Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Applications in Genetics and Molecular Biology Model-based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances Model-based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances

prior written permission of the publisher, bepress. Statistical Applications in Genetics and Molecular Biology is produced by The Berkeley Electronic Press (bepress). Abstract Nuclear Magnetic Resonance (NMR) spectroscopy is a key experimental technique used to study protein structure, dynamics, and interactions. NMR methods face the bottleneck of spectral analysis, in particular determining the resonance assignments, which help define the mapping between atoms in the protein and peaks in the spectra. A substantial amount of noise in spectral data, along with ambiguities in interpretation, make this analysis a daunting task, and there exists no generally accepted measure of uncertainty associated with the resulting solutions. This paper develops a model-based inference approach that addresses the problem of characterizing uncertainty in backbone resonance assignment. We argue that NMR spectra are subject to random variation, and ignoring this stochasticity can lead to false optimism and erroneous conclusions. We propose a Bayesian statistical model that accounts for various sources of uncertainty and provides an automatable framework for inference. While assignment has previously been viewed as a deterministic optimization problem, we demonstrate the importance of considering all solutions consistent with the data, and develop an algorithm to search this space within our statistical framework. Our approach is able to characterize the uncertainty associated with backbone resonance assignment in several ways: 1) it quantifies of uncertainty in the individually assigned resonances in terms of their posterior standard deviations; 2) it assesses the information content in the data with a posterior distribution of plausible assignments; and 3) it provides a measure of the overall plausibility of assignments. We demonstrate the value of our approach in a study of experimental data from two proteins, Human Ubiquitin and Cold-shock protein A from E. coli. In addition, we provide simulations showing the impact of experimental conditions on uncertainty in the assignments.
Random Power Control for Uncorrelated Rayleigh Fading Channels

When the channel measurement update rate is very slow compared to the channel fluctuations, the performance of conventional power control algorithms is greatly reduced. In this paper we introduce novel method to update the transmit power in such extreme situations. We propose to use random power allocation with certain distribution function and then using the channel measurements to update the statistics of this random power rather the power value itself. The truncated inverted exponential distribution is one candidate for the power distribution which is used in this paper. This distribution has one parameter which can be easily updated according to the channel quality. The signal-to-interference and noise ratio (SINR) is used as an indicator for the channel quality. The probability of outage when using the proposed power allocation is also given in mathematical form. Simulations show that, one may improve the average SINR when using the proposed algorithm compared to the conventional distributed power control algorithm.
Compact and Scalable Graph Neighborhood Sketching

The all-distances sketch (ADS) has recently emerged as a promising paradigm of graph neighborhood sketching. An ADS is a probabilistic data structure that is defined for each vertex of a graph. ADSs facilitate accurate estimation of many useful indicators for network analysis with the guarantee of accuracy, and the ADSs for all the vertices in a graph can be computed in near-linear time. Because of these useful properties, ADS has attracted considerable attention. However, a critical drawback of ADS is its space requirement, which tends to be much larger than that of the graph itself. In the present study, we address this issue by designing a new graph sketching scheme, namely, sketch retrieval shortcuts (SRS). Although SRSs are more space-efficient than ADSs by an order of magnitude, an ADS of any vertex can be quickly retrieved from the SRSs. The retrieved ADSs can be used to estimate the aforementioned indicators in exactly the same manner as with plain ADSs, inheriting the same accuracy guarantee. Our experiments on real-world networks demonstrate the usefulness of SRSs as a practical back-end of large-scale graph data mining.
Solvency II

The insurance industry needs to be regulated to protect policyholders. This is the main objective of the Solvency II directive – the new insurance regulations for the European Economic Area. In short, it requires insurance companies to act responsibly with the money they have been entrusted with. It is estimated that implementing Solvency II will cost 2-3 billion Euro. It has the potential to change a lot in the way insurance companies operate, and these changes will hopefully benefit not just policyholders but also the insurance companies in the long run. In this report we outline the main points of the directive and the reasoning behind them. The report is mostly a joint effort, with Sandra focusing on the parts about capital requirements and Oskar on the parts about supervision.
Association of rheumatoid arthritis with allergic diseases: A nationwide population-based cohort study.

