Miracle-dz/UniFAR-FTUs huggingface dataset:
Removal of Endotoxins from Bacteriophage Preparations by Extraction with Organic Solvents

Lipopolysaccharide (LPS, endotoxin, pyrogen) constitutes a very troubling contaminant of crude phage lysates produced in Gram-negative bacteria. Toxicity of LPS depends on the strong innate immunity response including the cytokines. Therefore, its removal is important for bacteriophage applications. In this paper, we present a procedure for extractive removal of endotoxin from bacteriophage preparations with water immiscible solvents (1-octanol or 1-butanol). During extraction most of the phage lytic activity is retained in the aqueous phase, while endotoxin accumulates in the organic solvent. The levels of endotoxin (expressed as endotoxin units, EU) in the aqueous bacteriophage-containing fraction determined by limulus amebocyte lysate or EndoLISA assay were exceptionally low. While the initial endotoxin levels in the crude phage lysates ranged between 103 and 105 EU/ml the average level after organic extraction remaining in the aqueous fraction was 5.3 EU/ml. These values when related to phage titers decreased from 103-105 EU/109 PFU (plaque forming units) down to an average of 2.8 EU/109 PFU. The purification procedure is scalable, efficient and applicable to all the bacteriophages tested: T4, HAP1 (E. coli) and F8 (P. aeruginosa).
Geometrically Influenced Photon Mapping 1

Ben Ball Yuriy Stejko Final Project Report Motivation The photon mapping we implemented in class worked well under most circumstances, however there were some specific situations where the result of rendering did not look entirely realistic [Image 2]. One situation where the problem was apparent was the rendering of edges. When two edges with a sharp change in photon quantity were rendered, photons from the bright edge would sometimes fall within the spherical region of photons for determining the color and brightness of a given point increase the brightness near that edge. The effect would also make the edge of the brighter polygon look darker then is should as it received less photons per unit area. Although one way to solve the brightening problem on the darker edge would be to simply ignore all photons that had an angle of approach of 90 degrees or more away from the normal of the side, this would not solve the problem of darkening bright edges and could cause the edge of the darker side to become even darker than it should be.
Impact of Write Pulse and Process Variation on 22 nm FinFET-Based STT-RAM Design: A Device-Architecture Co-Optimization Approach

Spin-transfer torque random access memory (STT-RAM) is a promising candidate for universal memory due to its speed, scalability, and non-volatility. A wide range of write speeds from <inline-formula><tex-math>$1$</tex-math><alternatives><inline-graphic xlink:type="simple" xlink:href="xu-ieq1-2509960.gif"/></alternatives></inline-formula> to <inline-formula><tex-math>$100\,\mathrm {ns}$</tex-math><alternatives><inline-graphic xlink:type="simple" xlink:href="xu-ieq2-2509960.gif"/></alternatives></inline-formula> have been reported for STT-RAM. As the storage element of an STT-RAM cell, the switching current of magnetic tunnel junction (MTJ) is inversely proportional to the write pulse width. In this work, we propose a methodology to design STT-RAM for different optimization goals such as read performance, write performance, and write energy by leveraging the trade-off between write current and write time of MTJ. To enable STT-RAM design in advanced technology nodes beyond 22 nm, we model perpendicular MTJ (PMTJ) as the storage element and FinFET as the access transistor. Our study shows that reducing write pulse width will harm read latency and energy. It is observed that “sweet spots” of write pulse width which minimize the write energy or write latency of an STT-RAM macro may exist. The optimal write pulse width depends on both the device and the architecture specifications. The impact of process variations including the MTJ and the FinFET access transistor are also analyzed.
Scolicidal Effects of Chitosan–Curcumin Nanoparticles on the Hydatid Cyst Protoscolices

In the current era, cystic echinococcosis (CE), as larval stage of Echinococcus granulosus, is considered as a threat to human health. Scolicidal agents used in the surgery of cysts have different side effects. Therefore, the present study aimed to assess the effects of chitosan nanoparticles containing curcumin (Ch–Cu NPs) on the protoscolices of the hydatid cyst in vitro. Ch–Cu NPs were synthesized using a simple co-precipitation method and their structural and morphological properties were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), zeta analyzer, and Fourier transform infrared (FT-IR) spectroscopy. Then, the effects of different concentrations of Ch–Cu NPs (0.25, 0.05, 1, 2, and 4 mg/mL) on the fatality rate, and the length and width of protoscolices in different times (5, 10, 20, 30, and 60 min) were investigated. In addition, the SEM technique was used to evaluate the structure of the protoscolices after treatment. Based on the results, the presence of curcumin on the chitosan nanoparticles was confirmed by FT-IR analysis. Further, XRD analysis approved the crystal structure of chitosan NPs. Furthermore, the highest fatality rate was 68% in 4 mg/mL concentration of Ch–Cu NPs. The length and width of protoscolices decreased based on the high concentrations of Ch–Cu NPs, compared to the control group. Finally, Ch–Cu NPs expressed good scolicidal activities, which made them suitable to be considered as an anti-protoscolex agent.
The eighth annual MLSP competition: Overview

