Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Sphingolipid and Phospholipid Profiles in Alcohol and Nicotine-Derived Nitrosamine Ketone-Associated White Matter Degeneration.

BACKGROUND Alcohol-mediated neurodegeneration is associated with white matter (WM) atrophy due to targeting of myelin and oligodendrocytes. However, variability in disease severity suggests cofactors contribute to WM degeneration. We examined the potential cofactor role of the tobacco-specific nitrosamine, nicotine-derived nitrosamine ketone (NNK), because smoking causes WM atrophy and most heavy drinkers consume tobacco products. METHODS This 8-week study of Long Evans rats had 4 treatment groups: control; NNK-2 mg/kg, 3×/wk in weeks 3 to 8; ethanol (EtOH) (chronic-26% caloric + binge-2 g/kg, 3×/wk in weeks 7 to 8); and EtOH + NNK. Exposure effects on WM lipid biochemical profiles and in situ distributions were examined using matrix-assisted laser desorption/ionization imaging mass spectrometry and tandem mass spectrometry. RESULTS NNK mainly caused WM fiber degeneration and fiber loss, EtOH caused demyelination, and dual exposures had additive effects. EtOH and EtOH + NNK decreased WM (including corpus callosum) and/or gray matter (hypothalamus, cortex, medial temporal) levels of several phosphatidylserine, phosphatidylinositol, and sphingolipid (sulfatide [ST]) species, while NNK increased or had minimal effect on these lipids. EtOH + NNK had broader and larger inhibitory effects on phospholipids and ST than EtOH or NNK alone. Principal component analysis clustered control with NNK, and EtOH with EtOH + NNK groups, highlighting the independent EtOH- rather than NNK-driven responses. CONCLUSIONS Chronic EtOH exposures decreased several phospholipid and sphingolipid species in brain, while concomitant NNK exposures exacerbated these effects. These findings support our hypothesis that tobacco smoking is a pathogenic cofactor in alcohol-mediated WM degeneration.
Research on Transportation-Related Emissions: Current Status and Future Directions

Abstract Transportation-related emissions are the dominant contributing source of air pollutants today. Considering the negative impacts of transportation-related emissions on our social and economic environment, extensive efforts have been made by researchers and practitioners attempting to find solutions to reduce the emissions. To synthesize these research efforts, researchers have conducted various reviews of relevant studies. However, because of the diversity of the topics, most of existing reviews have only focused on specific and narrowed areas. Furthermore, none of the existing reviews have attempted to summarize the researchers’ opinions on the current research and their prospects of the future research directions. Therefore, this paper is intended to fill this gap by conducting an extensive survey of transportation emissions professionals. In the paper, a review of existing research and developments on each of the emissions-related topics is provided, followed by a presentation of the respective survey results and analysis. At the conclusion of these reviews and the analysis of the survey, some future research directions in this field are presented.
Topic-Sensitive Search Engine Evaluation

Purpose – This work aims to investigate the sensitivity of ranking performance with respect to the topic distribution of queries selected for ranking evaluation.Design/methodology/approach – The authors reweight queries used in two TREC tasks to make them match three real background topic distributions, and show that the performance rankings of retrieval systems are quite different.Findings – It is found that search engines tend to perform similarly on queries about the same topic; and search engine performance is sensitive to the topic distribution of queries used in evaluation.Originality/value – Using experiments with multiple real‐world query logs, the paper demonstrates weaknesses in the current evaluation model of retrieval systems.
A Multi-objective Ab-initio Model for Protein Folding Prediction at an Atomic Conformation Level

