Miracle-dz/UniFAR-FTUs huggingface dataset:
Multidimensional Gene Set Analysis of Genomic Data

Understanding the functional implications of changes in gene expression, mutations, etc., is the aim of most genomic experiments. To achieve this, several functional profiling methods have been proposed. Such methods study the behaviour of different gene modules (e.g. gene ontology terms) in response to one particular variable (e.g. differential gene expression). In spite to the wealth of information provided by functional profiling methods, a common limitation to all of them is their inherent unidimensional nature. In order to overcome this restriction we present a multidimensional logistic model that allows studying the relationship of gene modules with different genome-scale measurements (e.g. differential expression, genotyping association, methylation, copy number alterations, heterozygosity, etc.) simultaneously. Moreover, the relationship of such functional modules with the interactions among the variables can also be studied, which produces novel results impossible to be derived from the conventional unidimensional functional profiling methods. We report sound results of gene sets associations that remained undetected by the conventional one-dimensional gene set analysis in several examples. Our findings demonstrate the potential of the proposed approach for the discovery of new cell functionalities with complex dependences on more than one variable.
) surface: Density Functional Theory

The atomic geometry and electronic structure of a single and double-layer of Thallium (Tl) on the Si(111)-( 7 √ × 3 √ ) surface have been studied using density functional theory. For Tl layer, we considered three cases: (i) Tl single layer as H3 (Tl is directly above a fourth-layer Si atom) and T4 (Tl is directly above a second-layer Si atom) sites, (ii) Tl double layer as H3–T4 (the first Tl layer at H3 site while the second layer at the T4 site) and T4–H3 (the first Tl layer at T4 site while the second layer at the H3 site) sites, and (iii) Tl double layer as rectangular (rect) and hexagonal (hex) sites. We have calculated the electronic band structures and the electronic charge densities of the energetically favourable cases. While the Tl single-layer makes the Si(111) surface semiconductor character, the double-layer Tl makes electronically the Si (111) surface metallic which agrees with the recent experimental measurements. ARTICLE HISTORY Received 18 January 2018 Accepted 21 February 2019
Implementing distribution and persistence aspects with aspectJ

This paper reports our experience using AspectJ, a general-purpose aspect-oriented extension to Java, to implement distribution and persistence aspects in a web-based information system. This system was originally implemented in Java and restructured with AspectJ. Our main contribution is to show that AspectJ is useful for implementing several persistence and distribution concerns in the application considered, and other similar applications. We have also identified a few drawbacks in the language and suggest some minor modifications that could significantly improve similar implementations. Despite the drawbacks, we argue that the AspectJ implementation is superior to the pure Java implementation. Some of the aspects implemented in our experiment are abstract and constitute a simple aspect framework. The other aspects are application specific but we suggest that different implementations might follow the same aspect pattern. The framework and the pattern allow us to propose architecture-specific guidelines that provide practical advice for both restructuring and implementing certain kinds of persistent and distributed applications with AspectJ.
Device-free positioning using a ceiling-based visible light sensing system

OF THE THESIS Device-Free Positioning Using a Ceiling-Based Visible Light Sensing System By MINITHA JAWAHAR Thesis Director: Marco Gruteser Positioning systems to determine the coordinates of a person inside a building or a room have been gaining popularity in recent years. Device-free positioning can be of use in many applications; for example, in a smart home, it would be useful for the lights in the bedroom to turn on once a person enters, and for it to turn off once they get into bed. However, existing solutions need expensive hardware installation, or require the user to hold a device to act like a receiver in order to be positioned, which is inconvenient. In addition, due to factors such as multipath and wall attenuation in closed areas, common localization strategies such as trilateration and triangulation struggle to provide a low localization error. LED bulbs are steadily becoming ubiquitous in modern society due to their energy efficiency and shelf life, so using visible light sensing for indoor localization is a good way to reduce the amount of external hardware needed to be installed. When a person is in a particular location in the room, shadows form on the floor due to the LED lamps on the ceiling. A highly sensitive prototype is designed and developed to detect the exact position and length of these shadows. These unique shadow patterns can be used in turn to estimate the position of the person. Using this setup, a low localization error of 2 feet is obtained. Finally, this setup is compared to existing technology, showing it to be more suitable for these applications while leveraging existing infrastructure.
Stability analyses of wheelchair robot based on “Human-in-the-Loop” control theory

The eight leg-wheels hybrid stair climbing wheelchair robot, was developed for aged and disabled person helping them moving freely in structured three-dimensional environment. The efforts of motion automation have been partly implemented, such as climbing up/down the stairs, traversing slope and obstacles, nevertheless without carrying the person. The person is the passenger, also the control object, as the same time the pilot of the wheelchair. Since the person in wheelchair changes his/her posture uncertainly, it is difficult to obtain a better solution of control only by thinking the model of wheelchair. This paper uses the wheelchair as the platform, and describes the entire closed-loop modeling and stability analysis together with its passenger, based on the control theory of “Human-in-the-Loop”.
The effect of endothelialization on the epidermal differentiation in human three-dimensional skin constructs - A morphological study.

