Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Immune Dominant Cytomegalovirus Epitopes Using Quantitative Real-Time Polymerase Chain Reactions to Measure Interferon-&ggr; Production by Peptide-Stimulated Peripheral Blood Mononuclear Cells

The identification of HLA restricted immune dominant cytotoxic T cell (CTL) epitopes limits immune therapy. Cytomegalovirus (CMV) disease remains a significant cause of morbidity after allogeneic stem cell transplantation. Adoptive immune therapy using CTLs stimulated with immune dominant CMV pp65 peptides may be effective in preventing CMV disease, but immune dominant CMV peptides have been identified for only a few HLA class I molecules. The purpose of this study was to use a novel molecular system to establish a rapid and precise method to identify new HLA-restricted CMV epitopes. Cytomegalovirus pp65 peptides expected to bind to the HLA-24 molecule were identified with a computer algorithm. Five candidate peptides were screened by direct ex vivo stimulation of peripheral blood mononuclear cells (PBMCs) from CMV-seropositive HLA-A*2402 individuals, and quantitative real time PCR (qRT-PCR) was used to evaluate CTL responses by measuring interferon-&ggr; (IFN-&ggr;) transcripts. One of the five candidate peptides, pp65341–350 (QYDPVAALFF), induced significant quantities of IFN-&ggr; mRNA production after 3 hours. PBMCs from CMV-seropositive HLA-A*2402 individuals sensitized in vitro with pp65341–350 also recognized CMV-infected targets. In conclusion, the measurement of IFN-&ggr; mRNA by qRT-PCR can be used to detect CTL responses 3 hours after peptide stimulation of a small quantity of PBMCs. This method has an advantage over other methods used to identify immune dominant epitopes in that it does not require in vitro expansion of CTLs with cytokines or virally infected targets. As a result, this method measures naturally induced immune reactions.
Fine-grained layered multicast

Traditional approaches to receiver-driven layered multicast have advocated the benefits of cumulative layering, which can enable coarse-grained congestion control that complies with TCP-friendliness equations over large time scales. In this paper, we quantify the costs and benefits of using non-cumulative layering and present a new, scalable multicast congestion control scheme which provides a fine-grained approximation to the behavior of TCP additive increase/multiplicative decrease (AIMD). In contrast to the conventional wisdom, we demonstrate that fine-grained rate adjustment can be achieved with only modest increases in the number of layers and aggregate bandwidth consumption, while using only a small constant number of control messages to perform either additive increase or multiplicative decrease.
Dairy Product, Saturated Fatty Acid, and Calcium Intake and Prostate Cancer in a Prospective Cohort of Japanese Men

Many epidemiologic studies have reported a positive association between dairy products and prostate cancer. Calcium or saturated fatty acid in dairy products has been suspected as the causative agent. To investigate the association between dairy products, calcium, and saturated fatty acid and prostate cancer in Japan, where both the intake of these items and the incidence of prostate cancer are low, we conducted a population-based prospective study in 43,435 Japanese men ages 45 to 74 years. Participants responded to a validated questionnaire that included 138 food items. During 7.5 years of follow-up, 329 men were newly diagnosed with prostate cancer. Dairy products were associated with a dose-dependent increase in the risk of prostate cancer. The relative risks (95% confidence intervals) comparing the highest with the lowest quartiles of total dairy products, milk, and yogurt were 1.63 (1.14-2.32), 1.53 (1.07-2.19), and 1.52 (1.10-2.12), respectively. A statistically significant increase in risk was observed for both calcium and saturated fatty acid, but the associations for these were attenuated after controlling for potential confounding factors. Some specific saturated fatty acids increased the risk of prostate cancer in a dose-dependent manner. Relative risks (95% confidence intervals) on comparison of the highest with the lowest quartiles of myristic acid and palmitic acid were 1.62 (1.15-2.29) and 1.53 (1.07-2.20), respectively. In conclusion, our results suggest that the intake of dairy products may be associated with an increased risk of prostate cancer. (Cancer Epidemiol Biomarkers Prev 2008;17(4):930–7)
Ginsenoside Rg3 induces ginsenoside Rb1-comparable cardioprotective effects independent of reducing blood pressure in spontaneously hypertensive rats

