Miracle-dz/UniFAR-FTUs huggingface dataset:
UCCA: A Semantics-based Grammatical Annotation Scheme

Syntactic annotation is an indispensable input for many semantic NLP applications. For instance, Semantic Role Labelling algorithms almost invariably apply some form of syntactic parsing as preprocessing. The categories used for syntactic annotation in NLP generally reflect the formal patterns used to form the text. This results in complex annotation schemes, often tuned to one language or domain, and unintuitive to non-expert annotators. In this paper we propose a different approach and advocate substituting existing syntax-based approaches with semantics-based grammatical annotation. The rationale of this approach is to use manual labor where there is no substitute for it (i.e., annotating semantics), leaving the detection of formal regularities to automated statistical algorithms. To this end, we propose a simple semantic annotation scheme, UCCA for Universal Conceptual Cognitive Annotation. The scheme covers many of the most important elements and relations present in linguistic utterances, including verb-argument structure, optional adjuncts such as adverbials, clause embeddings, and the linkage between them. The scheme is supported by extensive typological crosslinguistic evidence and accords with the leading Cognitive Linguistics theories.
Transcriptome Analysis of Scorpion Species Belonging to the Vaejovis Genus

Scorpions belonging to the Buthidae family have traditionally drawn much of the biochemist’s attention due to the strong toxicity of their venoms. Scorpions not toxic to mammals, however, also have complex venoms. They have been shown to be an important source of bioactive peptides, some of them identified as potential drug candidates for the treatment of several emerging diseases and conditions. It is therefore important to characterize the large diversity of components found in the non-Buthidae venoms. As a contribution to this goal, this manuscript reports the construction and characterization of cDNA libraries from four scorpion species belonging to the Vaejovis genus of the Vaejovidae family: Vaejovis mexicanus, V. intrepidus, V. subcristatus and V. punctatus. Some sequences coding for channel-acting toxins were found, as expected, but the main transcribed genes in the glands actively producing venom were those coding for non disulfide-bridged peptides. The ESTs coding for putative channel-acting toxins, corresponded to sodium channel β toxins, to members of the potassium channel-acting α or κ families, and to calcium channel-acting toxins of the calcin family. Transcripts for scorpine-like peptides of two different lengths were found, with some of the species coding for the two kinds. One sequence coding for La1-like peptides, of yet unknown function, was found for each species. Finally, the most abundant transcripts corresponded to peptides belonging to the long chain multifunctional NDBP-2 family and to the short antimicrobials of the NDBP-4 family. This apparent venom composition is in correspondence with the data obtained to date for other non-Buthidae species. Our study constitutes the first approach to the characterization of the venom gland transcriptome for scorpion species belonging to the Vaejovidae family.
Minimax Rates of Estimation for Sparse PCA in High Dimensions

We study sparse principal components analysis in the high-dimensional setting, where $p$ (the number of variables) can be much larger than $n$ (the number of observations). We prove optimal, non-asymptotic lower and upper bounds on the minimax estimation error for the leading eigenvector when it belongs to an $\ell_q$ ball for $q \in [0,1]$. Our bounds are sharp in $p$ and $n$ for all $q \in [0, 1]$ over a wide class of distributions. The upper bound is obtained by analyzing the performance of $\ell_q$-constrained PCA. In particular, our results provide convergence rates for $\ell_1$-constrained PCA.
mplications of pH manipulation methods for metal toxicity : Not all acidic nvironments are created equal

The toxicity of many metals is impacted by environmental pH, through both competition and complexation by hydroxide and carbonate ions. To establish safe environmental regulation it is important to properly define the relationship between pH and metal toxicity, a process that involves manipulating the pH of test water in the lab. The current study compares the effects of the three most common pH manipulation methods (carbon dioxide, acid–base addition, and chemical buffers) on acute Pb toxicity of a model fish species, Pimephales promelas. Acidification of test water revealed that the Pb and Pb2+ LC50 values were impacted by the pH manipulation method, with the following order of effects: HCl < CO2 < MOPS. Conversely no differences in toxicity were observed when test pH was alkalinized using MOPS or NaOH. The different impacts of pH manipulation methods on Pb toxicity are likely due to different physiolog-
FNDC5/Irisin Is Not Only a Myokine but Also an Adipokine

