Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual Control of Replication Timing

In mammalian cells, DNA replication proceeds according to a precise temporal order during the S phase, but how this program is controlled remains poorly understood. We analyzed the replication-dependent bromodeoxyuridine banding of chromosomes in Chinese hamster cells treated with the spindle poison nocodazole. In these cells, nocodazole induces a transient mitotic arrest, followed by DNA re-replication without intervening cell division. Nuclear fragmentation is often observed in tetraploid derivatives, and previous studies suggest that replication timing of chromosomes could be affected when they are segregated into different micronuclei. Here we show that the onset of replication is frequently asynchronous on individual chromosomes during the re-replication process. Moreover, fluorescence in situ hybridization analysis revealed that replication synchrony is equally altered in fragmented and non-fragmented nuclei, indicating that asynchronous onset of replication is not dependent on physical separation of the chromosomes into isolated compartments. We also show that the ordered program of replication is always preserved along individual chromosomes. Our results demonstrate that the onset of replication of individual chromosomes in the same nuclear compartment can be uncoupled from the time of S-phase entry and from the programmed replication of chromosome sub-domains, revealing that multi-level controls contribute to establish replication timing in mammalian cells.
Posttranslational modification of differentially expressed mitochondrial proteins in the retina during early experimental autoimmune uveitis

Purpose Posttranslational modification of proteins plays an important role in cellular functions and is a key event in signal transduction pathways leading to oxidative stress and DNA damage. In this study, we used matrix-assisted laser desorption/ionization- time of flight (MALDI-TOF) to investigate the posttranslational modifications of the differentially expressed proteins in the retinal mitochondria during early experimental autoimmune uveitis (EAU). Methods EAU was induced in 18 B10RIII mice with 25 µg of inter-photoreceptor retinoid-binding protein (IRBP) emulsified with complete Freund’s adjuvant (CFA); 18 mice treated with CFA without IRBP served as controls. Retinas were removed from the experimental and control groups on day 7 post immunization; mitochondrial fractions were extracted and subjected to 2 dimentional-difference in gel electrophoresis (2D-DIGE); and the protein spots indicating differential expression were subjected to MALDI-TOF for protein identification and indication of any posttranslational modifications. Results Of the 13 proteins found to be differentially expressed by 2D-DIGE (including upregulated aconitase, mitochondrial heat shock protein (mtHsp) 70, lamin-1, syntaxin-binding protein, αA crystallin, βB2 crystallin, along with downregulated guanine nucleotide-binding protein and ATP synthase) nine were found to undergo posttranslational modification. Oxidation was a common modification found to occur on aconitase, mtHsp 70, ATP synthase, lamin-1, βB2-crystallin, guanine nucleotide-binding protein, and manganese superoxide dismutase (MnSOD). In addition, aconitase hydratase, mtHsp 70, guanine nucleotide-binding protein, ATP synthase, syntaxin-binding protein, βB2-crystallin, and lamin-1 were also modified by carbamidomethylation. αA-crystallin had a pyro-glu modification. Conclusions Several proteins present in the retinal mitochondria are posttranslationally modified during early EAU, indicating the presence of oxidative stress and mitochondrial DNA damage. The most common modifications are oxidation and carbamidomethylation. A better understanding of the proteins susceptible to posttranslational modifications in the mitochondria at the early stage of the disease may serve to advance therapeutic interventions to attenuate disease progression.
Spatio-Temporal Locality Characterization

Reducing data communication over memory is one of the main current engineering challenges. To achieve this, optimization done solely at the application level is no longer sufficient. Holistic design-space exploration is necessary to evaluate the suitability of hardware architectures for a given application. Furthermore, a software-hardware co-design is needed to be able to leverage the inherent locality of programs and reduce data motion in the system. For this to be possible, the locality has to first be properly quantified. In this work, we propose a new approach to characterizing both the spatial and the temporal locality of a program using a hardware-architecture agnostic, generalized reuse distance metric. We propose a locality characterization metric in the form of a probability distribution as well as a visualization tool that is able to express this metric in an easily understandable way. We apply our new approach to the study of several algorithms. We show that the output of our visualization tool in the form of 2D locality plots, that we refer to as locality heat-maps or simply heat-maps, is able to clearly express the program’s spatial locality, even in cases where existing metrics have proven less insightful. By quantifying both the spatial and temporal aspects of locality, the approach we propose can thus supply useful input not only to cache memory design, but also to systems based on emerging technologies such as nonvolatile memory, systems that aim at bringing computation closer to data.
Segmental anchoring of pitch movements: Autosegmental association or gestural coordination?