Ginsenoside Rg3 (Rg3) is a rare type of ginsenoside used as an anti-tumor medicine in China. Ginsenoside Rb1 (Rb1), which exhibits protective effects on the cardiovascular system, is similar to Rg3 in chemical structure. In the present study, Rb1 and Rg3 were administered for 6 weeks to spontaneously hypertensive rats (SHR) and their cardioprotective effects were assessed. According to echocardiography and histopathological examinations, the decrease in cardiac function and ventricular remodeling that occurred in SHR rats were attenuated by Rb1 and Rg3. However, tail-cuff blood pressure measurements indicated that Rb1 and Rg3 did not reduce blood pressure in SHR rats. The cardioprotective effects of Rb1 and Rg3 occurred independently of blood pressure reduction. Furthermore, immunohistochemistry (IHC) revealed that renin angiotensin system (RAS) activity in the myocardium of SHR was significantly attenuated by Rb1 and Rg3, whereas ELISA identified no significant changes of RAS activity in the serum. The results of IHC and reverse transcription-quantitative polymerase chain reaction demonstrated that levels of transforming growth factor β1, tumor necrosis factor-α, interleukin-6, interleukin-1 and endothelian-1 in the myocardium of SHR rats were reduced following Rb1 and Rg3 treatment. This may be due to the attenuation of RAS activity in the myocardium and the mechanisms of the cardioprotective effects of Rb1 and Rg3.
WiDS Checker: Combating Bugs in Distributed Systems

Despite many efforts, the predominant practice of debugging a distributed system is still printf-based log mining, which is both tedious and error-prone. In this paper, we present WiDS Checker, a unified framework that can check distributed systems through both simulation and reproduced runs from real deployment. All instances of a distributed system can be executed within one simulation process, multiplexed properly to observe the "happensbefore" relationship, thus accurately reveal full system state. A versatile script language allows a developer to refine system properties into straightforward assertions, which the checker inspects for violations. Combining these two components, we are able to check distributed properties that are otherwise impossible to check. We applied WiDS Checker over a suite of complex and real systems and found non-trivial bugs, including one in a previously proven Paxos specification. Our experience demonstrates the usefulness of the checker and allows us to gain insights beneficial to future research in this area.
Classification of Very High Spatial Resolution Imagery Based on a New Pixel Shape Feature Set

This letter presents a novel spatial features extraction method for the high spatial resolution multispectral imagery (HSRMI) classification. First, Canny filter algorithm is applied to extract the edge information to obtain the fuzzy edge map. Secondly, adaptive threshold value for each pixel's homogeneous region (PHR) calculation is determined based on the fuzzy edge map and original image. Next, the PHR for every pixel is obtained based on the fuzzy edge map, adaptive threshold value and original image. And then, the pixel shape feature set (PSFS) is extracted based on the PHR. Lastly, SVM classifier is applied to classify the hybrid spectral and PSFS. Two different experiments were performed to evaluate the performance of PSFS, in comparison with spectral, gray level co-occurrence matrix (GLCM) and the existing pixel shape index (PSI). Experimental results indicate that the PSFS achieved the highest accuracy, hence, providing an effective spectral-spatial classification method for the HSRMI.
Development of a Facial Emotion Recognition Method Based on Combining AAM with DBN