BACKGROUND Low-grade inflammation conditions, e.g., type 2 diabetes, have been shown to be associated with an increased risk of rheumatoid arthritis (RA). However, the association between other chronic inflammatory conditions, e.g., asthma, allergic rhinitis, and atopic dermatitis, is still unclear. OBJECTIVE To investigate the risk of RA in patients with allergic diseases, including asthma, allergic rhinitis, and atopic dermatitis, by using a nationwide health claims database. METHODS The Taiwan National Health Insurance Research Database was used to assemble a cohort of 170,570 patients ages 20 years old and older diagnosed with allergic diseases, including asthma, allergic rhinitis, or atopic dermatitis. A comparison cohort of 170,238 patients was constructed from the same data base, with frequency matching for sex, 10-year age group, and year of insurance enrollment. Cox proportional hazards regression analyses were conducted to assess the association between the allergic diseases and incident RA. RESULTS Asthma (adjusted hazard ratio [AHR] 1.67, [95% confidence interval {CI}], 1.32-2.62) and allergic rhinitis (AHR 1.62 [95% CI, 1.33-1.98]) were significantly associated with the incident RA. These associations remained significant even after excluding patients who had concurrent diagnoses of asthma and allergic rhinitis. Patients with more than one allergic disease had an increased risk of developing RA (AHR 1.98 [95% CI, 1.50-2.62]). Subgroup analysis further indicated that middle-aged and elderly female patients with more than one allergic disease exhibited a high risk of developing RA. CONCLUSION Significant associations between common allergic diseases and incident RA was found in this population-based cohort study. Our findings provided support to the hypothesis that allergic diseases and RA might share a similar underlying etiologic pathway related to chronic inflammatory responses.
Performance comparison of video streaming application between Mobile WiMAX and UMTS

Video streaming is the real time delivery process of video to the user's media player services. In multimedia streaming technique, the user can access data while it is being transferred. To meet the demand of providing high-quality of video streaming, it is important to design suitable QoS model. Hence, in this project, we designed around streaming services using an Internet topology on expected video performance. We evaluate the performance of the Mobile WiMAX and UMTS due to fading effect according to the performance metrics of throughput, packet loss, jitter and delay. It will stream the LOTR2 (Lord of the Ring 2) movie for 1 hour interval to all client subscribers in mobile WiMAX and UMTS. Simulation results show that mobile WiMAX has better performance to support video streaming compared to UMTS.
Dealing with small data and training blind spots in the Manhattan world

Leveraging Manhattan assumption we generate metrically rectified novel views from a single image, even for non-box scenarios. Our novel views enable the already trained classifiers to handle training data missing views (blind spots) without additional training. We demonstrate this on end-to-end scene text spotting under perspective. Additionally, utilizing our fronto-parallel views, we discover unsuspended invariant mid-level patches given a few widely separated training examples (small data domain). These invariant patches outperform various baselines on small data image retrieval challenge.
Language Specific and Language General Motivations of Production Choices: A Multi-Clause and Multi-Language Investigation

Cross-linguistic studies allow for analyses that would be impossible in a single language. To better understand the factors that underlie sentence production, we investigated production choices in main and relative clause production tasks in three languages: English, Japanese and Korean. The effects of both non-linguistic attributes (such as conceptual animacy) and language specific properties (such as word order) were investigated. Japanese and Korean are structurally similar to each other but different from English, which allowed for an investigation of the production consequences of non-linguistic attributes in different typological or word order contexts (when Japanese and Korean speakers make similar production choices that are unlike those of English speakers), as well as production choices that differ despite typological similarity (when Japanese and Korean speakers make different choices). Speakers of all three languages produced more passive utterances when describing animate entities, but the overall rate of passives varied by task and language. Further, the sets of items that were most likely to elicit passives varied by language, with Japanese and Korean speakers more likely to produce passives when patients were adversely affected by the depicted event. These results suggest a number of factors that contribute to language production choices across three languages, and how general cognitive constraints on sentence production may interact with the structure of a specific language.
Prevalence and clinical importance of gastroesophageal reflux in Chinese patients with systemic sclerosis.

