Miracle-dz/UniFAR-FTUs huggingface dataset:
Packed Dense Interest Points for Scene Image Retrieval

In this paper we propose a novel method to retrieval scene images, where packed dense interest points are extracted as visual signature and asymmetric piece-to-image matching scheme is adopted for similarity matching. Compared to general images, scene image contains large area of low contrast regions, such as sky, calm water, or flat road surface, which make it difficult for popular method to extract appropriate representation with both good coverage of the entire image and insures relatively high repeatability. To obtain appropriate representation of a scene image as its visual signature, our method extracts packed dense interest points, i.e. using dense interest points as point features then packing these features in groups according to their spatial relations. After that a piece-to-image matching scheme based on packed Dense Interest Points is applied to fulfill retrieval work. Our retrieval method enhances interpretation ability of signature for scene image and performs matching taking geometric constrains into account. We evaluate our approach on MIT 8 scene categories, and demonstrate clear improvements in retrieval over conventional purely appearance-based baselines.
Complex event extraction at PubMed scale

Motivation: There has recently been a notable shift in biomedical information extraction (IE) from relation models toward the more expressive event model, facilitated by the maturation of basic tools for biomedical text analysis and the availability of manually annotated resources. The event model allows detailed representation of complex natural language statements and can support a number of advanced text mining applications ranging from semantic search to pathway extraction. A recent collaborative evaluation demonstrated the potential of event extraction systems, yet there have so far been no studies of the generalization ability of the systems nor the feasibility of large-scale extraction. Results: This study considers event-based IE at PubMed scale. We introduce a system combining publicly available, state-of-the-art methods for domain parsing, named entity recognition and event extraction, and test the system on a representative 1% sample of all PubMed citations. We present the first evaluation of the generalization performance of event extraction systems to this scale and show that despite its computational complexity, event extraction from the entire PubMed is feasible. We further illustrate the value of the extraction approach through a number of analyses of the extracted information. Availability: The event detection system and extracted data are open source licensed and available at http://bionlp.utu.fi/. Contact: jari.bjorne@utu.fi
Adaptive multi-objective genetic algorithm using multi-pareto-ranking

This paper extends an elitist multi-objective evolutionary algorithm, named GAME, based on several Pareto fronts corresponding to various fitness definitions. An additional operator is defined to create an adaptive version of this algorithm, called aGAME. This new operator alternates different modes of exploration of the search space all through an aGAME execution. Mode switching is controlled according to the values of two performance indicators, in order to maintain a good compromise between the quality and diversity of the returned solutions. aGAME is compared with the previous version (GAME) and with the three best-ranking algorithms of the CEC 2009 competition, using seven bi-objective benchmarks and the rules of this competition. This experimental comparison shows that aGAME outperforms these four algorithms, which validates both the efficiency of the proposed dynamic adaptive operator and the algorithm performance.
The submodular secretary problem under a cardinality constraint and with limited resources

We study the submodular secretary problem subject to a cardinality constraint, in long-running scenarios, or under resource constraints. In these scenarios the resources consumed by the algorithm should not grow with the input size, and the online selection algorithm should be an anytime algorithm. We propose a $0.1933$-competitive anytime algorithm, which performs only a single evaluation of the marginal contribution for each observed item, and requires a memory of order only $k$ (up to logarithmic factors), where $k$ is the cardinality constraint. The best competitive ratio for this problem known so far under these constraints is $\frac{e-1}{e^2+e} \approx 0.1700$ (Feldman et al., 2011). Our algorithm is based on the observation that information collected during times in which no good items were selected, can be used to improve the subsequent probability of selection success. The improvement is obtained by using an adaptive selection strategy, which is a solution to a stand-alone online selection problem. We develop general tools for analyzing this algorithmic framework, which we believe will be useful also for other online selection problems.
Automated Verification of Web Sites Using Partial Rewriting

In this paper, we develop a framework for the automated verification of Web sites which can be used to specify integrity conditions for a given Web site, and then automatically check whether these conditions are fulfilled. First, we provide a rewriting-based, formal specification language which allows us to define syntactic as well as semantic properties of the Web site. Then, we formalize a verification technique which detects both incorrect/forbidden patterns as well as lack of information, that is, incomplete/missing Web pages, inside the Web site. Useful information is gathered during the verification process which can be used to repair the Web site. Our methodology is based on a novel rewriting-based technique, called partial rewriting, in which the traditional pattern matching mechanism is replaced by tree simulation, a suitable technique for recognizing patterns inside semistructured documents. The framework has been implemented in the preliminary prototype Verdi, which is publicly available.
Intracellular localization and dynamics of myosin-II and myosin-IC in live Acanthamoeba by transient transfection of EGFP fusion proteins

