Miracle-dz/UniFAR-FTUs huggingface dataset:
Copy-Number Variation: The Balance between Gene Dosage and Expression in Drosophila melanogaster

Copy-number variants (CNVs) reshape gene structure, modulate gene expression, and contribute to significant phenotypic variation. Previous studies have revealed CNV patterns in natural populations of Drosophila melanogaster and suggested that selection and mutational bias shape genomic patterns of CNV. Although previous CNV studies focused on heterogeneous strains, here, we established a number of second-chromosome substitution lines to uncover CNV characteristics when homozygous. The percentage of genes harboring CNVs is higher than found in previous studies. More CNVs are detected in homozygous than heterozygous substitution strains, suggesting the comparative genomic hybridization arrays underestimate CNV owing to heterozygous masking. We incorporated previous gene expression data collected from some of the same substitution lines to investigate relationships between CNV gene dosage and expression. Most genes present in CNVs show no evidence of increased or diminished transcription, and the fraction of such dosage-insensitive CNVs is greater in heterozygotes. More than 70% of the dosage-sensitive CNVs are recessive with undetectable effects on transcription in heterozygotes. A deficiency of singletons in recessive dosage-sensitive CNVs supports the hypothesis that most CNVs are subject to negative selection. On the other hand, relaxed purifying selection might account for the higher number of protein–protein interactions in dosage-insensitive CNVs than in dosage-sensitive CNVs. Dosage-sensitive CNVs that are upregulated and downregulated coincide with copy-number increases and decreases. Our results help clarify the relation between CNV dosage and gene expression in the D. melanogaster genome.
Advertising, Learning, and Consumer Choice in Experience Good Markets: A Structural Empirical Examin

This paper empirically analyzes di erent e ects of advertising in a nondurable, experience good market. A dynamic learning model of consumer behavior is presented in which we allow both \informative" e ects of advertising and \prestige" or \image" e ects of advertising. This learning model is estimated using consumer level panel data tracking grocery purchases and advertising exposures over time. Empirical results suggest that in this data, advertising's primary e ect was that of informing consumers. The estimates are used to quantify the value of this information to consumers and evaluate welfare implications of an alternative advertising regulatory regime. JEL Classi cations: D12, M37, D83 ' Economics Dept., Boston University, Boston, MA 02115 (ackerber@bu.edu). This paper is a revised version of the second and third chapters of my doctoral dissertation at Yale University. Many thanks to my advisors: Steve Berry and Ariel Pakes, as well as Lanier Benkard, Russell Cooper, Gautam Gowrisankaran, Sam Kortum, Mike Riordan, John Rust, Roni Shachar, and many seminar participants, including most recently those at the NBER 1997Winter IO meetings, for advice and comments. I thank the Yale School of Management for gratefully providing the data used in this study. Financial support from the Cowles Foundation in the form of the Arvid Anderson Dissertation Fellowship is acknowledged and appreciated. All remaining errors in this paper are my own.
UC San Diego Recent Work Title Trades and Quotes : A Bivariate Point Process Permalink

Recent empirical work has studied point processes of transactions in financial markets and observed clear time dependent patterns in these arrival times. However, these studies do not examine the timing of quoted price changes. This paper formulates a bivariate point process to jointly analyze transaction and quote arrivals. In microstructure models, transactions may reveal private information that is then incorporated into new prices. This paper examines the speed of this information flow and the circumstances that govern it. A joint likelihood function for trade and quote arrivals is specified which is a generalization of the ACD model of Engle and Russell (1998) and which recognizes that an intervening trade sometimes censors the time between a trade and the subsequent quote. Models of trades and quotes are estimated for 8 stocks using TAQ transaction data. A series of diagnostic tests and alternative estimates are presented. The essential finding for the arrival of price quotes, is that information flow variables, such as high transaction arrival rates, large volume per trade, and wide bid/ask spreads, all predict more rapid price revisions. This means prices respond more quickly to trades when information is flowing so that the price impacts of trades and ultimately the volatility of prices, are high in such circumstances. When quote arrivals that modify only depth are included as well, a somewhat different answer is found. Now the information variables such as volume and trade arrival rate and level of spread have a slowing or ambiguous effect on quote arrivals. This result is an indication that depth revisions are relatively more frequent when the market is slower. A possible explanation is that depth quotes are derived directly from the limit order book and limit orders are submitted more cautiously when the market shows informational trading.
Esophagitis in a High H. pylori Prevalence Area: Severe Disease Is Rare but Concomitant Peptic Ulcer Is Frequent

