Miracle-dz/UniFAR-FTUs huggingface dataset:
Early Host Responses of Seasonal and Pandemic Influenza A Viruses in Primary Well-Differentiated Human Lung Epithelial Cells

Replication, cell tropism and the magnitude of the host's antiviral immune response each contribute to the resulting pathogenicity of influenza A viruses (IAV) in humans. In contrast to seasonal IAV in human cases, the 2009 H1N1 pandemic IAV (H1N1pdm) shows a greater tropism for infection of the lung similar to H5N1. We hypothesized that host responses during infection of well-differentiated, primary human bronchial epithelial cells (wd-NHBE) may differ between seasonal (H1N1 A/BN/59/07) and H1N1pdm isolates from a fatal (A/KY/180/10) and nonfatal (A/KY/136/09) case. For each virus, the level of infectious virus and host response to infection (gene expression and apical/basal cytokine/chemokine profiles) were measured in wd-NHBE at 8, 24, 36, 48 and 72 hours post-infection (hpi). At 24 and 36 hpi, KY/180 showed a significant, ten-fold higher titer as compared to the other two isolates. Apical cytokine/chemokine levels of IL-6, IL-8 and GRO were similar in wd-NHBE cells infected by each of these viruses. At 24 and 36 hpi, NHBE cells had greater levels of pro-inflammatory cytokines including IFN-α, CCL2, TNF-α, and CCL5, when infected by pandemic viruses as compared with seasonal. Polarization of IL-6 in wd-NHBE cells was greatest at 36 hpi for all isolates. Differential polarized secretion was suggested for CCL5 across isolates. Despite differences in viral titer across isolates, no significant differences were observed in KY/180 and KY/136 gene expression intensity profiles. Microarray profiles of wd-NHBE cells diverged at 36 hpi with 1647 genes commonly shared by wd-NHBE cells infected by pandemic, but not seasonal isolates. Significant differences were observed in cytokine signaling, apoptosis, and cytoskeletal arrangement pathways. Our studies revealed differences in temporal dynamics and basal levels of cytokine/chemokine responses of wd-NHBE cells infected with each isolate; however, wd-NHBE cell gene intensity profiles were not significantly different between the two pandemic isolates suggesting post-transcriptional or later differences in viral-host interactions.
Statistical analysis of different artificial intelligent techniques applied to Intrusion Detection System

Intrusion Detection System (IDS) which are increasingly a key part of system defense are used to identify abnormal activities in a computer system. In general, the traditional IDS relies on the extensive knowledge of security experts, in particular, on their familiarity with the computer system to be protected. To reduce this dependence, various data-mining and machine learning techniques have been used in the literature. The experiments and evaluations of the proposed intrusion detection system are performed with the NSL-KDD intrusion detection dataset. We will apply different learning algorithms on NSL-KDD data set, to recognize between normal and attack connections and compare their performing in different scenarios- discretization, features selections and algorithm method for classification- using a powerful statistical analysis: ANOVA. In this study, both the accuracy of the configuration of different system and methodologies used, and also the computational time and complexity of the methodologies are analyzed.
Multi-Robot Fence Patrol in Adversarial Domains

This paper considers the problem of multi-robot patrolling along an open polyline, for example a fence, in the presence of an adversary trying to penetrate through the fence. In this case, the robots’ task is to maximize the probability of detecting penetrations. Previous work concerning multi-robot patrol in adversarial environments considered closed polygons. That situation is simpler to evaluate due to its symmetric nature. In contrast, if the robots patrol back and forth along a fence, then the frequency of their visits along the line is coherently non-uniform, making it easier to be exploited by an adversary. Moreover, previous work assumed perfect sensorial capabilities of the robots in the sense that if the adversary is in the sensorial range of the robot is will surely be detected. In this paper we address these two challenges. We first suggest a polynomial time algorithm for finding the probability of penetration detection in each point along the fence. We then show that by a small adjustment this algorithm can deal with the more realistic scenario, in which the robots have imperfect sensorial capabilities. Last, we demonstrate how the probability of penetration detection can be used as base for finding optimal patrol algorithms for the robots in both strong and weak adversarial environment.
Assigning the characteristics of an ATR dove prism for use with terahertz frequencies: Supplemented with molecular dynamic simulations

