Miracle-dz/UniFAR-FTUs huggingface dataset:
Locality-enhancing loop transformations for parallel tree traversal algorithms

Exploiting locality is critical to achieving good performance. For regular programs, which operate on dense arrays and matrices, techniques such as loop interchange and tiling have long been known to improve locality and deliver improved performance. However, there has been relatively little work investigating similar locality-improving transformations for irregular programs that operate on trees or graphs. Often, it is not even clear that such transformations are possible. In this paper, we discuss two transformations that can be applied to irregular programs that perform graph traversals. We show that these transformations can be seen as analogs of the popular regular transformations of loop interchange and tiling. We demonstrate the utility of these transformations on two tree traversal algorithms, the Barnes-Hut algorithm and raytracing, achieving speedups of up to 251% over the baseline implementation.
In-network adaptive cluster enumeration for distributed classification and labeling

A crucial first step for signal processing decentralized sensor networks with node-specific interests is to agree upon a common unique labeling of all observed sources in the network. The knowledge “who observes what” is required, e.g. in node-specific audio or video signal enhancement to form node clusters of common interest. Recently proposed in-network distributed adaptive classification and labeling algorithms assume knowledge on the number of objects (clusters), which is not necessarily available in real-world applications. Thus, we consider the problem of estimating the number of data-clusters in the distributed adaptive network set-up. We propose two distributed adaptive cluster enumeration methods. They combine the diffusion principle, where the nodes share information within their local neighborhood only (without fusion center), with the X-means and the PG-means cluster enumeration. Performance is evaluated via simulations and the applicability of the methods is illustrated using a distributed camera network where moving objects appear and disappear from the Line-of-Sight (LOS) and the number of clusters becomes time-varying.
The Physiology and Pathophysiology of the Hyperbaric and Diving Environments Comparison of electrical and magnetic stimulations to assess quadriceps muscle function

Verges S, Maffiuletti NA, Kerherve H, Decorte N, Wuyam B, Millet GY. Comparison of electrical and magnetic stimulations to assess quadriceps muscle function: electrical and magnetic quadriceps stimulations. J Appl Physiol 106: 701–710, 2009. First published 28 August 2008; doi:10.1152/japplphysiol.01051. 2007. —This study aimed to 1) compare electrical and magnetic stimulations for quadriceps muscle function assessment, and 2) ascertain whether the ratios of the second twitch elicited by supramaximal electrical and magnetic femoral nerve stimulation at 10 and 100 Hz (T210:100) and the total twitch force elicited by the same types of stimulations (Fpaired10:100) are equivalent to the standard lowto high-frequency force ratio associated with submaximal electrical tetanic stimulations (Ftet10:100). Quadriceps force and vastus lateralis EMG were recorded at rest (n 21 subjects), immediately after, and 30 min after a 30-min downhill run (n 10) when 1) supramaximal electrical nerve stimulation (ENS), 2) magnetic nerve stimulation (MNS) and 3) submaximal electrical muscle stimulation (EMS) were delivered in random order at 1 (single stimulation), 10, and 100 Hz (paired stimulations). Tenand 100-Hz 500-ms tetani were also evoked with EMS to determine Ftet10:100. Before exercise, contractile properties with single and paired stimulations were similar for ENS and MNS (all intraclass correlation coefficients k 0.90), but smaller for EMS (P 0.001). M-wave characteristics were also similar for ENS and MNS (all k 0.90). After exercise, changes in all parameters did not differ between methods. With fatigue, the changes in Ftet10:100 were inconsistently correlated with the changes in T210:100 (r 0.24–0.73, P 0.002–0.15) but better correlated with the changes in Fpaired10:100 (immediately after exercise: r 0.80–0.83, P 0.001; 30 min after exercise: r 0.46–0.82, P 0.001–0.03). We conclude that ENS and MNS provide similar quadriceps muscle function assessment, while Fpaired10:100 is a better index than T210:100 of lowto highfrequency fatigue of the quadriceps in vivo.
Stochastic approximation and user adaptation in a competitive resource sharing system

This paper is motivated by the work of Altman and Shimkin (1998). Customers arrive at a service center and must choose between two types of service; a channel that is shared by all currently in it, and a dedicated line. The mean service cost (or time) for any customer entering the shared resource depends on the decisions of all future arrivals up to the time of departure, and so has a competitive aspect. The system keeps a record of the (discounted) mean sample service costs (or times) for the shared resource, as a function of the number there when a new arrival joins, and the arriving customers use this to make their decisions. The decision rule of each arriving customer is based on its own immediate self interest, given the available data. They select the service with the smallest estimated service cost. But, if the current estimate of the cost for the shared resource equals that of the dedicated line, any decision is possible. The procedure is a type of learning algorithm. The long term behavior of the arrivals and its effect on the system averages is of interest. The convergence problem is one in asynchronous stochastic approximation, where the ODE has a set-valued right hand side. The set value arises due to the arbitrariness of the decision at certain values of the current estimates. It is shown that, asymptotically, the performance of the learning system is that for the symmetric Nash strategy, despite the allowed arbitrariness and lack of coordination.
A Model for Anesthetic Effects on Cell Membranes

