Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Imaging of Cell Death in Tumors. Increasing Annexin A5 Size Reduces Contribution of Phosphatidylserine-Targeting Function to Tumor Uptake

Objective Annexin A5 is a phosphatidylserine binding protein that binds dying cells in vivo. Annexin A5 is a potential molecular imaging agent to determine efficacy of anti-cancer therapy in patients. Its rapid clearance from circulation limits tumor uptake and, hence, its sensitivity. The aim of this study is to determine if non-invasive imaging of cell death in tumors will benefit from increasing circulation time of annexin A5 by increasing its size. Procedures Annexin A5 size was increased by complexation of biotinylated annexin A5 with Alexa-Fluor680-labeled streptavidin. The non-binding variant of annexin A5, M1234, was used as negative control. The HT29 colon carcinoma xenograft model in NMRI nude mice was used to measure tumor uptake in vivo. Tumor uptake of fluorescent annexin A5-variants was measured using non-invasive optical imaging. Results The annexin A5-streptavidin complex (4∶1, moles:moles, Mw ∼200 kDa) binds phosphatidylserine-expressing membranes with a Hill-coefficient of 5.7±0.5 for Ca2+-binding and an EC50 of 0.9±0.1 mM Ca2+ (EC50 is the Ca2+ concentration required for half maximal binding)(annexin A5: Hill-coefficient 3.9±0.2, EC50 1.5±0.2 mM Ca2+). Circulation half-life of annexin A5-streptavidin is ±21 minutes (circulation half-life of annexin A5 is ±4 min.). Tumor uptake of annexin A5-streptavidin was higher and persisted longer than annexin A5-uptake but depended less on phosphatidylserine binding. Conclusion Increasing annexin A5 size prolongs circulation times and increases tumor uptake, but decreases contribution of PS-targeting to tumor uptake and abolishes power to report efficacy of therapy.
A Second Glitch from the “Anomalous” X-Ray Pulsar 1RXS J170849.0–4000910

We report on 5.4 yr of phase-coherent timing, using the Rossi X-Ray Timing Explorer, of the X-ray pulsar 1RXS J170849.0-4000910 (1RXS J1708-4009), a member of the class known as "anomalous X-ray pulsars. " This object exhibited a rotational glitch in 1999. Here we report a second, much larger rotational glitch that occurred ~1.5 yr after the first. We show that the recoveries from the two glitches are significantly different, with the first showing only a possible slow, approximately linear recovery, while the second showed a nearly complete recovery on a timescale of ~50 days. The approximately exponential recovery timescale of the second glitch is similar to that seen recently in 1E 2259+586 at the time of a major outburst. This suggests that 1RXS J1708-4009 undergoes similar bursting behavior, although with our sparse observations we have detected no other evidence of bursts from this source.
Rate Regions for Multiple Access Channel With Conference and Secrecy Constraints

This paper studies the impact of partial encoder cooperation on the secrecy of the multiple access channel (MAC) with an external eavesdropper. In particular, two encoders, connected by two communication links with finite capacities, wish to send secret messages to the common intended decoder in the presence of a passive eavesdropper. The inner and outer bounds on the secrecy capacity are derived for the discrete memoryless channel. The derived inner bound rate region is achievable by combining Willems's coding for the MAC with partially cooperating encoders and Wyner's random binning for the wiretap channel. Then, both the inner and outer bounds are extended to the Gaussian case and the corresponding rate regions are established. Several simple achievable transmission schemes are proposed for the Gaussian channel and the numerical results show that the partial encoder cooperation can increase the achievable rate regions.
J.A.Gray's Reinforcement Sensitivity Theory (RST) of Personality