In this paper, novel methods for facial emotion recognition in facial image sequences are presented. Our facial emotional feature detection and extracting based on Active Appearance Models (AAM) with Ekman’s Facial Action Coding System (FACS). Our approach to facial emotion recognition lies in the dynamic and probabilistic framework based on Dynamic Bayesian Network (DBN) with Kalman Filter for modeling and understanding the temporal phases of facial expressions in image sequences. By combining AAM and DBN, the proposed method can achieve a higher recognition performance level compare with other facial expression recognition methods. The result on the BioID dataset show a recognition accuracy of more than 90% for facial emotion reasoning using the proposed method.
Gamebots: A 3D Virtual World Test-Bed For Multi-Agent Research

paper describes Gamebots, a multi-agent system infrastructure derived from an Internet-base d multi-player video game called Unreal Tournament. The game allows characters to be controlled over client-server network connections by feeding sensory information to client players (humans and agents). Unlike other standard test-beds, the Gamebots domain allows both human players and agents, or bots, to play simultaneously; thus providing the opportunity to study human team behavior and to construct agents that play collaboratively with humans. The Gamebots system provides a built-in scripting language giving interested researchers the ability to create their own multi-agent tasks and environments for the simulation.
Perception-Link Behavior Model: Supporting a Novel Operator Interface for a Customizable Anthropomorphic Telepresence Robot

A customizable anthropomorphic telepresence robot (CATR) is an emerging medium that might have the highest degree of social presence among the existing mediated communication mediums. Unfortunately, there are problems with teleoperating a CATR, and these problems can deteriorate the gesture motion in a CATR. These problems are the disruption during decoupling, discontinuity due to the unstable transmission and jerkiness due to the reactive collision avoidance. From the review, none of the existing interfaces can simultaneously fix all of the problems. Hence, a novel framework with the perception-link behavior model (PLBM) was proposed. The PLBM adopts the distributed spatiotemporal representation for all of its input signals. Equipping it with other components, the PLBM can solve the above problems with some limitations. For instance, the PLBM can retrieve missing modalities from its experience during decoupling. Next, the PLBM can handle up to a high level of drop rate in the network connection because it is dealing with gesture style and not pose. For collision prevention, the PLBM can tune the incoming gesture style so that the CATR can deliberately and smoothly avoid a collision. In summary, the framework consists of PLBM being able to increase the user’s presence on a CATR by synthesizing expressive user gestures.
Planar Quadrangle Quality Measures: Is There Really A Choice?

In this article some new results are presented about planar quadrangle quality measures. On the one hand, a modi cation of the triangle quality measure based on the Frobenius norm is proposed, in order to comply with the case where the reference element is no longer equilateral, but a right isosceles triangle. Provided this modi cation, a natural use of the Frobenius norm for quadrangular elements is proposed. On the other hand, generalizations of two triangle quality measures, based on edge to inradius ratios, to planar quadrangles are proposed and justi ed, and their limitations, depending on user's expectations, are exhibited, justifying the use of a more complex quality measure.
Constrained choice? Graduate early career job-to-job mobility in core and non-core regions in the Netherlands

The chapter investigates job-switch strategies of graduates from Dutch HEIs residing in core and non-core areas: to what extent are residential and workplace mobility coupled with switches across industrial sectors? Registry data from Statistics Netherlands enables us to track graduation cohorts from seven years before to eighteen years after graduation. Overall, the likelihood of labour-market dynamics varies strongly with the life-phase in which we find graduates. The chapter finds that, like migration, job mobility is not a random event. It occurs, in some cases, repeatedly, to specific groups who appear to operate at the edges of the job-opportunity space. The chapter finds that sector and workplace mobility appear contemporarily positively inter-related, persistent, but also inter-temporally competing. Residential mobility appears somewhat disconnected from labour-market dynamics, although it appears that some wait for a match to come to fruition before changing residences. Mobility is higher across the board for graduates residing in non-core areas, with non-core singles found to be relatively mobile. The chapter demonstrates that it is not the presence of a partner as such that limits spatial mobility, but whether or not he or she is economically active. Controlling for this, and contrary to what is often reported in migration literature, the chapter finds that couples without children, living in non-core areas, are more likely to exhibit residential mobility than singles. They are also more likely to engage in sectoral and workplace mobility. Non-core couples with children are also found to be more likely to engage in residential mobility than singles.
Qualitative image based localization in a large building