Arvaniti, Ladd and Mennen (1998) reported a phenomenon of ‘segmental anchoring’: the beginning and end of a linguistically significant pitch movement are anchored to specific locations in segmental structure, which means that the slope and duration of the pitch movement vary according to the segmental material with which it is associated. This finding has since been replicated and extended in several languages. One possible analysis is that autosegmental tones corresponding to the beginning and end of the pitch movement show secondary association with points in structure; however, problems with this analysis have led some authors to cast doubt on the ‘hypothesis’ of segmental anchoring. I argue here that segmental anchoring is not a hypothesis expressed in terms of autosegmental phonology, but rather an empirical phonetic finding. The difficulty of describing segmental anchoring as secondary association does not disprove the ‘hypothesis’, but shows the error of using a symbolic phonological device (secondary association) to represent gradient differences of phonetic detail that should be expressed quantitatively. I propose that treating pitch movements as gestures (in the sense of Articulatory Phonology) goes some way to resolving some of the theoretical questions raised by segmental anchoring, but suggest that pitch gestures have a variety of ‘domains’ which are in need of empirical study before we can successfully integrate segmental anchoring into our understanding of speech production.
Blunted Reward Sensitivity and Trait Disinhibition Interact to Predict Substance Use Problems

Reward-deficit models of addiction posit weaknesses in reward sensitivity to be promotive of substance dependence, whereas the externalizing spectrum model views substance problems as arising in large part from a general disinhibitory liability. In the current study we sought to integrate these perspectives by testing for separate and interactive associations of disinhibition and reward dysfunction with interview-assessed substance use disorders (SUDs). Community and college adults (N = 199) completed a scale measure of trait disinhibition and performed a gambling-feedback task yielding a neural index of reward sensitivity, the “Reward Positivity” (RewP). Disinhibition and blunted RewP independently predicted SUDs and also operated synergistically, such that participants—in particular, men—with high levels of disinhibition together with blunted RewP exhibited especially severe substance problems. Though limited by its cross-sectional design, this work provides new information about the interplay of disinhibition, reward processing, and gender in SUDs and suggests important directions for future research.
Discriminant Analysis and Its Application in DNA Sequence Motif Recognition

Identification of functional motifs in a DNA sequence is fundamentally a statistical pattern recognition problem. Discriminant analysis is widely used for solving such problems. This paper will review two basic parametric methods: LDA (linear discriminant analysis) and QDA (quadratic discriminant analysis). Their usage in recognition of splice sites and exons in the human genome will be demonstrated.
ACOUSTIC DAYLIGHT IMAGING: VISION IN THE OCEAN

Sound provides a natural means for exploring the ocean but current sonar systems, as used for example in swath-mapping applications, do not provide directly pictorial images of the ocean depths. Such systems are more akin to radar, which relies on travel-time information to map the environment. A new acoustic technique for providing real-time visual images of the interior of the ocean is currently under development, and the results from initial experiments at sea provide evidence in support of the concept. The imaging process relies on ambient noise, or “acoustic daylight”, as the source of illumination, the underlying idea being analogous to photography in the atmosphere with daylight illuminating the subject. An object in the noise field scatters the incident sound, and the scattered field is focussed with an acoustic lens to form an image on an array of transducers. After signal processing, the acoustic image is displayed as a pictorial image on a television monitor. Acoustic “colour”, characterizing the spectral reflectivity of he object, could be represented as artificially generated optical colour in the display, and a rapid refresh rate should yield moving images much like those from a conventional video camera.
Robust Recommendation Based On Association Rule Mining

