Miracle-dz/UniFAR-FTUs huggingface dataset:
Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets

The NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents. The Biodefense Resource Center (www.proteomicsresource.org) has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and heterogeneous data. Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases. Value-added annotations are provided for key proteins from experimental findings using controlled vocabulary. The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case studies presented here. (1) The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and human HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggesting that this protein can be prioritized for additional analysis and functional characterization. (2) The analysis of a vaccinia-human protein interaction network supplemented with protein accumulation levels led to the identification of human Keratin, type II cytoskeletal 4 protein as a potential therapeutic target. (3) Comparison of complete genomes from pathogenic variants coupled with experimental information on complete proteomes allowed the identification and prioritization of ten potential diagnostic targets from Bacillus anthracis. The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach to basic understanding of pathogenicity and target identification.
Compressed pseudo-lattices

This paper introduces the notion of a compressed pseudo-lattice and suggests its use as a data structure in areas of application related to Formal Concept Analysis. It is closely related to the line diagram of a lattice and its use as a computational tool in applications such as machine learning, information retrieval and knowledge discovery in databases is discussed. The data structure—essentially a bipartite graph that incorporates an embedded sublattice—combines desirable features of concept lattices in a structure that allows for a flexible mechanism of scaling the size of the embedded sublattice, using defined operations that compress and expand it by removing or adding atoms and coatoms. A compressed pseudo-lattice essentially represents a complete sublattice from which a number of atoms and/or coatoms have been removed. Additionally the relation of the sublattice to the context from which it was derived is preserved. An application-dependent compression strategy or criterion is required to guide this process. The intent operations of a lattice are defined as substitutes for the infimum and supremum operations in compressed pseudo-lattices. It is argued that the removal of concepts from a concept lattice may hold advantages over traditional approaches.
Improving BM3D on non-stationary Gaussian models for real image noise

Most of the work related to image denoising is based on artificial noise of stationary Gaussian distribution (synthetically added to the image in arrears). However, this choice is only a rough approximation of the real noise distribution. That is why, various research works were recently focusing on how to perfectly model the real noise inherent in captured images. In this paper, we model this distribution as non-stationary conditional Gaussian, where the standard deviation is depending on the pixel intensity. Experimental results show that this assumption models the real image noise more accurately (specifically when it comes to its adaptive removal). For that, we developed an extended version of BM3D called NBM3D. It is suitable for adaptive non-stationary noise removal in natural captured images where the original BM3D performance is relatively limited. To accurately verify the denoising performance under real case scenarios, we compute a "noise-free" ground truth image as the average of a sequence of images captured on a static scene by a non-moving monocular camera. Then, we estimate the conditional Gaussian distribution. The resulting model is used for the execution of NBM3D. The comparison between our method and the state-of-the-art BM3D is done by comparing the denoised images using both approaches against the ground truths. Results on three different cameras and 15 sequences with varying lighting conditions show that the proposed NBM3D provides consistent denoising improvements compared to state-of-the-art in terms of real noise removal.
3D ellipsoid fitting for multi-view gait recognition

Gait recognition approaches continue to struggle with challenges including view-invariance, low-resolution data, robustness to unconstrained environments, and fluctuating gait patterns due to subjects carrying goods or wearing different clothes. Although computationally expensive, model based techniques offer promise over appearance based techniques for these challenges as they gather gait features and interpret gait dynamics in skeleton form. In this paper, we propose a fast 3D ellipsoidal-based gait recognition algorithm using a 3D voxel model derived from multi-view silhouette images. This approach directly solves the limitations of view dependency and self-occlusion in existing ellipse fitting model-based approaches. Voxel models are segmented into four components (left and right legs, above and below the knee), and ellipsoids are fitted to each region using eigenvalue decomposition. Features derived from the ellipsoid parameters are modeled using a Fourier representation to retain the temporal dynamic pattern for classification. We demonstrate the proposed approach using the CMU MoBo database and show that an improvement of 15–20% can be achieved over a 2D ellipse fitting baseline.
Bidirectional pose estimation

This paper presents a method for relative pose estimation between two devices. Typically pose estimation is based on detecting positions of known feature points of a tracked object. I literally take a new viewpoint to this problem by considering two camera-enabled devices tracking each other. The method requires only two feature points, which can be unobtrusively integrated to small, portable devices such as mobile phones. Both devices detect each others feature points and share the positions over a wireless network connection. The combined position data can then be used to calculate the six degrees of freedom (DOF) transformation between the devices. I compared the pose estimation accuracy with a conventional method using a simulation and a real world experiment. The results show that the bidirectional method is significantly more accurate and robust to noise. It is also less affected by the target distance.
An Investigation of the Latent Semantic Analysis Technique for Document Retrieval

