Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust Estimation in Non-Linear State-Space Models With State-Dependent Noise

In this paper, we present a robust estimation algorithm for non-linear state-space models driven by state-dependent noise. The algorithm is robust to outliers in the data. We derive the algorithm step by step from first principles, from theory to implementation. The implementation is straightforward and consists mainly of two components: 1) a slightly modified version of the Rauch-Tung-Striebel recursions, and 2) a backtracking line search strategy. Since it preserves the underlying chain structure of the problem, its computational complexity grows linearly with the number of data. The algorithm is iterative and is guaranteed to converge, under mild assumptions, to a local optimum from any starting point. We validate our approach via experiments on synthetic data from a multi-variate stochastic volatility model.
Transfer Learning by Distribution Matching for Targeted Advertising

We address the problem of learning classifiers for several related tasks that may differ in their joint distribution of input and output variables. For each task, small - possibly even empty - labeled samples and large unlabeled samples are available. While the unlabeled samples reflect the target distribution, the labeled samples may be biased. This setting is motivated by the problem of predicting sociodemo-graphic features for users of web portals, based on the content which they have accessed. Here, questionnaires offered to a portion of each portal's users produce biased samples. We derive a transfer learning procedure that produces resampling weights which match the pool of all examples to the target distribution of any given task. Transfer learning enables us to make predictions even for new portals with few or no training data and improves the overall prediction accuracy.
Increased Plasma Levels of the APC-Interacting Protein MAPRE1, LRG1, and IGFBP2 Preceding a Diagnosis of Colorectal Cancer in Women

Longitudinal blood collections from cohort studies provide the means to search for proteins associated with disease before clinical diagnosis. We investigated plasma samples from the Women's Health Initiative (WHI) cohort to determine quantitative differences in plasma proteins between subjects subsequently diagnosed with colorectal cancer (CRC) and matched controls that remained cancer-free during the period of follow-up. Proteomic analysis of WHI samples collected before diagnosis of CRC resulted in the identification of six proteins with significantly (P < 0.05) elevated concentrations in cases compared with controls. Proteomic analysis of two CRC cell lines showed that five of the six proteins were produced by cancer cells. Microtubule-associated protein RP/EB family member 1 (MAPRE1), insulin-like growth factor–binding protein 2 (IGFBP2), leucine-rich alpha-2-glycoprotein (LRG1), and carcinoembryonic antigen (CEA) were individually assayed by enzyme linked immunosorbent assay (ELISA) in 58 pairs of newly diagnosed CRC samples and controls and yielded significant elevations (P < 0.05) among cases relative to controls. A combination of these four markers resulted in a receiver operating characteristics curve with an area under the curve value of 0.841 and 57% sensitivity at 95% specificity. This combination rule was tested in an independent set of WHI samples collected within 7 months before diagnosis from cases and matched controls resulting in 41% sensitivity at 95% specificity. A panel consisting of CEA, MAPRE1, IGFBP2, and LRG1 has predictive value in prediagnostic CRC plasmas. Cancer Prev Res; 5(4); 655–64. ©2012 AACR.
Querying structured information sources on the web

To provide access to distributed and heterogeneous sources, information integration systems have traditionally relied on the availability of a mediated schema, along with mappings between this schema and the schema of the information sources. Queries posed to the mediated schema are then reformulated in terms of the source schemas. On the Web, where sources are plentiful, autonomous and extremely volatile, a system based on the existence of a pre-defined mediated schema and mapping information presents several drawbacks. Notably, the cost of keeping the mappings up to date as new sources are found or existing sources change can be prohibitively high. In this paper, we propose a new querying mechanism for integrating a large number of sources that requires neither a mediated schema nor source mappings. In the absence of a mediated schema, the user formulates queries based on what she expects to find. These queries are rewritten using a best-effort approach: the rewriting component compares a user query against the source schemas and produces a set of rewritings based on the matches found. We demonstrate the feasibility of this approach by providing a query interface for integrating hundreds of (real) structured Web information sources. We also discuss experimental results which indicate that our query rewriting algorithm can be effective.
Parallel external memory graph algorithms

In this paper, we study parallel I/O efficient graph algorithms in the Parallel External Memory (PEM) model, one o f the private-cache chip multiprocessor (CMP) models. We study the fundamental problem of list ranking which leads to efficient solutions to problems on trees, such as computing lowest common ancestors, tree contraction and expression tree evaluation. We also study the problems of computing the connected and biconnected components of a graph, minimum spanning tree of a connected graph and ear decomposition of a biconnected graph. All our solutions on a P-processor PEM model provide an optimal speedup of Θ(P) in parallel I/O complexity and parallel computation time, compared to the single-processor external memory counterparts.
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

