Miracle-dz/UniFAR-FTUs huggingface dataset:
De novo transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set

High‐throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without a high‐quality reference genome. For every stage of analysis – from assembly to annotation to variant discovery – researchers have to distinguish technical artefacts from the biological realities of their data before they can make inference. In this work, I explore these challenges by generating a large de novo comparative transcriptomic data set data for a clade of lizards and constructing a pipeline to analyse these data. Then, using a combination of novel metrics and an externally validated variant data set, I test the efficacy of my approach, identify areas of improvement, and propose ways to minimize these errors. I find that with careful data curation, HTS can be a powerful tool for generating genomic data for non‐model organisms.
Lost in Translation: Strategies Japanese Language Learners Use in Communicating Culturally Specific L1 Expressions in English.

Communicating in a second language could be seen as a process requiring the deconstruction and reconstruction of cultural meanings. If this is the case, how do second language (L2) learners express cultural meanings of their first language (L1) expressions that do not have semantically equivalent L2 expressions? Twentynine Japanese students learning English as a second language in the US were asked to translate Japanese cultural expressions that do not have equivalent English expressions. This study found that the students either (a) entirely eliminated the expression from the statement, (b) replaced the expression with an English expression commonly used in a similar context, but with a different meaning, or (c) literally translated the expression into an English expression that made little sense. The study suggests the importance of helping L2 learners develop this bicultural capability to convey rich cultural meanings of L1-specific expressions in L2-based communication.
Process for Measuring and Visualizing an Open Innovation Platform: Case Demola

Open innovation breaks the traditional pattern for developing new innovation leading to new business and the activities toward it. Consequently, new requirements are posed to innovation measurement. Demola is an open innovation platform that takes real-life problems from companies and other organizations and puts together and facilitates projects where students from different universities come together to solve the problems. This paper describes a set of network visualizations and animations that were developed in co-creation with the Demola operators to make visible the activity that Demola has initiated. Moreover, the development process used to design the visualizations and the technical process that was applied are described and discussed. We claim that static network visualizations and animations of an open innovation platform development are useful in presenting, describing, marketing and selling the platform for existing and new stakeholders. Our experience shows that in order to develop visualizations and animations that meet the requirements set by the different stakeholders, an iterative and incremental development process is needed. Moreover, we claim that taking a data-driven approach to visualization development is a key enabler in supporting the development.
Low-cost face biometry for visually impaired users

We present a work in progress on a face biometry system for visually impaired users - the result of a very close interaction among scientists, engineers, and a users group formed by visually impaired and social assistants. The prototype under development implements recent trends of video analysis and follows closely the suggestions given by the working group, with the ambitious goal of developing a device easy to use that can be an effective help to improve communication and inclusion of visually impaired population. The prototype works real-time processing the incoming video stream to the purpose of locating the presence of people and spotting known faces. Each event of interest produces a simple audio feedback to the user, allowing him or her to locate the presence of people before they start talking or highlighting known faces in noisy environments. So far the prototype has been quantitatively validated through a set of experiments carried out in lab; also a qualitative evaluation by a heterogeneous group of perspective users, users' relatives, social workers, and experts gave us many positive comments and useful feedbacks for future work.
Addressing Emerging Risks: Scientific and Regulatory Challenges Associated with Environmentally Persistent Free Radicals

Airborne fine and ultrafine particulate matter (PM) are often generated through widely-used thermal processes such as the combustion of fuels or the thermal decomposition of waste. Residents near Superfund sites are exposed to PM through the inhalation of windblown dust, ingestion of soil and sediments, and inhalation of emissions from the on-site thermal treatment of contaminated soils. Epidemiological evidence supports a link between exposure to airborne PM and an increased risk of cardiovascular and pulmonary diseases. It is well-known that during combustion processes, incomplete combustion can lead to the production of organic pollutants that can adsorb to the surface of PM. Recent studies have demonstrated that their interaction with metal centers can lead to the generation of a surface stabilized metal-radical complex capable of redox cycling to produce ROS. Moreover, these free radicals can persist in the environment, hence their designation as Environmentally Persistent Free Radicals (EPFR). EPFR has been demonstrated in both ambient air PM2.5 (diameter < 2.5 µm) and in PM from a variety of combustion sources. Thus, low-temperature, thermal treatment of soils can potentially increase the concentration of EPFR in areas in and around Superfund sites. In this review, we will outline the evidence to date supporting EPFR formation and its environmental significance. Furthermore, we will address the lack of methodologies for specifically addressing its risk assessment and challenges associated with regulating this new, emerging contaminant.
Online bicast allocation algorithm for contention-free-routing NoCs