Exercise provides clear beneficial effects for the prevention of numerous diseases. However, many of the molecular events responsible for the curative and protective role of exercise remain elusive. The recent discovery of FNDC5/irisin protein that is liberated by muscle tissue in response to exercise might be an important finding with regard to this unsolved mechanism. The most striking aspect of this myokine is its alleged capacity to drive brown-fat development of white fat and thermogenesis. However, the nature and secretion form of this new protein is controversial. The present study reveals that rat skeletal muscle secretes a 25 kDa form of FNDC5, while the 12 kDa/irisin theoretical peptide was not detected. More importantly, this study is the first to reveal that white adipose tissue (WAT) also secretes FNDC5; hence, it may also behave as an adipokine. Our data using rat adipose tissue explants secretomes proves that visceral adipose tissue (VAT), and especially subcutaneous adipose tissue (SAT), express and secrete FNDC5. We also show that short-term periods of endurance exercise training induced FNDC5 secretion by SAT and VAT. Moreover, we observed that WAT significantly reduced FNDC5 secretion in fasting animals. Interestingly, WAT of obese animals over-secreted this hormone, which might suggest a type of resistance. Because 72% of circulating FNDC5/irisin was previously attributed to muscle secretion, our findings suggest a muscle-adipose tissue crosstalk through a regulatory feedback mechanism.
Allergic Airway Inflammation is Differentially Exacerbated by Daytime and Nighttime Ultrafine and Submicron Fine Ambient Particles: Heme Oxygenase-1 as an Indicator of PM-Mediated Allergic Inflammation

Ambient particulate matter (PM) originates from a range of sources and differs in composition with respect to season, time of day, and particle size. In this study, ambient PM samples in the ultrafine and submicrometer fine range were tested for the potential to exacerbate a murine model of allergic airway inflammation when exposure occurs solely during allergic sensitization, but not during subsequent allergen challenge. Temporally resolved and size-segregated PM samples were used to understand how summer or winter, day or night, and ambient ultrafine and submicrometer fine particle size influence PM’s ability to exacerbate allergic inflammation. PM was collected in urban Fresno, CA. BALB/c mice were exposed to PM and house dust mite allergen (HDM) via intranasal aspiration on d 1, 3, and 5. HDM challenge occurred on d 12–14, with inflammation assessed 24 h following final challenge. While season or particle size did not predict allergic inflammation, daytime ultrafine and submicrometer fine particles significantly increased total cellular inflammation, specifically lymphocyte and eosinophil infiltration, compared to allergic controls. Further studies examined PM-mediated changes within the lung during the period where allergen sensitization occurred by measuring direct effects of PM on pulmonary oxidative stress and inflammation. Pulmonary levels of heme oxygenase-1 (HO-1), a biomarker of oxidative stress, but not cellular inflammation, demonstrated a remarkable correlation with the degree of allergic inflammation in animals sensitized to allergen and PM concomitantly, suggesting acute PM-mediated HO-1 levels may serve as a predictive indicator of a particle’s ability to exacerbate allergic airway inflammation.
Reusing Stack Traces: Automated Attack Surface Approximation