This marks the eighth year the Machine Learning for Signal Processing (MLSP) Technical Committee has hosted a data analysis competition, which is held in conjunction with the annual MLSP workshop. For this year's competition, which was sponsored by Amazon Corporation, entrants were asked to write an algorithm that attempts to automatically provision an employee's access to company resources in an optimal manner. In this paper, we (the organizers of the competition) briefly describe the application, the data, the rules, and the outcomes of the competition. A total of 4 teams entered the contest. We provided real (declassified) training data to the entrants and tested the algorithms using disjoint test data. The two teams with the best performing entries describe the approach they used in two separate companion papers, both of which appear in this year's conference proceedings.
Job Type Approach for Deciding Job Scheduling in Grid Computing Systems

Problem statement: Meta-scheduling has become very important due to the increased number of submitted jobs for execution. Approach: We considered the job type in the scheduling decision that was not considered previously. Each job can be categorized into two types namely, data-intensive and computational-intensive in a specific ratio. Job ratio reflected the exact level of the job type in two specific numbers in the form of ratio and was computed to match the appropriate sites for the jobs in order to decrease the job turnaround time. Moreover, the number of jobs in the queue was considered in the batch decision to ensure server-load balancing. Results: The new factor that we considered namely, the job ratio can reduce the job turnaround time by submitting jobs in batches rather than submitting the jobs one by one. Conclusion: Our proposed system can be implemented in any middleware to provide job scheduling service.
Accurate stereochemistry for two related 22,26-epiminocholestene derivatives

Regioselective opening of ring E of solasodine under various conditions afforded (25R)-22,26-epiminocholesta-5,22(N)-diene-3β,16β-diyl diacetate (previously known as 3,16-diacetyl pseudosolasodine B), C31H47NO4, or (22S,25R)-16β-hydroxy-22,26-epiminocholesta-5-en-3β-yl acetate (a derivative of the naturally occurring alkaloid oblonginine), C29H47NO3. In both cases, the reactions are carried out with retention of chirality at the C16, C20 and C25 stereogenic centers, which are found to be S, S and R, respectively. Although pseudosolasodine was synthesized 50 years ago, these accurate assignments clarify some controversial points about the actual stereochemistry for these alkaloids. This is of particular importance in the case of oblonginine, since this compound is currently under consideration for the treatment of aphasia arising from apoplexy; the present study defines a diastereoisomerically pure compound for pharmacological studies.
Optimizing Druid with Roaring bitmaps

In the current Big Data era, systems for collecting, storing and efficiently exploiting huge amounts of data are continually introduced, such as Hadoop, Apache Spark, Dremel, etc. Druid is one of theses systems especially designed to manage such data quantities, and allows to perform detailed real-time analysis on terabytes of data within sub-second latencies. One of the important Druid's requirements is fast data filtering. To insure that, Druid makes an extensive use of bitmap indexes. Previously, we introduced a new compressed bitmap index scheme called Roaring bitmap that has shown interesting results when compared to the bitmap compression scheme adopted by Druid: Concise. Since, Roaring bitmap has been integrated to Druid as an indexing solution. In this work, we produce an extensive series of experiments in order to compare Roaring bitmap and Concise time-space performances when used to accelerate Druid's OLAP queries and other kinds of operations Druid realizes on bitmaps, like: retrieving set bits from bitmaps, computing bitmap complements, aggregating several bitmaps with logical ORs and ANDs operations. Roaring bitmap has shown to improve up to ≈ 5× analytical queries response times under Druid compared to Concise.
Magnetic Driving of Relativistic Outflows in Active Galactic Nuclei. I. Interpretation of Parsec-Scale Accelerations

There is growing evidence that relativistic jets in active galactic nuclei undergo extended (parsec-scale) acceleration. We argue that, contrary to some suggestions in the literature, this acceleration cannot be purely hydrodynamic. Using exact semianalytic solutions of the relativistic MHD equations, we demonstrate that the parsec-scale acceleration to relativistic speeds inferred in sources such as the radio galaxy NGC 6251 and the quasar 3C 345 can be attributed to magnetic driving. Additional observational implications of this model will be explored in future papers in this series.
Stochastic fluctuations in the Gross–Pitaevskii equation