Ion channels in the plasma membrane are the functional units of neurons and their misregulation by anesthetic compounds is thought to be the proximate cause of the organism-level anesthetic response. However, the mechanism through which general anesthetics affect these channels remains an open question: although many drugs function by binding to receptors in the cell membrane, the variability in compounds that act as anesthetics suggests that they may have a different mode of operation. Recent experiments have shown that anesthetics lower the transition temperature, TC , of a liquid-liquid miscibility critical point of Giant Plasma Membrane-derived Vesicles (GPMVs), and further that the magnitude of this effect is well correlated with the potency of the anesthetic. To understand how anesthetics affect TC , we developed a simple Ising model for the membrane as a 2D binary liquid. In our model, Ising spins represent membrane lipids; annealed vacancies, which solubilize the two liquid phases, represent anesthetic molecules. We provide theoretical predictions for 1) the change in Tc of the membrane as a function of the potency-normalized amount of anesthetic in a volume surrounding it and 2) the mole fraction of anesthetic in the membrane at anesthetic dose. We demonstrate that these predictions are in good agreement with results from GPMV assays and synthetic bilayers, respectively. Ofer Kimchi ’16 Department of Physics Program in Applied and Computational Mathematics Princeton University Advisor: Benjamin Machta Second Reader: William Bialek This paper represents my own work in accordance with University regulations.
How to Overcome the Domain Barriers in Pattern-Based Machine Translation System

One of difficult issues in pattern-based machine translation system is maybe to find how to overcome the domain difference in adapting a system from one domain to other domain. This paper describes how we have resolved such barriers among domains as default target word of any domain, domain-specific patterns, and domain adaptation of engine modules in pattern-based machine translation system, especially English-Korean pattern-based machine translation system. For this, we will discuss two types of customization methods which mean a method adapting an existing system to new domain. One is the pure customization method introduced for patent machine translation system in 2006 and another is the upgraded customization method applied to scientific paper machine translation system in 2007. By introducing an upgraded customization method, we could implement a practical machine translation system for scientific paper translation within 8 months, in comparison with the patent machine translation system that was completed even in 24 months by the pure customization method. The translation accuracy of scientific paper machine translation system also rose 77.25% to 81.10% in spite of short term of 8 months.
Culture, Context and Structure: A Test on Hong Kong Banks

This research examined both context and home society culture as predictors of organizational structure in 39 multinational banks operating in Hong Kong. Organizational structure and context were operationalized using the Aston instru ments and culture was operationalized using Hofstede's measures of power dis tance and uncertainty avoidance. The results showed that the contextual variable of size was more strongly associated with structural differentiation while the cultural variable of power distance was more strongly associated with authority. These findings help explain the inconsistent relationships reported in previous studies.
New approaches to support vector ordinal regression

In this paper, we propose two new support vector approaches for ordinal regression, which optimize multiple thresholds to define parallel discriminant hyperplanes for the ordinal scales. Both approaches guarantee that the thresholds are properly ordered at the optimal solution. The size of these optimization problems is linear in the number of training samples. The SMO algorithm is adapted for the resulting optimization problems; it is extremely easy to implement and scales efficiently as a quadratic function of the number of examples. The results of numerical experiments on benchmark datasets verify the usefulness of these approaches.
On the effectiveness of anonymizing networks for web search privacy

Web search has emerged as one of the most important applications on the internet, with several search engines available to the users. There is a common practice among these search engines to log and analyse the user queries, which leads to serious privacy implications. One well known solution to search privacy involves issuing the queries via an anonymizing network, such as Tor, thereby hiding one's identity from the search engine. A fundamental problem with this solution, however, is that user queries are still obviously revealed to the search engine, although they are "mixed" among the queries issued by other users of the same anonymization service. In this paper, we consider the problem of identifying the queries of a user of interest (UOI) within a pool of queries received by a search engine over an anonymizing network. We demonstrate that an adversarial search engine can extract the UOI's queries, when it is equipped with only a short-term user search query history, by utilizing only the query content information and off-the-shelf machine learning classifiers. More specifically, by treating a selected set of 60 users --- from the publicly-available AOL search logs --- as the users of interest performing web search over an anonymizing network, we show that each user's queries can be identified with 25.95% average accuracy, when mixed with queries of 99 other users of the anonymization service. This average accuracy drops to 18.95% when queries of 999 other users of the anonymization service are mixed together. Though the average accuracies are not so high, our results indicate that few users of interest could be identified with accuracies as high as 80--98%, even when their queries are mixed among queries of 999 other users. Our results cast serious doubts on the effectiveness of anonymizing web search queries by means of anonymizing networks.
Bayesian Agglomerative Clustering with Coalescents

