Miracle-dz/UniFAR-FTUs huggingface dataset:
WSISA: Making Survival Prediction from Whole Slide Histopathological Images

Image-based precision medicine techniques can be used to better treat cancer patients. However, the gigapixel resolution of Whole Slide Histopathological Images (WSIs) makes traditional survival models computationally impossible. These models usually adopt manually labeled discriminative patches from region of interests (ROIs) and are unable to directly learn discriminative patches from WSIs. We argue that only a small set of patches cannot fully represent the patients survival status due to the heterogeneity of tumor. Another challenge is that survival prediction usually comes with insufficient training patient samples. In this paper, we propose an effective Whole Slide Histopathological Images Survival Analysis framework (WSISA) to overcome above challenges. To exploit survival-discriminative patterns from WSIs, we first extract hundreds of patches from each WSI by adaptive sampling and then group these images into different clusters. Then we propose to train an aggregation model to make patient-level predictions based on cluster-level Deep Convolutional Survival (DeepConvSurv) prediction results. Different from existing state-of-the-arts image-based survival models which extract features using some patches from small regions of WSIs, the proposed framework can efficiently exploit and utilize all discriminative patterns in WSIs to predict patients survival status. To the best of our knowledge, this has not been shown before. We apply our method to the survival predictions of glioma and non-small-cell lung cancer using three datasets. Results demonstrate the proposed framework can significantly improve the prediction performance compared with the existing state-of-the-arts survival methods.
HyperNetworks with statistical filtering for defending adversarial examples

Deep learning algorithms have been known to be vulnerable to adversarial perturbations in various tasks such as image classification. This problem was addressed by employing several defense methods for detection and rejection of particular types of attacks. However, training and manipulating networks according to particular defense schemes increases computational complexity of the learning algorithms. In this work, we propose a simple yet effective method to improve robustness of convolutional neural networks (CNNs) to adversarial attacks by using data dependent adaptive convolution kernels. To this end, we propose a new type of HyperNetwork in order to employ statistical properties of input data and features for computation of statistical adaptive maps. Then, we filter convolution weights of CNNs with the learned statistical maps to compute dynamic kernels. Thereby, weights and kernels are collectively optimized for learning of image classification models robust to adversarial attacks without employment of additional target detection and rejection algorithms. We empirically demonstrate that the proposed method enables CNNs to spontaneously defend against different types of attacks, e.g. attacks generated by Gaussian noise, fast gradient sign methods (Goodfellow et al., 2014) and a black-box attack(Narodytska & Kasiviswanathan, 2016).
Predictive analytics based on CEP for logistic of sensitive goods

Reducing the amount of lost and damaged perishable goods (food and medicines) during transportation and storage represents a substantial global challenge, which imply the implementation of cold chain monitoring at all levels of the supply chains. The main objective of this work is to develop an IoT enabled infrastructure, which supports the development of smart transportation specific applications. The proposed infrastructure contains an emulator, which can be used for emulating the conditions inside a truck during the transportation process and some CEP based tools for processing the data generated by the sensors.
An overview of the COBRA-ABS high level synthesis system for multi-FPGA systems

This paper presents an overview of the COBRA-ABS behavioural high-level synthesis tool. COBRA-ABS has been designed to synthesise custom architectures for arithmetic intensive algorithms, specified in C, for implementation on multi-FPGA Custom Computing Machine (FCCM) platforms. It performs globally optimising high level synthesis using simulated annealing, integrating all partitioning, scheduling, binding and allocation operations in one optimisation step, and has been designed to be retargetable to different board architectures. COBRA-ABS synthesises a custom Very Long Instruction Word (VLIW) architecture for the given algorithm for implementation on the specified FCCM. The paper gives details of the architectural issues which have influenced the design of the tool, looks at how it fits into the overall design flow and reviews the fundamental concepts and implementation of the globally optimising synthesis methodology. To illustrate the operation of the tool, a number of results for synthesis of a Fast Fourier Transform algorithm are presented.
Estimation of gait stability based on accelerometer signals

An estimation of gait stability based on accelerometer signal is presented. The walking process of a human body is a complex task that involves the muscular, joint and nervous systems. The gait cycle is divided into swing and stance phases. Gait stability is defined as repetition of the gait cycle with minimum variability. In order to assets the gait stability a series of parameter are estimated, such parameters include, duration of the gait cycle, length of the left and right step, average speed of the gait and number of samples per cycle. The first step toward establish gait stability is estimated the beginning and ending of a cycle. This process is achieved by a series of filter that isolated 2Hz component that is produce by heel strike. Once the cycles have been localized, the rest of the parameters are estimated. The algorithm was tested on a set of 40 healthy persons from ages 20 to 59. The results show that the stability decreases with age, as expected, since our neuromotor system deteriorates with age.
Pre-service teachers’ motivation, sense of teaching efficacy, and expectation of reality shock