Jeffrey Gray's (1976, 1982) behavioural inhibition system (BIS) theory of anxiety has stood well the test of time. This theory of personality – which is now widely known as reinforcement sensitivity theory (RST) – has gradually evolved over the past 30 years, seeing its major revision in 2000 by Gray and McNaughton, and even further elaborations and refinements subsequently (McNaughton and Corr, 2004, 2008; Corr and McNaughton, 2008). However, recent data that have strengthened the general foundations of the neural basis of the theory have also forced significant modifications of, and additions to, its superstructure. These changes are not inconsequential; as such, predictions cannot now be based on prior knowledge of the 1982 version. These changes, we contend, have the potential to lead to confusion. A major purpose of this chapter is to review the current scientific status of Gray's RST and draw out some of its major implications for future research. RST is built upon a state description of neural systems and associated, relatively short-term, emotions and behaviours, which, according to the theory, give rise to longer-term trait dispositions of emotion and behaviour. This theory argues that statistically defined personality factors are sources of variation that are stable over time and that derive from underlying properties of an individual; it is these, and current changes in the environment, that comprise the neuropsy-chological foundations of 'personality'. This assertion is demanded by the fact that personality traits account for behavioural differences between individuals presented with identical environments; also, behavioural differences show consistency across time. Thus, the ultimate goal of personality research is to identify the relatively static (underlying) biological variables that determine the (superficial) factor structure measured in behaviour. It would, of course, be a mistake to deny the relevance of the environment in controlling behaviour, but to produce consistent long-term effects, environmental influences must be mediated by, and instantiated in, biological systems.
A two-sided relaxation scheme for Mathematical Programs with Equilibrium Constraints

We propose a relaxation scheme for mathematical programs with equilibrium constraints (MPECs). In contrast to previous approaches, our relaxation is two-sided: both the complementarity and the nonnegativity constraints are relaxed. The proposed relaxation update rule guarantees (under certain conditions) that the sequence of relaxed subproblems will maintain a strictly feasible interior---even in the limit. We show how the relaxation scheme can be used in combination with a standard interior-point method to achieve superlinear convergence. Numerical results on the MacMPEC test problem set demonstrate the fast local convergence properties of the approach.
Styrket feedback gennem studerendes selvevaluering

Studerende er ofte utilfredse med såvel kvaliteten som kvantiteten af feedback på skriftligt arbejde. Ligeledes kan det som underviser være svært at afgive feedback, der tager udgangspunkt i de studerendes respektive læringssituationer, hvis man ikke har andet afsæt end opgavetekster. Denne artikel beskriver derfor to eksperimenter med brug af selvevaluering som kvalificerende mellemled i ekstern feedback på skriveøvelser. Eksperimenternes formål er at styrke den formative læring ved skriftligt arbejde. I det første eksperiment bestod feedbacken af underviser-feedback, mens det andet eksperiment indebar peer-feedback og fælles feedback. I begge tilfælde blev selvevalueringen foretaget med udgangspunkt i en kriteriebaseret retteguide. Eksperimenterne medførte, at den eksterne feedback blev målrettet og kvalificeret i forhold til den enkelte studerende, mens selve skriveprocessen mod forventning kun blev påvirket i mindre grad. Endelig blev den formative læring bedst styrket hos de studerende, der i forvejen var engageret i egen læring. En medvirkende årsag hertil var, at nogle studerende oplevede retteguiden som irrelevant eller svært tilgængelig. Students are often dissatisfied with both the quality and quantity of the feedback they receive on their written work. Furthermore, teachers may find it difficult to provide feedback relevant to the learning situation of individual students solely on the basis of written papers. Consequently, this article describes two experiments with students' self-assessments as a qualifying mediator for external feedback. The purpose of the experiments is to improve the formative learning from written papers. The first experiment used self-assessment to mediate individual feedback from the lecturer whereas the second experiment made use of peer-feedback in groups followed by general feedback from the lecturer. In both cases self-assessment was conducted using a criteria based scoring guide. The experiments revealed that self-assessment strengthens external feedback through shared and explicit criteria while also making it specific to individual students. However, contrary to expectations, self-assessment influenced the writing process itself to a lesser extent. Finally, formative learning through self-assessment was most evident with students already actively engaged with their own learning, while some of the other students perceived the scoring guide as irrelevant and inaccessible.
Oncosuppressive functions of decorin

