Miracle-dz/UniFAR-FTUs huggingface dataset:
Complex discovery from weighted PPI networks

MOTIVATION Protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein interactions, which makes it possible to predict protein complexes from protein-protein interaction (PPI) networks. However, protein interaction data produced by high-throughput experiments are often associated with high false positive and false negative rates, which makes it difficult to predict complexes accurately. RESULTS We use an iterative scoring method to assign weight to protein pairs, and the weight of a protein pair indicates the reliability of the interaction between the two proteins. We develop an algorithm called CMC (clustering-based on maximal cliques) to discover complexes from the weighted PPI network. CMC first generates all the maximal cliques from the PPI networks, and then removes or merges highly overlapped clusters based on their interconnectivity. We studied the performance of CMC and the impact of our iterative scoring method on CMC. Our results show that: (i) the iterative scoring method can improve the performance of CMC considerably; (ii) the iterative scoring method can effectively reduce the impact of random noise on the performance of CMC; (iii) the iterative scoring method can also improve the performance of other protein complex prediction methods and reduce the impact of random noise on their performance; and (iv) CMC is an effective approach to protein complex prediction from protein interaction network. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Towards an Analysis of Garbage Collection Techniques for Embedded Real-Time Java Systems

From a real-time perspective, the garbage collector (GC) introduces unpredictable pauses that are not tolerated by real-time tasks. Real-time collectors eliminate this problem but introduce a high overhead. Another approach is to use memory regions (MR) within which allocation and deallocation are customized. This facility is supported by the memory model of the real-time specification for Java (RTSJ). This paper provides an indepth analytical investigation of the problems and solutions of Java garbage collection techniques regarding it use in embedded real-time systems
SPUDD: Stochastic Planning using Decision Diagrams

Recently, structured methods for solving factored Markov decisions processes (MDPs) with large state spaces have been proposed recently to allow dynamic programming to be applied without the need for complete state enumeration. We propose and examine a new value iteration algorithm for MDPs that uses algebraic decision diagrams (ADDs) to represent value functions and policies, assuming an ADD input representation of the MDP. Dynamic programming is implemented via ADD manipulation. We demonstrate our method on a class of large MDPs (up to 63 million states) and show that significant gains can be had when compared to tree-structured representations (with up to a thirty-fold reduction in the number of nodes required to represent optimal value functions).
Textile yarn thermocouples for use in fabrics

Thermocouples are mainly used for accurate temperature measurements, but they can also be used for the generation of electric energy at low voltage and low power. If inserted into wearable garments, these thermocouples can be used to supply the electric energy required by portable electronic devices. The heat from the human body gives rise to a temperature gradient which can be converted into electric power. In this article, we study the possibility to create a thermocouple and thermopile from pure conductive textile yarns. Among the materials tested, nickel-coated carbon fiber in combination with stainless steel yarn, polypyrrole-coated carbon fiber, or carbon fiber has good potential to be a textile-based thermocouple. We also successfully made a 10-pair carbon fiber–nickel-coated carbon fiber junction thermopile from a single nickel-coated carbon fiber yarn by removing the nickel selectively through etching process.
Access to Mental Health Services Among Patients at Health Centers and Factors Associated with Unmet Needs

Cross-sectional 2009 Health Center Patient Survey data describe the mental health status of health center patients, utilization of mental health services, and factors associated with unmet need for mental health treatment. One in five health center patients accessed mental health services in the past year, and over half of the patients who received counseling received this treatment at a health center. Patients who were unable to access mental health care cited affordability as a concern. Unmet need for mental health treatment was reported by one in three patients. Multivariate analysis found that the odds of reporting unmet need were higher for patients who lacked a usual source of care and patients with serious mental illness.
The impact of storage effects in biobanks on biomarker discovery in systems biology studies

Sample handling and storage conditions in specimens frozen over long periods of time can severely impact marker levels. If laboratory technologies, practices and related protocols change over time, biomarker studies are potentially biased and report erroneous results. These issues and pitfalls are often overlooked in system biology studies using previously collected and stored materials, and are likely to be one notable cause for biomarker candidates failing to be validated. We present results from simulation studies quantifying the loss in statistical power to detect true biomarkers, due to diminishing concentration of analytes in samples subject to poor handling and storage conditions.
Circulating Tumor Cells In Colorectal Cancer.