Background Few data are available on the prevalence of erosive and severe esophagitis in Western countries. Objective To retrospectively determine the prevalence and the factors predicting erosive esophagitis and severe esophagitis in a large series of endoscopies in Spain. Design Retrospective observational study. A multivariate analysis was performed to determine variables predicting severe esophagitis. Setting Databases of 29 Spanish endoscopy units. Patients Patients submitted to a diagnostic endoscopy during the year 2005. Interventions Retrospective review of the databases. Main Outcome Measurements Esophagitis severity (graded according to the Los Angeles classification) and associated endoscopic findings. Results Esophagitis was observed in 8.7% of the 93,699 endoscopies reviewed. Severe esophagitis (LA grade C or D) accounted for 22.5% of cases of the disease and was found in 1.9% of all endoscopies. Incidences of esophagitis and those of severe esophagitis were 86.2 and 18.7 cases per 100,000 inhabitants per year respectively. Male sex (OR 1.89) and advanced age (OR 4.2 for patients in the fourth age quartile) were the only variables associated with severe esophagitis. Associated peptic ulcer was present in 8.8% of cases. Limitations Retrospective study, no data on individual proton pump inhibitors use. Conclusions Severe esophagitis is an infrequent finding in Spain. It occurs predominantly in males and in older individuals. Peptic ulcer disease is frequently associated with erosive esophagitis.
A model-based method for building reconstruction

Model-based reconstruction methods are applied to the detailed reconstruction of buildings from close-range images. The 3D points obtained through image matching are segmented into a coarse polyhedral model with a robust regression algorithm, then the geometry of this model is refined with predefined shape templates in order to automatically recover a CAD-like model of the building surface. Reprojection of the 3D shape templates is used to optimally fit their parameters to the image information. Throughout the paper the investigated methods are demonstrated on real datasets.
Modeling of Human Arm Movement: A Study on Daily Movement

Mimicking human arm motion has become a challenging topic for the researchers among the field of Human rehabilitation, motor control and perception, biomechanics, and several other related research topics. Considering human-robot cooperation, this paper is focused on modeling human arm while performing planner motion. In this work human arm is assumed as a mass-spring-damper system and based on this assumption the related mathematical model is developed. The desired movement in this study is one of the daily activities with obstacle. Mathematical model is developed with the help of the robotic principle, mechanical system analysis method, and also with the help of biological data. The kinematic and dynamic data is then analyzed. In this work kinematic data are taken from the ShapTape® device. The different components of the position, velocity and acceleration are compared. Besides, the analysis of the simulated torques is done. MATLAB is used for the simulation. These observations are expected to give several ideas for designing a controller for upper limb exoskeleton for rehabilitation purposes.
Circadian regulation of the light input pathway in Neurospora crassa

FREQUENCY (FRQ) is a critical element of the circadian system of Neurospora. The white collar genes are important both for light reception and circadian function. We show that the responsiveness of the light input pathway is circadianly regulated. This circadian modulation extends to light‐inducible components and functions that are not rhythmic themselves in constant conditions. FRQ interacts genetically and physically with WHITE COLLAR‐1, and physically with WHITE COLLAR‐2. These findings begin to address how components of the circadian system interact with basic cellular functions, in this case with sensory transduction.
IFS CODING USING AN MPC NETWORK