The demand on network-on-chips (NoCs) with quality of service guarantees for real-time applications has been massively increasing in the last few years. One of the main techniques used for providing such networks is time-division-multiplexing (TDM) since it provides hard bandwidth and latency guarantees along with better resources utilization. In this paper, a runtime bicast algorithm is proposed for allocating the TDM slots in a contention-free-routing NoC. The proposed algorithm is evolved from a state-of-the art TDM allocation algorithm for point-to-point connections. The bicast algorithm shows merit in time-to-bandwidth efficiency for 80.12% of the total possible bicast connections with an average improvement of 37.76% compared with the unicast algorithm.
Swelling Behaviour of Carboxymethylated Tamarind Gum

Chemical composition and swelling behaviour of crude tamarind gum from Tamarindus indica seed were observed and compared with modified gums as used carboxymethylation reaction. The condition of carboxymethylation at 70°C for 60 min of reaction time and methanol as solvent media was used. Different mole ratios of sodium hydroxide to monochloroacetic acid (nNaOH/nMCA) from 1 to 2.78 were studied and then its degree of substitution (DS) of both crude and carboxymethylated tamarind gums was also determined and compared. Then the swelling property of all samples was evaluated by using gravimetric technique (weight difference between dry and wet polymer). The results from swelling test showed that crude tamarind gum behaved low swelling while carboxymethylated tamarind gums showed high swelling profiles, ranged from 17 to 81% during 60 min. This is a preliminary assessment to expressing pharmaceutical application possibility of tamarind gum as disintegrant, diluent and drug release controlling agent.
Resonant amplification of delivered volume during high-frequency ventilation.

The volume of gas delivered from a high-frequency ventilation (HFV) circuit was measured with an ultrasonic flowmeter. The measurements were done in vitro (20-liter air-filled glass bottle) and in vivo (9 anesthetized dogs lying supine) at oscillation frequencies ranging from 4 to 23 Hz and stroke volumes of the pump ranging from 36 to 150 ml. We varied the length and diameter of the tube connecting the pump with the endotracheal tube, the length and diameter of the bias outflow tube, the diameter of the endotracheal tube, and the stroke volume of the pump. Both in vitro and in vivo, there was resonant amplification of the delivered gas volume; i.e., the delivered gas volume exceeded the stroke volume at certain frequencies. Altering the dimensions of connecting tube, endotracheal tube, bias outflow tube, or stroke volume, i.e., changing the resistance to gas flow, gas compliance, and/or gas inertance in these elements, altered the ratio of gas delivered to stroke volume that could be predicted by an electric analog. These data indicate that the delivered gas volume during HFV depends critically on the configuration of the HFV circuit, the size of the endotracheal tube, the oscillation frequency, and the pump stroke volume. Knowledge of the delivered gas volume during HFV and appreciation of the phenomenon of resonant amplification of the delivered gas volume will permit a more accurate description of factors contributing to gas transport during HFV.
Function flow: making synchronization easier in task parallelism

Expressing synchronization in task parallelism remains a significant challenge because of the complicated relationships between tasks. In this paper, we propose a novel parallel programming model, namely function flow, where synchronization is easier to express. We release the burden of synchronizing by the virtue of parallel functions and functional wait. In function flow, parallel functions are defined to represent parallel tasks. Functional wait is designed to coordinate relationships of parallel functions at task-level. The main aspects of functional waits are boolean-expressions which are coupled with parallel functions' invocations. The functional wait mechanisms, based on parallel functions, provide powerful semantic supports and compiling time checking on relationships of parallel tasks. Our preliminary result of function flow shows that a wide range of realistic parallel programs can be easily expressed with performance coming close to well-tuned multi-threaded programs using barriers/sync. The overhead of task-level coordination is very low, not exceed 8%.
Vision-based simultaneous localization and mapping with two cameras

In this paper, we propose a novel method for the simultaneous localization and mapping (SLAM) problem with two cameras. A single camera based approach suffers from a lack of information for feature initialization and the instability of covariance of the 3D camera location and feature position. To solve this problem, we use two cameras which move independently, unlike the stereo camera. We derive new formulations for the extended Kalman filter and map management of two cameras. We also present a method for the new features initialization and feature matching with two cameras. In our method, the covariance of camera and feature location converges more rapidly. This characteristic enables a reduction of the computational complexity by fixing the feature position whose covariance converges. Experimental results prove that our approach estimates the 3D camera location and feature position more accurately and the covariance of camera and feature location converges more rapidly when compared with the single camera case.
Highly Restricted T Cell Repertoire Shaped by a Single Major Histocompatibility Complex–Peptide Ligand in the Presence of a Single Rearranged T Cell Receptor β Chain