Engineering Computer Science Msc. System Engineering and Computation by David Camilo Becerra Romero This thesis focuses on the protein structure prediction problem, one of the most important problems tackled by bioinformatics and molecular biology. The basic problem consists of predicting the three-dimensional structure of a protein from its amino-acid sequence. Specifically, in this work a parallel multiobjective ab-initio approach at an atomic conformation level for protein structure prediction is proposed. The proposed model incorporated several existing software tools combined with others developed by us. Experiments were carried out over a set of different proteins (1ROP, 1PLW, 1UTG, 1CRT and 1ZDD) to validate the model obtaining very promising results. The most important features of the experimental framework are: i) A trigonometric representation was chosen to represent and compute the backbone and side-chain torsion angles of a protein; ii) The Chemistry at HARvard Macromolecular Mechanics (CHARMm) function was used in order to evaluate the structure of protein conformations; iii) The multi-objective genetic algorithm (NSGA-II) was used to evolve protein conformations directed by an atom-interaction scoring function; iv) An island model of the evolutionary algorithm was developed to speed up the process and to improve the effectiveness of the algorithm. NATIONAL UNIVERSITY OF COLOMBIA
Global Output Regulation of A Class of Nonlinear Systems with Nonlinear Exosystems

This paper deals with global output regulation with nonlinear exosystems for a class of uncertain nonlinear output feedback systems. The circle criterion is exploited for the internal model design to accommodate the nonlinearities in the exosystems, and the explicit conditions are given for the exosystems such that proposed internal model design can be applied. The uncertainties of the output feedback systems are in the form of unknown constant parameters, and adaptive control techniques are used to ensure the global stability of the proposed control design for output regulation
Few-photon-level two-dimensional infrared imaging by coincidence frequency upconversion

We demonstrate few-photon-level infrared imaging at 1040 nm by coincidence frequency upconversion with a high conversion efficiency of 33.5%. By synchronous pulse pumping at 1549 nm, the infrared object image was spectrally upconverted into the visible regime. The upconverted image was captured by a silicon electron multiplying charged coupled device without any scanning devices, thus gaining in simplicity and speed. The imaging sensitivity was improved by reducing the background noise with coincidence pulsed pumping at long wavelength.
ToxoDB : an integrated genomic database for the study of Toxoplasma gondii and Neospora caninum

Integrated databases resources are integral to the study of biology and of host-pathogen interactions. Tremendous strides in technology have permitted the generation of large, valuable data sets for many life cycle stages of numerous pathogens and/or their hosts. The Toxoplasma genome database (http://ToxoDB.org) currently hosts, and integrates, a wide array of diverse, large-scale data sets (1). ToxoDB contains three fully annotated genome sequences for Toxoplasma gondii (GT1, VEG and ME49 strains) and the annotated genome sequence of the closely related Neospora caninum (2). Additionally, the database contains all available EST sequence data, 13 microarray experimental datasets for tachyzoites and bradyzoites, 2 SAGETag data sets, 1 tachyzoite RNA-Seq experiment from both T. gondii VEG and N. caninum, and ChIP-on-chip data sets from precipitation with several different histone antibodies. The database also contains 21 proteomic data sets, SNPs and ortholog and synteny determinations between all Toxoplasma strains and Neospora. The database is part of the NIH-funded Eukaryotic Pathogen Database, (http://EuPathDB.org) (3). The integrated data are presented in an intuitive interface that permits strategic data mining across the data sets using our strategy system (4). For example, it is possible to identify all annotated genes that contain a signal peptide, are expressed in tachyzoites, but not bradyzoites, have evidence of protein expression and are conserved in Neospora with only a few clicks of the cursor. The database, which has been in existence since 2003 (5), is a free community resource that is linked to other prominent apicomplexan organisms (Plasmodium, Thileria, Babesia and Cryptosporidium) as well as other prominent eukaryotic pathogens (Giardia, Entamoeba, Leishmania, Trypanosoma, Microsporidia and Trichomonas) via the EuPathDB.org portal. The EuPathDB portal permits queries of Toxoplasma and any other organism contained within the database simultaneously. For example, it is possible to search for genes with certain properties that are conserved in Toxoplasma and Neospora but not other Apicomplexa. References 1. Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, et al. ToxoDB: An integrated Toxoplasma gondii database resource. Nucleic Acids Res. 2008;36(Database issue):D553-6.http://www.sanger. ac.uk/resources/downloads/protozoa/neosporacaninum.html. 2. Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, et al. EuPathDB: A portal to eukaryotic pathogen databases. Nucleic Acids Res. 2010;38(Database issue):D415-9. 3. Fischer S, Aurrecoechea C, Brunk BP, Gao X, Harb OS, Kraemer ET, et al. The strategies WDK: A graphical search interface and web development kit for functional genomics databases. DATABASE The Journal of Biological Databases and Curation. In press. 4. Kissinger JC, Gajria B, Li L, Paulsen IT, Roos DS. ToxoDB: Accessing the Toxoplasma gondii genome. Nucleic Acids Res. 2003;31:234-6.
SWI/SNF chromatin remodeling complex is obligatory for BMP2‐induced, Runx2‐dependent skeletal gene expression that controls osteoblast differentiation

