Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating EMR-Linked and In Vivo Functional Genetic Data to Identify New Genotype-Phenotype Associations

The coupling of electronic medical records (EMR) with genetic data has created the potential for implementing reverse genetic approaches in humans, whereby the function of a gene is inferred from the shared pattern of morbidity among homozygotes of a genetic variant. We explored the feasibility of this approach to identify phenotypes associated with low frequency variants using Vanderbilt's EMR-based BioVU resource. We analyzed 1,658 low frequency non-synonymous SNPs (nsSNPs) with a minor allele frequency (MAF)<10% collected on 8,546 subjects. For each nsSNP, we identified diagnoses shared by at least 2 minor allele homozygotes and with an association p<0.05. The diagnoses were reviewed by a clinician to ascertain whether they may share a common mechanistic basis. While a number of biologically compelling clinical patterns of association were observed, the frequency of these associations was identical to that observed using genotype-permuted data sets, indicating that the associations were likely due to chance. To refine our analysis associations, we then restricted the analysis to 711 nsSNPs in genes with phenotypes in the On-line Mendelian Inheritance in Man (OMIM) or knock-out mouse phenotype databases. An initial comparison of the EMR diagnoses to the known in vivo functions of the gene identified 25 candidate nsSNPs, 19 of which had significant genotype-phenotype associations when tested using matched controls. Twleve of the 19 nsSNPs associations were confirmed by a detailed record review. Four of 12 nsSNP-phenotype associations were successfully replicated in an independent data set: thrombosis (F5,rs6031), seizures/convulsions (GPR98,rs13157270), macular degeneration (CNGB3,rs3735972), and GI bleeding (HGFAC,rs16844401). These analyses demonstrate the feasibility and challenges of using reverse genetics approaches to identify novel gene-phenotype associations in human subjects using low frequency variants. As increasing amounts of rare variant data are generated from modern genotyping and sequence platforms, model organism data may be an important tool to enable discovery.
Destination Branding in Relation to Airports: The Case of the City of Valencia

This study investigates various factors that contribute to the success of destination branding efforts where success is defined as the increase in airplane passenger numbers to a destination and its linked air transportation. Drawing on in-depth interviews and snowball sampling, the study examines the roles of many of the key actors involved in the efforts to increase passenger numbers. Using the City of Valencia in Spain as a case study, the role of its airport is examined as a factor of particular interest. The study concludes that Valencia has positioned itself among neighbouring destinations on the Spanish Mediterranean coast by its focus on high profile events and cultural tourism. However, other actors have taken a more active role in the effort to increase the number of tourists than the Valencia Airport that has taken a more passive role. Another finding is that the persistence in seeking resources for the costly branding efforts was another influential factor that explains the increase in Valencia tourism.
Heterogenous Forecasting and Federal Reserve Information

December 2001 We provide evidence that private forecasters and the staff of the Federal Reserve use different forecasting models to predict inflation and GNP growth and heterogeneity of forecasting models is the norm in the market place. We thus argue that neither the Fed nor commercial forecasters know the "true" model of the economy. We demonstrate that their forecast errors are correlated with information available at the time when the forecasts were made and hence, by studying the systematic patterns of these forecast errors, we can deduce a great deal about their assessments of economic conditions in general and their view of monetary policy in particular. We also show that (i) although all private forecasters have the same information, their diverse forecasting models result in a distribution of forecasts which fluctuates over time. The distribution shows no tendency for convergence. The "consensus" median forecaster is a random member whose identity changes over time; (ii) the evidence shows that at any date there is a whole set of private forecasts who agree with the Fed's forecasts but the Fed forecasts are less volatile than the volatility of private forecasts measured by the variance of the cross-sectional distribution of private forecasts; (iv) diverse assessments of the impact of monetary policy on inflation and growth are important factors which contribute to the heterogeneity of forecasts. A surprising result reveals that although there is strong evidence for heterogeneity among forecasters, we also find similarity in qualitative patterns of forecast errors of all participants, including the Fed. Qualitative similarity implies similarity in the basic ideas underlying the forecasting models even when these ideas are wrong. This implies a degree of correlation among the subjective beliefs of divergent agents in the economy. (v) although all forecasts violate the standard orthogonality conditions of Rational Expectations, we argue in this paper that this should not be interpreted as irrational behavior. We provide an introduction to the theory of Rational Belief (see Kurz (1994), (1997)) and demonstrate that in contrast to the rejection of Rational Expectations, the pattern of estimated parameters is consistent with the predictions of the theory of Rational Beliefs (see Kurz (1994), (1997)). In opposition to some (e.g. De Bondt and Thaler (1985), (1990)), we argue that rejection of rational expectations should not be interpreted to imply irrational behavior. Working Papers Index
β-Thymosins and Hemocyte Homeostasis in a Crustacean