The T cell repertoire is shaped by positive and negative selection of thymocytes through the interaction of α/β-T cell receptors (TCR) with self-peptides bound to self-major histocompatibility complex (MHC) molecules. However, the involvement of specific TCR-peptide contacts in positive selection remains unclear. By fixing TCR-β chains with a single rearranged TCR-β irrelevant to the selecting ligand, we show here that T cells selected to mature on a single MHC–peptide complex express highly restricted TCR-α chains in terms of Vα usage and amino acid residue of their CDR3 loops, whereas such restriction was not observed with those selected by the same MHC with diverse sets of self-peptides including this peptide. Thus, we visualized the TCR structure required to survive positive selection directed by this single ligand. Our findings provide definitive evidence that specific recognition of self-peptides by TCR could be involved in positive selection of thymocytes.
Silent Synapse Activation in Epilepsy

Epilepsy is a life-threatening chronic disease in a state of neuronal over electric activity. The precise nature of the seizure recurrence has not been clearly. Synapses can be divided into silent and functional synapse.Silent synapses, defined as structural specializations for neurotransmission that do not produce a physiological response in the receiving cell, may occur frequently in neural circuits. Models of synaptic plasticity, such as long-term potentiation (LTP) and long-term depression (LTD) of glutamatergic synapses, are believed to underlie the seizure occurrence. Silent synapses containing only NMDA receptors are transformed within minutes into activated synapses postsynaptically AMPA receptor insertion and presynaptic transmitter releasing (BDNF-Cdc42 (brain derived neurotrophic factor-) signaling, Calcium influx,cAMP(Cyclic Adenosine monophosphate) signal pathway. All previous mentioned genes and proteins were abnormal in epilepsy patients and animal models. Future experimental and clinical studies are needed a better understanding on the mechanisms of silent synapses in epilepsy.
Hardware Implementation of MUSIC Algorithm for Airborne Digital Direction Finding System

To solve the issue of high complexity and poor real time in conventional array direction finding system of multiple signal classification algorithms, a digital solution based on field programmable gate array (FPGA) is presented. The solution includes real time quadrate demodulation and pretreatment, coordinate rotation digital computing (CORDIC) algorithm in rotation mode to realize singular value decomposition in order to reduce computation, and finally achieves the real time array direction finding. Hardware simulation and tests show that the system works stably and can ensure the deviation is less than 0.5 degree with over 64 snapshots, which can be used in precise positioning and measurement.
Basics of Self Micro Emulsifying Drug Delivery System

About 70-75% of drugs is taken orally and is found not to be as useful as desired. A self-micro emulsifying drug delivery system (SMEDDS) is a drug delivery system that uses a micro-emulsion achieved by chemical rather than mechanical means. Micro-emulsions have significant potential for use in drug delivery, and SMEDDS are the best of these systems. SMEDDS are of particular value in increasing the absorption of lipophilic drugs taken orally. SMEDDS are mixtures of natural or synthetic oils, solid or liquid surfactants, or alternatively, one or more hydrophilic solvents and co-solvents/surfactants that have a unique ability of forming fine oil-in-water (o/w) micro emulsions upon mild agitation followed by dilution in aqueous media, such as GI fluids. SMEDDS spread readily in the GI tract, and the digestive motility of the stomach and the intestine provide the agitation necessary for self-emulsification. SMEDDS can be encapsulated in hard or soft gelatin capsules or can be converted to solid state (Solid SEDDS/SMEDDS). This review article provides an overview of SMEDDS and its advantages over conventional dosage forms. Keywords: SMEDDS, Micro-emulsions, Co-solvents
Asymptotic Evaluation of Eigenvalue Distribution and Ergodic Capacity under Outdoor-Indoor MIMO Measured Channel

This paper analyzes the asymptotic distribution of the channel eigenvalues and the asymptotic ergodic channel capacity using measured multiple-input multiple-output (MIMO) data. A realistic propagation environment in the presence of spatial fading correlation under an outdoor-indoor scenario at 5.25 GHz, which has important applications for data transmission in future cellular as well as wireless local area networks (WLAN) systems, is taken into account. The analytic results of the asymptotic distribution of the channel eigenvalues and the asymptotic ergodic channel capacity, which assume that the number of antenna elements approaches infinity, are reviewed. We show that these closed-form solutions are also valid for realistic channel and realistic number of antenna elements. In this paper, the outdoor-indoor scenario including the channels in an office room and corridors is investigated.
Multi-store metadata-based supervised mobile app classification

The mass adoption of smartphone and tablet devices has boosted the growth of the mobile applications market. Confronted with a huge number of choices, users may encounter difficulties in locating the applications that meet their needs. Sorting applications into a user-defined classification scheme would help the app discovery process. Systems for automatically classifying apps into such a classification scheme are thus sorely needed. Methods for automated app classification have been proposed that rely on tracking how the app is actually used on users' mobile devices; however, this approach can lead to privacy issues. We present a system for classifying mobile apps into user-defined classification schemes which instead leverages information publicly available from the online stores where the apps are marketed. We present experimental results obtained on a dataset of 5,993 apps manually classified under a classification scheme consisting of 50 classes. Our results indicate that automated app classification can be performed with good accuracy, at the same time preserving users' privacy.
Fatty acid composition in feeds and plasma of Canadian premature infants