INTRODUCTION Inducing vascularization in three-dimensional skin constructs continues to be difficult. In this study, two variations of human full-thickness skin constructs were examined. Type KCFB consists of keratinocytes (epidermal equivalent) and fibroblasts that were embedded in a collagen matrix (dermal equivalent). Type KCFB-EC consists of keratinocytes as well as fibroblasts and vascular endothelial cells. The epidermal equivalent of KCFB-EC constructs underwent cellular alterations in their differentiation possibly induced by the presence of endothelial cells. The objective of the study was to assess the effect of endothelial cells, i.e., endothelialization of the dermal equivalent on the differentiation of keratinocytes by comparing the morphology and ultrastructure of the two types of skin constructs, as well as to excised normal human skin. HYPOTHESIS The differentiation of keratinocytes is influenced by the presence of endothelial cells. METHODS, PATIENTS, MATERIAL KCFB constructs (keratinocytes, fibroblasts) and KCFB-EC skin constructs(kera-tinocytes, fibroblasts, endothelial cells) were prepared according to Küchler et al. [25]. After two weeks, the skin constructs were processed for analysis by light microscopy (LM) and electron microscopy (TEM), followed by quantitative, semi-quantitative as well as qualitative assessment. For comparison, analysis by LM and TEM of excised normal human skin was also performed. RESULTS Both KCFB and KCFB-EC skin constructs and the human skin had all strata of stratified soft-cornified epidermis present. The comparison of the respective layers of the skin constructs brought the following characteristics to light: The KCFB-EC constructs had significantly more mitotic cells in the stratum spinosum, more cell layers in the stratum granulosum and more keratohyalin granules compared to KCFB skin constructs. Additionally, the epidermal architecture was unorganized in the endothelialized constructs and features of excessive epidermal differentiation appeared in KCFB-EC skin constructs. CONCLUSION The endothelialization of the dermal equivalent caused changes in the differentiation of the epidermis of KCFB-EC skin constructs that may be interpreted as an unbalanced, i.e., uncontrolled or enhanced maturation process.
A cross‐sectional evaluation of the validity of a smartphone otoscopy device in screening for ear disease in Nepal

Hearing loss is a neglected international health problem. The greatest burden of ear disease is in low‐income countries where there is also a lack of resources. In this context, screening for otological disease may be worthwhile. Cupris© has developed an otoscopy device that offers the possibility of low‐cost mass screening in remote communities. We evaluated the validity of this device in diagnosing ear disease and in determining whether referral to an ENT centre is warranted.
Model‐based reconstruction for T1 mapping using single‐shot inversion‐recovery radial FLASH

Quantitative parameter mapping in MRI is typically performed as a two‐step procedure where serial imaging is followed by pixelwise model fitting. In contrast, model‐based reconstructions directly reconstruct parameter maps from raw data without explicit image reconstruction. Here, we propose a method that determines T1 maps directly from multi‐channel raw data as obtained by a single‐shot inversion‐recovery radial FLASH acquisition with a Golden Angle view order. Joint reconstruction of a T1, spin‐density and flip‐angle map is formulated as a nonlinear inverse problem and solved by the iteratively regularized Gauss‐Newton method. Coil sensitivity profiles are determined from the same data in a preparatory step of the reconstruction. Validations included numerical simulations, in vitro MRI studies of an experimental T1 phantom, and in vivo studies of brain and abdomen of healthy subjects at a field strength of 3 T. The results obtained for a numerical and experimental phantom demonstrated excellent accuracy and precision of model‐based T1 mapping. In vivo studies allowed for high‐resolution T1 mapping of human brain (0.5–0.75 mm in‐plane, 4 mm section thickness) and liver (1.0 mm, 5 mm section) within 3.6–5 s. In conclusion, the proposed method for model‐based T1 mapping may become an alternative to two‐step techniques, which rely on model fitting after serial image reconstruction. More extensive clinical trials now require accelerated computation and online implementation of the algorithm. © 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26, 254–263, 2016
Solution Processing of Small Molecule Organic Semiconductors: From In situ Investigation to the Scalable Manufacturing of Field Effect Transistors