The extracellular matrix is rapidly emerging as a prominent contributor to various fundamental processes of tumorigenesis. In particular, decorin, a member of the small leucine-rich proteoglycan gene family, is assuming a central role as a potent soluble tumor repressor. Decorin binds and antagonizes various receptor tyrosine kinases and inhibits downstream oncogenic signaling in several solid tumors. Among other functions, decorin evokes cell cycle arrest, apoptosis, and antimetastatic, and antiangiogenic programs. Recent work has revealed a paradigmatic shift in our understanding of the molecular mechanisms underlying its tumoricidal properties. Decorin adversely compromises the genetic signature of the tumor microenvironment and induces endothelial cell autophagy downstream of VEGFR2. Moreover, decorin selectively evokes destruction of tumor cell mitochondria downstream of Met through mitophagy. Acting as a partial agonist, decorin signals via proautophagic receptors and triggers procatabolic processes that parallel the classical tumoricidal properties of this multifaceted proteoglycan.
Healthy 50-Year-Old Men LDL Particle Size Distribution Is Associated With Carotid Intima-Media Thickness in

Results of cross-sectional and prospective studies have suggested that small, dense low-density lipoprotein (LDL) particles predispose to coronary heart disease. We investigated the relationships between plasma concentrations of LDL subfractions and intima-media thickness (IMT) of the common carotid artery (CCA), quantified by B-mode ultrasound, in 94 healthy, 50-year-old men, all of whom were homozygous for the apolipoprotein E3 allele. A novel 3% to 7.5% polyacrylamide gradient gel was developed to provide separation of LDL subfractions with high resolution, as was a procedure to quantify plasma concentrations of these LDL subspecies. The LDL particle size distribution pattern obtained by the gradient gel electrophoresis procedure was in good agreement with the one obtained by a well-established, single-spin density gradient ultracentrifugation technique. LDL-II (particle size, 23.5 to 25.0 nm) was the most abundant subfraction, and its plasma concentration correlated closely with the total LDL cholesterol concentration (r50.61, P,0.001) but not with CCA IMT ( r520.13, NS). In contrast, the plasma concentration of the predominant small, dense LDL particle subfraction (LDL-III; particle size, 22.5 to 23.5 nm) correlated strongly with CCA IMT (r50.42,P,0.001). In multivariate analysis, the plasma concentration of the LDL-III subfraction contributed significantly to the variation in CCA IMT (R50.19). When plasma triglycerides and LDL cholesterol were forced into the multivariate model, 10% of the variation in CCA IMT was still accounted for by the LDL-III subfraction. In summary, use of a novel and sensitive gradient gel electrophoresis method for evaluation of LDL heterogeneity provided the basis for demonstrating an independent relation between the plasma concentration of small LDL and IMT of the CCA in healthy, middle-aged men. (Arterioscler Thromb Vasc Biol . 1999;19:2422-2430.)
The Non-Essential Mycolic Acid Biosynthesis Genes hadA and hadC Contribute to the Physiology and Fitness of Mycobacterium smegmatis

Gram positive mycobacteria with a high GC content, such as the etiological agent of tuberculosis Mycobacterium tuberculosis, possess an outer membrane mainly composed of mycolic acids (MAs), the so-called mycomembrane, which is essential for the cell. About thirty genes are involved in the biosynthesis of MAs, which include the hadA, hadB and hadC genes that encode the dehydratases Fatty Acid Synthase type II (FAS-II) known to function as the heterodimers HadA-HadB and HadB-HadC. The present study shows that M. smegmatis cells remain viable in the absence of either HadA and HadC or both. Inactivation of HadC has a dramatic effect on the physiology and fitness of the mutant strains whereas that of HadA exacerbates the phenotype of a hadC deletion. The hadC mutants exhibit a novel MA profile, display a distinct colony morphology, are less aggregated, are impaired for sliding motility and biofilm development and are more resistant to detergent. Conversely, the hadC mutants are significantly more susceptible to low- and high-temperature and to selective toxic compounds, including several current anti-tubercular drugs.
Does Performance Budgeting Work?: An Analytical Review of the Empirical Literature