Development of bone tissue requires maturation of osteoblasts from mesenchymal precursors. BMP2, a member of the TGFβ superfamily, and the Runx2 (AML3/Cbfa1) transcription factor, a downstream BMP2 effector, are regulatory signals required for osteoblast differentiation. While Runx2 responsive osteogenic gene expression has been functionally linked to alterations in chromatin structure, the factors that govern this chromatin remodeling remain to be identified. Here, we address the role of the SWI/SNF chromatin remodeling enzymes in BMP2‐induced, Runx2‐dependent development of the osteoblast phenotype. For these studies, we have examined calvarial cells from wild‐type (WT) mice and mice that are homozygous for the Runx2 null allele, as well as the C2C12 model of BMP2‐induced osteogenesis. By the analysis of microarray data, we find that several components of the SWI/SNF complex are regulated during BMP2‐mediated osteoblast differentiation. Brg1 is an essential DNA dependent ATPase subunit of the SWI/SNF complex. Thus, functional studies were carried out using a fibroblast cell line that conditionally expresses a mutant Brg1 protein, which exerts a dominant negative effect on SWI/SNF function. Our findings demonstrate that SWI/SNF is required for BMP2‐induced expression of alkaline phosphatase (APase), an early marker reflecting Runx2 control of osteoblast differentiation. In addition, Brg1 is expressed in cells within the developing skeleton of the mouse embryo as well as in osteoblasts ex vivo. Taken together these results support the concept that BMP2‐mediated osteogenesis requires Runx2, and demonstrates that initiation of BMP2‐induced, Runx2‐dependent skeletal gene expression requires SWI/SNF chromatin remodeling complexes. © 2004 Wiley‐Liss, Inc.
Integrated Circuit Design Based on Carbon Nanotube Field Effect Transistor

As complementary metal-oxide semiconductor (CMOS) continues to scale down deeper into the nanoscale, various device non-idealities cause the I-V characteristics to be substantially different from well-tempered metal-oxide semiconductor field-effect transistors (MOSFETs). The last few years witnessed a dramatic increase in nanotechnology research, especially the nanoelectronics. These technologies vary in their maturity. Carbon nanotubes (CNTs) are at the forefront of these new materials because of the unique mechanical and electronic properties. CNTFET is the most promising technology to extend or complement traditional silicon technology due to three reasons: first, the operation principle and the device structure are similar to CMOS devices and it is possible to reuse the established CMOS design infrastructure. Second, it is also possible to reuse CMOS fabrication process. And the most important reason is that CNTFET has the best experimentally demonstrated device current carrying ability to date. This paper discusses and reviewsthe feasibility of the CNTFET`s application at this point of time in integrated circuits design by investigating different types of circuit blocks considering the advantages that the CNTFETs offer.
Asymmetric Shocks in a Currency Union: The Role of Central Bank Collateral Policy

Currency unions limit the ability of the central bank to use interest rate policy to accommodate asymmetric shocks. I show that collateral policy can serve to dampen asymmetric shocks in a currency area when these shocks also affect the collateral held by banks and when collateral portfolios of banks differ systematically across countries. In my model banks from 2 countries use collateral to borrow from the money market or a central bank that targets a level of interest rate (or investment) in each economy. The distressed bank may enter a “collateral crunch” regime where it is constrained in its access to funding due to a moral hazard problem. The central bank faces an heterogeneous transmission of its interest rate: a unit change in rate has a smaller effect on the economy rate of the distressed country. The central bank therefore sets a high interest rate which is well transmitted in the booming economy and relaxes the haircut on the collateral owned by the distressed bank.
Nonblind and semiblind space-time-frequency multiuser detection for space-time block-coded MC-CDMA