Latent semantic analysis (LSA) application in information retrieval promises to offer better performance by overcoming some limitations that plagues traditional term-matching techniques. These term-matching techniques have always relied on matching query terms with document terms to retrieve the documents having terms matching the query terms. However, by use of these traditional retrieval techniques, users' needs have not been adequately served. While users want to search through information based on conceptual content, natural languages have limited the expression of these concepts. They present synonymy problem (a situation where several words may have the same meaning) and polysemy problem (a situation where a word may have several meanings). Due to these natural language problems, individual words contained in users' queries, may not explicitly specify the intended user's concept, which may result in the retrieval of some irrelevant documents. LSA seems to be a promising technique in overcoming these natural language problems especially synonymy problem. It deals with exploiting the global relationships between terms and documents and then mapping these documents and terms in a proximity space, where terms and documents that are closely related are mapped close to each other in this space. Queries are then mapped to this space with documents being retrieved based on similarity measures. In this report, LSA performance in documents retrieval is investigated and compared with traditional term-matching techniques. Declaration I hereby declare that I have personally authored this entire project report and that no other sources other than the ones listed at the end of the report have been used. The report is therefore, original and it has not been published in Germany or in any other country. All the registered trademarks, names, logos and icons appearing in this report are the property of their respective owners.
THE ROLE OF ANTICIPATED AFFECTIVE AMBIVALENCE IN THE ENTREPRENEURIAL PROCESS

Recent theoretical and empirical studies suggest that emotions play a significant role in the entrepreneurial process. In the present study, we investigated the role of anticipated affective ambivalence (that is, future oriented affect relating to the expectancy of feeling both positive and negative affect) from nascent entrepreneurship in students’ entrepreneurial intent. Based on extant theory, we propose that students’ anticipated affective ambivalence moderates the impact of attitudes towards entrepreneurship, perceived behavioral control and subjective norm, on entrepreneurial intent. We empirically tested our propositions using a sample of 1624 students from different universities in Greece and data were analyzed using structural equation modeling. We discuss the implications of our results in the light of the increasing interest of universities in Europe to promote entrepreneurship and develop suitable educational programs.
Reproducibility in echocardiographic assessment of the left ventricular global and regional function, the HUNT study.

AIMS The study aimed to compare the inter-observer reproducibility of new and traditional measurements of the left ventricular (LV) global and regional function. METHODS AND RESULTS Two experienced echocardiographers performed 20 complete echo/Doppler examinations and 50 analyses on ten healthy subjects. All recordings were analysed for systolic and diastolic conventional and deformation measurements by both echocardiographers. Inter-observer mean error (absolute difference divided by the mean) was 4% and lowest (P = 0.001) for systolic M-mode annulus excursion. Mean error for the regional deformation indices was significantly higher than for all the global measurements (all P < 0.001). Mean error for analyses of the same recording was 34% (P = 0.002) lower for global systolic indices and 44% (P < 0.001) lower for global diastolic indices than inter-observer mean error for analyses made in separate recordings. CONCLUSION Systolic M-mode annulus excursion showed better inter-observer reproducibility than other traditional and newer measurements of LV systolic and diastolic function. Repeated analyses of the same recordings underestimate the more clinically relevant inter-observer reproducibility by approximately 40% for most measurements of LV function.
Interactive effect of stressful life events and the serotonin transporter 5-HTTLPR genotype on posttraumatic stress disorder diagnosis in 2 independent populations.