Robert D. Dony1 Edward R. Vrscay2 1School of Engineering University of Guelph Guelph, ON N1G 2W1 email: rdony@uoguelph.ca 2Deptartment of Applied Mathematics University of Waterloo Waterloo, ON N2L 2G1 email: ervrscay@links.uwaterloo. ca ABSTRACT This paper examines the relationship between iterated function systems (IFS), a fractal approach to image compression, and mixutre of principal components (MPC), a neural network approach to image compression. Both can be fundamentally expressed as a local linear transformation. In IFS, the basis vector comes from the image itself and evolves during the iterations while in MPC, the trained network contains the basis basis vectors. A new method of image compression is presented which uses an MPC network as a library for reducing the search for the large domain blocks in IFS. The resulting hybrid approach has better rate-distortion characteristics relative to standard IFS when tested on a standard image.
Prediction of Performance on Cross-Lingual Information Retrieval by Regression Models

The purpose of this paper is to examine empirically factors having effects on performance of cross-lingual information retrieval. In order to obtain experimental data, at the NTCIR-4 CLIR task, we submitted search results of Japanese monolingual run and three bilingual runs retrieving the Japanese document collection (i.e., Chinese-Japanese, Korean-Japanese and English-Japanese runs). It turns out that a regression model of which independent variables are “quality” of query translation and “difficulty” of the search in itself explains well variations of values of average precision by CLIR runs. The “quality” of translations was measured as a score assigned by a human assessor based on the degree to which each translation is coincident with the corresponding term in the Japanese topic that the task organizers provided, and the “difficulty” of the search was represented as a value of average precision by a run using the Japanese topic (i.e., monolingual run).
Decision-making in abstract trust games: A user interface perspective

To understand the processes involved in trust-based judgments in a computer-mediated multi-agent setting, a user interface (UI) was developed and an experiment was devised based on the Iterated Diner's Dilemma, a variation of the n-player Prisoner's Dilemma. Analysis of the experiment resulted in two major findings: (1) UI composition and information presentation have an impact on human trust and cooperation behavior, and (2) a strong positive correlation between Situation Awareness (SA) and performance is confirmed. There was a significant effect for UI levels on our main performance metric, total participant dining points. , at the p=0.041 level. Also, there was a marginal effect for UI levels on participant cooperation at the p=0.084 level. Total participant dining points and SA were strongly correlated, r (92) = 0.62. Similarly, participant cooperation and SA were strongly correlated, r (92) = 0.61.
Collaboration modes and advantages in supply chain

This research aims to address supply chain collaboration with a perspective of broader three-dimensional relationship, not a linear two-dimensional relationship discussed broadly in previous research. Case study was adopted for this research, and data collection was mainly conducted via interview. The research results highlighted that supply chain collaborations are common practice across all levels of the pharmaceutical supply chain. The results also indicated that the different strengthen levels of barging power among collaborative partners will influence the achieved advantages at different supply chain levels, including strategic, operational and political levels.
Coupling beamforming with spatial and spectral feature based spectral enhancement and its application to meeting recognition

This paper discusses microphone array based interference reduction approaches for robust automatic speech recognition. A model based multichannel spectral enhancement approach has recently been proposed for effectively reducing interference by exploiting both the spatial and spectral features of the signals. With the goal of further improving the effectiveness of this approach, we propose a new framework that combines this approach with a microphone-array based beamforming approach. Because the two approaches can work in a complementary manner in the proposed framework, they can greatly improve the interference reduction performance. We apply the proposed framework to the recognition of actual meetings, and show that it is superior to the use of beamforming or spectral enhancement alone in terms of the word error rates.
Help me Obi-Wan: the influence of facial dominance on perceptions of helpfulness