Thymosin proteins are well known for their actin-binding activity. Thymosin beta 4 (Tβ4) has been associated with biological activities in tissue repair and cell migration via interaction with ATP-synthase in vertebrates, while the information of similar thymosin functions in invertebrates is limited. We have shown previously that ATP-synthase is present on the surface of crayfish hematopoietic tissue (HPT) cells, and that astakine 1 (Ast1, an invertebrate cytokine) was found to interact with this β-subunit of ATP synthase. Here, we identified five different β-thymosins from Pacifastacus leniusculus, designated Pl-β-thymosin1-5. The two dominant isoforms in brain, HPT and hemocytes, Pl-β-thymosin1 and 2, were chosen for functional studies. Both isoforms could bind to the β-subunit of ATP-synthase, and Pl-β-thymosin1, but not Pl-β-thymosin2, significantly increased extracellular ATP formation. Moreover, Pl-β-thymosin1 stimulated HPT cell migration in vitro and Ast1 blocked this effect. Pl-β-thymosin2 increased the circulating hemocyte number at an early stage after injection. Additionally, in vivo injection of Pl-β-thymosin1 resulted in significant reduction of reactive oxygen species (ROS) production in crayfish HPT whereas Pl-β-thymosin2 had a similar but transient effect. Both Pl-β-thymosins induced the expression of Ast1 and superoxide dismutase (SOD) transcripts, while silencing of endogenous Pl-β-thymosin 1 and 2 by RNAi resulted in significant reduction of the Ast1 and SOD transcripts. The diverse effects exhibited by Pl-β-thymosin1 and Pl-β-thymosin2 indicates that these proteins are involved in a complex interaction that regulates the hematopoietic stem cell proliferation and differentiation.
Budget reform in OECD member countries: Common trends

From the early 1990s, the fiscal position of OECD member countries improved steadily each year, from a deficit of 5% of GDP for member countries as whole in 1993 to a perfect balance in the year 2000, i.e. neither a deficit nor a surplus. In 2001, member countries experienced a deficit of 1% of GDP. Table 1 depicts the general government financial balances of selected OECD member countries. This goes to show the historical pattern in member countries: achieving fiscal consolidation is a slow process and successes in fiscal consolidation can quickly dissipate. A very short time ago, several OECD member countries believed that they were on a long-term track for fiscal surpluses; the era of deficits had been overcome. This did not turn out to be the case; surpluses turned out to be a very short-lived phenomenon for many countries.
Fate of Carbohydrates and Lignin during Composting and Mycelium Growth of Agaricus bisporus on Wheat Straw Based Compost

In wheat straw based composting, enabling growth of Agaricus bisporus mushrooms, it is unknown to which extent the carbohydrate-lignin matrix changes and how much is metabolized. In this paper we report yields and remaining structures of the major components. During the Phase II of composting 50% of both xylan and cellulose were metabolized by microbial activity, while lignin structures were unaltered. During A. bisporus’ mycelium growth (Phase III) carbohydrates were only slightly consumed and xylan was found to be partially degraded. At the same time, lignin was metabolized for 45% based on pyrolysis GC/MS. Remaining lignin was found to be modified by an increase in the ratio of syringyl (S) to guaiacyl (G) units from 0.5 to 0.7 during mycelium growth, while fewer decorations on the phenolic skeleton of both S and G units remained.
Spontaneous Event Recommendations on the Go