The present study investigated how pre-service teachers’ motivation and their sense of teaching efficacy influence their expectation about reality shock during the first year of professional teaching. A total of 533 pre-service teachers at a state university in the US Midwest participated in this study. The results showed that the pre-service teachers’ expectation of reality shock was negatively related to teacher efficacy and intrinsic motivation while it was positively related to introjected and external motivation. The results of a hierarchical regression analysis revealed that pre-service teachers’ sense of efficacy and introjected motivation were strong predictors of their expectation of reality shock, when gender difference was controlled for. There was an interaction effect between intrinsic motivation and teachers’ sense of efficacy in predicting the reality shock expectation. We discussed the educational implications for future research in an endeavour to reduce the reality shock among novice teachers.
A Cellular Automata-based Model for Simulating Restitution Property in a Single Heart Cell

Ventricular fibrillation is the cause of the most sudden mortalities. Restitution is one of the specific properties of ventricular cell. The recent findings have clearly proved the correlation between the slope of restitution curve with ventricular fibrillation. This; therefore, mandates the modeling of cellular restitution to gain high importance. A cellular automaton is a powerful tool for simulating complex phenomena in a simple language. A cellular automaton is a lattice of cells where the behavior of each cell is determined by the behavior of its neighboring cells as well as the automata rule. In this paper, a simple model is depicted for the simulation of the property of restitution in a single cardiac cell using cellular automata. At first, two state variables; action potential and recovery are introduced in the automata model. In second, automata rule is determined and then recovery variable is defined in such a way so that the restitution is developed. In order to evaluate the proposed model, the generated restitution curve in our study is compared with the restitution curves from the experimental findings of valid sources. Our findings indicate that the presented model is not only capable of simulating restitution in cardiac cell, but also possesses the capability of regulating the restitution curve.
Cloning and sequence analysis of the Pichia pastoris TRP1, IPP1 and HIS3 genes

The Pichia pastoris TRP1 and HIS3 genes were cloned by complementation of the Saccharomyces cerevisiae trp1 and his3 mutants, respectively, and their nucleotide sequence was determined. The P. pastoris TRP1 gene includes an open reading frame (ORF) of 714 nucleotides corresponding to a polypeptide of 237 amino acids whose sequence shares about 40% identity with that of TRP1 encoding proteins in other yeast species. DNA sequencing showed that an ORF of 858 nucleotides, encoding a protein of 285 amino acids with high homology to inorganic pyrophosphatases (IPP1), is located downstream of the P. pastoris TRP1 gene. Both genes converge in this chromosomal region, showing a genetic organization analogous to that found in the Kluyveromyces lactis genome. The P. pastoris HIS3 gene possesses an ORF of 675 nucleotides, encoding a polypeptide of 224 amino acids which shows 74·1% identity to the homologous S. cerevisiae protein. The hexameric consensus GCN4 binding sequence (TGACTC), characteristic of many amino acid biosynthetic genes, is present in the promoter region. The TRP1 and IPP1 sequences were deposited in the EMBL databank under Accession Number AJ001000. The Accession Number of the HIS3 gene is U69170. © 1998 John Wiley & Sons, Ltd.
Augmented non-visual distance sensing with the EyeCane

How can we sense distant objects without vision? Vision is the main distal sense used by humans, thus impairing distance and spatial perception for sighted individuals in the dark or for people with visual impairments. We suggest augmenting distance perception via other senses such as using auditory or haptic cues, and have created the EyeCane for this purpose. The EyeCane is a minimal Sensory Substitution Device that enables users to perform tasks such as distance estimation, and obstacle detection and avoidance up to 5m away on-visually. In the demonstration, visitors will receive a brief training with the device, and then use it to detect objects and estimate distances while blindfolded.
Beyond Minimally Important Change: Defining a Successful Outcome of Physical Therapy for Patients With Low Back Pain