The open nature of collaborative recommender systems present a security problem. Attackers that are indistinguishable from ordinary users may inject biased profiles, degrading the objectivity and accuracy of the system over time. Standard memory-based collaborative filtering algorithms, such as k-nearest neighbor, have been shown quite vulnerable to such attacks. Model-based techniques, including k-means clustering and probabilistic latent semantic analysis, have shown different degrees of improvement over k-nn with respect to robustness in the face of profile injection attacks. In this paper, we examine the robustness of a model-based recommendation algorithm based on the data mining technique of association rule mining. In particular, our preliminary results show that the Apriori algorithm offers significant improvement in stability and robustness compared to k-nearest neighbor and other model-based techniques we have studied.
"The European Neighbourhood Policy (ENP): Extending Governance beyond Borders?"

In this paper I argue that the development of the European Neighbourhood Policy (ENP) can be understood as a form of ‘externalization of EU governance’. In 2004 and 2007, the EU enlarged to encompass twelve new member states and thus acquired a new neighbourhood, notably in Eastern Europe. Russia, Ukraine, Belarus and Moldova now share a common border with the EU. Since 2001/02, the EU has been developing the ENP to cope with the challenges resulting from this new political landscape, and as such, the ENP is now the primary instrument through which EU governance is externalized. With the exception of Belarus and Russia, the European Union’s Eastern neighbours are intent on acquiring EU membership. The EU, in turn, is keen on maintaining its Eastern borders safe and secure from external risks such as illegal migration, environmental degradation and economic crisis. In order to meet these objectives, the EU promotes democratic and economic reforms in the countries located along its Eastern border and in doing so strives to foster political stability and security in the wider Europe. While hierarchy and negotiation constitute the dominant modes of governance in enlargement, this paper will demonstrate that coordination and competition – albeit in the shadow of hierarchy – are the most central modes of governance discernible within the European Neighbourhood Policy.
Blogvox 2 : A Modular Domain Independent Sentiment Analysis System

Title of Thesis: Blogvox2: A Modular Domain Independent Sentiment Analysis System. Sandeep Balijepalli, Masters of Science, 2007 Thesis directed by: Dr. Tim Finin, Professor Department of Computer Science and Electrical Engineering Bloggers make a huge impact on society by representing and influencing the people. Blogging by nature is about expressing and listening to opinion. Good sentiment detection tools, for blogs and other social media, tailored to politics can be a useful tool for today’s society. With the elections around the corner, political blogs are vital to exerting and keeping political influence over society. Currently, no sentiment analysis framework that is tailored to Political Blogs exist. Hence, a modular framework built with replicable modules for the analysis of sentiment in blogs tailored to political blogs is thus justified. I propose Blogvox2, an information retrieval based domain independent sentiment analysis framework that uses customized pattern matching techniques, such as nave bayesian filter, bag of words and part of speech tagging are used for opinion extraction in blogs. We also developed prototype two-panel and four-panel search applications of the query results. In addition, we also analyze opinionated sentences to identify trends on the hot and top topics. The modular framework of of Blogvox2 provides a platform where new modules for different domains can be easily plugged in. The framework provides the date of publishing, permanent link and the urls of the sentences that expresses opinions based on the analysis. Based on the analysis of the blogvox2 on political domain, our system performs well with unigram approach. We investigated our framework with pattern matching techniques, bigram technique, combining the unigram and bigram techiniques and incorporating parts of speech tagging, which have not fared as well as unigram techniques. We also investigated the reasons for the performance degradation or enhancements on each approach. Based on our analysis, we developed different applications to ease the use of our framework.
An Evolutionary Model of Cooperation, Fairness and Altruistic Punishment in Public Good Games