In this paper, we summarize our previous work in the field of event recommendations and give an outlook on future work. We developed a recommender system which implements a hybrid recommendation technique to provide accurate recommendations. A two-week user study showed that our system delivers promising results. Nevertheless, we believe that this approach mainly supports users who are looking for recommendations a long time in advance. Other possible situations in which people could be open for recommendations are more spontaneous, for example, when they are already out exploring the city. We give an overview of aspects which have to be considered fur such spontaneous recommendations on the go and the role of social context in this scenario.
Scheduling Self-Suspending Real-Time Tasks with Rate-Monotonic Priorities

Recent results have shown that the feasibility problem of scheduling periodic tasks with self-suspensions is NP-hard in the strong sense. We observe that a variation of the problem statement that includes sporadic tasks instead of periodic tasks results in a simple characterization of the critical scheduling instant. This in turn leads to an exact characterization of the critical instant for self-suspending tasks with respect to the interference (preemption) from higher-priority sporadic tasks. Using this characterization, we provide pseudo-polynomial response-time tests for analyzing the schedulability of such self-suspending tasks. Self-suspending tasks can also result in more worst-case interference to lower-priority tasks than their equivalent non-suspending counterparts with zero suspension intervals. Hence, we develop a dynamic slack enforcement scheme, which guarantees that the worst-case interference caused by suspending sporadic tasks is no more than the worst-case interference arising from equivalent non-suspending sporadic tasks without suspension intervals. The worst-case response time of self-suspending sporadic tasks themselves is also shown to be unaffected by dynamic slack enforcement, thereby making it optimal. In order to reduce the runtime complexity of slack enforcement, a static slack enforcement scheme is also developed. Empirical analysis of these schemes and the previously studied period enforcement algorithm shows that static slack enforcement achieves within 3% of the breakdown utilization of dynamic slack enforcement, while period enforcement achieves within 14% of dynamic slack enforcement. System designers can take advantage of these different execution control policies depending on their taskset utilizations and implementation constraints.
Active discs for automated optic disc segmentation

Glaucoma is currently one of the major causes of vision loss worldwide. Though the lost vision capability cannot be recovered, preventive steps such as clinical diagnosis and necessary treatment can be taken in order to minimize visual impairment due to glaucoma. The process of clinical diagnosis needs manual examination and outlining of the optic disc and cup, which is subjective and time consuming. In this paper, we propose a methodology for automatic segmentation and outlining of the optic disc using an active disc formulation. The method uses a disc template as a prototype. The initialization is automated using a matched filtering technique. We choose the disc to be isotropic, and allow for translation, isotropic scaling, and optimization of the corresponding parameters. The active disc is evolved towards the boundary of the optic disc by minimizing a local energy function. We report validations on three publicly available databases MES-SIDOR, DRIONS-DB, and Drishti-GS containing 1200, 110, and 101 retinal fundus images, respectively. The corresponding F-scores 0.8456, 0.8380, and 0.9077, respectively, for the databases show robustness, and high correlation of the proposed algorithm with the expert segmentation.
Dynamic road scene classification: Combining motion with a visual vocabulary model