In this paper, a novel space–time-frequency minimum mean squared error (STF-MMSE)-based parallel interference cancellation receiver is proposed for space–time block-coded multicarrier code division multiple access systems in time-varying fading channels. The signal processing of this new detector is jointly implemented in space, time, and frequency domains, which leads to a powerful capability of combating interference coming from different sources. An adaptive implementation based on subspace estimation is proposed for slow-varying fading channels. Furthermore, based on the characteristic function of a complex Gaussian random vector, an analytical method to calculate the bit error probability of the proposed STF-MMSE receiver is presented. Representative examples of the detector are provided to demonstrate its superior performance.
A GPU-based correlator X-engine implemented on the CHIME Pathfinder

We present the design and implementation of a custom GPU-based compute cluster that provides the correlation X-engine of the CHIME Pathfinder radio telescope. It is among the largest such systems in operation, correlating 32,896 baselines (256 inputs) over 400MHz of radio bandwidth. Making heavy use of consumer-grade parts and a custom software stack, the system was developed at a small fraction of the cost of comparable installations. Unlike existing GPU backends, this system is built around OpenCL kernels running on consumer-level AMD GPUs, taking advantage of low-cost hardware and leveraging packed integer operations to double algorithmic efficiency. The system achieves the required 105 TOPS in a 10kW power envelope, making it one of the most power-efficient X-engines in use today.
PBTI in HKMG nMOS Transistors— Effect of Width, Layout, and Other Technological Parameters

This paper discusses in detail the effects of transistor width, layout, and technological parameters like gate dielectric and Lanthanum capping layer thickness on positive bias temperature instability (PBTI) of nMOS transistors fabricated using 28-nm gate-first High-<inline-formula> <tex-math notation="LaTeX">${K}$ </tex-math></inline-formula> metal gate CMOS technology. It is shown that the PBTI reduces with decrease in width (<inline-formula> <tex-math notation="LaTeX">${W}$ </tex-math></inline-formula>), increase in capping layer thickness and decrease in high-<inline-formula> <tex-math notation="LaTeX">${K}$ </tex-math></inline-formula> dielectric thickness. The physical mechanisms responsible for these dependencies are investigated and attributed to the modulation of preexisting traps in the high-<inline-formula> <tex-math notation="LaTeX">${K}$ </tex-math></inline-formula> dielectric and the modulation of electron injection into these traps. It is also shown that the PBTI of the devices could be improved by dividing a single active into multiple actives, by increasing active-to-active spacing and gate pitch.
"Wrapping" X3DOM around Web Audio API

Spatial sound has a conceptual role in the Web3D environments, due to highly realism scenes that can provide. Lately the efforts are concentrated on the extension of the X3D/ X3DOM through spatial sound attributes. This paper presents a novel method for the introduction of spatial sound components in the X3DOM framework, based on X3D specification and Web Audio API. The proposed method incorporates the introduction of enhanced sound nodes for X3DOM which are derived by the implementation of the X3D standard components, enriched with accessional features of Web Audio API. Moreover, several examples-scenarios developed for the evaluation of our approach. The implemented examples established the achievability of new registered nodes in X3DOM, for spatial sound characteristics in Web3D virtual worlds.
Dose‐Response Models Incorporating Aerosol Size Dependency for Francisella tularensis

The effect of bioaerosol size was incorporated into predictive dose‐response models for the effects of inhaled aerosols of Francisella tularensis (the causative agent of tularemia) on rhesus monkeys and guinea pigs with bioaerosol diameters ranging between 1.0 and 24 μm. Aerosol‐size‐dependent models were formulated as modification of the exponential and β‐Poisson dose‐response models and model parameters were estimated using maximum likelihood methods and multiple data sets of quantal dose‐response data for which aerosol sizes of inhaled doses were known. Analysis of F. tularensis dose‐response data was best fit by an exponential dose‐response model with a power function including the particle diameter size substituting for the rate parameter k scaling the applied dose. There were differences in the pathogen's aerosol‐size‐dependence equation and models that better represent the observed dose‐response results than the estimate derived from applying the model developed by the International Commission on Radiological Protection (ICRP, 1994) that relies on differential regional lung deposition for human particle exposure.
Consensus of rankings