Security requirements around software systems have become more stringent as society becomes more interconnected via the Internet. New ways of prioritizing security efforts are needed so security professionals can use their time effectively to find security vulnerabilities or prevent them from occurring in the first place. The goal of this work is to help software development teams prioritize security efforts by approximating the attack surface of a software system via stack trace analysis. Automated attack surface approximation is a technique that uses crash dump stack traces to predict what code may contain exploitable vulnerabilities. If a code entity (a binary, file or function) appears on stack traces, then Attack Surface Approximation (ASA) considers that code entity is on the attack surface of the software system. We also explore whether number of appearances of code on stack traces correlates with where security vulnerabilities are found. To date, feasibility studies of ASA have been performed on Windows 8 and 8.1, and Mozilla Firefox. The results from these studies indicate that ASA may be useful for practitioners trying to secure their software systems. We are now working towards establishing the ground truth of what the attack surface of software systems is, along with looking at how ASA could change over time, among other metrics.
Design of low power 3D hybrid memory by non-volatile CBRAM-crossbar with block-level data-retention

As one of the newly introduced resistive random access memory (ReRAM) devices, this paper has shown an in-depth study of conductive-bridging random access memory (CBRAM) for non-volatile memory (NVM) computing. Firstly, a CBRAM-crossbar based memory is evaluated with accurate physical-level model and circuit-level characterization. It is then deployed as NVM component with a 3D hybrid integration of SRAM/DRAM, where one layer of CBRAM-crossbar is designed for data-retention under power gating to reduce leakage power from SRAM/DRAM at other layers. Moreover, a block-level data-retention scheme is designed to only write back dirty data from SRAM/DRAM to CBRAM-crossbar. When compared to the hybrid memory using phase-change random access memory (PCRAM) as data-retention, our CBRAM-based hybrid memory achieves 16x faster migration time and 4x less migration power for hibernating transition. When compared to the FeRAM-based bit-wise data-retention, our approach also achieves 17x smaller area and 8x smaller power under the same data migration speed.
Digital Demodulation of Interferometric Signals

The marriage of optical sensing techniques with sophisticated digital signal processing has resulted in a myriad of practical metrology systems. Optical metrology systems offer many attractive measurement features. These systems are inherently non-contacting, nondestructive, and immune from electromagnetic interference. In addition, since light is used as the sensing probe, the measurement system is capable of high sensitivity, fine resolution (both spatial and temporal), and absolute calibration.
Achieving Data Utility Fairness in Periodic Dissemination for VANETs

In addition to safety, Vehicular Ad-hoc Networks (VANETs) enable the development of new information-rich applications that disseminate relevant data to vehicles. One key challenge in such networks is to use the available bandwidth efficiently when there is: (i) a short connectivity time due to the rapidly changing road environment, and (ii) bandwidth congestion due to continuous collection and dissemination of data. Numerous solutions were proposed to alleviate bandwidth congestion by using transmission power and beaconing rate control. However, the reduction of data messages transmitted by using priority- based data selection mechanisms has not been fully explored. In this work, we propose a periodic data dissemination protocol for non-safety applications which distributes data utility fairly among vehicles with conflicting data interests. Furthermore, given a defined maximum network load allowed, only the least relevant data is suppressed. Fairness is achieved using the concept of Nash Bargaining from game theory. Simulation results show that our approach leads to an efficient bandwidth utilization in terms of utility per message received and higher fairness index compared with other approaches.
Plane-wave and cylindrical-wave admittance method for simulation of classical and photonic-crystal-based VCSELs

In this paper we present the application of a novel fully vectorial and three-dimensional computational method for planar devices to simulation of electromagnetic modes in classical and photonic-crystal-based VCSELs. We show the mathematical basis of the method and present results of computations of a resonant wavelength, optical losses, and a threshold gain of a classical arsenide VCSEL with oxide confinement and also of a purely photonic-crystal confined one. Furthermore we analyze the analytical reduction of computational domain to two dimensions in axisymmetric geometries with cylindrical-wave expansion, discuss the mathematical problems which occurs in such coordinates and suggest a method to overcome them.
Cross-domain item recommendation based on user similarity