The majority of studies in scene classification have focused on still images, ignoring potentially informative temporal cues. This paper explores the combination of multi-scale appearance and motion features for classification of scenes captured from a moving vehicle under real-world driving. The objective is to classify unknown scenes in one out of a set of predefined typical road scene classes that are learnt during training. The method is studying the performance of a state-of-the-art scene classification visual vocabulary model (known also as bag of features model) when appearance image features and video motion features are combined for SVM learning and classification. The sequence of scenes is captured from a moving vehicle equipped with a frontal camera sensor. Video driving data used for evaluation were available by two test vehicles (a passenger car and a truck) participating in the European interactIVe IP. It is shown that a notable performance increase is realized by appearance-temporal approach in comparison to purely appearance or purely temporal methods. The quantitative evaluation has been performed using manually annotated video sequences.
Adaptive routing protocols for hypercube interconnection networks

A taxonomy for characterizing adaptive routing protocols for hypercube interconnection networks (HINs) is presented. The taxonomy is based on classes of routing decisions common to any HIN. This taxonomy is used to discuss existing and proposed protocols. Rather than an exhaustive enumeration of related research, the protocols selected for discussion are intended to be representative of the classes defined by the taxonomy. These protocols are candidates for use in massively parallel architectures configured with HINs. To provide some insight into their behavior in very large HINs, results of simulation studies of representative protocols are presented. <<ETX>>
DataGrid Authentication via GSI Certificates Within a Very Large Global File System

Grid computing is moving from the domain of the unrealized research project to the heavily production oriented world of the National Science Foundation’s TeraGrid and other organizations. A critical part of such efforts is the ability of users to access their data quickly, efficiently, and independently of physical location. Whereas in small Grid communities it may be feasible to transfer the applicable data from place to place by file transfer utilities such as GridFTP, in large supercomputing communities the Global File System approach seems much more appropriate. This paradigm has been implemented within the TeraGrid and has been in production since October, 2005. The use of a Global File System has necessitated a rethink of the authentication process: unlike a very tightly coupled grid, the UIDs are not unified across sites. To enable the concept of file ownership to survive journeys between sites, it has been necessary to implement a GSI certificate to UID mapping. This has been completed and is in production. The extension of this paradigm to Group Authentication is more complex, and the exact approach is under discussion. In this paper we report on our experiences and intended future work.
Ant-Based Simulation of Opinion Spreading in Online Social Networks

An increasing number of people are socializing within online networks. By means of interaction, network members influence one another’s opinion. For companies, it is important to know how opinions spread throughout networks in order to be able to take appropriate marketing actions. A new approach is presented which simulates the spread of opinions within online social networks. The principles of opinion formation are first revealed by ant mining algorithms coming from swarm intelligence and then applied to simulate the spread of opinions.
The Oxfam Poverty Report

* Acknowledgements * Introduction 1. Poverty 2. A world at war 3. Structural adjustment 4. International trade 5. Ecological footprints 6. Aid, dept, and development finance 7. Anagenda for change * Notes * Index * Information on the international Oxfam group
A general few-projection method for tomographic reconstruction of samples consisting of several distinct materials

We present a method for tomographic reconstruction of objects containing several distinct materials, which is capable of accurately reconstructing a sample from vastly fewer angular projections than required by conventional algorithms. The algorithm is more general than many previous discrete tomography methods, as: (i) a priori knowledge of the exact number of materials is not required; (ii) the linear attenuation coefficient of each constituent material may assume a small range of a priori unknown values. We present reconstructions from an experimental x-ray computed tomography scan of cortical bone acquired at the SPring-8 synchrotron.
Innovation in the Service Sector and the Role of Patents and Trade Secrets

Abstract This study, using Japanese firm-level data, presents empirical findings on innovation in the service sector and the role of patents and trade secrets. Service firms have fewer product innovations than manufacturing firms do, but the productivity of innovative service firms is very high. Service firms have a low propensity to hold patents, but their holding of trade secrets is comparable to that of manufacturing firms. Product/service innovations have positive relationships with holding patents and trade secrets in both industries, but a positive association of process innovations is found only with holding trade secrets in the manufacturing industry.
Motion-Tracking and Speech Recognition for Hands-Free Mouse-Pointer Manipulation