CONTEXT The 5-HTTLPR polymorphism in the promoter region of the serotonin transporter gene (SLC6A4) has been found to moderate several categories of emotional response after stressful life events. Previous studies generally focused on its effect on depressive symptoms; little is known about its moderation of the development of posttraumatic stress disorder (PTSD). OBJECTIVE To examine the effects of childhood adversity, adult traumatic events, 5-HTTLPR genotypes, and gene x environment interactions on the etiology of PTSD. DESIGN A cross-sectional study in which participants in several studies investigating the genetics of substance dependence were also screened for lifetime PTSD. The triallelic system of 5-HTTLPR was genotyped. Logistic regression modeling was used in the analyses. SETTING General community. PARTICIPANTS Five hundred eighty-two European American and 670 African American individuals who reported experiences of childhood adversity, adult traumatic events, or both. Main Outcome Measure Diagnosis of PTSD, defined by DSM-IV diagnostic criteria and assessed through the Semi-Structured Assessment for Drug Dependence and Alcoholism interview. RESULTS Childhood adversity and adult traumatic events both predicted PTSD. Although the 5-HTTLPR genotype alone did not predict the onset of PTSD, it interacted with adult traumatic events and childhood adversity to increase the risk for PTSD, especially for those with high rates of both types of trauma exposure (European American: odds ratio [OR], 2.86; 95% confidence interval [CI], 1.50-5.45; P = .002; African American: OR, 1.88; 95% CI, 1.04-3.40; P = .04; pooled: OR, 2.31; 95% CI, 1.50-3.56; P < .001). CONCLUSIONS Participants who had both childhood adversity and adult traumatic events were more likely to develop lifetime PTSD compared with those who experienced either type of adverse event. The risk was increased in individuals with 1 or 2 copies of the S' (S) allele compared with the L' (L) homozygotes. Our study provides additional direct evidence that PTSD is influenced by the interactive effect of environmental and genetic factors.
Hierarchical background subtraction algorithm using Gabor filter

Detection of a moving object in a non-stationary scene is a very critical and challenging step for visual surveillance applications. Background subtraction (BS) is a widely used algorithm for moving object detection in the presence of static cameras. Its performance purely depends on the choice of features used for background modeling. The traditional BS assumes that the background is static or near-static. This assumption does not hold for practical scenarios and their performance degrades in the presence of non-stationary scenes such as swaying of trees, sprouting of water from fountain, ripples in water, flag fluttering in the wind, camera jitters and noise. In this paper, we have combined both block-based and pixel-based approaches in our hierarchical BS algorithm. Both coarse and fine level background modeling is done using the magnitude feature obtained from the Gabor filter. First coarse level background modeling is done for identifying the blocks which are fully or partially occupied by the foreground objects. Every pixel in the foreground blocks is further classified using the Gabor feature for improving the precision of the detected moving object. The proposed algorithm is a single modal based BS scheme. Quantitative and qualitative results justify our algorithm for efficient moving object detection in the presence of complex dynamic backgrounds.
Ideal Affect: Cultural Causes and Behavioral Consequences

Most research focuses on actual affect, or the affective states that people actually feel. In this article, I demonstrate the importance and utility of studying ideal affect, or the affective states that people ideally want to feel. First, I define ideal affect and describe the cultural causes and behavioral consequences of ideal affect. To illustrate these points, I compare American and East Asian cultures, which differ in their valuation of high-arousal positive affective states (e.g., excitement, enthusiasm) and low-arousal positive affective states (e.g., calm, peace-fulness). I then introduce affect valuation theory, which integrates ideal affect with current models of affect and emotion and, in doing so, provides a new framework for understanding how cultural and temperamental factors may shape affect and behavior.
SENSORIMOTOR WORKING MEMORY CAPACITY LIMITS

ii Co-Authorship . iii Acknowledgements . iv List of Figures . vii List of Tables . viii List of Abbreviations . ix Chapter 1: General Introduction . 1 1.1 Preface . 1 1.2 Working Memory and Capacity Limitations . 2 1.3 “Slot” vs “Shared Resource” Explanation of Working Memory . 5 1.5 Sensorimotor Predictions When Lifting Objects . 8 1.6 Internal Model Framework . 11 1.7 Implicated Neural Mechanisms . 12 1.8 Outline of Experiments and Hypotheses . 14 Chapter 2: Natural Learning of Object Weight . 16 2.1 Abstract . 16 2.2 Introduction . 16 2.3 Materials and Methods . 20 2.3.1 Participants . 20 2.3.2 Stimulus Objects . 20 2.3.3 Tabletop Workspace . 22 2.3.4 Procedure . 22 2.3.5 Data Analysis . 23 2.4 Results . 25 2.5 Discussion . 33 Chapter 3: Change Detection for Object Weighti . 39 3.1 Abstract . 39 3.2 Introduction . 39 3.3 Materials and Methods . 43 3.3.1 Participants . 43 3.3.2 Stimulus Objects . 44 3.3.3 Tabletop Workspace . 45 vi 3.3.4. Liquid Crystal Goggles . 46 3.3.5. Cognitive Tasks . 46 3.3. 6. Procedure . 47 3.3. 7. Data Analysis . 48 3.4 Results . 49 3.4.1 Perceptual Data . 49 3.4.2 Lifting Data . 53 3.4.3 Cognitive Data . 56 3.4.4 Correlational Results . 57 3.5 Discussion . 58 Chapter 4: General Discussion . 65 4.1 Summary of studies and principle findings . 65 4.2 Sensorimotor Working Memory Capacity Limits . 66 4.3 Future Directions . 67 4.4 Conclusions . 69 References . 71 Appendix A : Tables of means and standard deviations . 79
Solid state disk: A new storage device for video storage server