We study from a mathematical point of view a model equation for a Bose–Einstein condensation, in the case where the trapping potential varies randomly in time. The model is the so-called Gross–Pitaevskii equation, with a quadratic potential with white noise fluctuations in time. We prove the existence of solutions in 1D and 2D in the energy space. The blow-up phenomenon is also discussed under critical and super critical nonlinear interactions in the attractive case.
An Original Way of Building a TIN with Complex Urban Structures

Geographical Information System (GIS) software often models a Digital Terrain Model (DTM) by using triangulations (TINs). Computer Aided Design (CAD) is then used to model complex city structures and superimpose them on the TINs. Since the terrain surface is not connected to the built-up structures, no further spatial analysis (for example, neighbourhood analysis, flow modelling) is possible. Bridges and tunnels are parts of complex urban structures which may be difficult or impossible to be modeled in those TINs. An original way of building the TIN model may help to solve this problem. The use of the “boundary-representation” structure from CAD systems, the triangulation structure of TINs and the Quad-Edge structure from Computational Geometry are combined to alleviate the problem. The Quad-Edge structure forms the base of the model and CAD-type Euler Operators are the intermediate level operators for building the TIN model. To extend the TIN model with bridges, holes and buildings, additional Euler Operators are used. This original way of building the terrain model not only permits the extrusion of buildings and the formation of bridges and tunnels, but also the development of topological queries and analysis, for example, runoff modelling. It is a simple and reliable method and is illustrated with examples of interactive modelling of part of the Hong Kong city.
Distributed fair scheduling with distributed coordination function in WLAN

With the rapid growth of the Internet and other Internet-protocol related applications, many improvements have been made at the data link layer in wireless systems to support a wider variety of data services. However, further improvements in packet data admission, scheduling and policing between nodes in the network are necessary to maximize throughput and user satisfaction. In the above three, scheduling has the greatest impact on system throughput. Also, proper scheduling can provide user satisfaction. In this paper, a combination of an Inter Frame Space (IFS) based Distributed Fair Scheduling (IDFS) with the backbone of IEEE 802.11 DCF is designed to achieve better performance in terms of throughput and fairness. Such an attempt has not been made so far in the literature up to our knowledge. By implementing this mechanism, it is proved that improved throughput is achieved compared to traditional DCF and Inter Frame Space (IFS) based Distributed Fair Queuing (IDFQ) separately. It involves a Cross-Layer Approach by considering the physical characteristics of wireless channel and designing a mapping function at Medium Access control (MAC) layer. The inclusion of weighted fair service discipline in the system remedies the performance anomaly problem of IEEE 802.11 Medium Access Control. The proposed methodology avoids collisions of packets to the greater extent and thus helps to improve the throughput in the simulated environment. It is also shown that better performance measure is achieved when validated with NS2 simulations.
Evaluating the Effectiveness of Interactive Map Interface Designs: A Case Study Integrating Usability Metrics with Eye-Movement Analysis

This paper proposes combining traditional usability methods with the analysis of eye movement recordings to evaluate interactive map interfaces, and presents a case study in support of this approach. The case study evaluates two informationally equivalent, but differently designed online interactive map interfaces presented to novice users. In a mixed factorial experiment, thirty participants were asked to solve three typical map-use tasks using one of the two interfaces; we then measured user satisfaction, efficiency (completion time) and effectiveness (accuracy) with standard SEE usability metrics. While traditional (bottom line) usability metrics can reveal a range of usability problems, they may be enhanced by additional procedural measures such as eye movement recordings. Eye movements have been shown to help reveal the amount of cognitive processing a display requires and where these cognitive resources are required. Therefore, we can establish how a display may or may not facilitate task completion by analyzing eye movement recordings. User satisfaction information related to tested stimuli (i.e., collected through standardized questionnaires) can also be linked to eye tracking data for further analysis. We hope that the presented methodology and case study will help cartographers and map interface designers to better identify design issues in their products, and that these insights will eventually lead to more effective and efficient online map interfaces.
A low-order linear functional observer for time delay systems

This paper presents an efficient technique to design low-order state function observers for linear time-delay systems. Assuming the existence of a linear state feedback controller to achieve stability or some control performance criteria of the time-delay system, a design procedure is proposed for reconstruction of the state feedback control action. The procedure involves solving an optimisation problem with the objective to generate a matrix that is as close as possible to the given feedback gain of the required feedback controller. A condition for robust stability of the time-delay system using the observer-based control scheme is given. The attractive features of the proposed design procedure are that the resulted linear functional state observer is of a very low order and it requires information of a small number of outputs. Numerical examples are given to demonstrate the design procedure and its merits.
Automatic Answer Validation System on English language