In this paper we characterize an in house attenuated total reflection (ATR) sample cell unit, for use with a table top Terahertz-Time domain system (THz-TDS) spectrometer. The custom designed ATR unit offers several key advantages compared to conventional transmission spectrometry. Solid, liquid and powdered samples can easily be prepared for analysis and are easily removed and accessed without the need of dismantling the sample cell. Multiple reflections between the windows in transmission cells are no longer present with the ATR setup. If required the prism can be removed and replaced with a more traditional transmission cell without interfering with the spectrometers optics and optical beam path. The ATR unit was tested with a series of water-isopropyl alcohol (IPA) mixtures, to measure the performance and sensitivity of the ATR unit. The series of mixtures ranged from 0-100% IPA with increments of 10%. The ATR unit was shown to define each increment, with a steady and linear drop of in THz absorbance with added IPA. The real and imaginary parts of the refractive index and therefore, dielectric constants were also calculated at each sample interval. The refractive index increased linearly at the measured THz range from 0.5 and 1 THz from a refractive index of 1 at pure IPA to a maximum of 3 at pure water. To further our understanding of the ATR results, molecular dynamic simulations of the IPA mixtures were performed using an OPLS/AA force field. These simulations produced a series of trajectories from which the auto correlated Fourier transform was calculated from the total dipole moment magnitude of each frame. This gives us the spectral density of each IPA-water mixture which is directly comparable to the THz spectrum experimentally seen with the ATR unit. These simulations repeated the same pattern showing a decrease in THz absorbance with increasing IPA solute. From these results, we conclude the ATR unit is an effective tool in terahertz spectroscopy. The agreement with the simulated results gives us confidence the ATR unit is performing as designed.
The Impact of Health Insurance Status on Treatment Intensity and Health Outcomes

This paper uses the abrupt changes in health insurance coverage at age 65 arising from the Medicare program eligibility rules to evaluate the impact of insurance status on treatment intensity and health outcomes. Drawing from several million hospital discharge records for the State of California, the authors begin by identifying a subset of patients who are admitted through the emergency room for non-deferrable conditions-diagnoses with the same daily admission rates on weekends and weekdays. Among this subset of patients there is no discernable rise in the number of admissions at age 65, suggesting that the severity of illness is similar for patients who are just under 65 and those who are just over 65. The fraction of patients in this group who lack health insurance, however, falls sharply at age 65, while the proportion with Medicare as their primary insurer rises. Tracking health-related outcomes of the group, they find significant increases in treatment intensity at the age 65 barrier, including increases in the number of procedures performed, and total list charges. They also find a rise in the probability that patients are transferred to other units within the same hospital, coupled with a reduction in the probability of discharge to home. Finally, they estimate a drop in the rate of re-admission within one month of the initial discharge.
Author-Specific Sentiment Aggregation for Polarity Prediction of Reviews

In this work, we propose an author-specific sentiment aggregation model for polarity prediction of reviews using an ontology. We propose an approach to construct a Phrase Annotated Author Specific Sentiment Ontology Tree (PASOT), where the facet nodes are annotated with opinion phrases of the author, used to describe the facets, as well as the author’s preference for the facets. We show that an author-specific aggregation of sentiment over an ontology fares better than a flat classification model, which does not take the domain-specific facet importance or author-specific facet preference into account. We compare our approach to supervised classification using Support Vector Machines, as well as other baselines from previous works, where we achieve an accuracy improvement of 7.55% over the SVM baseline. Furthermore, we also show the effectiveness of our approach in capturing thwarting in reviews, achieving an accuracy improvement of 11.53% over the SVM baseline.
Defense Technical Information Center Compilation Part Notice ADP 014821

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DESIGN AND IMPLEMENTATION OF CACHE MANAGER FOR HYBRID STORAGE

The technology and cost barrier of the SSD motivated many research groups and companies to merge the SSD with low cost and large capacity storage device, Hard Disk Drive (HDD). As the NAND flash memory technology is getting more advanced, price of NAND flash memory dropped dramatically. As number of bits per cell in NAND flash memory is increasing, the price of $/GByte is reduced. This trend will continue until the market sought for another media as a stable and fast storage media. NAND flash based Solid State Drive (SSD) is considered as a choice for replacing Hard Disk Drive (HDD) to reduce and minimize the gap between IO latency DRAM of a storage device. In this work, we first examine three existing cache manager solutions and study if advertised measurements hold in in-house benchmark environment. We describe what has to be considered in implementing cache managers, and also describe design and implementation of a cache manager and measure its caching performance.
Adaptive Fuzzy Sliding Mode Control Algorithm for a Non-Affine Nonlinear System