Cross-domain recommender systems adopt multiple methods to build relations from source domain to target domain in order to alleviate problems of cold start and sparsity, and improve the performance of recommendations. The majority of traditional methods tend to associate users and items, which neglected the strong influence of friend relation on the recommendation. In this paper, we propose a cross-domain item recommendation model called CRUS based on user similarity, which firstly introduces the trust relation among friends into cross-domain recommendation. Despite friends usually tend to have similar interests in some domains, they share differences either. Considering this, we define all the similar users with the target user as Similar Friends. By modifying the transfer matrix in the random walk, friends sharing similar interests are highlighted. Extensive experiments on Yelp data set show CRUS outperforms the baseline methods on MAE and RMSE.
BIOMIMETIC MANUFACTURING OF CUSTOMISED NOVEL FIBRE PROTEINS FOR SPECIALISED APPLICATIONS

Abstract Using spider silk and collagen as a model, we have investigated the role that various protein primary structural components play in fibre production. Spidroins, spider dragline silk protein components, are essentially characterised by an amino-acid repeat containing a glycine-rich motif (amorphous) followed by an alanine-rich motif (crystalline, putatively responsible for fibre strength). We have tested the importance of alanine runs in these proteins and the role of this motif in the mechanical properties of the resulting fibre. To test the importance of alanine-rich motifs in the spidroin-1 proteins, we engineered three types of spidroin-1-like genes containing sequence encoding for different amounts of alanine repeats in the protein (normal, low, and no alanine residues). We also have engineered three copolymer collagen-spidroin-1 genes using each of the three spidroin-1 synthetic genes. These copolymers were mimicked on the existing natural block collagensilk- like protein copolymer found in the byssus thread of marine mussels. All of these constructs were introduced in yeast (Pichia pastoris) for protein production. We are currently purifying each of the recombinant proteins for structural analysis (CDspectroscopy).
The geometry of partial fitness orders and an efficient method for detecting genetic interactions

We present an efficient computational approach for detecting genetic interactions from fitness comparison data together with a geometric interpretation using polyhedral cones associated to partial orderings. Genetic interactions are defined by linear forms with integer coefficients in the fitness variables assigned to genotypes. These forms generalize several popular approaches to study interactions, including Fourier–Walsh coefficients, interaction coordinates, and circuits. We assume that fitness measurements come with high uncertainty or are even unavailable, as is the case for many empirical studies, and derive interactions only from comparisons of genotypes with respect to their fitness, i.e. from partial fitness orders. We present a characterization of the class of partial fitness orders that imply interactions, using a graph-theoretic approach. Our characterization then yields an efficient algorithm for testing the condition when certain genetic interactions, such as sign epistasis, are implied. This provides an exponential improvement of the best previously known method. We also present a geometric interpretation of our characterization, which provides the basis for statistical analysis of partial fitness orders and genetic interactions.
Joint Design-Time and Post-Silicon Minimization of Parametric Yield Loss using Adjustable Robust Optimization

Parametric yield loss due to variability can be effectively reduced by both design-time optimization strategies and by adjusting circuit parameters to the realizations of variable parameters. The two levels of tuning operate within a single variability budget, and because their effectiveness depends on the magnitude and the spatial structure of variability their joint co-optimization is required. In this paper we develop a formal optimization algorithm for such co-optimization and link it to the control and measurement overhead via the formal notions of measurement and control complexity. We describe an optimization strategy that unifies design-time gate-level sizing and post-silicon adaptation using adaptive body bias at the chip level. The statistical formulation utilizes adjustable robust linear programming to derive the optimal policy for assigning body bias once the uncertain variables, such as gate length and threshold voltage, are known. Computational tractability is achieved by restricting optimal body bias selection policy to be an affine function of uncertain variables. We demonstrate good run-time and show that 5-35% savings in leakage power across the benchmark circuits are possible. Dependence of results on measurement and control complexity is studied and points of diminishing returns for both metrics are identified
Benchmarking Stream-Based XPath Engines Supporting Simultaneous Queries for Service Oriented Networking