ICEberg (http://db-mml.sjtu.edu.cn/ICEberg/) is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. We propose that ICEberg will facilitate efficient, multi-disciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.
Robust stability analysis in the *-norm and Lyapunov-Razumikhin functions for the stability analysis of time-delay systems

Lyapunov-Krasovskii functionals have been shown to have connections with input-output techniques considering delay operators mapping L2 to L2. It is shown here that Lyapunov-Razumikhin functions can also be connected to the input-output framework by considering operators on L∞ and the corresponding Small-Gain Theorem. Several important results from the Lyapunov-Razumikhin Theorem are retrieved and extended.
Effect of Electric Convulsion Therapy on Urinary Excretion of 3′, 5′ Cyclic Adenosine Monophosphate

Electric convulsion therapy (E.C.T.) was used in the treatment of 13 women inpatients suffering from depressive symptoms. Twelve of the patients showed a significant increase in urinary excretion of 3′, 5′ cyclic adenosine monophosphate (cAMP) on the day of treatment, whereas four controls who received all or part of the preliminary treatment but no electric shock showed a reduction. The results of this study are consistent with the hypothesis that the antidepressant action of E.C. T. is mediated through an increased production of cAMP in brain tissue.
Energy-Aware Optimisation for Run-Time Reconfiguration

Run-time reconfiguration has been shown to produce power and energy efficient designs. However, it is important to take into account the energy overhead of the reconfiguration process itself. This paper presents an analytical model that covers the effects of power consumption and configuration speed of the reconfiguration process. Based on this model, a method is introduced that establishes the optimal degree of parallelism for designs supporting partial run-time reconfiguration. Our energy-aware approach is illustrated by optimising designs for software-defined radio: a reconfigurable FIR filter is shown to be up to 49% more energy efficient and up to 87% more area efficient than a non-reconfigurable design.
Mining RCS Data

As software systems evolve, it becomes important to know and to track the evolution of a system and its components. Data mining tools helps us to find the relationships between these components from patterns in the attributes of the data. The purpose of this paper is to describe how relationships between the attributes in the RCS (Revision Control System) change data can be found. These relationships may include which components of the system undergo repeated maintenance, how many lines of code are changed, the span of time in which files undergo change, as well as the type of maintenance (according to certain keywords used in the log). The technique is illustrated on a flight simulator system consisting of 409 RCS files.
The Mitochondria-Targeted Antioxidant Mitoquinone Protects against Cold Storage Injury of Renal Tubular Cells and Rat Kidneys

The majority of kidneys used for transplantation are obtained from deceased donors. These kidneys must undergo cold preservation/storage before transplantation to preserve tissue quality and allow time for recipient selection and transport. However, cold storage (CS) can result in tissue injury, kidney discardment, or long-term renal dysfunction after transplantation. We have previously determined mitochondrial superoxide and other downstream oxidants to be important signaling molecules that contribute to CS plus rewarming (RW) injury of rat renal proximal tubular cells. Thus, this study's purpose was to determine whether adding mitoquinone (MitoQ), a mitochondria-targeted antioxidant, to University of Wisconsin (UW) preservation solution could offer protection against CS injury. CS was initiated by placing renal cells or isolated rat kidneys in UW solution alone (4 h at 4°C) or UW solution containing MitoQ or its control compound, decyltriphenylphosphonium bromide (DecylTPP) (1 μM in vitro; 100 μM ex vivo). Oxidant production, mitochondrial function, cell viability, and alterations in renal morphology were assessed after CS exposure. CS induced a 2- to 3-fold increase in mitochondrial superoxide generation and tyrosine nitration, partial inactivation of mitochondrial complexes, and a significant increase in cell death and/or renal damage. MitoQ treatment decreased oxidant production ∼2-fold, completely prevented mitochondrial dysfunction, and significantly improved cell viability and/or renal morphology, whereas DecylTPP treatment did not offer any protection. These findings implicate that MitoQ could potentially be of therapeutic use for reducing organ preservation damage and kidney discardment and/or possibly improving renal function after transplantation.
MARES Project: Hydrographic data of the San Jorge Gulf from
R/V Coriolis II cruise in 2014