* The study was created at the Medical University in Łódż, grant number 502-03/5-120-02/502-54-047 Colorectal tumors are considered as the third most common neoplasms in the male population and second in case of female patients (1). The five-year survival of patients with colorectal cancer depends on the clinical stage of the disease, amounting to 90% in case of stage I and 11% in case of stage IV (2). According to The National Cancer Registry the incidence of colorectal carcinoma in Poland (2010) amounted to 12% considering the male population, and 10% in case of female patients (total of 15,800 patients) (3). Available imaging diagnostic methods (CT, MRI) only allow to determine the local advancement of the disease, as well as already existing metastatic foci, which are a significant prognostic factor and main cause of death. Other confirmed prognostic factors of colorectal carcinoma include: – depth of tumor infiltration, – stage of the disease, according to the TNM classification, – histological differentiation, – infiltration of vascular and lymph vessels, – infiltration of local lymph nodes (4, 5). Surgery is the basic therapeutic method in case of colorectal carcinoma, and if necessary, adjuvant chemotherapy. In reality, despite the implementation of all possible therapeutic methods, 25-50% of patients with colorectal cancer stage I and II present with cancer recurrence (6). Therefore, the search for prognostic factors which would accurately determine the likelihood of recurrence. Circulating tumor cells (CTCs) seem to pose such an opportunity.
Perceptual Video Quality Metric for 3D video quality assessment

One method of evaluating the quality of stereoscopic video is the use of conventional two dimensional (2D) objective metrics. Metrics with good representation of the Human Visual System (HVS) will present more accurate evaluation. In this paper we propose a perceptual based objective metric for 2D videos for 3D video quality evaluation. The proposed Perceptual Quality Metric (PQM) shows better results for 3D video quality evaluation and outperforms the Video Quality Metric (VQM); as it is sensitive to slight changes in image degradation and error quantification starts at pixel level right up to the sequence level. Verifications are done through series of subjective tests to show the level of correlation of PQM and user scores.
Evaluation of Tumour Necrosis Factor Alpha, Interleukin-2 Soluble Receptor, Nitric Oxide Metabolites, and Lipids as Inflammatory Markers in Type 2 Diabetes Mellitus

This study compared the results of tumour necrosis factor alpha (TNF-α), interleukin-2 soluble receptor (sIL-2R), nitric oxide metabolites (NOx), C-reactive protein (CRP), and lipids (total cholesterol, high-density lipoprotein (HDL-cholesterol), lowdensity lipoprotein (LDL-cholesterol), and triglycerides) between control group (nondiabetic subjects) and overweight type 2 DM subjects. To restrict the influence of variables that could interfere in the interpretation of data, subjects with obesity and/or acute or chronic inflammatory disease, haemoglobinopathies, recent use of antibiotics, antiinflammatory drugs, and trauma were excluded. Type 2 DM patients (n = 39; age 53.3 ± 9.0 years; median glycated haemoglobin A1c < 8%) presented higher levels of TNF-α, triglycerides (P < .01), NOx and sIL-2R (P < .05) than control group (n = 28; age 39.7 ± 14.1 years). CRP, LDL-cholesterol, total cholesterol, and HDL-cholesterol did not differ among groups. Diabetic women (n = 21) had higher levels of TNF-α, total cholesterol, LDL-cholesterol, and HDL-cholesterol than diabetic men (n = 18) (P < .05), but there were no differences among sexes in the control group. This study indicates that increased level of proinflammatory markers occurs in type 2 DM even in the absence of obesity and marked hyperglycaemia, confirming that the inflammation course of the atherosclerotic process is more severe in diabetic patients than in nondiabetic subjects.
Smart cane location guide for blind using GPS