We developed a reliable method for transient transfection of Acanthamoeba using Superfect (Qiagen) and a vector with the Acanthamoeba ubiquitin promoter and enhanced green fluorescent protein (EGFP) as the reporter gene. The transfection efficiency was 3% for profilin-I-EGFP and EGFP-myosin-II tail, and less than 0.5% for larger constructs such as full length myosin-II or myosin-IC. Profilin-I-EGFP was distributed throughout the cytoplasm as observed previously with rhodamine-labeled profilin, while EGFP alone accumulated in the nucleus. EGFP fused to full length myosin-II or to the C-terminal 256 residues of the myosin-II tail concentrated in fluorescent spots similar to thick filaments and minifilaments identified previously in fixed cells with fluorescent antibodies. Thick filaments were located in the dorsal cytoplasm and along the lateral margins of the back half of the cell. Thick filaments formed behind the leading edge and moved continuously towards the rear of the cell, where they disassembled. If phosphorylation of the myosin-II heavy chain was prevented by mutation of all three phosphorylated serines to alanine, thick filaments of unphosphorylated myosin-II accumulated around vesicles of various sizes. EGFP-myosin-IC was spread throughout the cytoplasm but concentrated transiently around contractile vacuoles and macropinocytosis cups providing that the construct included both the head and a tail with the SH3 domain.
Perceived health status and morbidity and mortality: evidence from the Kuopio ischaemic heart disease risk factor study.

BACKGROUND Previous studies have reported an increased risk of death in those who report their health is poor, however, the role of underlying and subclinical disease in this association has not been carefully studied. METHODS The associations between perceived health status and mortality from all causes and cardiovascular disease, incidence of myocardial infarction, carotid atherosclerosis, forced expiratory volume, and maximal exercise capacity were studied in the Kuopio Ischaemic Heart Disease Risk Factor Study, a population-based study of 2682 men, aged 42-60, in eastern Finland. RESULTS There were strong, statistically significant, age-adjusted associations between level of perceived health and mortality from all causes (RH(bad versus good) = 3.67), cardiovascular causes (RH(bad versus good) = 6.64), and incidence of myocardial infarction (RH(bad versus good) = 3.87). Perceived health levels were strongly associated with risk factors and disease indicators. The associations with mortality and myocardial infarction outcomes were considerably weakened with progressive adjustment for eight risk factors and prevalent disease. Higher levels of perceived health were associated with less carotid atherosclerosis, and greater forced expiratory volume and maximal exercise capacity. Associations between level of perceived health and these indicators were considerably stronger in those with prevalent diseases than in those who were healthy. CONCLUSIONS The overall pattern of results suggests that perceived health levels mainly reflect underlying disease burden.
The clinical gaze – ascribed gender(ed) identities in a mental health service context

ABSTRACTThis article focuses on gender(ed) ascribed identities of service users in a mental health service context in Sweden. The empirical data were collected through observations of weekly team conferences. The examples can be described as ‘frozen images’ or ideal types in the sense that they illustrate the different ways service providers describe the service users’ problems at a certain time in a certain context. This article illustrates that the ‘the gaze’ of the service providers was value-laden, making moral judgements tied to the notion of responsibility. However, the same kind of behaviour or diagnoses can be accounted for in different ways and hence lead to different outcomes for the service user, which illustrates ‘severe mental illness’ as a stretchable phenomenon. The team discussions also mirror the service users’ strategies to handle professional and institutional power, that is, challenge the power position of professionals, with regard to the construction of service users as passive recip.
Hidden Markov Models with Applications to DNA Sequence Analysis

The Hidden Markov Model (HMM) is a model with a finite number of states, each associated with a probability distribution. The transitions between states cannot be directly measured (hidden), but in a particular state an observation can be generated. It is the observations and not the states themselves which are visible to an outside observer. However, by applying a series of statistical techniques it is possible to gain insight into the hidden states via the observations they generate. In the case of DNA analysis, we observe a strand of DNA which we believe can be segmented into homogeneous regions to identify the specific functions of the DNA strand. Through the use of HMMs we can determine which parts of the strand belong to which segments by matching segments to hidden states. HMMs have been applied to a wide range of applications including speech recognition, signal processing and econometrics to name a few. Here we will discuss the theory behind HMMs and the applications that they have in DNA sequence analysis. We shall be specifically interested in discussing “how can we determine from which state our observations are being generated? ”, “how do we determine the parameters of our model? ” and “how do we determine the sequence of hidden states given our observations? ” While there are many applications of HMMs we shall only be concerned with their use in terms of DNA sequence analysis and shall cover examples in this literature where HMMs have been successfully used. In this area we shall compare approaches to using HMMs for DNA segmentation. Firstly, the approach taken when the number of hidden states is known and secondly, how it is possible to segment a DNA sequence when the number of hidden states is unknown?
Using SPIN to model check concurrent algorithms, using a translation from C to Promela