Rankings are widely used in many information systems. In information retrieval, a ranking is a list of ordered documents, in which a document with lower position has higher ranking score than the documents behind it. This paper studies the consensus measure for a given set of rankings, in order to understand the degree to which the rankings agree and the extent to which the rankings are related. The proposed multi-facet approach, without the need for pairwise comparison between rankings, allows to measure the consensus in a set of rankings, with respect to the length of common patterns, the number of common patterns for a given length, and the number of all common patterns. The experiments show that the proposed approach can be used to compare the search engines in terms of closeness of the returned results when semantically related key words are sent to them.
Molecular epidemiological analysis of the transboundary transmission of 2003 highly pathogenic avian influenza H7N7 outbreaks between the Netherlands and Belgium.

The 2003 outbreak of Highly pathogenic avian influenza (HPAI) A(H7N7) in the Netherlands, Belgium and Germany resulted in significant genetic diversification that proved informative for tracing transmission events. Building on previous investigations on the Dutch outbreak, we focused on the potential transnational transmissions between the Netherlands and Belgium. Although no clear epidemiological links could be identified from the tracing data, the transmission network based on concatenated HA-NA-PB2 sequences supports at least three independent introductions from the Netherlands to Belgium and suggests one possible introduction form Belgium back to the Netherlands. Two introductions in the Belgian province of Limburg occurred from nearby farms in the Dutch province of Limburg. One introduction resulted in three secondary infected farms, while a second introduction did not cause secondary infections. The third introduction into Belgium occurred in the north of the Antwerp province, very close to the national border, and originated from the North of the Dutch province Brabant (long distance transmission, >65 km). The virus spread to two additional Belgian farms, one of which may be the source of a secondarily infected farm in the Netherlands. One infected turkey farm in the province of Antwerp (Westmalle) was geographically close to the latter introduction, but genetically clustered with the first introduction event in the Limburg province. Epidemiological tracing data could neither confirm nor exclude whether this outbreak was a result from long distance contacts within Belgium or whether this farm presented a fourth independent transboundary introduction. These multiple transnational transmissions of HPAI in spite of reinforced biosecurity measures and trade restrictions illustrate the importance of international cooperation, legislation and standardization of tools to combat transboundary diseases.
Combining behavior trees with MAXQ learning to facilitate CGFs behavior modeling

In simulation based military training, behaviors of Computer generated forces (CGFs) are usually constrained by doctrine and goal hierarchy. Behavior Tree (BT) is a popular AI scripting technique to encode such behavior, but suffers from time-consuming, repetitive endeavor and lack of nuanced variations. This paper proposes a novel approach MAXQ-BT, which combines BT with MAXQ learning to facilitate constrained and adaptive behavior generation. We first allow subject matter expert (SME) to encode goal hierarchy and temporal constrains with an initial BT, then a modified MAXQ learner is combined to generate specific behavior policy for selector node subtree. Finally, the learned policy is reorganized transparently as condition nodes of original selected behavior. Preliminary experiments in a predator-prey simulation scenario show that MAXQ-BT can facilitate behavior trees generation easily for CGF to achieve better behavior performance than handcrafted products.
Carrier Phase Estimation for 32-QAM Optical Systems Using Quasi-QPSK-Partitioning Algorithm

In this letter, we propose a quasi-quadrature phase shift keying (QPSK) partitioning to replace the conventional QPSK partitioning in the first stage of the carrier phase estimation (CPE) algorithms for 32-QAM optical systems. By using the proposed quasi-QPSK-partitioning method, the ability of the CPE algorithms to track changes of phase is greatly enhanced. For 1-dB SNR penalty at bit error rate of 1E-2, the proposed method can achieve an improvement of 85% in combined linewidth symbol duration product tolerance when compared with the conventional method for single stage. With the help of the fine estimation stages, the maximum tolerable combined linewidth symbol duration product can be up to 5.1E-5.