Solution Processing of Small Molecule Organic Semiconductors: From In situ Investigation to the Scalable Manufacturing of Field Effect Transistors Muhammad Rizwan Khan Niazi Solution-processed organic field effect transistors (OFETs) are strong contenders to become a part of electronic circuitry because of being compatible with cost-effective high throughput roll-to-roll technology. Single crystal based OFETs can fulfill the stringent performance demands in terms of carrier mobility, switching speed, etc. and uniformity over large areas, but these suffer from major scale-up challenges. To achieve device performance approaching that of single crystals with scalable and industry-compatible manufacturing of small molecule organic semiconductors (OSCs) based FETs, requires understanding and ultimately controlling the solution-to-solid phase transformation phenomenon to produce high-quality thin films. In this thesis, we develop an understanding of the process-structure-property-performance relationship in OSCs that bring fresh insights into the nature of solution crystallization and lead to novel ways to control OSC crystallization, and finally help achieve fabrication of high-performance OFETs by scalable, high throughput and industry-compatible blade coating method. We probe the solution crystallization of OSCs by employing a suite of ex & in situ characterization techniques. This leads us to an important finding that OSC molecules aggregate to form a dense amorphous intermediate state and nucleation happens from this intermediate state during blade coating under a wide window of coating
Study of optical fiber as new radiation dosimeter

New preliminary results obtained in the study of optical fiber properties, for the development of a new radiation dosimeter sensitive to high energy photon beams, are presented in this paper. Optical fiber has been exposed to high energy photon beam generated by ALIN 10 linear accelerator. The exposure of the optical fibers to the high energy photon beam has produced an increase in radiation induced attenuation (RIA), a physical quantity used to exposure dose quantification. Attenuation in the optical fibers was measured before, during and after irradiation, for two wavelength values. The experimental results show that the optical fiber has a good response to radiation exposure and, therefore, can be useful in achieving the purposes of this study.
High Performance and Low Power Hardware Implementation for Cryptographic Hash Functions

Since hash functions are cryptography's most widely used primitives, efficient hardware implementation of hash functions is of critical importance. The proposed high performance hardware implementation of the hash functions used sponge construction which generates desired length digest, considering two key design metrics: throughput and power consumption. Firstly, this paper introduces unfolding transformation which increases the throughput of hash function and pipelining and parallelism design techniques which reduce the delay. Secondly, we propose a frequency trade-off technique which can give us a scope of frequency value for making a trade-off between low dynamic power consumption and high throughput. Finally, we use load-enable based clock gating scheme to eliminate wasted toggle rate of signals in the idle mode of hash encryption system. We demonstrated the proposed design techniques by using 45 nm CMOS technology at 10 MHz. The results show that we can achieve up to 47.97 times higher throughput, 6.31% delay reduction, and 13.65% dynamic power reduction.
Efficacy of cognitive behavioural therapy for children and adolescents with traumatic brain injury

Purpose. Behavioural and psychological disorders after traumatic brain injury (TBI) are very common. The purposes of this study were to estimate the frequency of these problems in our sample, to evaluate the effectiveness of cognitive behavioural therapy (CBT) and to assess the predictive value of important clinical variables for the treatment outcome. Method. Forty patients aged 4–18 years were included in this study. Twenty-eight patients received CBT at our Institute (clinical group), while 12 patients did not receive any treatment at all (control group). The CBCL/4-18 and the VABS were administered to parents at the beginning of the study and after 12 months. Results. A high frequency of psychological and behavioural problems was found in both groups of patients. After CBT, the clinical group showed a significant advantage on several CBCL scales and a greater increase in adaptive behaviour on the VABS Socialisation domain. The Glasgow Coma Scale score, days of unconsciousness and age at injury were not predictors of the severity of psychological problems at the follow-up for the patients of the clinical group. Conclusions. Our results suggest that CBT is an effective intervention for young patients with psychological problems after TBI.
An Overview of Evolutionary Algorithms for Parameter Optimization

Three main streams of evolutionary algorithms (EAs), probabilistic optimization algorithms based on the model of natural evolution, are compared in this article: evolution strategies (ESs), evolutionary programming (EP), and genetic algorithms (GAs). The comparison is performed with respect to certain characteristic components of EAs: the representation scheme of object variables, mutation, recombination, and the selection operator. Furthermore, each algorithm is formulated in a high-level notation as an instance of the general, unifying basic algorithm, and the fundamental theoretical results on the algorithms are presented. Finally, after presenting experimental results for three test functions representing a unimodal and a multimodal case as well as a step function with discontinuities, similarities and differences of the algorithms are elaborated, and some hints to open research questions are sketched.
Hindered diffusion of MRI contrast agents in rat brain extracellular micro-environment assessed by acquisition of dynamic T1 and T2 maps.