This paper addresses the problem of automatically verifying correctness of concurrent algorithms, e.g., as found inconcurrent implementations of common data structures, using model checking. In order to use a model checker to analyze programs in, e.g., C, one must first translate programs to the input language of the model checker. Since our aim is to use SPIN, we present an automated translation from a subset of C to Promela. This translation is able to handle features not covered by previous such translations, notable pointer structures and function calls. We illustrate the application of our translation to a concurrent queue algorithm by Michael and Scott.
A Novel Vehicular Information Network Architecture Based on Named Data Networking (NDN)

Vehicular information network and Internet of Things (IoT) technologies have been receiving a lot of attention in recent years. As one of the most important and promising IoT areas, a vehicular information network aims to implement a myriad of applications related to vehicles, traffic information, drivers, passengers, and pedestrians. However, intervehicular communication (IVC) in a vehicular information network is still based on the TCP/IP protocol stack which is not efficient and scalable. To address the efficiency and scalability issues of the IVC, we leverage the named data networking (NDN) paradigm where the end user only cares about the needed content and pays no attention to the actual location of the content. The NDN model is highly suitable for the IVC scenario with its hierarchical content naming scheme and flexible content retrieval and caching support. We design a novel vehicular information network architecture based on the basic communication principle of NDN. Our proposed architecture aims to improve content naming, addressing, data aggregation, and mobility for IVC in the vehicular information network. In addition, the key parameter settings of the proposed schemes are analyzed in order to help guide their actual deployment.
The COP9 signalosome is vital for timely repair of DNA double-strand breaks

The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ring ubiquitin ligase (CRL) complexes by removing the ubiquitin-like protein, NEDD8, from their cullin scaffold. We find that the CSN is physically recruited to DSB sites in a neddylation-dependent manner, and is required for timely repair of DSBs, affecting the balance between the two major DSB repair pathways—nonhomologous end-joining and homologous recombination repair (HRR). The CSN is essential for the processivity of deep end-resection—the initial step in HRR. Cullin 4a (CUL4A) is recruited to DSB sites in a CSN- and neddylation-dependent manner, suggesting that CSN partners with CRL4 in this pathway. Furthermore, we found that ATM-mediated phosphorylation of CSN subunit 3 on S410 is critical for proper DSB repair, and that loss of this phosphorylation site alone is sufficient to cause a DDR deficiency phenotype in the mouse. This novel branch of the DSB response thus significantly affects genome stability.
A Cross-Layer Reliability Design Methodology for Efficient, Dependable Wireless Receivers

Continued progressive downscaling of CMOS technologies threatens the reliability of chips for future embedded systems. We developed a novel design methodology for dependable wireless communication systems which exploits the mutual trade-offs of system performance, hardware reliability, and implementation complexity. Our cross-layer approach combines resilience techniques on hardware level with algorithmic techniques exploiting the available flexibility in the receiver. The overhead is minimized by recovering only from those hardware errors that have a strong impact on the system behavior. We apply our new methodology on a double-iterative MIMO-BICM receiver which belongs to the most complex systems in current communication standards.
Social Learning in Continuous Time: When are Informational Cascades More Likely to Be Inefficient?

In an observational learning environment rational agents may mimic the actions of the predecessors even when their own signal suggests the opposite. In case early movers’ signals happen to be incorrect society may settle on a common inefficient action, resulting in an inefficient informational cascade. This paper models observational learning in continuous time with endogenous timing of moves. This permits the analysis of comparative statics results. The effect of an increase in signal quality on the likelihood of an inefficient cascade is shown to be nonmonotonic. If agents do not have strong priors, an increase in signal quality may lead to a higher probability of inefficient herding. The analysis also suggests that markets with quick response to investment decisions, such as financial markets, may be more prone to inefficient collapses.
Efficacy of a needling device for the treatment of acne scars: a randomized clinical trial.

