conventional statistical analysis showed that OS converged in the sunitinib and placebo arms (median 72.7 vs. 64.9 weeks; HR, 0.876; P = 0.306) as expected, given the cross-over design. RPSFT analysis estimated median OS for placebo of 39.0 weeks (HR, 0.505, 95% CI, 0.262–1.134; P = 0.306). No new safety concerns emerged with extended sunitinib treatment. No consistent associations were found between the pharmacodynamics of angiogenesis-related plasma proteins during sunitinib treatment and clinical outcome. Conclusions: The cross-over design provided evidence of sunitinib clinical benefit based on prolonged time to tumor progression during the double-blind phase of this trial. As expected, following cross-over, there was no statistical difference in OS. RPSFT analysis modeled the absence of cross-over, estimating a substantial sunitinib OS benefit relative to placebo. Long-term sunitinib treatment was tolerated without new adverse events. Clin Cancer Res; 18(11); 3170–9. ©2012 AACR.
Modeling for Short-Form HTTP Adaptive Streaming Considering Memory Effect

With the rapid development of Information and Communication Technology, mobile HTTP adaptive streaming (HAS) technologies have gained popularity. Thusly, the ability to evaluate users' Quality of Experience (QoE) is important. However, changing the transmitted video quality as employed by HAS poses more psychological impact like memory effect on subjectively perceived video quality and modeling HAS QoE considering memory effect is still a challenge. In this paper, we propose a QoE model for short-form HAS video considering memory effect. In order to assess the effect that each segment has in the overall video quality, a subjective online test based on the wisdom of the crowds is conducted. The result shows primacy effect is more obvious than recency effect in short-form videos. The proposed method is validated by plenty subjective tests and the simulation results show that our QoE model for short-form video is powerful.
Arms Race between Enveloped Viruses and the Host ERAD Machinery

Enveloped viruses represent a significant category of pathogens that cause serious diseases in animals. These viruses express envelope glycoproteins that are singularly important during the infection of host cells by mediating fusion between the viral envelope and host cell membranes. Despite low homology at protein levels, three classes of viral fusion proteins have, as of yet, been identified based on structural similarities. Their incorporation into viral particles is dependent upon their proper sub-cellular localization after being expressed and folded properly in the endoplasmic reticulum (ER). However, viral protein expression can cause stress in the ER, and host cells respond to alleviate the ER stress in the form of the unfolded protein response (UPR); the effects of which have been observed to potentiate or inhibit viral infection. One important arm of UPR is to elevate the capacity of the ER-associated protein degradation (ERAD) pathway, which is comprised of host quality control machinery that ensures proper protein folding. In this review, we provide relevant details regarding viral envelope glycoproteins, UPR, ERAD, and their interactions in host cells.
Mycosis Fungoides Presentation in Emergency

We present the case of a young lady who presented to the department of emergency medicine (DEM) for evaluation of painful breast swelling and skin indurations involving 90% of the body surface. She stayed long in the DEM for 3 days and managed for breast abscess she was consulted to dermatology for evaluation of skin lesions and prelimi- nary diagnosed as rare skin T cell lymphoma. Final diagnosis based on clinical and histopathological was Mycosis Fun- goids (MF). This case reveals that prompt referral from the DEM to the concerned speciality even for the rare type of dis- eases like MF can facilitate diagnosis and management and overall positive impact on disease outlook. Our patient was fi- nally admitted under oncology unit and managed appropriately.
Tensor decomposition of dense SIFT descriptors in object recognition

In machine vision, Scale-invariant feature transform (SIFT) and its variants have been widely used in image classification task. How- ever, the high dimensionality nature of SIFT features, usually in the or- der of multiple thousands per image, would require careful consideration in place to achieve accurate and timely categorization of objects within images. This paper explores the possibility of processing SIFT features as tensors and uses tensor decomposition techniques on high-order SIFT tensors for dimensionality reduction. The method focuses on both accu- racy and efficiency aspects and the validation result with the Caltech 101 dataset confirms the improvement with notable margins.
Combining functional and imperative programming for multicore software: An empirical study evaluating Scala and Java

Recent multi-paradigm programming languages combine functional and imperative programming styles to make software development easier. Given today's proliferation of multicore processors, parallel programmers are supposed to benefit from this combination, as many difficult problems can be expressed more easily in a functional style while others match an imperative style. Due to a lack of empirical evidence from controlled studies, however, important software engineering questions are largely unanswered. Our paper is the first to provide thorough empirical results by using Scala and Java as a vehicle in a controlled comparative study on multicore software development. Scala combines functional and imperative programming while Java focuses on imperative shared-memory programming. We study thirteen programmers who worked on three projects, including an industrial application, in both Scala and Java. In addition to the resulting 39 Scala programs and 39 Java programs, we obtain data from an industry software engineer who worked on the same project in Scala. We analyze key issues such as effort, code, language usage, performance, and programmer satisfaction. Contrary to popular belief, the functional style does not lead to bad performance. Average Scala run-times are comparable to Java, lowest run-times are sometimes better, but Java scales better on parallel hardware. We confirm with statistical significance Scala's claim that Scala code is more compact than Java code, but clearly refute other claims of Scala on lower programming effort and lower debugging effort. Our study also provides explanations for these observations and shows directions on how to improve multi-paradigm languages in the future.
Minimal-invasive magnetic heating of tumors does not alter intra-tumoral nanoparticle accumulation, allowing for repeated therapy sessions: an in vivo study in mice

Localized magnetic heating treatments (hyperthermia, thermal ablation) using superparamagnetic iron oxide nanoparticles (MNPs) continue to be an active area of cancer research. For generating the appropriate heat to sufficiently target cell destruction, adequate MNP concentrations need to be accumulated into tumors. Furthermore, the knowledge of MNP bio-distribution after application and additionally after heating is significant, firstly because of the possibility of repeated heating treatments if MNPs remain at the target region and secondly to study potential adverse effects dealing with MNP dilution from the target region over time. In this context, little is known about the behavior of MNPs after intra-tumoral application and magnetic heating. Therefore, the present in vivo study on the bio-distribution of intra-tumorally injected MNPs in mice focused on MNP long term monitoring of pre and post therapy over seven days using multi-channel magnetorelaxometry (MRX). Subsequently, single-channel MRX was adopted to study the bio-distribution of MNPs in internal organs and tumors of sacrificed animals. We found no distinct change of total MNP amounts in vivo during long term monitoring. Most of the MNP amounts remained in the tumors; only a few MNPs were detected in liver and spleen and less than 1% of totally injected MNPs were excreted. Apparently, the application of magnetic heating and the induction of apoptosis did not affect MNP accumulation. Our results indicate that MNP mainly remained within the injection side after magnetic heating over a seven-days-observation and therefore not affecting healthy tissue. As a consequence, localized magnetic heating therapy of tumors might be applied periodically for a better therapeutic outcome.
Watermarking Algorithm using Genetic Algorithm and HVS

In this work, a watermarking algorithm is proposed using Genetic algorithm and discrete wavelet transformation. The algorithm proposed is to improve both robustness and fidelity of the watermarked image. Fuzzy Inference system is used to determine the embedding strength based on HVS properties of the image. To test the robustness different attacks are performed and the NC (Normalized cross correlation) is computed. The algorithms showed better results and good quality for watermarked image. General Terms Genetic Algorithms, Watermarking, Security, Algorithm, Fuzzy logic.