Solid state disk (SSD) is a new storage device that utilizes semiconductor memory chips (e.g. RAM, EEPROM, flash memory) to store data rather than using conventional spinning platters and moving heads found in conventional magnetic disk drive. The term of “solid state” means there are no moving parts involve in accessing, storing and retrieving required data on the drive. Several benefits offered by the SSD drives due to absent of moving mechanical components are high access speed, light weight, ruggedness, low latency, low power consumption, and silent operation. This paper discusses the architecture and the advantage offered by SSD in using the drive as a storage device in video server.
Macrophages Promote Axon Regeneration with Concurrent Neurotoxicity

Activated macrophages can promote regeneration of CNS axons. However, macrophages also release factors that kill neurons. These opposing functions are likely induced simultaneously but are rarely considered together in the same experimental preparation. A goal of this study was to unequivocally document the concurrent neurotoxic and neuroregenerative potential of activated macrophages. To do so, we quantified the length and magnitude of axon growth from enhanced green fluorescent protein-expressing dorsal root ganglion (DRG) neurons transplanted into the spinal cord in relationship to discrete foci of activated macrophages. Macrophages were activated via intraspinal injections of zymosan, a potent inflammatory stimulus known to increase axon growth and cause neurotoxicity. Using this approach, a significant increase in axon growth up to macrophage foci was evident. Within and adjacent to macrophages, DRG and spinal cord axons were destroyed. Macrophage toxicity became more evident when zymosan was injected closer to DRG soma. Under these conditions, DRG neurons were killed or their ability to extend axons was dramatically impaired. The concurrent induction of pro-regenerative and neurotoxic functions in zymosan-activated macrophages (ZAMs) was confirmed in vitro using DRG and cortical neurons. Importantly, the ability of ZAMs to stimulate axon growth was transient; prolonged exposure to factors produced by ZAMs enhanced cell death and impaired axon growth in surviving neurons. Lipopolysaccharide, another potent macrophage activator, elicited a florid macrophage response, but without enhancing axon growth or notable toxicity. Together, these data show that a single mode of activation endows macrophages with the ability to simultaneously promote axon regeneration and cell killing.
Örgütlerde Stres Kaynaklarının Çalışanların İş-Aile Çatışması Üzerine Etkisi

Work and family are the two concepts that people give importance utmost importance in their lives. One of the factors that influence today’s work lives is the conflict employees have between their family lives and work lives. Work stress has a critical place in terms of the performance, productivity, job satisfaction and social relations of employees. This study was conducted among sugar factory employees to examine the relations between work stress factors and work- family conflict. Besides, the relations between the variables in question and socio-economic variables have also been studied. Questionnaire technique was used for the study. The result of the study shows that there is a low and negative relation between work stress factors and work- family conflict; positive and meaningful relations between work control and social support, factors of work stress. It is seen that the work responsibilities of employees do not affect their family lives. Moreover, the employees state that they are content with social support items the most. There is no difference between work stress and work- family conflict in terms of demographic variables, gender, marital status, age, income and number of children. Those working three shifts have relatively more work- family conflict when compared with those working day shift on a permanent basis. It is seen that the civil servants have more decision- making rights and workloads than do the workers, as to the education variable, elementary schools graduates have fewer decision- making rights than do university graduates.
Equity volatility and credit yield spreads

We show that a simple structural model of credit risk is able to generate credit yield spreads for the low-rated bonds close to the historical spreads once the recent trends in the stock volatility are taken into account. We study the idiosyncratic and market volatility of stock returns in the cross-section of credit ratings. We flnd that the increase in the level of the flrm-speciflc volatility, demonstrated recently by Campbell et al. (2001), refers only to the low-rated stocks. A time-varying deterministic volatility process is used to imply the asset volatilities, the asset risk premia and the default boundaries from the historical default rates. Stock volatility is modeled as an autoregressive process. Physical default probability of an investment-grade bond is primarily linked to the drift of the flrm value process and default probability of a low-rated bond to the total asset volatility. We conflrm this by flnding that an increase in the flrm-speciflc volatility afiects credit spreads of the low-rated bonds and does not have an observable impact on the investment-grade bonds.