ABSTRACT We all occasionally need the help of others whom we do not know well. In four studies, we studied the influence of the facial appearance of both the potential helper and the help seeker on such a decision. In three studies (1a-1c), across different help domains, participants rated a person with submissive facial appearance as more likely to help. This was mediated via the perception of the submissive person as caring and helpful. The notion that submissive individuals will be perceived as more likely to help when a dominant person asks was only supported in the context of financial help. The preference for a submissive potential helper was also found when participant had to choose a helper for themselves (Study 2). (120 words)
MUSIC, maximum likelihood, and Cramer-Rao bound

The performance of the MUSIC and ML methods is studied, and their statistical efficiency is analyzed. The Cramer-Rao bound (CRB) for the estimation problems is derived, and some useful properties of the CRB covariance matrix are established. The relationship between the MUSIC and ML estimators is investigated as well. A numerical study is reported of the statistical efficiency of the MUSIC estimator for the problem of finding the directions of two plane waves using a uniform linear array. An exact description of the results is included. <<ETX>>
Synergy of Intellectual Property and Traditional Knowledge: Holy Grail for Protection and Sustainable Future

The symbiosis of Intellectual Property Rights (IPR) and Traditional Knowledge (TK) has become indispensable for its creators and for the world's intellectual community at large. Evidently, the need for preservation, protection and promotion of TK has become inevitable for self-sustenance, economic prosperity of knowledge holders and competitive business advantage. Obviously, the promotion of TK is now widely recognized and it plays an eminent role in supporting TK-based community's livelihood and cultures. The exponential growth of TK has galvanized new forms of IP protection, especially for traditional medicine (TM). The traditional healthcare problems, complexities linked to IP in TK, and community knowledge are posing a gargantuan challenge to sustainable development, intellectual and cultural vitality. This paper stresses on the scope of TK, the avenues to protect it under the existing IPR regime. It incisively highlights the challenges faced by TK holders and the subsequent need for its protective regulation. The paper enunciates the Traditional Knowledge Digital Library (TKDL) as a versatile global regulatory device to obviate the usurpation of documented knowledge. It imparts the vital prerequisites for TKDL and delineates the crucial role it plays, in preserving prized heritage and acceleration of modern research on Ayurveda. The synergy of IPR and TK continues to be nebulous but empirical evidence suggests the rationale for protecting TK within the IPR ambit. The sine qua non of TK protection is to tackle the major concerns like equity, conservation, preservation of traditional culture, bio-piracy, promotion and evolution of TK. The cardinal focus here is the urgent need for international coordination and cooperation to efficaciously safeguard and leverage TK. Any protective strategy should take into account the ethnic community and the attendant global dimensions. The bottom-line is that such a protection should be effectual, comprehensible and accessible to TK holders. Interfacing IPRs with TK rights will only pave the way for TK protection, knowledge enrichments on TM, well- articulated human resources creation and nourishment of TK culture.
Exploring Syntactic Features for Relation Extraction using a Convolution Tree Kernel

This paper proposes to use a convolution kernel over parse trees to model syntactic structure information for relation extraction. Our study reveals that the syntactic structure features embedded in a parse tree are very effective for relation extraction and these features can be well captured by the convolution tree kernel. Evaluation on the ACE 2003 corpus shows that the convolution kernel over parse trees can achieve comparable performance with the previous best-reported feature-based methods on the 24 ACE relation subtypes. It also shows that our method significantly outperforms the previous two dependency tree kernels on the 5 ACE relation major types.
Progressive Authentication: Deciding When to Authenticate on Mobile Phones