OBJECTIVES To estimate the prevalence of gastroesophageal reflux (GER) and its clinical relevance with other manifestations in Chinese patients with systemic sclerosis (SSc). METHODS A prospective cross-sectional study of 205 Chinese patients with SSc was conducted at Peking Union Medical College Hospital (PUMCH). GER was diagnosed as mild heartburn or regurgitation ≥2 days per week, or moderate/severe heartburn or regurgitation ≥1 day a week. PAH was defined as pulmonary artery systolic pressure (PASP) >45mmHg at rest as estimated by transthoracic echocardiography (TTE). Demographic, clinical, and laboratory data were calculated between GER and non-GER groups, and relative examinations including a six-minute walk test, pulmonary function test and modified Rodnan skin score (mRSS) were also performed. RESULTS The prevalence of GER was 43.90% (90/205) among 205 Chinese patients with SSc. The presence of Raynaud phenomenon (98.9% vs. 92.2%), fingertip ulcers (56.7% vs. 51.3%), pulmonary arterial hypertension (PAH) (18.89% vs. 6.96%, respectively), and all gastrointestinal tract manifestations occurred significantly more frequent in patients with GER than in patients without GER, respectively (p<0.05). There were no differences in the development of any autoantibody between GER patients and non-GER patients (p>0.05). Echocardiography showed that the left ventricular ejection fraction (LVEF) was lower (62.27±10.48 vs. 70.09±5.26, respectively) and pericarditis was more frequent (22.6% vs. 11.0%, respectively) in SSc-related GER than in SSc patients without GER, respectively. The New York Heart Association (NYHA) functional class of SSc-related GER was worse than patients without GER (p=0.015). A pulmonary function test showed that forced vital capacity FVC% (78.93±17.90 vs. 84.55±17.45, respectively, p=0.042), forced expiratory volume FEV1% (77.12±15.65 vs. 84.30±16.25, respectively, p=0.004), and diffusing capacity DLCO% (4.76±1.76 vs. 5.63±2.12, respectively, p<0.001) were lower, and the FVC%/DLCO% ratio (1.46±0.42 vs. 1.28±0.27, respectively, p=0.001)was higher in SSc-related GER than non-GER patients (p<0.05). We also found that GER was an independent risk factor of PAH in SSc patients (p=0.030, OR=7.532). CONCLUSIONS GER is common in Chinese patients with SSc, and patients with GER are susceptible to microvascular damage. Therefore, SSc patients presenting with GER should be screened for PAH.
Milwaukee Voucher-School Leaders’ Views on Accountability: What Are They, and Why Do They Matter?

ABSTRACT This article uses originally collected survey data to determine how leaders of private schools in the nation’s oldest school-voucher program define accountability and perceive the state agency charged with holding them accountable. The results indicate voucher-school administrators’ views on accountability are influenced by their school’s level of dependence on government revenues, their school’s academic performance, and their own personal views on regulation. The findings add to a body of research showing how accountability frameworks and perceptions influence the actions and performance of organizations and their stakeholders.
User-Control of Personalised Intelligent Environments which Support Health

This research project aims at supporting workers in the mining and construction industries and older adults at home, in monitoring the risks of their daily work or living situation. A goal is to create awareness in the individual about risks and how to decrease risks. Methods and knowledge-based applications are developed, which synthesise knowledge about the user, the user's activities, the environment and generic domain knowledge for the purpose of providing tailored support and advice to individuals. This knowledge is also what the user can relate to, interact with and control through different methods. In this paper we investigate different approaches to user control of intelligent environments and propose a dialogue-based method for user control.
The European Community and European government: harmonization, mobility and space

Although the European Community does not possess many of the usual attributes of a nation state, it is none the less expected to provide a framework within which Europe's economic and social problems might be governed. This paper examines the methods with which the Community has sought to establish the possibility of European government. The focus of the paper is on the single market programme and the associated project of ‘harmonization’. It is argued that the harmonization project can be seen both as a way of realizing a novel organization of European space, and as a process directed at establishing this space as a governable entity. The paper examines the specific character of this spatial order, and its articulation with neo-liberal and neo-social democratic conceptions of European government.
Epidemiology of heartwater in Nigeria.

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G protein‐coupled receptors in natural killer cells

Natural killer (NK) cells are capable of killing tumor as well as virally infected cells. How these cells migrate toward the infected sites in the body is not completely understood. Chemokine receptors that belong to the heptahelical family of receptors and characteristically bind heterotrimeric G proteins are present in most NK cells. Recent results showed that resting NK cells highly express constitutive chemokine receptors (CCR4, CCR7, CXCR4, and CX3CR1) with low expression of a limited repertoire of inflammatory chemokine receptors (CCR1 and CXCR3). However, only a subset of these cells expressing the CD56dim and adhesion moleculehigh phenotype is capable of in vivo binding to vascular endothelium. Under pathological conditions where inflammatory cytokines are present, these cells are induced to express inflammatory chemokine receptors. Resting as well as activated NK cells also express receptors for another member of the heptahelical family of receptors that bind phosphorylated or glycosylated lysolipids. These include sphingosine 1‐phosphate (S1P)1, S1P4, and S1P5, the receptors for S1P; lysophosphatidic acid (LPA)1, LPA2, and LPA3, the receptors for LPA; and T cell death‐associated gene 8, the receptor for psychosine. Similar to chemokines, S1P, LPA, and psychosine induce the chemotaxis of NK cells through heterotrimeric G proteins. However, in contrast to chemokines, which enhance the cytotoxicity of NK cells, lysolipids inhibit this function. We hope that gaining knowledge regarding the distribution of activated NK cells toward the sites of tumor growth or virally infected sites will give an advantage in designing strategies using these cells as tools for the prevention and treatment of immunodeficiencies.
DNA binding by c‐Ets‐1, but not v‐Ets, is repressed by an intramolecular mechanism.

