Miracle-dz/UniFAR-FTUs huggingface dataset:
Physics-Based Simulations for Fluid Mixtures

Physics-Based Simulations for Fluid Mixtures Dongwoon Lee Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2007 We develop a physics-based particle method to simulate various fluid mixture effects. A particle method is chosen over a grid-based method because we believe a particle method is more intuitive and better suited for handling physical and chemical interactions between fluids. Since a particle carries the physical attributes of the fluid (e.g, density and velocity), transfer of these attributes between particles can be computed easily using a particle method. Also, arbitrary shapes of the fluid mixture can be modeled based on the particles’ spatial configuration, which is updated throughout the simulation.
Meta-Stars: Dynamic, Schemaless, and Semantically-Rich Topic Hierarchies in Social BI

A key role in OLAP analyses of textual user-generated content for social business intelligence (SBI) is played by topics, i.e., concepts of interest within a subject area. Topic hierarchies are irregular, heterogeneous, dynamic, and possibly schemaless; besides, unlike in traditional OLAP, di↵erent semantics for topic aggregation can be envisioned. In this demonstration we present an architecture for SBI based on meta-stars, a novel approach to topic modeling in ROLAP systems. By coupling meta-modeling with navigation tables, meta-stars can cope with changes in the schema of irregular hierarchies and with schemaless ones; besides, they enable a new class of OLAP queries based on semantically-aware aggregation. The demonstration will focus both on the hierarchy update process and on the querying expressiveness.
SCAM: A Copy Detection Mechanism for Digital Documents

Copy detection in Digital Libraries may provide the necessary guarantees for publishers and newsfeed services to offer valuable on-line data. We consider the case for a registration server that maintains registered documents against which new documents can be checked for overlap. In this paper we present a new scheme for detecting copies based on comparing the word frequency occurrences of the new document against those of registered documents. We also report on an experimental comparison between our proposed scheme and COPS [6], a detection scheme based on sentence overlap. The tests involve over a million comparisons of netnews articles and show that in general the new scheme pbetter in detecting documents that have partial overlap. Keywords: Copy Detection, Plagiarism, Registration Ser-ver, Databases
DNA polymerase β contains a functional nuclear localization signal at its N-terminus

Abstract DNA polymerase β (pol β) requires nuclear localization to fulfil its DNA repair function. Although its small size has been interpreted to imply the absence of a need for active nuclear import, sequence and structural analysis suggests that a monopartite nuclear localization signal (NLS) may reside in the N-terminal lyase domain. Binding of this domain to Importin α1 (Impα1) was confirmed by gel filtration and NMR studies. Affinity was quantified by fluorescence polarization analysis of a fluorescein-tagged peptide corresponding to pol β residues 2–13. These studies indicate high affinity binding, characterized by a low micromolar Kd, that is selective for the murine Importin α1 (mImpα1) minor site, with the Kd strengthening to ∼140 nM for the full lyase domain (residues 2–87). A further reduction in Kd obtains in binding studies with human Importin α5 (hImpα5), which in some cases has been demonstrated to bind small domains connected to the NLS. The role of this NLS was confirmed by fluorescent imaging of wild-type and NLS-mutated pol β(R4S,K5S) in mouse embryonic fibroblasts lacking endogenous pol β. Together these data demonstrate that pol β contains a specific NLS sequence in the N-terminal lyase domain that promotes transport of the protein independent of its interaction partners. Active nuclear uptake allows development of a nuclear/cytosolic concentration gradient against a background of passive diffusion.
UTU at SemEval-2016 Task 10: Binary Classification for Expression Detection (BCED)

The SemEval 2016 DiMSUM Shared Task concerns the detection of minimal semantic units from text and prediction of their coarse lexical categories known as supersenses. Our approach is to define this task as a binary classification problem approachable by straightforward machine learning methods. We start by detecting semantic units by matching text spans against several large dictionaries, including the English WordNet, expressions derived from the Yelp Academic Dataset and concepts from the English Wikipedia, generating a set of potential supersenses for each matched span. For each potential supersense and text span pair a binary machine learning example is defined. We classify these examples using an ensemble method, taking as the final predicted supersense the one with the highest confidence score. Our system achieves good performance on the supersense classification task but has limited performance for detection of multi-word semantic units. We show that the task of supersense prediction can be effectively defined as a binary classification task.
Comparing and contrasting different algorithms leads to increased student learning