This paper concerns the design of robust controller for a nonlinear system that can be represented or approximated in a non-affine form. The control algorithm is based on sliding mode control that incorporates a fuzzy tuning technique, and it superposes equivalent control, switching control, and fuzzy control. An equivalent control law is firstly designed based on a nominal system model that was obtained by using curve fitting techniques under MATLAB. Switching control is then added to guarantee that the state reaches the sliding surface in the presence of parameter and disturbance uncertainties. Also, fuzzy tuning schemes, which can be supported by learning techniques derived from neural networks, are employed to improve control performance and to reduce chattering in the sliding mode. To verify the performance of this controller, an experimental platform of a pneumatically actuated top-guided single-seated control valve, which belongs to a classical complex nonlinear system, was constructed. Also, the experimental results show that high performance and attenuated chatter are achieved and thus verify the validity of the proposed control approach to dynamic systems characterized by severe uncertainties.
Morphological Analysis of White Cement Clinker Minerals: Discussion on the Crystallization-Related Defects

The paper deals with a formation of artificial rock (clinker). Temperature plays the capital role in the manufacturing process. So, it is useful to analyze a poor clinker to identify the different phases and defects associated with their crystallization. X-ray fluorescence spectroscopy was used to determine the clinker's chemical composition. The amounts of the mineralogical phases are measured by quantitative XRD analysis (Rietveld). Scanning electron microscopy (SEM) was used to characterize the main phases of white Portland cement clinker and the defects associated with the formation of clinker mineral elements. The results of a study which focused on the identification of white clinker minerals and defects detected in these noncomplying clinkers such as fluctuation of the amount of the main phases (alite (C3S) and belite (C2S)), excess of the free lime, occurrence of C3S polymorphs, and occurrence of moderately-crystallized structures are presented in this paper.
An ALU Based Online BIST for Varying Word Widths of RAM

On-line testing of word oriented memories is fast becoming a basic feature of digital systems, not only for critical applications, but also for highly-available applications. With the use of transparent BIST (built in self test) schemes for testing of RAMs, preservation of memory contents during periodic testing is assured but, it requires more hardware for signature prediction and more time for testing. Symmetric Transparent BIST skips the signature prediction phase, thus reducing the hardware and test time. Previously, one ALU was used for testing one RAM which increases the hardware of BIST circuit. The proposed method uses a symmetric transparent BIST scheme and an ALU capable of testing more than one RAM thus decreasing the hardware required to test RAM modules on a die. Different word widths of RAMs can be tested by using addition and subtraction operation of ALU with the help of series of March elements. Four RAM modules are tested using one ALU module in a roving manner. Due to the decrease in hardware overhead of proposed scheme the test time is also reduced.
Proton core imaging of the nuclear burn in inertial confinement fusion implosions

A proton emission imaging system has been developed and used extensively to measure the nuclear burn regions in the cores of inertial confinement fusion implosions. Three imaging cameras, mounted to the 60-beam OMEGA laser facility [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)], use the penetrating 14.7MeV protons produced from DHe3 fusion reactions to produce emission images of the nuclear burn spatial distribution. The technique relies on penumbral imaging, with different reconstruction algorithms for extracting the burn distributions of symmetric and asymmetric implosions. The hardware and design considerations required for the imaging cameras are described. Experimental data, analysis, and error analysis are presented for a representative symmetric implosion of a fuel capsule with a 17-μm-thick plastic shell and 18atm DHe3 gas fill. The radial burn profile was found to have characteristic radius Rburn, which we define as the radius containing half the DHe3 reactions, of 32±2μm (burn radii measure.
Dynamic Early Stopping for Naive Bayes

Energy efficiency is a concern for any software running on mobile devices. As such software employs machine-learned models to make predictions, this motivates research on efficiently executable models. In this paper, we propose a variant of the widely used Naive Bayes (NB) learner that yields a more efficient predictive model. In contrast to standard NB, where the learned model inspects all features to come to a decision, or NB with feature selection, where the model uses a fixed subset of the features, our model dynamically determines, on a case-by-case basis, when to stop inspecting features. We show that our approach is often much more efficient than the current state of the art, without loss of accuracy.
Phytohormone Involvement in the Ustilago maydis– Zea mays Pathosystem: Relationships between Abscisic Acid and Cytokinin Levels and Strain Virulence in Infected Cob Tissue

Ustilago maydis is the causative agent of common smut of corn. Early studies noted its ability to synthesize phytohormones and, more recently these growth promoting substances were confirmed as cytokinins (CKs). Cytokinins comprise a group of phytohormones commonly associated with actively dividing tissues. Lab analyses identified variation in virulence between U. maydis dikaryon and solopathogen infections of corn cob tissue. Samples from infected cob tissue were taken at sequential time points post infection and biochemical profiling was performed using high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI MS/MS). This hormone profiling revealed that there were altered levels of ABA and major CKs, with a marked reduction in CK glucosides, increases in methylthiol CKs and a particularly dramatic increase in cisZ CK forms, in U. maydis infected tissue. These changes were more pronounced in the more virulent dikaryon relative to the solopathogenic strain suggesting a role for cytokinins in moderating virulence during biotrophic infection. These findings highlight the fact that U. maydis does not simply mimic a fertilized seed but instead reprograms the host tissue. Results underscore the suitability of the Ustilago maydis– Zea mays model as a basis for investigating the control of phytohormone dynamics during biotrophic infection of plants.
Mammalian Base Excision Repair: Functional Partnership between PARP-1 and APE1 in AP-Site Repair