We introduce a new Bayesian model for hierarchical clustering based on a prior over trees called Kingman's coalescent. We develop novel greedy and sequential Monte Carlo inferences which operate in a bottom-up agglomerative fashion. We show experimentally the superiority of our algorithms over the state-of-the-art, and demonstrate our approach in document clustering and phylolinguistics.
Developmental Changes in Synaptic AMPA and NMDA Receptor Distribution and AMPA Receptor Subunit Composition in Living Hippocampal Neurons

AMPA and NMDA receptors mediate most excitatory synaptic transmission in the CNS. We have developed antibodies that recognize all AMPA or all NMDA receptor variants on the surface of living neurons. AMPA receptor variants were identified with a polyclonal antibody recognizing the conserved extracellular loop region of all four AMPA receptor subunits (GluR1–4, both flip andflop), whereas NMDA receptors were immunolabeled with a polyclonal antibody that binds to an extracellular N-terminal epitope of the NR1 subunit, common to all splice variants. In non-fixed brain sections these antibodies gave labeling patterns similar to autoradiographic distributions with particularly high levels in the hippocampus. Using these antibodies, in conjunction with GluR2-specific and synaptophysin antibodies, we have directly localized and quantified surface-expressed native AMPA and NMDA receptors on cultured living hippocampal neurons during development. Using a quantitative cell ELISA, a dramatic increase was observed in the surface expression of AMPA receptors, but not NMDA receptors, between 3 and 10 d in culture. Immunocytochemical analysis of hippocampal neurons between 3 and 20 d in vitro shows no change in the proportion of synapses expressing NMDA receptors (∼60%) but a dramatic increase (∼50%) in the proportion of them that also express AMPA receptors. Furthermore, over this period the proportion of AMPA receptor-positive synapses expressing the GluR2 subunit increased from ∼67 to ∼96%. These changes will dramatically alter the functional properties of hippocampal synapses.
GENIA corpus - a semantically annotated corpus for bio-textmining

MOTIVATION Natural language processing (NLP) methods are regarded as being useful to raise the potential of text mining from biological literature. The lack of an extensively annotated corpus of this literature, however, causes a major bottleneck for applying NLP techniques. GENIA corpus is being developed to provide reference materials to let NLP techniques work for bio-textmining. RESULTS GENIA corpus version 3.0 consisting of 2000 MEDLINE abstracts has been released with more than 400,000 words and almost 100,000 annotations for biological terms.
Towards a Taxonomy of Provenance in Scientific Workflow Management Systems

Scientific Workflow Management Systems (SWfMS) have been helping scientists to prototype and execute in silico experiments. They can systematically collect provenance information for the derived data products to be later queried. Despite the efforts on building a standard Open Provenance Model (OPM), provenance is tightly coupled to SWfMS. Thus scientific workflow provenance concepts, representation and mechanisms are very heterogeneous, difficult to integrate and dependent on the SWfMS. To help comparing, integrating and analyzing scientific workflow provenance, this paper presents a taxonomy about provenance characteristics. Its classification enables computer scientists to distinguish between different perspectives of provenance and guide to a better understanding of provenance data in general. The analysis of existing approaches will assist us in managing provenance data from distributed heterogeneous workflow executions.
Which Identities Matter? A Mixed-Method Study of Group, Organizational, and Professional Identities and Their Relationship to Burnout

Considerable research views group, organizational, and professional identities as theoretically and methodologically similar. This study suggests that these identities are generically different. An explanatory sequential mixed data analysis of survey and interview data collected at an information technology organization (N = 111 workers) was used to examine the relationships between identities and the experience of burnout and to understand the communicative behaviors associated with types of identity and burnout. Survey data revealed that controlling for communication activity, work group identification was associated with lower depersonalization while professional identification was associated with increased personal accomplishment. No relationship was found between organizational identification and burnout. Semistructured interviews revealed three themes related to identification: (a) Being Yourself in the Work Group, (b) Valuing the Role of the IT Professional, and (c) Othering the Organization. Implications for organizational communication with respect to theorizing and measuring organizational identity are discussed.
The Fluorescent Pigment of Pseudomonas fluorescens : Biosynthesis, Purification and Physicochemical Properties