Comparing and contrasting different solution approaches is known in math education and cognitive science to increase student learning -- what about CS? In this experiment, we replicated work from Rittle-Johnson and Star, using a pretest--intervention--posttest--follow-up design (n=241). Our intervention was an in-class workbook in CS2. A randomized half of students received questions in a compare-and-contrast style, seeing different code for different algorithms in parallel. The other half saw the same code questions sequentially, and evaluated them one at a time. Students in the former group performed better with regard to procedural knowledge (code reading & writing), and flexibility (generating, recognizing & evaluating multiple ways to solve a problem). The two groups performed equally on conceptual knowledge. Our results agree with those of Rittle-Johnson and Star, indicating that the existing work in this area generalizes to CS education.
3D-CITY MODEL SUPPORTING FOR CCTV MONITORING SYSTEM

Closed circuit television (CCTV) monitoring system is widely used in many important fields to monitor fixed objectives or special areas due to its reliable capability of visual remote surveillance and control. In tradition, the CCTV system design is a complex process including field survey, plan and selecting proposed cameras sites. The visual design method is introduced in CCTV system design and maintenance. This paper suggests that the visual design method should be introduced and advantages of spatial analysis and information query of GIS and 3D city model should be fully used to aid CCTV monitoring system in design and maintenance.
Autologous peptides eluted from acute myeloid leukemia cells can be used to generate specific antileukemic CD4 helper and CD8 cytotoxic T lymphocyte responses in vitro.

BACKGROUND AND OBJECTIVES The poor prognosis of acute myeloid leukemia (AML) treated with conventional chemotherapy justifies seeking additional immunotherapeutic approaches to eliminate minimal residual disease. Hence, we evaluated the feasibility of generating in vitro antileukemic immune responses, which would bypass the need for epitope identification and rely on antigen presentation by autologous dendritic cells. DESIGN AND METHODS Naturally processed peptides were extracted by acid elution from circulating AML cells of six patients at diagnosis. Mature dendritic cells (mDC) were derived from autologous monocytes obtained when the patients were in complete remission, and were loaded with the pool of eluted peptides to stimulate autologous T lymphocytes in vitro. RESULTS We were able to induce in vitro antileukemic Th1 responses characterized by CD4(+) T-cell proliferation, significant interferon-gamma secretion by both CD4+ and CD8(+) T lymphocytes by recognition of autologous AML cells and generation of cytotoxic CD8(+) T lymphocytes. INTERPRETATION AND CONCLUSIONS These results demonstrate that naturally processed peptides eluted from AML cells and presented by differentiated autologous mDC could be immunogenic in vitro. Although more in vitro data will be needed to check the safety of such an approach, notably to rule out possible autoimmune adverse effects, these results lay the basis for a potentially effective antileukemic immunotherapy for high-risk AML patients with minimal residual disease.
Observing the BitTorrent universe through Telescopes

Recent analysis of the latest peer-to-peer trends worldwide indicates that BitTorrent is the most popular file sharing protocol, taking more than half of the P2P traffic in some geographical locations. Despite several studies about the dynamics of the “BitTorrent universe”, there exists no methodology to systematically observe it. This is mainly due to the challenges that need to be faced in order to observe the BitTorrent universe, the specificity of existing studies, and the ad hoc nature of the monitoring methods employed so far. In this paper, we propose a novel monitoring architecture (called TorrentU) that allows the systematic observation of large numbers of BitTorrent networks. Complementary monitoring strategies are flexibly combined to allow varying degrees of network/geographic coverage, information accuracy and richness of detail. To show the concept and technical feasibility of TorrentU, we implemented a prototype with the key parts of the architecture, and evaluated it through a case study with a rich set of monitoring campaigns running on PlanetLab nodes.
Detection and characterization of extended-spectrum β-lactamases (blaCTX-M-1 and blaSHV) producing Escherichia coli, Salmonella spp. and Klebsiella pneumoniae isolated from humans in Mizoram

Aim: The present study was conducted to isolate and characterize the extended spectrum β-lactamases (ESBLs) producing enteric bacteria in human beings in Mizoram, India. Materials and Methods: Fecal samples were collected from human beings with or without the history of diarrhea from different hospitals of Mizoram. Samples were processed for isolation and identification of Escherichia coli, Salmonella and Klebsiella pneumoniae. All the isolates were subjected to antibiotic sensitivity assays. Phenotypically, ESBLs production ability was determined by double discs synergy test (DDST) method. ESBLs producing isolates were subjected to polymerase chain reaction (PCR) for detection of ESBLs genes. Plasmids were cured by acridine orange. Transfer of resistance from a donor to recipient strains was done by in vitro horizontal method. Results: A total of 414 enteric bacteria were isolated from 180 fecal samples (113 were from diarrheic patients and 67 were from non-diarrheic patients), of which 333 (80.44%), 52 (12.56%), and 29 (7.00%) were E. coli, K. pneumoniae and Salmonella spp. , respectively. Double discs synergy test (DDST) exhibited 72 (21.62%) E. coli, 12 (23.08%) K. pneumoniae and 4 (13.79%) Salmonella spp. were ESBLs producers. Altogether, 24 (13.04%) isolates were found to be positive for at least one resistance genes under this study. A total of 36 (8.70%) E. coli, 4 (0.97%) K. pneumoniae and 2 (0.48%) Salmonella spp. were found to be positive for blaCTX-M-1 gene by PCR. Similarly, 5 (1.21%) E. coli and 4 (0.97%) K. pneumoniae isolates were found to be positive for blaSHV gene. A total of 3 (0.72%) K. pneumoniae isolates were recorded as positive for both blaCTX-M-1 and blaSHV genes. All the isolates were carrying plasmids ranging between 0.9 kb and ~30 kb. The resistance plasmid could not be transferred to a recipient by in vitro horizontal gene transfer method. Conclusion: ESBLs producing enteric bacteria are circulating in human population in North Eastern Region of India. Indiscriminate use of antibiotics should be avoided to control the menace of multidrug resistance bacteria in the environment, animals, and human beings.
NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs

We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1–25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.
When Flexibility Is Stable: Implicit Long-Term Shaping of Olfactory Preferences

Preferences are traditionally assumed to be stable. However, empirical evidence such as preference modulation following choices calls this assumption into question. The evolution of such postchoice preference over long time spans, even when choices have been explicitly forgotten, has so far not been studied. In two experiments, we investigated this question by using a variant of the free choice paradigm: In a first session, participants evaluated the pleasantness of a number of odors. We then formed pairs of similarly rated odors, and asked participants to choose their favorite, for each pair. Participants were then presented with all odors again, and asked for another pleasantness rating. In a second session 1 week later, a third pleasantness rating was obtained, and participants were again asked to choose between the same options. Results suggested postchoice preference modulation immediately and 1 week after choice for both chosen and rejected options, even when choices were not explicitly remembered. A third experiment, using another paradigm, confirmed that choice can have a modulatory impact on preferences, and that this modulation can be long-lasting. Taken together, these findings suggest that although preferences appear to be flexible because they are modulated by choices, this modulation also appears to be stable over time and even without explicit recollection of the choice. These results bring a new argument to the idea that postchoice preference modulation could rely on implicit mechanisms, and are consistent with the recent proposal that cognitive dissonance reduction could to some extent be implicit.
Performance analysis of multicarrier CDMA multiuser detection with channel mismatch

Using the replica method originally developed for statistical physics, we provide asymptotic (large-system limit) so- lutions to the output signal-to-interference ratio (SIR) of the mul- tiuser detections (MUDs) with channel mismatch in multi-carrier code-division-multiple-access (MC-CDMA) systems. Among sys- tem performances of the MUDs, we cover both 1) linear detectors such as the linear minimum mean-square error (LMMSE) detec- tor, the linear decorrelator (LDD), and matched-filter (MF) de- tector, and 2) nonlinear detector such as the maximum posterior marginal (MPM) detector and the maximum a posteriori (MAP) detector. Through numerical experiments for finite systems, we show that the asymptotic solutions can produce highly accurate results for MC-CDMA systems.
Oscillator-controlled bipedal walker with pneumatic actuators

The development of an oscillator controller for a bipedal robot with antagonistic pairs of pneumatic actuators is reported. Periodic motions of the legs switch between the swinging and supporting stages based on the phase of the oscillators. The oscillators receive touch sensor signals at the end of the legs as feedback when the leg touches the ground and compose a steady limit cycle of the total periodic dynamics of bipedal locomotion. The effectiveness and performance of the proposed controller were evaluated with numerical simulations and experiments with the hardware.
A Lack of Experience-Dependent Plasticity After More Than a Decade of Recovered Sight

In 2000, monocular vision was restored to M. M. , who had been blind between the ages of 3 and 46 years. Tests carried out over 2 years following the surgery revealed impairments of 3-D form, object, and face processing and an absence of object- and face-selective blood-oxygen-level-dependent responses in ventral visual cortex. In the present research, we reexamined M. M. to test for experience-dependent recovery of visual function. Behaviorally, M. M. remains impaired in 3-D form, object, and face processing. Accordingly, we found little to no evidence of the category-selective organization within ventral visual cortex typically associated with face, body, scene, or object processing. We did observe remarkably normal object selectivity within lateral occipital cortex, consistent with M. M. ’s previously reported shape-discrimination performance. Together, these findings provide little evidence for recovery of high-level visual function after more than a decade of visual experience in adulthood.
Optimal TDMA time slot and cycle length allocation for hard real-time systems