Visually impaired have a deficiency in their vision which has limitations in terms of mobility. On the other side, the blind must also run their daily activities. Sometimes, the blind must performs a mobility from one building to another building in some area which has a distance like campus, mall and others. In order to make the visually impaired mobility becomes easier, we created a tool that can help them to detect the location of the destination buildings or inform them where the position of the standing place through the sound as the output information. Prototype made using the GPS module, keypad, earphone and raspberry Pi. The results show that the functional testing tools can detect the location area of interest with a deviation of less than 8 m. Also based on the friendly user testing, this prototype categorized good enough to be used by the blind.
Evidence for Protection against Chronic Hepatitis C Virus Infection in Chimpanzees by Immunization with Replicating Recombinant Vaccinia Virus

ABSTRACT Given the failures of nonreplicating vaccines against chronic hepatitis C virus (HCV) infection, we hypothesized that a replicating viral vector may provide protective immunity. Four chimpanzees were immunized transdermally twice with recombinant vaccinia viruses (rVV) expressing HCV genes. After challenge with 24 50% chimpanzee infective doses of homologous HCV, the two control animals that had received only the parental VV developed chronic HCV infection. All four immunized animals resolved HCV infection. The difference in the rate of chronicity between the immunized and the control animals was close to statistical significance (P = 0.067). Immunized animals developed vigorous gamma interferon enzyme-linked immunospot responses and moderate proliferative responses. To investigate cross-genotype protection, the immunized recovered chimpanzees were challenged with a pool of six major HCV genotypes. During the acute phase after the multigenotype challenge, all animals had high-titer viremia in which genotype 4 dominated (87%), followed by genotype 5 (13%). However, after fluctuating low-level viremia, the viremia finally turned negative or persisted at very low levels. This study suggests the potential efficacy of replicating recombinant vaccinia virus-based immunization against chronic HCV infection.
Combined Treatment with Anisodamine and Neostigmine Inhibits Joint Inflammation in Collagen‐Induced Arthritis Mice

Rheumatoid arthritis (RA) is a complicated and treatment refractory autoimmune disease that is characterized by a chronic inflammatory infiltration of immune cells 1. The central nervous system plays an important role in limiting inflammatory responses via an inflammatory reflex of the vagus nerve termed as “the cholinergic antiinflammatory pathway” 2. Acetylcholine, the principal neurotransmitter of the vagus nerve, interacts with α7 nicotinic acetylcholine receptor (α7nAChR) expressed on macrophages and other cells and could inhibit the production of proinflammatory cytokines such as TNFα, interleukin (IL)-1β, and IL-6. Decreased level of vagus nerve activity is correlated with increased serum concentration of late-phase inflammation cytokine high-mobility group box chromosomal protein 1 in patients with RA. Stimulation of nicotinic acetylcholine receptors attenuates collagen-induced arthritis (CIA) in mice. Lack of α7nAChR aggravates the development of CIA 3.
Examining Performance of Bluetooth Network In The Presence of Wi-Fi System

More recently, there has been a growing interest in cognitive techniques, which allow devices and even whole networks to monitor the environment in order to dynamically select and use the channel that affects the least interference. This study aims at Simulation of Bluetooth performance with IEEE 802.11b interference and determination of the Bit Error Rate (BER) using Advanced Design System (ADS 2011 C). The study which employed the Agilent Advance Design system 2011 (ADS 2011) as methodology, reveals that the frequency offset and relative interference power of IEEE 802.11b with Bluetooth signal affect the Bluetooth network performance in terms of BER. Thus the study recommends that measurement should be done in order to include the impact of these components on Bluetooth network performance with the interference from IEEE 802.1lb system.
RISKY SEX: How Cultural Norms Regarding Sexuality Inhibit Condom Use Among Kenyan Youth