The E26 avian retrovirus causes an acute leukemia in chickens and transforms both myeloid and erythroid cells. The virus encodes a 135 kDa fusion protein which contains amino acid sequences derived from the viral Gag protein and the two cellular transcription factors c‐Myb and c‐Ets‐1p68. Previously we have shown that like v‐myb, v‐ets on its own is also active in transformation, but only within the erythroid lineage. To understand better the mechanisms involved in the oncogenic activation of c‐Ets‐1p68, we used the polyoma PEA3 element, a known Ets binding site, to compare the sequence‐specific DNA binding and transactivating properties of v‐Ets and c‐Ets‐1p68. Using Ets protein synthesized in rabbit reticulocyte lysate in gel retardation assays, we detected little binding of c‐Ets‐1p68 to an oligonucleotide containing the PEA3 motif whereas v‐Ets bound strongly. However, in transient cotransfection assays in chicken embryo fibroblasts both c‐Ets‐1p68 and v‐Ets transactivated transcription from a heterologous promoter linked to PEA3 elements. Interestingly, fragments of c‐Ets‐1p68 with strong DNA binding activity could be produced by limited proteolysis, indicating that the DNA binding domain is repressed within the full‐length molecule. By deletion mapping the DNA binding domain was localized to the most highly conserved region of the Ets‐related proteins known as the ETS domain. The C‐terminus as well as a region in the middle of the polypeptide chain are involved in repression of DNA binding in c‐Ets‐1p68. Significantly, v‐Ets contains a 16 amino acid substitution at the C‐terminus. Our results suggest that intramolecular repression of DNA binding is a regulatory mechanism in c‐Ets‐1p68 which is lost in v‐Ets.
Liquid FM: Recommending Music through Viscous Democracy

Most modern recommendation systems use the approach of collaborative filtering: users that are believed to behave alike are used to produce recommendations. In this work we describe an application (Liquid FM) taking a completely different approach. Liquid FM is a music recommendation system that makes the user responsible for the recommended items. Suggestions are the result of a voting scheme, employing the idea of viscous democracy. Liquid FM can also be thought of as the first testbed for this voting system. In this paper we outline the design and architecture of the application, both from the theoretical and from the implementation viewpoints.
Security Impact Ratings Considered Harmful

In this paper, we question the common practice of assigning security impact ratings to OS updates. Specifically, we present evidence that ranking updates by their perceived security importance, in order to defer applying some updates, exposes systems to significant risk. We argue that OS vendors and security groups should not focus on security updates to the detriment of other updates, but should instead seek update technologies that make it feasible to distribute updates for all disclosed OS bugs in a timely manner.
A framework and tool support for the systematic testing of model-based specifications

Formal specifications can precisely and unambiguously define the required behavior of a software system or component. However, formal specifications are complex artifacts that need to be verified to ensure that they are consistent, complete, and validated against the requirements. Specification testing or animation tools exist to assist with this by allowing the specifier to interpret or execute the specification. However, currently little is known about how to do this effectively.This article presents a framework and tool support for the systematic testing of formal, model-based specifications. Several important generic properties that should be satisfied by model-based specifications are first identified. Following the idea of mutation analysis, we then use variants or mutants of the specification to check that these properties are satisfied. The framework also allows the specifier to test application-specific properties. All properties are tested for a range of states that are defined by the tester in the form of a testgraph, which is a directed graph that partially models the states and transitions of the specification being tested. Tool support is provided for the generation of the mutants, for automatically traversing the testgraph and executing the test cases, and for reporting any errors. The framework is demonstrated on a small specification and its application to three larger specifications is discussed. Experience indicates that the framework can be used effectively to test small to medium-sized specifications and that it can reveal a significant number of problems in these specifications.
Solving Imperfect Recall Games ( Doctoral Consortium )

Imperfect recall games remain an unexplored part of the game theory, even though recent results in abstraction algorithms show that the imperfect recall might be the key to solving the immense games found in the real world efficiently. Our research objective is to develop the first algorithm capable of outperforming the state-of-the-art solvers applied directly to perfect recall games, by creating and solving its imperfect recall abstraction. To achieve this, we need to answer a set of open questions considering the imperfect recall games. Namely (1) what properties allow the existence of Nash equilibrium in behavioral strategies in imperfect recall games and (2) what information are the players allowed to forget to guarantee that the resulting imperfect recall game can be used to solve the original game with a bounded error.