Stream-based simultaneous XPath processing plays a critical role in service oriented networking, where the processing must scale well in terms of concurrent input streams and number of XPath queries. However, there are no benchmarks or evaluation methodology in existing literatures that benchmark stream-based XPath engines supporting simultaneous queries. In this paper, we describe a novel benchmarking methodology for evaluating XPath engines which handle simultaneous queries on streaming traffics. With structured data model, query model, and control model in our benchmark, we conduct well controlled experiments to assess and isolate various performance factors. We also demonstrate that our structured, quantified approach with wide data set coverage, enables accurate performance measurements, and easy bottleneck isolations of a real-world XPath engine implementation.
Modular Focused Proof Systems for Intuitionistic Modal Logics

Focusing is a general technique for syntactically compartmentalizing the non-deterministic choices in a proof system, which not only improves proof search but also has the representational benefit of distilling sequent proofs into synthetic normal forms. However, since focusing is usually specified as a restriction of the sequent calculus, the technique has not been transferred to logics that lack a (shallow) sequent presentation, as is the case for some of the logics of the modal cube. We have recently extended the focusing technique to classical nested sequents, a generalization of ordinary sequents. In this work we further extend focusing to intuitionistic nested sequents, which can capture all the logics of the intuitionistic S5 cube in a modular fashion. We present an internal cut-elimination procedure for the focused system which in turn is used to show its completeness.
Enhanced Viral Etiological Diagnosis of Respiratory System Infection Outbreaks by Use of a Multitarget Nucleic Acid Amplification Assay

ABSTRACT A study was undertaken to assess the utility of the xTAG respiratory viral panel (RVP) for enhanced laboratory investigation of respiratory outbreaks. Specimens (n = 1,108) from 244 suspected respiratory virus outbreaks in 2006 and 2007 in Alberta, Canada, were included in the study. Testing by direct fluorescent antigen detection (DFA) and various in-house nucleic acid amplification tests (NATs) for common respiratory viruses provided an etiological diagnosis in 177 outbreaks (72.5%), with 524 samples testing positive (47.3%) for a respiratory virus. Two hundred samples from 51 unresolved outbreaks were further tested by RVP retrospectively. Fifty-eight samples from 30 unresolved outbreaks had a respiratory virus detected by RVP (47 picornavirus-positive, 9 coronavirus-positive, and 2 influenza virus A-positive samples). Overall, detection of a viral etiological agent was achieved in 90.8% of outbreaks using a combination of DFA, NATs, and RVP. Use of RVP enhances the laboratory investigation of respiratory virus outbreaks and facilitates appropriate patient and outbreak management.
Evidence of Conjoint Activation of the Anterior Insular and Cingulate Cortices during Effortful Tasks

The ability to perform effortful tasks is a topic that has received considerable interest in the research of higher functions of the human brain. Neuroimaging studies show that the anterior insular and the anterior cingulate cortices are involved in a multitude of cognitive tasks that require mental effort. In this study, we investigated brain responses to effort using cognitive tasks with task-difficulty modulations and functional magnetic resonance imaging (fMRI). We hypothesized that effortful performance involves modulation of activation in the anterior insular and the anterior cingulate cortices, and that the modulation correlates with individual performance levels. Healthy participants performed tasks probing verbal working memory capacity using the reading span task, and visual perception speed using the inspection time task. In the fMRI analysis, we focused on identifying effort-related brain activation. The results showed that working memory and inspection time performances were directly related. The bilateral anterior insular and anterior cingulate cortices showed significantly increased activation during each task with common portions that were active across both tasks. We observed increased brain activation in the right anterior insula and the anterior cingulate cortex in participants with low working memory performance. In line with the reported results, we suggest that activation in the anterior insular and cingulate cortices is consistent with the neural efficiency hypothesis (Neubauer).