Interest in indoor localization is growing because it is an important component of many applications. Imagebased localization, using naturally-occurring features in the environment, is an attractive solution to this problem. A challenge is to be able perform this on a mobile device with limited computing power. Another challenge is that buildings can have locations with a similar appearance, which can confuse an image-based recognition system. Since many applications do not need exact location, we focus on qualitative localization, which is the problem of the problem of determining approximate location by matching a query image to a database of images. We propose a novel approach that uses an efficient hashing scheme to quickly identify candidate locations, then applies a strong geometric constraint to reject matches that have similar appearance. On experiments in a large campus building, we show that this approach can localize a query image with high accuracy and has potential to run in real time on a mobile device. Keywords-computer vision; indoor localization; image retrieval; vision based navigation.
Sodium channel NaV1.9 mutations associated with insensitivity to pain dampen neuronal excitability

Voltage-gated sodium channel (NaV) mutations cause genetic pain disorders that range from severe paroxysmal pain to a congenital inability to sense pain. Previous studies on NaV1.7 and NaV1.8 established clear relationships between perturbations in channel function and divergent clinical phenotypes. By contrast, studies of NaV1.9 mutations have not revealed a clear relationship of channel dysfunction with the associated and contrasting clinical phenotypes. Here, we have elucidated the functional consequences of a NaV1.9 mutation (L1302F) that is associated with insensitivity to pain. We investigated the effects of L1302F and a previously reported mutation (L811P) on neuronal excitability. In transfected heterologous cells, the L1302F mutation caused a large hyperpolarizing shift in the voltage-dependence of activation, leading to substantially enhanced overlap between activation and steady-state inactivation relationships. In transfected small rat dorsal root ganglion neurons, expression of L1302F and L811P evoked large depolarizations of the resting membrane potential and impaired action potential generation. Therefore, our findings implicate a cellular loss of function as the basis for impaired pain sensation. We further demonstrated that a U-shaped relationship between the resting potential and the neuronal action potential threshold explains why NaV1.9 mutations that evoke small degrees of membrane depolarization cause hyperexcitability and familial episodic pain disorder or painful neuropathy, while mutations evoking larger membrane depolarizations cause hypoexcitability and insensitivity to pain.
CMAP: Complement Map Database

SUMMARY The human complement system is increasingly perceived as an intricate protein network of effectors, inhibitors and regulators that drives critical processes in health and disease and extensively communicates with associated physiological pathways ranging from immunity and inflammation to homeostasis and development. A steady stream of experimental data reveals new fascinating connections at a rapid pace; although opening unique opportunities for research discoveries, the comprehensiveness and large diversity of experimental methods, nomenclatures and publication sources renders it highly challenging to keep up with the essential findings. With the Complement Map Database (CMAP), we have created a novel and easily accessible research tool to assist the complement community and scientists from related disciplines in exploring the complement network and discovering new connections. AVAILABILITY http://www.complement. us/cmap. CONTACT lambris@upenn.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Finding appropriate clinical trials: evaluating encoded eligibility criteria with incomplete data

We describe our work on creating a system that selects appropriate clinical trials by automating the evaluation of eligibility criteria. We developed a data model of eligibility for breast cancer clinical trials, upon which the criteria were encoded. Standard vocabularies are utilized to represent concepts used in the system, and retrieve their hierarchical relationships. The system incorporates Bayesian networks to handle missing patient information. Protocols are ranked by the belief that the patient is eligible for each of them. In a preliminary evaluation, we found good agreement (kappa 0.86) between the system and an independent physician in selection of protocols, but poor agreement (kappa 0.24) in protocol ranking. We conclude that our approach is feasible, and potentially useful in assisting both physicians and patients in the task of selecting appropriate trials.
Distributed estimation for feedback-linearizable nonlinear systems

In a multi sensor-agent network we tackle the distributed estimation problem for multi-inputs-multi-outputs feedback-linearizable nonlinear systems. Given a plant of this class, supposing that a sensors network measures its outputs, we will provide a sufficient condition to guarantee the existence of a distributed observer able to estimate the state by each single sensor. After having motivated, contextualized and formulated the problem we will prove our main result and will test its efficiency through a simulation.
Elevation-based upscaling of organic carbon stocks in High-Arctic permafrost terrain: a storage and distribution assessment for Spitsbergen, Svalbard