The knowledge of brain tissues characteristics (such as extracellular space and tortuosity) represents valuable information for the design of optimal MR probes for specific biomarkers targeting. This work proposes a methodology based on dynamic acquisition of relaxation time maps to quantify in vivo MRI contrast agent concentration after intra-cerebral injection in rat brain. It was applied to estimate the hindered diffusion in brain tissues of five contrast agents with different hydrodynamic diameters (Dotarem(®) ≈ 1 nm, P846 ≈ 4 nm, P792 ≈ 7 nm, P904 ≈ 22 nm and Gd-based emulsion ≈ 170 nm). In vivo apparent diffusion coefficients were compared with those estimated in an obstacle-free medium to determine brain extracellular space and tortuosity. At a 2 h imaging timescale, all contrast agents except the Gd-based emulsion exhibited significant diffusion through brain tissues, with characteristic times compatible with MR molecular imaging (<70 min to diffuse between two capillaries). In conclusion, our experiments indicate that MRI contrast agents with sizes up to 22 nm can be used to perform molecular imaging on intra-cerebral biomarkers. Our quantification methodology allows a precise estimation of apparent diffusion coefficients, which is helpful to calibrate optimal timing between contrast agent injection and MRI observation for molecular imaging studies.
Energy Conservation Scheme for IEEE 802.15.4 Based Battery-Free Wireless Sensor Networks

In Battery-free Wireless Sensor Network (BF-WSN), the nodes harvest energy from ambient energy sources to power their microprocessors, sensors, radio transceivers, etc. It is critical to design an energy conservation scheme for the nodes to save energy. Considering contemporary Wireless Sensor Network (WSN) adopts IEEE 802.15. 4 standard in its Medium Access Control (MAC) layer and Physical (PHY) layer, we model the 802.15. 4 based BF-WSN using Markov chain so that the expected number of packets waiting in the node's transmission/reception buffer and the buffer overflow probability are derived. In addition, the Optimization Problem (OP) is formulated that minimizes the node's energy consumption under the constraints on capacitor-charging time, buffer overflow probability, data rate, and the maximum number of transmission retrials set in the MAC layer. Moreover, the OP Based Energy Management Scheme (OBEMS) is presented, which uses the solution of the OP. Simulation results show the proposed scheme is able to reduce energy consumption while maintaining a higher Packet Delivery Ratio (PDR).
Regional lung function after pneumonectomy

Hall, D. R. (1974). Thorax, 29, 425-431. Regional lung function after pneumonectomy. Regional lung function was studied with xenon-133 in 10 patients with bronchial carcinoma before and again three to six months after pneumonectomy. It was found that ventilation and perfusion were often considerably reduced in the tumour-bearing lung and that the greater part of the cardiac output had apparently been diverted to the unaffected lung before operation. The regional distribution of ventilation and perfusion in the lung remaining after surgery was essentially unchanged from that measured in the same lung preoperatively and no different from the pattern seen in 10 normal volunteers.
Compacting Neural Network Classifiers via Dropout Training

We introduce dropout compaction, a novel method for training feed-forward neural networks which realizes the performance gains of training a large model with dropout regularization, yet extracts a compact neural network for run-time efficiency. In the proposed method, we introduce a sparsity-inducing prior on the per unit dropout retention probability so that the optimizer can effectively prune hidden units during training. By changing the prior hyperparameters, we can control the size of the resulting network. We performed a systematic comparison of dropout compaction and competing methods on several real-world speech recognition tasks and found that dropout compaction achieved comparable accuracy with fewer than 50% of the hidden units, translating to a 2.5x speedup in run-time.
Indoor Environment Navigation for Blind with Voice Feedback in zigbee network

: This paper presents visually impaired assistive system which focuses on independent mobility of visually impaired or blind people who suffer in an unknown environment without any manual assistance. This system employs Radio Frequency Identification (RFID) to achieve an objective of identifying certain paths for the user navigation as well as provide certain features such as object recognition, log records of all users’ tag access, emergency button and user track information. This proposed system on the user side include a mobile RFID reader module with an integrated microcontroller, zigbee transceiver for transmitting the tag’s information and TTS for playing information to the user and on the server side zigbee transceiver for wireless communication. In path identification technique, RFID passive tag network is employed on the path and for object recognition required tools and other objects in the house or building will be embedded with passive RFID tags. A text data unique to each object and path location, resides on the server. The reader reads the tags and transmits the data wirelessly to the server PC which in turn scans for the received Tag ID in the database and respond to the user with its related text data which is played at the user side by converting it from text to speech with the help of SAPI module.
Outlier mining based Automatic Incident Detection on urban arterial road

Nowadays, Floating Car Data (FCD), which is becoming an important way to acquire traffic information, has been widely taken to estimate speed or travel time on road. In this paper, we introduce the concept of outlier mining into Automatic Incident Detection (AID) based on FCD and propose a novel AID approach on urban arterial road. According to the characteristics of incident, feature vector is selected from both spatial analysis and temporal analysis. Then a multilevel detection method that consists of filtering, outlier detection, and delay monitoring is proposed. The evaluation on real incident data and FCD gives the result that DR = 81.5% while FAR = 1.83%, which proves that the approach can achieve considerable effectiveness.