Mobile users are often faced with a trade-off between security and convenience. Either users do not use any security lock and risk compromising their data, or they use security locks but then have to inconveniently authenticate every time they use the device. Rather than exploring a new authentication scheme, we address the problem of deciding when to surface authentication and for which applications. We believe reducing the number of times a user is requested to authenticate lowers the barrier of entry for users who currently do not use any security. Progressive authentication, the approach we propose, combines multiple signals (biometric, continuity, possession) to determine a level of confidence in a user's authenticity. Based on this confidence level and the degree of protection the user has configured for his applications, the system determines whether access to them requires authentication. We built a prototype running on modern phones to demonstrate progressive authentication and used it in a lab study with nine users. Compared to the state-of-theart, the system is able to reduce the number of required authentications by 42% and still provide acceptable security guarantees, thus representing an attractive solution for users who do not use any security mechanism on their devices.
Index-Based Processing of Similarity Queries for Set and Sequence-Valued Attributes

Many complex real world objects can be easily modeled using sets or sequences. Attributes containing sets or sequences of elements appear in various application domains, e.g. in telecommunication and retail databases, multimedia systems, web server logs, genetic and molecular databases, etc. However, the support for such attributes is usually limited to definition and storage in flat relational tables. Currently available database systems support neither indexing nor advanced querying of attributes containing sets or sequences. SQL language does not offer any primitives to express set containment or set similarity queries. In this paper we investigate similarity queries for set and sequence-valued attributes. We present the notion of a similarity query and we review similarity measures proposed so far for sets and sequences. We present hierarchical bitmap index, an efficient indexing technique for sets, and we show how the hierarchical bitmap index framework can be extended to incorporate sequences as well. We introduce a new similarity measure that can be successfully used with sequences. We present algorithms for efficient similarity query processing using hierarchical bitmap index and its variants. Our paper concludes with the results of conducted experi-
Sequences with Subword Complexity 2n G Unter Rote Sequences with Subword Complexity 2n G Unter Rote

Some typographical errors have been corrected. Figure 2 of this report is not complete in this version because it should contain some hand-drawn additional arcs. The reader, however, is able work out the details for herself. Abstract We construct and discuss innnite 0-1-sequences which contain 2n diierent sub-words of length n, for every n.
Improved preparation of chick embryonic samples for magnetic resonance microscopy

Previous work demonstrated the power of three‐dimensional (3D) magnetic resonance microscopy (MRM) to follow complicated morphologic development in the embryonic cardiovascular system. In this study we describe a new dual‐contrast method for specimen preparation that combines perfusion fixation and immersion in fixative with macro‐ and small molecular gadolinium agents to provide enhanced definition of both the heart wall and chamber. MRM was performed at 9.4 T with image resolutions of 25, 31, and 50 μm isotropic voxels for three stages of chick embryos (day 4, day 5.5, and day 9), and compared to histological sections of the same embryos. The results show considerable improvement of image quality over previous efforts, with better signal‐to‐noise ratio (SNR) and contrast between the cardiac chamber and myocardial wall. Excellent correlation was shown between the MRM images and histological sections. Thus, 3D high‐resolution MRM in combination with the dual‐contrast technique is useful for acquiring quantitative 3D morphologic data regarding heart development. Magn Reson Med 49:1192–1195, 2003. © 2003 Wiley‐Liss, Inc.
Polyhedral Bubble Insertion: A Method to Improve Nested Loop Pipelining for High-Level Synthesis

High-level synthesis (HLS) allows hardware to be directly produced from behavioral description in C/C++, thus accelerating the design process. Loop pipelining is a key transformation of HLS, as it improves the throughput of the design at the price of a small hardware overhead. However, for small loops, its use often results in a poor hardware utilization due to the pipeline latency overhead. Overlapping the iterations of the whole loop nest instead of only overlapping the innermost loop is a way to overcome this difficulty, but currently available techniques are restricted to perfectly nested loops with constant bounds, involving uniform dependences only. Using the polyhedral model, we extend the applicability of the nested loop pipelining transformation by proposing a new legality check and a new loop correction technique, called polyhedral bubble insertion. This method was implemented in a source-to-source compiler targeting HLS, and results on benchmark kernels show that polyhedral bubble insertion is effective in practice on a much larger class of loop nests.