ABSTRACT Accurate quantity and distribution estimates of permafrost soil organic carbon (SOC) stocks are needed to project potential feedbacks to climate, following warming. Still, upscaling from local field observations to regional estimates to circumarctic assessments remains a challenge. Here we explore elevation-based upscaling techniques for High-Arctic permafrost SOC stocks. We combine two detailed, high-resolution SOC inventories on Spitsbergen (Svalbard) with regional validation data. We find a clear relationship between elevation and SOC content, and use this observed exponential correlation, as well as discrete elevation classes, as upscaling models for Spitsbergen. We estimate the total amount of permafrost SOC currently present in soils on Spitsbergen to be 105.36 Tg (0.11 Pg), with a mean SOC content of 2.84 ± 0.74 kg C m−2 (mean ± 95% confidence interval). Excluding glaciers and permanent snowfields, exposed land is currently estimated to contain 6.26 ± 1.47 kg C m−2.
Uncanny Valley of Androids and Its Lateral Inhibition Hypothesis

The "uncanny valley" must be avoided from the viewpoint of communication robot design, while this is an essential phenomenon for discovering the principles relevant to establishing social interaction between human and robot. Studying the uncanny valley allows us to explore the boundary of human-likeness. We have empirically and experimentally obtained evidence to show the uncanny valley. We have also obtained experimental evidence to suggest that the uncanny valley varies owing to the development of individuals. We refer to this variable uncanny valley as the age-dependent uncanny valley. We assume that the uncanny valley is induced by a lateral inhibition effect, and is referred to herein as the lateral inhibition hypothesis of the uncanny valley;. The present paper presents evidence concerning the uncanny valley and describes the likelihood of the present hypothesis.
Ultra low-power DFF based shift registers design for CMOS image sensors applications

Various implementations of D-flip-flops (DFF) for shift register designs in CMOS image sensors are proposed. Driven by requirements of low-area and low-power dissipation, the presented FF allow implementation of power-efficient shift registers, used for signal readout control and windows of interest definition in CMOS image sensors and are optimized for operation at low frequencies. Power dissipation of the presented DFF is significantly reduced by leakage control using the stack effect. A variety of DFF and a shift-register, using the stacking effect approach, have been implemented in 0.18 /spl mu/m standard CMOS technology to compare the proposed DFF and shift-register structures with existing alternatives, showing an up to 63 % reduction in power dissipation of a shift-register at 30 Hz frequency. Operation of the proposed circuits is discussed and simulation results are reported.
Goethe, Hegel and Marx

Hegel's philosophical system rested on an appropriation of the concept which lay at the heart of Goethe's scientific work, the Urphanomen (archetypal phenomenon). In a sense, the Urphanomen is the Urphanomen of Hegel's philosophy: Hegel transformed and expanded this idea in his Logic, in which the place of the Urphanomen is taken by a Concept rather than a phenomenon. Marx in turn took this idea as the foundation for Capital, with the practice of commodity exchange being the Urphanomen of bourgeois society; but changed the relationship between conceptual and practical development. Each link in this chain turns the Urphanomen “inside out” in the act of appropriating it.
High precision quantum query algorithm for computing AND-based boolean functions

Quantum algorithms can be analyzed in a query model to compute Boolean functions. Function input is provided in a black box, and the aim is to compute the function value using as few queries to the black box as possible. The complexity of the algorithm is measured by the number of queries on the worst-case input. In this paper we consider computing AND Boolean function. First, we present a quantum algorithm for AND of two bits. Our algorithm uses one quantum query and correct result is obtained with a probability p=4/5, that improves previous results. The main result is generalization of our approach to design efficient quantum algorithms for computing composite function AND(f1,f2) where fi is a Boolean function. Finally, we demonstrate another kind of an algorithm for AND of two variables, that has a correct answer probability p=9/10, but cannot be extended to compute AND(f1,f2).