This paper attempts to ascertain what light the empirical literature sheds on the efficacy of performance budgeting. Performance budgeting refers to procedures or mechanisms intended to strengthen links between the funds provided to public sector entities and their outcomes and/or outputs through the use of formal performance information in resource allocation decision making. The paper seeks to identify and examine the literature on 'government-wide' performance budgeting systems - that is, systems used by central budget decision makers (ministry of finance and political executive) to link the funding they provide to those agencies' performance. Performance budgeting principles are, however, applied not only on a government wide basis, but also in funding systems applied to specific categories of government services. This paper does not attempt to review the empirical literature on all such 'sectoral' performance budgeting systems. Rather, it undertakes a case study of the literature on one specific sectoral system - output-based hospital funding systems.
What Does the Future Hold for Restricted Patterns ?

As one can see, without several examples worked out with a pencil and paper, this formal definition is not very insightful. To understand where restricted patterns really originated from, we draw on visual imagery and replace “one-dimensional” permutations by “twodimensional” objects, matrices. In doing so, we shall violate the customary labeling of the top row as the “first” row of a matrix. Instead, we shall coordinatize our matrices from the bottom left corner, just like in a Cartesian coordinate system; thus, the origin will always be placed at the bottom left corner of the matrix (cf. Fig. 1) so that our first row will be the bottom row, and our first column will be (as usual) the leftmost column of a matrix. This is done in order to keep the resemblance with the “shape” of permutations, in other words, with their graphs as functions π : [n] → [n].
Privacy-Preserving Queries over Outsourced Data with Access Pattern Protection

One of the concerns about database outsourcing is that the service provider may not be trustworthy. Besides protecting data against outsiders, it is necessary to hide sensitive information from the service provider. For single-server environments, data encryption is commonly used to protect data confidentiality. To use server computational resources for processing queries, data are encrypted in tuple-level. Indexing tags are computed and attached to the encrypted tuples such that the server can check if an encrypted tuple satisfies the query predicate without learning exact data values. However, with additional information of some time-based events, service providers can still infer information of the encrypted data through query access patterns if there are observed linkages between the access patterns and the time-based events. In this paper, we study the problem of information disclosure in such a scenario. We first illustrate how to launch the inference attack. Then, we formally define the problem and propose techniques for protecting access privacy. Instead of providing total privacy with a high overhead, our approach aims to lower the confidence of service providers' inferences. Experiment results show that a high level of access privacy can be achieved with a reasonable overhead.
Cluster Based Under-Sampling for Unbalanced Cardiovascular Data

Most medical datasets are not balanced in their class labels. Indeed in some cases it has been no ticed that the given class labels do not accurately represent characteristics of the data record. Most existing classification methods tend not to perform well on minority class examples when the dataset is extremely imbalanced. This is because they aim to optimize the overall accuracy without considering the relative distribution of each class. In this paper we propose a cluster based under sampling technique that solves the class imbalance problem for our cardiovascular data. It shows significant better performance than existing methods.
Expertise Evaluation using PathFinder Networks Scaling in Ranking of Satellite Images

In this article we propose a methodology to evaluate the level of expertise of image analysts when searching domain-specific images by semantics. We apply our methodology to ranking high-resolution satellite images by semantics. Our methodology applies PathFinder Network Scaling methods to create concept maps for representing associations of semantics to regions of a feature space for each image analyst. The relevance of each node in a concept map is evaluated using a hits authority algorithm. The expertise of each image analyst is then evaluated by comparing to ground truth models using the Kendall tau rank correlation coefficient. Our system allows us to identify areas of expert disagreement by evaluating the relative difference individual models place on features as well as recommend areas of that needs to be stressed by novice image analysts.
PopCover: a method for selecting of peptides with optimal population and pathogen coverage