We present an Answer Validation System (AV) based on Textual Entailment and Question Answering. The important features used to develop the AV system are Named Entity Recognition, Textual Entailment, Question-Answer type Analysis and Chunk Boundary and Dependency relations. Separate AV modules have been developed for each of these features. We first combine the question and the answer into Hypothesis (H) and the Supporting Text as Text (T) to check the entailment relation as either “VALIDATED” or “REJECTED”. The important lexical features used for the Textual Entailment Module in the present system are: WordNet based unigram match, bigram match and skip-gram. The results obtained from the four answer validation modules are integrated using a voting technique. Evaluation scores obtained on the AVE 2008 test set show 67% precision for “VALIDATED” decisions.
The Data Centre Nature and Landscape (DNL): Service Oriented Architecture, Metadata Standards and Semantic Technologies in an Environmental Information System

The Data Centre Nature and Landscape, intended as a database for biotope information, constantly evolved over the last 11 years to become a virtual data centre connecting several databases located all over Switzerland. It was en-riched with a user-friendly Web-interface, partially modularized into a Service Oriented Architecture and finally of-fers open and intuitive search facilities based on semantic technologies. This paper shall give an overview of the hurdles that had to be taken and the many lessons to be learned during the last decade sharing our experience developing and maintaining environmental information systems.
Multimodal Man-Machine Interface for Mission PlanningA

This paper presents a multimodalinterface featuring fusion of multiple modalities for natural human-computer interaction. The architecture of the interface and the methods applied are described, and the results of the real-time multimodal fusion are analyzed. The research in progress concerning a mission planning scenario is discussed and other possible future directions are also presented.
Numerical Study on the Formation of Shear Fracture Network

Shear fracture network is important to the hydraulic fracturing treatment of a shale gas reservoir. In this paper, the formation of shear fracture network is investigated by a Displacement Discontinuity Method (DDM) based model. The results show that the sliding of fracture surface is irreversible but may change significantly after fluid pressure dissipates. The final sliding distance is different for natural and hydraulic fractures. Most of the shear fractures are natural fractures while the newly formed hydraulic fractures tend to be totally closed after pressure dissipates. The effects of in situ stress are investigated. The affected area reaches its maximum value when the maximum principle stress direction is perpendicular to the principal fracture direction. The effects of the injection rate are also investigated. The increasing of the injection rate is helpful in increasing the fracture aperture, but has no effect on the final sliding distance. Moreover, the effects of the injection rate on the affected area depend on the connectivity of natural fractures. The affected area increases with the injection rate when the connectivity is poor but decreases slightly with injection rate when the connectivity is good.
Model Reference Adaptive Control based-on Neural Networks for Nonlinear time-varying System

This paper presents a Direct Model Reference Adaptive Control (MRAC) for nonlinear time-varying system. A mechanism adaptation algorithm is proposed. This corresponding algorithm depends on the error between the actual plant output and the output of the reference model, and also is depending on variable learning rate. The control strategy is based on two-steps; the first is initialization parameters of the controller using reduced number of observation. In the second phase, the parameters of the controller are directly tuned from the training data via the tracking error. The simulation results show that the proposed algorithm is simple to implement and may be extended to multivariable system. Keywords—Nonlinear system; neural network; adaptive control; model reference
A Novel 3-D Mineralized Tumor Model to Study Breast Cancer Bone Metastasis

Background Metastatic bone disease is a frequent cause of morbidity in patients with advanced breast cancer, but the role of the bone mineral hydroxyapatite (HA) in this process remains unclear. We have developed a novel mineralized 3-D tumor model and have employed this culture system to systematically investigate the pro-metastatic role of HA under physiologically relevant conditions in vitro. Methodology/Principal Findings MDA-MB231 breast cancer cells were cultured within non-mineralized or mineralized polymeric scaffolds fabricated by a gas foaming-particulate leaching technique. Tumor cell adhesion, proliferation, and secretion of pro-osteoclastic interleukin-8 (IL-8) was increased in mineralized tumor models as compared to non-mineralized tumor models, and IL-8 secretion was more pronounced for bone-specific MDA-MB231 subpopulations relative to lung-specific breast cancer cells. These differences were pathologically significant as conditioned media collected from mineralized tumor models promoted osteoclastogenesis in an IL-8 dependent manner. Finally, drug testing and signaling studies with transforming growth factor beta (TGFβ) confirmed the clinical relevance of our culture system and revealed that breast cancer cell behavior is broadly affected by HA. Conclusions/Significance Our results indicate that HA promotes features associated with the neoplastic and metastatic growth of breast carcinoma cells in bone and that IL-8 may play an important role in this process. The developed mineralized tumor models may help to reveal the underlying cellular and molecular mechanisms that may ultimately enable more efficacious therapy of patients with advanced breast cancer.