Abstract. PROMESse (Multidisciplinary program for the study of the ecosystem and marine geology of San Jorge Gulf and the coast of the Province of Chubut) was an international cooperation research program among the Ministry of Science and Technology (MINCyT), the National Scientific and Technical Research Council (CONICET), the Province of Chubut (Argentina) and the University of Quebec at Rimouski (UQAR/ISMER, Canada). Within the framework of this program two projects were carried out, MARES (Marine Ecosystem Health of the San Jorge Gulf: Present status and Resilience capacity) and MARGES (Marine Geology). The main goal of MARES was to conduct a comprehensive study of the dynamics of physical, chemical and biological parameters vitals for the San Jorge Gulf ecosystem. The observational component of this project consisted on a multidisciplinary oceanographic cruise on board of the research vessel Coriolis II in Feb. 2014 integrated by three legs designed to identify and characterize areas of high primary productivity, which will serve as indicators of the ecosystem health. This paper reports the hydrographic data collected during the second leg of the Coriolis II cruise. This leg was aimed to study the frontal dynamics associated to a region of high tidal dissipation rate south of the Gulf, and to study the vertical displacements of the pycnocline at a fixed site in the center of the Gulf mouth. To this end, high-resolution data was collected in the southern tidal front, including quasi-continuous CTD vertical profiles, underway surface temperature and salinity, Scanfish II CTD and shipboard ADCP data. The data sets are available in the National Oceanographic Data Center (NODC) from NOAA. DOI: doi:10.7289/V5MP51J2.
Realising Common Knowledge Assumptions in Agent Auctions

Game theory is popular in agent systems for designing auctions with desirable properties. However, many of these properties will only hold if the game and its properties are common knowledge among the agents. For example, in an auction where truthful bidding is an equilibrium strategy, unless this is common knowledge, it may not be rational for an agent to bid truthfully. It is currently not clear how this state of common knowledge can be achieved, especially in open agent societies where agents may encounter previously unseen auction specifications. We need a method for communicating the rules of the game to the agents, and the agents need to be able to determine its properties. We present a machine-readable language in which the rules of the game can be written. We show that it is not feasible for an agent to determine the properties of any arbitrary specification, unless information about the properties is communicated and/or certain restrictions are placed on the specification. We look at two special cases where common knowledge is achievable: auctions with identical players where the two highest bidders determine the price, and Groves mechanisms with a restriction on the pricing rule.
Diversity gain using a repeater in a wireless personal area network

In this paper we show that a one-hop repeater in an ultra-wideband (UWB) communication system for a wireless personal area network (WPAN) can be used to achieve diversity gain in a Rayleigh fading channel. We use maximal ratio combining (MRC) in the transmitter-repeater link and space-time coding (STC) in the repeater-receiver link, where the repeater has two antennas for transmission as well as reception. The repeater transmits at a higher rate than the transmitter so that the symbols are properly synchronized. We then derive the closed-form expression for the probability of bit error and show that there exists a trade-off between the bit error rate (BER) performance and the transmit powers of the transmitter and the repeater. Based on our BER curves, we then show that the performance of the proposed system is much better than a conventional repeater as well as the traditional communication system.
DESIRED CHARACTERISTICS OF MODULATION SPECTRUM FOR ROBUST AUTOMATIC SPEECH RECOGNITION

We report on the effect of band-pass filtering of the time trajectories of spectral envelopes on speech recognition. Several types of filter (linear-phase FIR, DCT, DFT) are studied. Results indicate the relative importance of different components of the modulation spectrum of speech for ASR. General conclusions are: (1) most of the useful linguistic information is in modulation frequency components from the range between 1 and 16 Hz, with the dominant component at around 4 Hz, (2) it is important to preserve the phase information in modulation frequency domain, (3) The features which include components at around 4 Hz in modulation spectrum outperform the conventional delta features, (4) The features which represent the several modulation frequency bands with appropriate center frequency and band width increase recognition performance.
Kinetics of Nucleotide Incorporation Opposite DNA Bulky Guanine N2 Adducts by Processive Bacteriophage T7 DNA Polymerase (Exonuclease–) and HIV-1 Reverse Transcriptase*

Six oligonucleotides with carcinogen derivatives bound at the N2 atom of deoxyguanosine were prepared, including adducts derived from butadiene, acrolein, crotonaldehyde, and styrene, and examined for effects on the replicative enzymes bacteriophage DNA polymerase T7– (T7–) and HIV-1 reverse transcriptase for comparison with previous work on smaller DNA adducts. All of these adducts strongly blocked dCTP incorporation opposite the adducts. dATP was preferentially incorporated opposite the acrolein and crotonaldehyde adducts, and dTTP incorporation was preferred at the butadiene- and styrene-derived adducts. Steady-state kinetic analysis indicated that the reduced catalytic efficiency with adducted DNA involved both an increased Km and attenuated kcat. Fluorescence estimates of Kd and pre-steady-state kinetic measurements of koff showed no significantly decreased affinity of T7– with the adducted oligonucleotides or the dNTP. Pre-steady-state kinetics showed no burst phase kinetics for dNTP incorporation with any of the modified oligonucleotides. These results indicate that phosphodiester bond formation or a conformational change of the enzyme• DNA complex is rate-limiting instead of the step involving release of the oligonucleotide. Thio elemental effects for dNTP incorporation were generally relatively small but variable, indicating that the presence of adducts may sometimes make phosphodiester bond formation rate-limiting but not always.
Otitic hydrocephalus