A major challenge when selecting T cell epitopes for diagnostic or preventive purposes stems from the vast genomic variation of pathogens and the diversity of the host cellular immune system. Here, we describe a rational epitope selection strategy, called PopCover that aims at dealing with both of these challenges. The method integrates pan-specific MHC binding predictions with information about MHC allelic prevalence in a given population, and select pools of peptides that in concert will provide broad coverage of both pathogen genomic and the HLA diversity. The method was benchmarked against HIV as a case story. A small set of Gag, Nef, Tat and Pol peptides were selected from a large set of full sequenced HIV genomes covering the 5 major subtypes to provide optimal class II epitope coverage of a population with Caucasian HLA prevalence. Using the PopCover method these peptide pools were, in a simulation experiment, demonstrated to provide potential epitope coverage of between 52% and 100% of virtual patient infected with HIV. These numbers are significantly higher than what was obtained using selection strategies defined by sequence conservation and HLA promiscuity alone.
Robustness of Gaussian Hedges and the Hedging of Fixed Income Derivatives

The effect of model and parameter misspecification on the effectiveness of Gaussian hedging strategies for derivative financial instrumens is analyzed, showing that Gaussian hedges in the "natural" hedging instruments are particularly robust. This is true for all models that imply Balck/Scholes - type formulas for option prices and hedging strategies. In this paper we focus on the hedging of fixed income derivatives and show how to apply these results both within the framework of Gaussian term structure models as well as the increasingly popular market models where the prices for caplets and swaptions are given by the corresponding Black formulas. By explicitly considering the behaviour of the hedging strategy under misspecification we also derive the El Karoui, Jeanblanc-Picque and Shreve (1995, 1998) and Avellaneda, Levy and Paras (1995) results that a superhedge is obtained in the Black/Scholes model if the misspecified volatility dominates the true volatility. Furthermore, we show that the robustness and superhedging result do not hold if the natural hedging instruments are unavailable. In this case, we study criteria for the optimal choice from the instruments that are available.
Semantics Sensitive Segmentation and Annotation of Natural Images

In this paper, we present new perceptual techniques for segmentation and annotation of natural images. The image segmentation approach is a multilevel clustering method based on a new proposed non-parametric clustering algorithm, called adaptive medoidshift (AMS) and normalized cuts (N-cut). The AMS method locally clusters the image color composition by considering their spatial distribution into uniform segments, which are then perceptually group together using N-cut into meaningful semantic sensitive salient regions. The proposed image annotation approach assigns labels at segment and scene level to represent semantic content and concept of image respectively. The low level features are extracted from the obtained salient regions and are used by support vector machine (SVM) classifiers to assign segment labels, which are then used to derive scene labels. This effectively reduces the ¿semantic gap¿ between low level features and high level semantics. Experiments show the effectiveness of proposed algorithms on variety of natural images.
Sample Size Calculation of RNA-sequencing Experiment-A Simulation-Based Approach of TCGA Data

Power and sample size calculation is an essential component of experimental design in biomedical research. For RNA-sequencing experiments, sample size calculations have been proposed based on mathematical models such as Poisson and negative binomial; however, RNA-seq data has exhibited variations, i.e. over-dispersion, that has caused past calculation methods to be under- or over-power. Because of this issue and the field’s lack of a simulation-based sample size calculation method for assessing differential expression analysis of RNA-seq data, we developed this method and applied it to three cancer sites from the Tumor Cancer Genome Atlas. Our results showed that each cancer site had its own unique dispersion distribution, which influenced the power and sample size calculation.
Book Section: Essay and Review: Evaluation of Sexually Violent Predators

This is a controversial area. Educated professionals can debate which mechanism best meets society's need to protect itself from individuals who are predatory and remorseless in their sexual drives, but the civil commitment of some of the very highest risk sexual offenders seems like a reasonable place to start. Some of the scholarly articles on this topic take a polemical approach challenging these laws based on a number of justifiable reasons. Emotions run high, and many of the criticisms have tremendous face validity. I sometimes joke that my ACLU card burns in my wallet whenever I work in this field.