IMPORTANCE Neocollagenesis can be achieved using a dermal rolling needle device, thereby reducing the appearance of acne scars. OBJECTIVE To determine the efficacy of a needling device for treatment of acne scars. DESIGN, SETTING, AND PARTICIPANTS We performed a single-center, rater-blinded, balanced (1:1), split-face, placebo-controlled, parallel-group randomized clinical trial at an urban academic institution. The study took place from November 30, 2009, through July 27, 2010. Twenty healthy adults (age range, 20-65 years) with acne scars on both sides of the face were enrolled. Fifteen individuals completed the study, and no enrolled participants were withdrawn for adverse effects. INTERVENTIONS For each participant, one side of the face was randomized for needling. Three needling treatments were performed at 2-week intervals. MAIN OUTCOMES AND MEASURES Two blinded dermatologists separately rated participants' acne scars based on standard digital photographs obtained at baseline and at the 3-month and 6-month follow-up visits on the quantitative global scarring grading system. RESULTS Mean scar scores were significantly lower in the treatment group compared with baseline at 6 months (mean difference, 3.4; 95% CI, 0.2-6.5; P = .03) and nominally but not significantly lower compared with baseline at 3 months (mean difference, 2.4; 95% CI, -0.01 to 4.8; P = .052). In the control group, mean scar scores did not vary significantly from baseline at 3 months (mean difference, 1.0; 95% CI, -1.4 to 3.4; P = .96) and at 6 months (mean difference, 0.4; 95% CI, -2.3 to 3.5; P > .99). The needling procedure was not particularly painful, with a mean pain rating of 1.08 of 10. Participants perceived a 41% mean improvement in overall scar appearance on the treated side. No adverse events were reported. CONCLUSIONS AND RELEVANCE After 3 needling treatments, there was improvement in the appearance of acne scars over time compared with the control group, with minimal pain reported. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00974870.
Replication Protein A Links Cell Cycle Progression and the Onset of Neurogenesis in Drosophila Optic Lobe Development

Stem cell self-renewal and differentiation must be carefully controlled during development and tissue homeostasis. In the Drosophila optic lobe, neuroepithelial cells first divide symmetrically to expand the stem cell population and then transform into asymmetrically dividing neuroblasts, which generate medulla neurons. The mechanisms underlying this cell fate transition are not well understood. Here, we show a crucial role of some cell cycle regulators in this transition. We find that loss of function in replication protein A (RPA), which consists of three highly conserved protein subunits and functions in DNA replication, leads to disintegration of the optic lobe neuroepithelium and premature differentiation of neuroepithelial cells into medulla neuroblasts. Clonal analyses of RPA loss-of-function alleles indicate that RPA is required to prevent neuroepithelial cells from differentiating into medulla neuroblasts. Inactivation of the core cell cycle regulators, including the G1/S regulators E2F1, Cyclin E, Cdk2, and PCNA, and the G2/M regulators Cyclin A, Cyclin B, and Cdk1, mimic RPA loss-of-function phenotypes, suggesting that cell cycle progression is required for both maintaining neuroepithelial cell identity and suppressing neuroblast formation. We further find that RPA or E2F1 inactivation in the neuroepithelial cells correlates with downregulation of Notch signaling activity, which appears to result from Numb mislocalization. Thus, we have shown that the transition from neuroepithelial cells to neuroblasts is directly regulated by cell cycle regulators and propose a model in which the inhibition of neuroepithelial cell cycle progression downregulates Notch signaling activity through Numb, which leads to the onset of neurogenesis.
ADIPOSE SENSORY NERVES: FUNCTIONAL AND NEUROANATOMICAL EVIDENCE FOR THEIR EMERGING ROLE IN ENERGY BALANCE

White adipose tissue (WAT) lipolysis is initiated via direct sympathetic nervous system (SNS) innervation and activation. SNS control to WAT is vital to maintaining homeostasis in response to metabolic challenges such as food deprivation and cold exposure. Using transneuronal viral tract tracers, we have identified sensory nerves from WAT that project to brainstem and forebrain areas critical to metabolic function. In addition, these sensory circuits from fat communicate with SNS outflow neurons that project back to fat—forming neural feedback loops throughout the CNS—providing neuroanatomical evidence for sensory WAT-SNS crosstalk. It is unclear, however, what role these WAT-specific sensory nerves serve to inform the CNS of acute and dynamic metabolic challenges to which it can then respond. Here we tested mechanisms of activation of WAT sensory nerves and present a working model to deepen our understanding of why these neural circuits act as conduits for acute metabolic feedback signals from WAT. Neurochemical, neuroanatomical, and neurophysiological evidence supports the presence of: 1) WAT lipolytic sensors from a neural population known to be capable of controlling SNS outflow; and 2) functional neural links among fat depots mediated via the peripheral and central nervous systems. INDEX WORDS: SS-SNS crosstalk, adipose afferent reflex, free fatty acids ADIPOSE SENSORY NERVES: FUNCTIONAL AND NEUROANATOMICAL EVIDENCE FOR THEIR EMERGING ROLE IN ENERGY BALANCE
Semi-Automated Reconstruction of Curvilinear Structures in Noisy 2D images and 3D image stacks

We propose a new approach to semi-automated delineation of curvilinear structures in a wide range of imaging modalities. Earlier approaches lack robustness to imaging noise, do not provide radius estimates for the structures and operate only on single channel images. In contrast, ours makes use of the color information, when available, and generates accurate centreline location and radius estimates with minimal supervision. We demonstrate this on a wide range of datasets ranging from a 2D dataset of aerial images to 3D micrographs of neurites.