We identify and explain the mechanisms that account for the emergence of fairness preferences and altruistic punishment in voluntary contribution mechanisms by combining an evolutionary perspective together with an expected utility model. We aim at filling a gap between the literature on the theory of evolution applied to cooperation and punishment, and the empirical findings from experimental economics. The approach is motivated by previous findings on other-regarding behavior, the co-evolution of culture, genes and social norms, as well as bounded rationality. Our first result reveals the emergence of two distinct evolutionary regimes that force agents to converge either to a defection state or to a state of coordination, depending on the predominant set of self- or other-regarding preferences. Our second result indicates that subjects in laboratory experiments of public goods games with punishment coordinate and punish defectors as a result of an aversion against disadvantageous inequitable outcomes. Our third finding identifies disadvantageous inequity aversion as evolutionary dominant and stable in a heterogeneous population of agents endowed initially only with purely self-regarding preferences. We validate our model using previously obtained results from three independently conducted experiments of public goods games with punishment.
Human Blood Mononuclear Cells

IL-18 is synthesized as a precursor molecule without a signal peptide but requires the IL-1 b converting enzyme (ICE, caspase-1) for cleavage into a mature peptide. Human precursor IL-18 was expressed, purified, and cleaved by ICE into a 18-kD mature form. Mature IL-18 induced IL-8, macrophage inflammatory protein-1 a , and monocyte chemotactic protein-1 in human peripheral blood mononuclear cells in the absence of any co-stimuli. Blocking IL-1 with IL-1 receptor antagonist resulted in a 50% reduction in IL-8. Neutralization of TNF with TNF binding protein resulted in a 66% reduction in IL-1 b , an 80% reduction of IL-8, and an 88% reduction in mean TNF a mRNA. In purified CD14 1 cells but not CD3 1 /CD4 1 , IL-18 induced gene expression and synthesis of IL-8 and IL-1 b . TNF a production was induced in the non-CD14 1 population and there was no induction of TNF b by IL-18. In purified natural killer cells, IL-18 induced IL-8 that was also inhibited by TNF binding protein. IL-18 did not induce antiinflammatory cytokines, IL-1Ra, or IL-10, although IL-18 induction of TNF a was inhibited by IL-10. In the presence of IFN g , IL-18–induced TNF a was enhanced and there was an increase in the mature form of IL-1 b . We conclude that IL-18 possesses proinflammatory properties by direct stimulation of gene expression and synthesis of TNF a from CD3 1 /CD4 1 and natural killer cells with subsequent production of IL-1 b and IL-8 from the CD14 1 population. ( J. Clin. Invest. 1998. 101:711– 721.)
Repairing topological inconsistency of mesh sequences

We propose a novel approach for repairing topological inconsistency of mesh sequences with a few user interactions. The main idea of our approach is to leverage curve skeletons to detect the inconsistency of a mesh sequence. The skeleton of one mesh in the sequence is edited by user, which produces a prototype skeleton. We propagate this prototype using graph matching in‐between frames. By using temporal coherence cues, the matching procedure can be dramatically accelerated. Finally, the mesh sequence is repaired according to the inconsistencies by comparing matched skeletons and original skeletons. As demonstrated in the results, our approach avoids manually editing in all meshes, and is able to output a mesh sequence with consistent topology. Copyright © 2010 John Wiley & Sons, Ltd.
ORQA: modeling energy and quality of service within AUTOSAR models

Electric vehicles embed a low amount of energy, so their devices need to be managed efficiently to optimize the vehicle autonomy. A vehicle management is achieved by the embedded systems, modeled following the AUTOSAR standard. AUTOSAR covers most of the automotive concerns, but it lacks energy consumption and user-oriented Quality of Service models. This paper presents ORQA, a framework to model and manage the electric vehicle devices through energy consumption and user-oriented Quality of Service. At design time, the architects choose and tune the actual vehicle device models through their power requirements and, if appropriate, quality levels. The generated implementation is then embedded in the existing AUTOSAR models. Thus, at run-time, the vehicle's system is able to evaluate the global consumption of a trip and to propose the user a specific driving strategy. The optional devices are managed throughout the trip, based on the driver preferences. ORQA is illustrated with a classic use-case: a work to home trip.
Adding Once-Daily Lixisenatide for Type 2 Diabetes Inadequately Controlled by Established Basal Insulin