We present an analytic method to determine the provably smallest possible slot length that must be allocated in a TDMA resource, to serve an event-triggered hard real-time load with arbitrary deterministic timing behavior. Based on this method, we then present constructive methods to find all feasible as well as the optimal cycle length in a TDMA resource, and we show how to determine the minimum required bandwidth of a TDMA resource. We demonstrate the applicability and computational efficiency of the presented methods in a case study of a large distributed embedded system with a TDMA bus, where we find the optimal parameter set for the TDMA bus
Integrating 2D mouse emulation with 3D manipulation for visualizations on a multi-touch table

We present the Rizzo, a multi-touch virtual mouse that has been designed to provide the fine grained interaction for information visualization on a multi-touch table. Our solution enables touch interaction for existing mouse-based visualizations. Previously, this transition to a multi-touch environment was difficult because the mouse emulation of touch surfaces is often insufficient to provide full information visualization functionality. We present a unified design, combining many Rizzos that have been designed not only to provide mouse capabilities but also to act as zoomable lenses that make precise information access feasible. The Rizzos and the information visualizations all exist within a touch-enabled 3D window management system. Our approach permits touch interaction with both the 3D windowing environment as well as with the contents of the individual windows contained therein. We describe an implementation of our technique that augments the VisLink 3D visualization environment to demonstrate how to enable multi-touch capabilities on all visualizations written with the popular prefuse visualization toolkit.
Environmental Regulation, Pollution, and Public Health

In the first chapter, I investigate the effects of the Residential Lead Based Paint Hazard Reduction Act. Enacted in 1996, the lead hazard disclosure policy requires sellers and landlords to disclose known lead-based paint hazards to potential buyers or renters. Employing a difference-in-differences approach, I find evidence that the law prompted some families with children to reallocate toward homes without significant lead risks, increased lead mitigation in rental properties, and reduced blood-lead levels among children in rental properties. However, because white families appear to be more responsive to information disclosure than other groups, the information disclosure law might exacerbate racial disparities in lead exposure. In the second chapter, I estimate the spatio-temporal dynamics between wildfire and infant birthweight. Exposure to wildfire smoke is determined using the latitude and longitude coordinates of each infant's home address and a fine-scaled, spatial dataset of wildfire smoke plumes re-constructed in GIS from satellite images of the landscape. Using a difference-in-differences estimation strategy, model estimates show that wildfire smoke leads to a 4% to 6% reduction in birthweight. These effects are most pronounced among mothers exposed during their second and third trimesters of pregnancy and attenuate with respect to distance to a fire. We find no statistically significant relationships between proximity to wildfire and the birthweights of infants located outside the path of wildfire smoke. In the third chapter, I examine the relationship between hurricanes, the salience of flood risk, and residential property investment. Utilizing a difference-in-differences estimation strategy, I find a significant increase in the probability a homeowner invests in a damaged building located in a statutorily designated flood risk area. However, I find no change in the rate of property investment in damaged homes located outside of these areas. Results suggest that a recent storm may elevate households' perceptions of flood risk; however, we show that the primary mechanism driving these changes is a household's exposure to storm damage. We find no evidence of saliency effects in regions less proximate to storm damage. These findings cast doubt on the potential for an information-based regulation to align risk-perceptions with risk-actualities.
Multi-Class Constrained Normalized Cut With Hard, Soft, Unary and Pairwise Priors and its Applications to Object Segmentation

Normalized cut is a powerful method for image segmentation as well as data clustering. However, it does not perform well in challenging segmentation problems, such as segmenting objects in a complex background. Researchers have attempted to incorporate priors or constraints to handle such cases. Available priors in image segmentation problems may be hard or soft, unary or pairwise, but only hard must-link constraints and two-class settings are well studied. The main difficulties may lie in the following aspects: 1) the nontransitive nature of cannot-link constraints makes it hard to use such constraints in multi-class settings and 2) in multi-class or pairwise settings, the output labels have inconsistent representations with given priors, making soft priors difficult to use. In this paper, we propose novel algorithms, which can handle both hard and soft, both unary and pairwise priors in multi-class settings and provide closed form and efficient solutions. We also apply the proposed algorithms to the problem of object segmentation, producing good results by further introducing a spatial regularity term. Experiments show that the proposed algorithms outperform the state-of-the-art algorithms significantly in clustering accuracy. Other merits of the proposed algorithms are also demonstrated.
RISA: A Hardware Platform for Evolutionary Design

Reconfigurable integrated system array is a new form of field programmable digital device incorporating both hardware and software reconfigurable elements. RISA was developed specifically for implementing biologically inspired electronic systems. The architecture is particularly suited for investigating evolvable hardware due to the flexibility of RISA's configuration system. Fine grained partial reconfiguration is supported and random configuration bitstreams will not cause device damage. This paper describes the new RISA chip and the features that make it suitable for bio-inspired applications.