The biosynthesis of a yellow-green, fluorescent, water-soluble pigment by Pseudomonas fluorescens occurred only when the bacteria were iron-deficient and was not directly influenced by the nature of the organic carbon source. The pigment formed a very stable Fe3+ complex and was purified in this form. Pseudomonas fluorescens produced only one molecular species of fluorescent pigment; however, its lability under mild alkaline conditions led to the formation of several pigmented decomposition products. The spectral properties of the pure pigment, its molecular weight (1500 ± 75) and its stability constant for Fe3+ (of the order of 1032) were determined. Both its biosynthesis and its chemical properties (formation of a stable Fe3+ complex) suggest that the fluorescent pigment is a desferrisiderophore.
On road network utility based on risk-aware link choice

We have previously shown how it is possible to lower accident risk levels while at the same time increasing traffic flows with the aid of vehicular ad-hoc networks. In this paper, we extend the online traffic accident risk mitigation system to include link choice. We develop an algorithm that allows vehicles to choose road links that provide the current maximal utility, based on information received over a vehicular network, whilst remaining below acceptable risk levels. Additionally, we investigate how to improve the performance of this algorithm by considering the effect a vehicle's link choice has on the utility of other vehicles. We introduce a social penalty for reducing other vehicles' utility and investigate the effects of including this as a factor in vehicles' link choices. The resulting system sheds new light on the problem of effective link choice by route selection algorithms and highlights the potential that exists in VANET-based traffic management.
Separate resistances to arsenate and arsenite (antimonate) encoded by the arsenical resistance operon of R factor R773

The arsenical resistance operon of R factor R773 was analyzed by subcloning and insertional inactivation. The operon was found to have two functional regions, the promoter-proximal region encoding resistance to arsenite and antimonate and the promoter-distal region encoding arsenate resistance. A unique 1.6-kilobase fragment was shown to be sufficient to encode arsenate resistance and produce arsenate extrusion from intact cells.
Mumps Virus Matrix, Fusion, and Nucleocapsid Proteins Cooperate for Efficient Production of Virus-Like Particles

ABSTRACT Paramyxovirus particles, like other enveloped virus particles, are formed by budding from membranes of infected cells. To define mumps virus (MuV) proteins important for this process, viral proteins were expressed either singly or in combination in mammalian cells to produce virus-like particles (VLPs). Only the MuV matrix (M) protein when expressed by itself was capable of inducing particle release, but the quantity of these M-alone particles was very small. Efficient production of mumps VLPs occurred only when the M protein was coexpressed together with other viral proteins, with maximum production achieved upon coexpression of the viral M, nucleocapsid (NP), and fusion (F) proteins together. Electron microscopy analysis confirmed that VLPs were morphologically similar to MuV virions. The two MuV glycoproteins were not equal contributors to particle formation. The F protein was a major contributor to VLP production, while the hemagglutinin-neuraminidase protein made a smaller contribution. Evidence for the involvement of class E protein machinery in VLP budding was obtained, with mumps VLP production inhibited upon expression of dominant-negative versions of the class E proteins Vps4A and Chmp4b. Disruption of the sequence 24-FPVI-27 within the MuV M protein led to poor VLP production, consistent with findings of earlier studies of a related sequence, FPIV, important for the budding of parainfluenza virus 5. Together, these results demonstrate that different MuV structural proteins cooperate together for efficient particle production and that particle budding likely involves host class E protein machinery.
Are materialistic teenagers less motivated to learn? Cross-sectional and longitudinal evidence from the United Kingdom and Hong Kong.

Is materialism systematically related to teenagers' learning motivation as well as actual learning outcomes? The reported research tested a theoretical model of associations among materialism, achievement goals, and exam performance among teenagers. Study 1 tested the theoretical model in 4 groups of teenagers drawn from 2 different educational stages (Year 9 and Year 12) and two societies of different cultural heritage (United Kingdom and Hong Kong). Results supported the model that materialism was associated with lower intrinsic mastery goals, and higher extrinsic performance goals in all of the 4 groups. More important, 1-year longitudinal data from Hong Kong (Study 2) showed that a materialistic value orientation at an earlier time point explained decreases in mastery goals and increases in performance goals a year later. Furthermore, earlier endorsement of materialistic values also predicted later deterioration of school performance. Theoretical and practical implications of the findings are discussed.
Epithelial to mesenchymal transition in head and neck squamous carcinoma

Epithelial–mesenchymal transformations (EMT) are critical for the invasion, progression, and metastasis of epithelial carcinogenesis. The role of EMT in head and neck squamous carcinoma (HNSC) tumorigenesis remains unexplored. In the current study, the expressions of several factors associated with the induction of EMT in HNSC cell lines and tumor specimens were investigated to define their functional and pathologic role in HNSC.