Study Design. Prospective, longitudinal cohort study Objective. To examine the validity of a threshold that has been used to define a successful outcome for patients with low back pain (LBP), undergoing nonsurgical rehabilitation based on a 50% improvement on the Modified Oswestry disability index (ODI). Summary of Background Data. Making research findings interpretable is a goal of evidence-based practice. One attempt to improve interpretability is reporting treatment results as the percentage of patients achieving a threshold level of improvement within treatment groups along with mean between-group differences. The most recommended threshold is the minimum clinically important difference of the outcome tool. For clinical conditions with favorable natural histories such as LBP, thresholds requiring more than minimal improvement may be preferable for defining success. Methods. Patients with LBP receiving 4 weeks of physical therapy were examined. The ODI and measures of pain, fear-avoidance beliefs, and demographic characteristics were recorded at baseline and after treatment. A 15-point global rating of change was also completed after treatment. The percent ODI change with treatment was computed and compared between groups known to have different prognoses. The percent ODI change was compared to the global rating of change to determine the accuracy of various thresholds of success based on the percent ODI change. Results. A total of 243 subjects (mean age 37.2 ± 11.4 years, 44.9% female) were included. Mean percent ODI change was 43.1% (±40.5), and 109 subjects (44.9%) had a successful outcome (≥50% ODI improvement). As hypothesized, baseline factors with known prognostic importance were less likely to be present in subjects with a successful outcome. The 50% ODI improvement threshold for success had high sensitivity (0.84; 95% CI: 0.79, 0.88) and specificity (0.89; 95% CI: 0.85, 0.93) when compared with success based on the global rating of change. No other percent improvement threshold for the ODI had a higher accuracy than the 50% threshold when compared to the global rating of change. Conclusion. A threshold of 50% improvement on the ODI may be a valid measure for defining a successful outcome for patients with LBP.
Quantum circuit design of 8 /spl times/ 8 discrete Hartley transform

In this paper, the 8 /spl times/ 8 discrete Hartley transform will be implemented by using quantum elementary gates such as controlled NOT gates and Hadamard gates. Two steps involved are as follows: first, the discrete Hartley transform matrix is decomposed into the product of several sparse unitary matrices using the structure of fast Hartley transform algorithm. Then, each sparse matrix is implemented by elementary quantum gates and cascade them to obtain the final circuit. The design results show that the proposed design method has less circuit complexity than the conventional Cybenko's method.
Biomechanics analysis of human walking with load carriage.

BACKGROUND Comprehensive analysis of the inherent laws and the biomechanic principles of human walking with load carriage and building kinematics, and kinematics model of human walking with load carriage, are very meaningful for the development of devices and apparatus that are related to human walking with load carriage, such as a lower limb exoskeleton. OBJECTIVE The gait experiment of human walking with load carriage is designed and performed in this paper. METHODS The obtained video is marked and analyzed by using SIMI motion analytical software. The space motion coordinates at each body's mark point that is needed in the kinematics model of established human walking with load carriage is obtained. Based on inverse kinematics, a dynamic model of human walking with load carriage is established. The SPSS statistical analysis software is used for statistical processing for determining key gait parameters. RESULTS The influence of load and speed on the walking gait parameters is analyzed systematically. CONCLUSIONS The method provides a theoretical basis for the design of an exoskeleton.
1.5–3.3 GHz, 0.0077 mm2, 7 mW All-Digital Delay-Locked Loop With Dead-Zone Free Phase Detector in $0.13~\mu \text{m}$ CMOS

A 1.5–3.3 GHz, 7 mW, all-digital delay-locked loop (ADDLL) designed in a UMC 130-nm CMOS technology is presented in this paper. The proposed ADDLL uses the modified successive approximation register to control a NAND-based coarse delay line, which enables wider operating frequency range and small intrinsic delay. The inverter-based fine delay line is controlled by an XOR-based up/down counter with dead-zone free phase detector to overcome the dead-zone problem of conventional phase detectors. The D-type flip-flops in the phase detector are modified to detect sub-ps level delay difference between the input and output clocks, so that a delay resolution of better than 1 ps is achieved in the proposed design. The combination of both coarse and fine locking processes gives outstanding performance in terms of residual phase difference and output jitter. The overall design occupies 0.0077 mm2 area. The experimental results show that the peak-to-peak and root mean square jitters are 12 and 1.629 ps at 3.3 GHz, respectively, while the input jitter is 2.6 ps peak-to-peak and 612 fs rms.
Identification of Yersinia enterocolitica genes affecting survival in an animal host using signature‐tagged transposon mutagenesis

Pathogenic Yersinia species are associated with both localized and systemic infections in mammalian hosts. In this study, signature‐tagged transposon mutagenesis was used to identify Yersinia enterocolitica genes required for survival in a mouse model of infection. Approximately 2000 transposon insertion mutants were screened for attenuation. This led to the identification of 55 mutants defective for survival in the animal host, as judged by their ability to compete with the wild‐type strain in mixed infections. A total of 28 mutants had transposon insertions in the virulence plasmid, validating the screen. Two of the plasmid mutants with severe virulence defects had insertions in an uncharacterized region. Several of the chromosomal insertions were in a gene cluster involved in O‐antigen biosynthesis. Other chromosomal insertions identified genes not previously demonstrated as being required for in vivo survival of Y. enterocolitica. These include genes involved in the synthesis of outer membrane components, stress response and nutrient acquisition. One severely attenuated mutant had an insertion in a homologue of the pspC gene (phage shock protein C) of Escherichia coli. The phage shock protein operon has no known biochemical or physiological function in E. coli, but is apparently essential for the survival of Y. enterocolitica during infection.
Radiations évolutives, "innovations clés" et notions d'espèces dans le genre Euphorbia L. à Madagascar