OBJECTIVE To examine the efficacy and safety of adding the once-daily glucagon-like peptide-1 receptor agonist (GLP-1RA) lixisenatide to established basal insulin therapy alone or together with metformin, in people with type 2 diabetes and elevated glycated hemoglobin (HbA1c). RESEARCH DESIGN AND METHODS We conducted a double-blind, parallel-group, placebo-controlled trial. Patients (n = 495) with established basal insulin therapy but inadequate glycemic control were randomized to add lixisenatide 20 μg or placebo for 24 weeks. Basal insulin dosage was unchanged except to limit hypoglycemia. HbA1c reduction from baseline was the primary end point. RESULTS Mean duration of diabetes was 12.5 years, duration of insulin use was 3.1 years, insulin dosage was 55 units/day, and baseline HbA1c was 8.4%. With lixisenatide, the placebo-corrected change of HbA1c from baseline was –0.4% (95% CI –0.6 to –0.2; P = 0.0002), and mean HbA1c at end point was 7.8%. HbA1c <7.0% (53 mmol/mol) was attained by more lixisenatide (28%) than placebo (12%; P < 0.0001) participants. Lixisenatide reduced plasma glucose levels after a standardized breakfast (placebo-corrected reduction, –3.8 mmol/L; P < 0.0001); seven-point glucose profiles showed a reduction persisting through the day. Reductions in body weight (placebo corrected, –1.3 kg; P < 0.0001) and insulin dosage (–3.7 units/day; P = 0.012) were greater with lixisenatide. Main adverse events (AEs) with lixisenatide were gastrointestinal. Symptomatic hypoglycemia was 28% for lixisenatide and 22% for placebo; 4 of 328 subjects (1.2%) had severe hypoglycemia with lixisenatide vs. 0 of 167 with placebo. CONCLUSIONS By improving HbA1c and postprandial hyperglycemia without weight gain in type 2 diabetes with inadequate glycemic control despite stable basal insulin, lixisenatide may provide an alternative to rapid-acting insulin or other treatment options.
A credit-token-based spectrum etiquette framework for coexistence of heterogeneous cognitive radio networks

The coexistence of cognitive radio (CR) networks in the same swath of spectrum has become an increasingly important problem, which is especially challenging when coexisting networks are heterogeneous (i.e., use different air interface standards), such as the case in TV white spaces. In this paper, we propose a credit-token-based spectrum etiquette framework that enables spectrum sharing among distributed heterogeneous CR networks with equal priority. Specifically, we propose a game-auction coexistence framework. Each network acts as either an offerer or a requester, and coexists with other networks via a non-cooperative game and a truthful multi-winner auction. The framework addresses the trade-offs among social welfare and offerer's revenue in the auction and requester's utility in the game. We prove that the framework guarantees system stability. Our simulation results show that the proposed coexistence framework always converges to a near-optimal distributed solution and improves coexistence fairness and spectrum utilization.
When Pain Brings Gain: Soccer Players Behavior and Admissions Suggest Feigning Injury to Maintain a Favorable Scoreline

The rules of soccer dictate that play, once halted, cannot continue if a player is injured. Players may take advantage of this rule by feigning injury to preserve beneficial match positions. Thirty Euro 2008 matches, 90 Premier League matches and 63 World Cup 2010 matches were reviewed for the timing and severity of injuries. The number of injuries was compared between teams that benefited from stopping the game and those that did not benefit. The number of low-level injuries, not resulting in substitution or subsequent problems, was directly compared for Benefit and Non-Benefit teams for each 15-min period following kick off. Statistical significance was assessed using appropriate non-parametric tests. In addition, seven current players and three managers were interviewed and were asked about feigning injury. Teams that benefited from game stoppages suffered significantly more minor injuries in the last 15 min of matches compared with those that did not benefit. Four of the players directly admitted feigning injury. When it is beneficial, soccer players can and do successfully feign injury to stop the game. Consequently it is possible that others might also successfully feign injury, pain or disease when motivated to do so.