Amidst high rates of HIV infection in sub-Saharan African communities, it would seem that most new HIV/AIDS infection cases in Kenya occur among young adults and adolescents. Despite the implementation of numerous AIDS education campaigns and condom distribution programs, it would appear that, for these young people especially, the risk factors are associated primarily with lower levels of AIDSrelated knowledge and attitudes towards using condoms. The purpose of this research is to study the way in which cultural norms regarding sexuality and gender might contribute to risky sexual practices among Kenyan youth. To gain a better understanding of these cultural norms, thematic secondary analysis of data collected as part of the evaluation of the Primary School Action for Better Health (PSABH) programme was carried out with particular attention given to focus group discussions among primary school pupils aged 11 to 16 regarding Kenyan socio-sexual scripts and how these scripts may inhibit condom use and thus increase HIV risk. It is anticipated that a better understanding of cultural norms and how they may affect young people’s sexuality will allow for the development and implementation of more effective policies and programs to combat HIV in Kenya.
Bioinformatics Applications Note Sequence Type Analysis and Recombinational Tests (start)

The 32-bit Windows application START is implemented using Visual Basic and C ++ and performs analyses to aid in the investigation of bacterial population structure using multilocus sequence data. These analyses include data summary, lineage assignment, and tests for recombination and selection. Multilocus Sequence Typing (MLST) is a nucleotide sequence-based typing method that indexes the variation present in bacterial housekeeping genes, where most of the variation is selectively neutral (Maiden et al., 1998). Internal fragments of seven housekeeping genes, approximately 450–500 bp in length, are sequenced and novel alleles are assigned with arbitrary numbers sequentially to provide an allelic profile of seven integers that defines the Sequence Type (ST) of each isolate. The technique is designed primarily for global or long-term epidemiology and surveillance, and has the advantage over other typing methods, such as genetic fingerprinting, of electronic portability and unambiguous characterization of isolates. MLST schemes have been developed for a range of bacterial pathogens and databases for these organisms can be interrogated at the MLST web-site (http://www.mlst.net/) thus facilitating rapid comparisons of isolates typed using the method. A further advantage of MLST is that it provides large quantities of data that may be analyzed by a number of evolutionary approaches to yield insights into the structure of bacterial populations and the selective pressures which act upon them. With the increasing availability of MLST data, the need for software to describe and analyze datasets has become apparent. Sequence Type Analysis and Recombinational Tests (START) was written to address this need through the inclusion of multiple analytical techniques in an easy-to-use and intuitive interface for Windows 95/98/NT/2000 operating systems. Techniques available within the START program are divided into four categories: data summary, lineage assignment , tests for recombination and tests for selection. Two input files are required for many of the tests—allelic profiles, consisting of isolate identifiers and allele numbers , and allele sequences. Profile data can be entered into the program directly from the keyboard, by pasting from the clipboard or by loading a tab-delimited text file while allele sequences need to be in FASTA format. The program utilizes an embedded web-browser for output, enabling easy formatting of tables and inclusion of diagrams generated by the lineage assignment algorithms using HTML, as well as printing and saving of results. Graphical output from analyses is produced in the form of Windows Metafiles (WMF) embedded within the page and these may be …
Intelligent Systems Demonstration: The Secure Wireless Agent Testbed (SWAT)

We will demonstrate the Secure Wireless Agent Testbed (SWAT), a unique facility developed at Drexel University to study integration, networking and information assurance for next-generation wireless mobile agent systems. SWAT is an implemented system that fully integrates: 1) mobile agents, 2) wireless ad hoc multi-hop networks, and 3) security. The demonstration will show the functionality of a number of decentralized agent-based applications, including applications for authentication, collaboration, messaging, and remote sensor monitoring. The demonstration will take place on a live mobile ad hoc network consisting of approximately a dozen nodes (PDAs, tablet PCs, and laptops) and hundreds of mobile software agents.
Cosmological Implications of the Fundamental Relations of X-Ray Clusters

Based on the two-parameter family nature of X-ray clusters of galaxies obtained in a separate paper, we discuss the formation history of clusters and the cosmological parameters of the universe. Utilizing the spherical collapse model of cluster formation, and assuming that the cluster X-ray core radius is proportional to the virial radius at the time of the cluster collapse, the observed relations among the density, radius, and temperature of clusters imply that cluster formation occurs in a wide range of redshifts. The observed relations favor the low-density universe. Moreover, we find that the model of n ~ -1 is preferable.
Estrogen-related receptor alpha and mitochondria: tale of the titans