Geant parmi les plantes a fleurs, le genre Euphorbia L. (~ 2000 taxa) est caracterise par une diversite morphologique impressionnante et une distribution cosmopolite. Toutes les especes d’euphorbes presentent neamoins une inflorescence tres condensee, qui mime une fleur hermaphrodite et constitue la synapomorphie morphologique du genre. La variabilite morphologique des euphorbes, notamment lorsqu’elle est mise en relation avec leurs milieux de vie, constitue un sujet d’etude a priori particulierement prometteur pour amorcer une description formelle des liens entre les plantes et leurs conditions environnementales. Malheureusement, ces travaux sont limites par notre connaissance parcellaire du genre tant au niveau de son alpha-taxonomie que de son histoire evolutive. Cette etude a utilise l’exemple des euphorbes malgaches (~ 10% de la richesse specifique du genre) pour explorer les notions d’especes et de diversification dans le genre Euphorbia. En premier lieu, nous avons revise la taxonomie d’un groupe d’euphorbe malgache encore peu documente, le groupe d’E. Pachysantha ; deux especes nouvelles pour la science ont ete decrites. En vue de fournir une methode d’identification sure et rapide des especes d’euphorbes malgaches, nous avons teste l’approche du barcoding ADN ; le succes rencontre nous permet de suggerer la generalisation de l’utilisation de cet outil a l’ensemble du genre. Nous avons etudie la diversification dans le temps d’un clade d’euphorbes malgaches hyper-diversifie, le clade GDD (Euphorbia sections Goniostema, Denisophorbia et Deuterocalli). Les reconstructions hylogenetiques inferees a partir de huit regions de l’ADN nucleaire et chloroplastique et d’un echantillonnage representatif de la diversite specifique du clade, ont ete placees dans un cadre chronologique. A l’aide de methodes statistiques, nous avons caracterise le tempo de diversification du clade GDD au cours du temps. Dans le but d’elucider les liens entre la diversite morphologique des especes de ce clade et leurs conditions environnementales, nous avons teste les relations entre quelques grands traits morphologiques et un jeu de variables climatiques ; des associations entre l’evolution de la succulence au sein de la section Goniostema et certaines variables climatiques ont ete mises au jour. Compte tenu des avancees recentes dans la connaissance du genre Euphorbia, nous suggerons une extension de tous ces types de travaux a l’echelle du genre.
SCLEROSTIN IMMUNOREACTIVITY INCREASES WITHIN THE CORTICAL BONE OSTEOCYTES IN THE FEMUR OF AGING MICE

Sclerostin, a secreted glycoprotein, is known to down-regulate osteocyte differentiation from osteoblasts and acts as a negative modulator of bone formation. It is well established that serum sclerostin levels increase with age but the relationship between changes of cellular expression of sclerostin with age is not well known. Immunohistochemical staining and confocal microscopic analysis of sclerostin immunoreactivity (sclerostin-IR) in the femurs of 4, 9, and 24 month old adult C3H/HeJ male mice was performed. Detectable levels of sclerostin-IR were found in cortical bone osteocytes of the femur in all age groups using an antibody directed against sclerostin. Phalloidin and DAPI were used to mark all osteocytes in cortical bone to detect osteocyte/ sclerostin-IR colocalization. Sclerostin-negative and sclerostin-positive expressing osteocytes were detected in close proximity throughout the cortical bone. Only a subset of osteocytes expressed sclerostin and this ratio of sclerostin positive osteocytes increased with age, from 38.5 ± 1.6% to 43 ± 3.6% to 49 ± 2.3% in young, middle-aged, and old mice, respectively. Understanding the potential mechanisms that drive these age-related changes may influence the therapeutic potential of age-related diseases like osteoporosis. Introduction Aging inevitability comes with the heightened likelihood of bone degeneration, as bones become weaker (Zioupos 1998). As a result, age brings the increased risk of bone diseases like osteoporosis, the most common bone disease in aging humans. Osteoporotic patients show symptoms of significantly weakened bone strength, low bone mineral density (BMD), and an increased predisposition to fracture (Recker 2004; Pietschmann 2008). The two current primary
Spatial and Resource Factors Influencing High Microbial Diversity in Soil

ABSTRACT To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson’s index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.