The apurinic/apyrimidinic- (AP-) site in genomic DNA arises through spontaneous base loss and base removal by DNA glycosylases and is considered an abundant DNA lesion in mammalian cells. The base excision repair (BER) pathway repairs the AP-site lesion by excising and replacing the site with a normal nucleotide via template directed gap-filling DNA synthesis. The BER pathway is mediated by a specialized group of proteins, some of which can be found in multiprotein complexes in cultured mouse fibroblasts. Using a DNA polymerase (pol) β immunoaffinity-capture technique to isolate such a complex, we identified five tightly associated and abundant BER factors in the complex: PARP-1, XRCC1, DNA ligase III, PNKP, and Tdp1. AP endonuclease 1 (APE1), however, was not present. Nevertheless, the complex was capable of BER activity, since repair was initiated by PARP-1’s AP lyase strand incision activity. Addition of purified APE1 increased the BER activity of the pol β complex. Surprisingly, the pol β complex stimulated the strand incision activity of APE1. Our results suggested that PARP-1 was responsible for this effect, whereas other proteins in the complex had no effect on APE1 strand incision activity. Studies of purified PARP-1 and APE1 revealed that PARP-1 was able to stimulate APE1 strand incision activity. These results illustrate roles of PARP-1 in BER including a functional partnership with APE1.
Life cycle inventory of 23 dairy farms in south-western Sweden

In this study, data on resource use and emissions for dairy farms in southwestern Sweden were collected and analysed with Life Cycle Assessment (LCA) methodology. The purpose of the study was to gain increased knowledge of the environmental impact of today´s milk production and of the variations between farms regarding resource use and emissions. Data were collected from 23 dairy farms in the Halland and Västra Götlands regions. The farms were divided into three groups: 1) Conventional high (Conv High); producing >7 500 kg ECM/ha (nine farms) 2) Conventional medium (Conv Med); producing < 7 500 kg ECM/ha (eight farms) 3) Organic (six farms) Data on concentrate feed production were upgraded from earlier work by collating statistics and information from different feed and food industries. All the studied farms participated in the advisory programme " Greppa Näringen " and had detailed information on feed and fertiliser consumption. In addition to this, data on use of diesel, electricity, pesticides and plastic were collected at the farms. For ammonia, nitrate, nitrous oxide and methane, different emission models were used in order to infer the losses. The functional unit (reference unit) in the study was " one kg of energy corrected milk " at the farmgate. Emissions of ammonia and nitrate, as well as pesticide use, were also evaluated per hectare of arable land at the farms. The systems analysed included all phases in the life cycle of fertilisers, feed products, diesel, pesticides and plastics. Transport steps were also taken into account. Buildings, machinery and medicines were not included. Allocation between milk and meat was done on an economic basis, distributing 90 % of the impact to milk and 10 % to the meat. Economic allocation was also used in the Life Cycle Inventory (LCI) of concentrate feed. In the LCIs of the 23 dairy farms, the results were presented as use of resources (energy, nutrients and land), use of pesticides, emissions of greenhouse gases, emissions of nutrifying and acidifying substances. The LCI results were statistically analysed in oneway ANOVA to establish the results that showed the least significant difference between the three farm groups. There was no significant difference in the use of energy resources between the two conventional groups. The overall energy use was significantly lower for the organic farm group in comparison with the conventional groups, and it was the total lower use of fossil fuels that explained this difference …
An analysis of modal coupling effects during the glottal cycle: formant synthesizers from time-domain finite-difference simulations

Speech is typically modelled using time-domain or frequency-domain simulations of the acoustic ﬁeld in the vocal tract. Using a biorthogonal modal decomposition, it is shown that time-domain ﬁnite-difference simulations can be transformed algebraically into equivalent formant synthesizers, the parameters of which vary in time and are calculated directly from the laws of physics. Examining the structure of the equivalent formant synthesizer, it is observed that formant excitation is largely due to internal modal coupling effects, induced by rapid perturbation of the acoustic eigenmodes caused by vibration of the glottis, and does not rely precisely on external sources provided by boundary conditions. This leads to a novel interpretation and justiﬁcation of traditional models of the glottal source.