Abstract The estrogen-related receptor alpha (ERRα) governs multitude of biological functions by working as specific transcriptional regulator in animals. Over the past few years, one aspect of ERRα that has seen optimal progress is its control over the mitochondrial physiology. The ERRα not only regulates an array of nuclear genes devoted to mitochondrial functions but also numerous mitochondrial DNA genes that ultimately culminates into this organelle’s homeostasis. In fact, ERRα expression is correlated with genes whose functional products are part of the mitochondrial physiology. Studies have indicated that nearly half of the proteins encoded by the mitochondrial genome are regulated by ERRα. Moreover, ERRα controls vital mitochondrial processes such as oxidative metabolism through a network of protein kinases and by regulating the expression of sirtuins like Sirt3. Furthermore, new findings also show that ERRα regulate mitochondrial biogenesis in association with PGC family co-activators such as PGC-1-related co-activator and PGC-1β and also via cross-talk with mitogen-activated protein kinase kinases and PI3K/(AKT) signaling. The current understanding of the pathways and networks shows strong influence of ERRα in coordinating mitochondrial physiology. This review focuses on the new advances made in understanding the complex and important interface between ERRα and mitochondrial physiology.
Creativity as a Mental State: An EEG Study of Musical Improvisation

ii DEDICATION. iii ACKNOWLEDGMENTS . iv TABLE OF CONTENTS . v LIST OF TABLES . vii LIST OF FIGURES . viii LIST OF APPENDICES . ix CHAPTER 1: Introduction . 1 Organization of the Study . 4 Literature Review . 5 Concepts of Creativity Localizing the Construct . 5 Hierarchy of Consciousness . 10 Electroencephalography . 14 Alpha Activity during Creative Cognition . 15 Interpretations of Alpha Activity During Creative Cognition . 20 Heritability of Creativity . 22 Creativity as an Emergenic Phenomenon . 24 Gagné’s Theory of Talent Development . 27 Artists’ Experience of Creativity . 29 Studies of Artistic Creativity . 32 Assessment of Creativity. 35 Summary . 42 Aims, Research Questions, and Hypotheses . 45 CHAPTER 2: Method . 51
Expression of immunohistochemical markers on microglia in Creutzfeldt-Jakob disease and Alzheimer's disease: morphometric study and review of the literature.

INTRODUCTION Microglia are the resident immune cells of the CNS. They are involved in the pathogenesis of diverse neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease, prion diseases as well as multiple sclerosis, amyotrophic lateral sclerosis and AIDS dementia complex. Activated microglia up-regulate many surface receptors such as the major histocompatibility complex (MHC) or complement receptors and secrete a variety of soluble biologically active factors, which are either neurotrophic (e.g. Glia-Derived Neurotrophic Factor [GDNF]) or proinflammatory and neurotoxic (e.g. tumour necrosis factor alpha [TNF-α], interleukin 1β [IL-1β], nitric oxide [NO], superoxide, eicosanoids, quinolinic acid). AIM The aim of this work was to assess differences in the expression of microglial markers (ferritin, CD68, and HLA-DR) between AD and Creutzfeldt-Jakob disease (CJD) brains. MATERIAL AND METHODS Analyses were performed on 65 slices derived from 26 brains [46 CJD (20 brains), 12 AD (4 brains) and 7 controls (2 brains)]. Slices were labelled immunohistochemically using anti-ferritin, anti-HLA-DR and anti-CD68 antibodies. The nonparametric Mann-Whitney U test was used to assess quantitative differences between groups. RESULTS The expression of microglia markers (HLA-DR and CD68) is more noticeable in CJD than in AD or control brains. There is no difference between AD and controls. The latter statement is only true in the case of using HLA-DR or CD-68 labelling. Furthermore, ferritin is not a recommended marker in this context. CONCLUSIONS CNS inflammation is more prominent in CJD than in AD or controls. The lack of differences between AD and controls may result from a relatively advanced neurodegeneration in AD brains. In late phases of AD, inflammation is no longer present, in contrast to the early stages of the disease.