Otitic hydrocephalus is one of the less common intrncraninl complications of infectious ear disease, consisting of elevated intracranial pressure without focal neurologic abnormalities other than those due to the elevated pressure. A representative case is discussed in this report, followed by a review of the literature. The clinical course, diagnosis, treatment, and prognosis arc outlined. The etiology and the association with lateral sinus thrombosis remains obscure.
Sparse reconstruction of incomplete relative transfer function: Discrete and continuous time domain

Relative transfer functions (RTF) between microphones can often be estimated accurately but only for certain frequencies. For example, this happens in situations where the RTF is estimated from a noise-free signal of a target source whose spectrum does not span the whole frequency range. By combining a conventional RTF estimator and a selection of the active frequencies, an incomplete measurement of the RTF is obtained. We propose to retrieve the whole RTF estimate through finding the sparsest representation of the incomplete measurement in the discrete or continuous time-domain and compare both approaches. The RTF estimates are evaluated in terms of attenuation rate that measures the target signal cancellation at the output of a blocking matrix. It is shown by experiments that the reconstructed estimate can achieve significantly better attenuation than the initial (complete) estimate.
Hamiltonian-driven adaptive dynamic programming for nonlinear discrete-time dynamic systems

In this paper, based on the Hamiltonian, an alternative interpretation about the iterative adaptive dynamic programming (ADP) approach from the perspective of optimization is developed for discrete time nonlinear dynamic systems. The role of the Hamiltonian in iterative ADP is explained. The resulting Hamiltonian driven ADP is able to evaluate the performance with respect to arbitrary admissible policies, compare two different admissible policies and further improve the given admissible policy. The convergence of the Hamiltonian ADP to the optimal policy is proven. Implementation of the Hamiltonian-driven ADP by neural networks is discussed based on the assumption that each iterative policy and value function can be updated exactly. Finally, a simulation is conducted to verify the effectiveness of the presented Hamiltonian-driven ADP.
Verification of Analog/Mixed-Signal Circuits Using Labeled Hybrid Petri Nets

System on a chip design results in the integration of digital, analog, and mixed-signal circuits on the same substrate which further complicates the already difficult validation problem. This paper presents a new model, labeled hybrid Petri nets (LHPNs), that is developed to be capable of modeling such a heterogeneous set of components. This paper also describes a compiler from VHDL-AMS to LHPNs. To support formal verification, this paper presents an efficient zone-based state space exploration algorithm for LHPNs. This algorithm uses a process known as warping to allow zones to describe continuous variables that may be changing at variable rates. Finally, this paper describes the application of this algorithm to a couple of analog/mixed-signal circuit examples
Acinetobacter bacteraemia in Thailand: evidence for infections outside the hospital setting

SUMMARY Acinetobacter is a well-recognized nosocomial pathogen. Previous reports of community-associated Acinetobacter infections have lacked clear case definitions and assessment of healthcare-associated (HCA) risk factors. We identified Acinetobacter bacteraemia cases from blood cultures obtained <3 days after hospitalization in rural Thailand and performed medical record reviews to assess HCA risk factors in the previous year and compare clinical and microbiological characteristics between cases with and without HCA risk factors. Of 72 Acinetobacter cases, 32 (44%) had no HCA risk factors. Compared to HCA infections, non-HCA infections were more often caused by Acinetobacter species other than calcoaceticus–baumannii complex species and by antibiotic-susceptible organisms. Despite similar symptoms, the case-fatality proportion was lower in non-HCA than HCA cases (9% vs. 45%, P < 0·01). Clinicians should be aware of Acinetobacter as a potential cause of community-associated infections in Thailand; prospective studies are needed to improve understanding of associated risk factors and disease burden.
A parallel implementation of the Finite-Domain Time-Difference algorithm using MPJ express

This paper presents and evaluates a parallel Java implementation of the Finite-Difference Time-Domain (FDTD) method, which is a widely used numerical technique in computational electrodynamics. The Java version is parallelized using MPJ Express - a thread-safe messaging library. MPJ Express provides a full implementation of the mpiJava 1.2 API specification. This specification defines a MPI-like binding for the Java language. This paper describes our experiences of implementing the Java version of the FDTD method. Towards the end of this paper, we evaluate and compare the performance of the Java version against its C counterpart on a 32 processing core Linux cluster of eight compute nodes.