The design of traditional interfaces relies on the use of mouse and keyboard. For people with certain disabilities, however, using these devices presents a real problem. In this chapter we describe a graphical user interface navigation utility, similar in functionality to the traditional mouse pointing device. Movement of the pointer is achieved by tracking the motion of the head, while button-actions can be initiated by issuing a voice command. Foremost in our mind was the goal to make our system easy to use and affordable, and provide users with disabilities with a tool that promotes their independence and social interaction.
Respiration Gates Sensory Input Responses in the Mitral Cell Layer of the Olfactory Bulb

Respiration plays an essential role in odor processing. Even in the absence of odors, oscillating excitatory and inhibitory activity in the olfactory bulb synchronizes with respiration, commonly resulting in a burst of action potentials in mammalian mitral/tufted cells (MTCs) during the transition from inhalation to exhalation. This excitation is followed by inhibition that quiets MTC activity in both the glomerular and granule cell layers. Odor processing is hypothesized to be modulated by and may even rely on respiration-mediated activity, yet exactly how respiration influences sensory processing by MTCs is still not well understood. By using optogenetics to stimulate discrete sensory inputs in vivo, it was possible to temporally vary the stimulus to occur at unique phases of each respiration. Single unit recordings obtained from the mitral cell layer were used to map spatiotemporal patterns of glomerular evoked responses that were unique to stimulations occurring during periods of inhalation or exhalation. Sensory evoked activity in MTCs was gated to periods outside phasic respiratory mediated firing, causing net shifts in MTC activity across the cycle. In contrast, odor evoked inhibitory responses appear to be permitted throughout the respiratory cycle. Computational models were used to further explore mechanisms of inhibition that can be activated by respiratory activity and influence MTC responses. In silico results indicate that both periglomerular and granule cell inhibition can be activated by respiration to internally gate sensory responses in the olfactory bulb. Both the respiration rate and strength of lateral connectivity influenced inhibitory mechanisms that gate sensory evoked responses.
Decoding Articulatory Features from fMRI Responses in Dorsal Speech Regions

The brain's circuitry for perceiving and producing speech may show a notable level of overlap that is crucial for normal development and behavior. The extent to which sensorimotor integration plays a role in speech perception remains highly controversial, however. Methodological constraints related to experimental designs and analysis methods have so far prevented the disentanglement of neural responses to acoustic versus articulatory speech features. Using a passive listening paradigm and multivariate decoding of single-trial fMRI responses to spoken syllables, we investigated brain-based generalization of articulatory features (place and manner of articulation, and voicing) beyond their acoustic (surface) form in adult human listeners. For example, we trained a classifier to discriminate place of articulation within stop syllables (e.g., /pa/ vs /ta/) and tested whether this training generalizes to fricatives (e.g., /fa/ vs /sa/). This novel approach revealed generalization of place and manner of articulation at multiple cortical levels within the dorsal auditory pathway, including auditory, sensorimotor, motor, and somatosensory regions, suggesting the representation of sensorimotor information. Additionally, generalization of voicing included the right anterior superior temporal sulcus associated with the perception of human voices as well as somatosensory regions bilaterally. Our findings highlight the close connection between brain systems for speech perception and production, and in particular, indicate the availability of articulatory codes during passive speech perception. SIGNIFICANCE STATEMENT Sensorimotor integration is central to verbal communication and provides a link between auditory signals of speech perception and motor programs of speech production. It remains highly controversial, however, to what extent the brain's speech perception system actively uses articulatory (motor), in addition to acoustic/phonetic, representations. In this study, we examine the role of articulatory representations during passive listening using carefully controlled stimuli (spoken syllables) in combination with multivariate fMRI decoding. Our approach enabled us to disentangle brain responses to acoustic and articulatory speech properties. In particular, it revealed articulatory-specific brain responses of speech at multiple cortical levels, including auditory, sensorimotor, and motor regions, suggesting the representation of sensorimotor information during passive speech perception.