The objective of this exploratory study was to investigate how the fatty acid (FA) composition of different food sources for preterm infants including: breast milk (BM), formula (F), human milk fortifiers (HMFs) and total parenteral nutrition (TPN) impacted preterm infant's plasma FA. The associations between FA content of plasma with antioxidant enzyme activity and cognition were also evaluated.
Automatic lexical classification: bridging research and practice

Natural language processing (NLP)—the automatic analysis, understanding and generation of human language by computers—is vitally dependent on accurate knowledge about words. Because words change their behaviour between text types, domains and sub-languages, a fully accurate static lexical resource (e.g. a dictionary, word classification) is unattainable. Researchers are now developing techniques that could be used to automatically acquire or update lexical resources from textual data. If successful, the automatic approach could considerably enhance the accuracy and portability of language technologies, such as machine translation, text mining and summarization. This paper reviews the recent and on-going research in automatic lexical acquisition. Focusing on lexical classification, it discusses the many challenges that still need to be met before the approach can benefit NLP on a large scale.
Average dwell time approach robust stabilization of switched linear systems with time-delay

The robust stabilization for a class of uncertain switched linear systems with time-delay is studied. By using average dwell-time and matrix decomposition methods, the sufficient condition that makes the switched systems exponentially stable and the design method of switching law are obtained. The result can be expressed in the form of LMI, which can be evaluated easily. The simulation shows the validity of the result.
Analysis of melt spinning master-curves of low density polyethylene

The extensional rheological properties of a low density polyethylene (LDPE) melt were studied by using melt spinning technique. Based on the extension properties of the LDPE melt under experimental condi- tions, the melt spinning master-curves were plotted by introducing scaling factor b and the draw ratio k. The scal- ing factor b shows the combination effects on the preorien- tation before extension, the unwrapping and orientation of molecular chains during extension. Several linear relation- ships between b and temperature, log b and the logarithm of extrusion flow rate v0 (log v0) have been investigated. By using the values of b and the reference curve, the extension viscosity curves with different temperature and extrusion flow rate could be calculated, thus the measure- ment range of melt spinning technique would be extended effectively. V C 2012 Wiley Periodicals, Inc. J Appl Polym Sci 125: 2202-2206, 2012
MRE11 complex links RECQ5 helicase to sites of DNA damage

RECQ5 DNA helicase suppresses homologous recombination (HR) possibly through disruption of RAD51 filaments. Here, we show that RECQ5 is constitutively associated with the MRE11–RAD50–NBS1 (MRN) complex, a primary sensor of DNA double-strand breaks (DSBs) that promotes DSB repair and regulates DNA damage signaling via activation of the ATM kinase. Experiments with purified proteins indicated that RECQ5 interacts with the MRN complex through both MRE11 and NBS1. Functional assays revealed that RECQ5 specifically inhibited the 3′→5′ exonuclease activity of MRE11, while MRN had no effect on the helicase activity of RECQ5. At the cellular level, we observed that the MRN complex was required for the recruitment of RECQ5 to sites of DNA damage. Accumulation of RECQ5 at DSBs was neither dependent on MDC1 that mediates binding of MRN to DSB-flanking chromatin nor on CtIP that acts in conjunction with MRN to promote resection of DSBs for repair by HR. Collectively, these data suggest that the MRN complex recruits RECQ5 to sites of DNA damage to regulate DNA repair.
Study on the Mechanic Properties of DLC Films on Different Metal Substrates

To overcome the low adhesion of hydrogen-free DLC films on metal substrates, in this studying, DLC films (0.9μm) were prepared with 3 types of interlayer (2 types of Ti/TiCx/DLC interlayer and 1 type of Ti/TiNx/TiNxCy/DLC interlayer) on different substrates (W18Cr4V, Cr12, GCr15, TC4, 40Cr, 9Cr18 and Cr18Ni9Ti). The internal stress of the films was calculated by the bending of substrate (Si(100)). It was found that it is as high as 3.9GPa, and part of the high residual stress of the DLC films was dissipated through a compound interlayers, and the thick films achieved, and the pull tests found that the adhesion has been highly strengthened with a proper interlayer. The films structure qualities were investigated by Raman spectroscopy and the results indicate that the films have the same structure properties which suggests that the properties of the DLC films can not been affected by substrates. The hardness is about 5000HV, defined by nanoindentation techniques. The frictional properties were investigated by reciprocal sliding tests and the friction coefficient was about 0.1, independent of their substrates. Thus our DLC films may have great potential applications in precision parts tribological application.