Miracle-dz/UniFAR-FTUs huggingface dataset:
FROM MOLECULES TO INSECT COMMUNITIES - HOW FORMAL AGENT BASED COMPUTATIONAL MODELLING IS UNCOVERING NEW BIOLOGICAL FACTS

Agent-based approaches to modelling biological phenomena are becoming popular and proving successful in a number of areas. However, the underlying basis of these techniques is sometimes rather ‘ad-hoc’ and the models are often only applied to specific systems. This paper describes a general approach that is based on the use of fully general computational models, using a formal model of an agent and a rigorous approach to building systems of communicating agents within virtual environments. A collection of tools has been built which allow for efficient simulation of such systems and their visualisation. Included in this work is the implementation of the simulations on parallel clusters of computers to enable large numbers of agents to be simulated. Application areas where the method has been successfully applied include: • Signal transduction pathways, specifically the NF-κB pathway. This model has been validated using single cell data from GFP transvected cells. The model has enabled the prediction of the possible role of actin filaments in the sequestration and feedback control of IκB. • The epitheliome project involves building models of the development of both skin and urothelial tissue and the investigation of the role of calcium and juxtracrine signalling in the development and differentiation of tissue. Again, the models have been validated with ’in vitro’ tissue cultures under a number of important laboratory conditions. • Populations of Pharoah’s ants have been simulated and closely compared with real populations within the laboratory. The role of pheromone signalling has been studied and the modelling has led to a new understanding of the use of pheromone trails in foraging behaviour. This has shown that the geometry of the trails contains vital information that is used in the navigation of the trails by the insects.
Functional Group and Substructure Searching as a Tool in Metabolomics

Background A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases. Methodology We have developed a database named “Biochemical Substructure Search Catalogue” (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest. Conclusions This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed.
Frugal Coordinate Descent for Large-Scale NNLS

The Nonnegative Least Squares (NNLS) formulation arises in many important regression problems. We present a novel coordinate descent method which differs from previous approaches in that we do not explicitly maintain complete gradient information. Empirical evidence shows that our approach outperforms a state-of-the-art NNLS solver in computation time for calculating radiation dosage for cancer treatment problems.
Collecting broken frames: Error statistics in IEEE 802.11b/g links

We present a measurement method that allows to capture the complete set of all PSDU (PLCP Service Data Unit) transmissions and receptions in live IEEE 802.11b/g links with very high timing resolution. This tool provides an in-depth view of the statistics of frame-losses as it makes it possible to distinguish between different loss types such as complete miss, partial corruption and physical-layer capture. Getting access to this low-level statistics on nodes that actively participate in transmissions themselves is a challenging task since the software-interface provided to the network layer needs to remain untouched and cannot be used for tracing. In this contribution we describe in detail how to non-intrusively circumvent these restrictions and also present initial results.
Same-Sex Partnerships and the Health of Lesbian, Gay and Bisexual Older Adults

Same-Sex Partnerships and the Health of Lesbian, Gay and Bisexual Older Adults Mark Edward Williams Chair of the Supervisory Committee: Professor Nancy Hooyman School of Social Work While extensive research has examined associations between marriage, cohabitation and the health of heterosexual adults, it remains unclear whether similar patterns of health are associated with the same-sex partnerships for older adults. The following papers examine how having a same-sex partner may be related to general self-reported health, mental health, and satisfaction with life for older adults. Analyzing survey data collected from lesbian, gay, and bisexual (LGB) adults 50 years of age and older, the first paper reports findings that those with same-sex partners have significantly better self-reported health, fewer depressive symptoms, less perceived stress, and greater life satisfaction, controlling for gender, age, education, income, sexuality, and relationship duration. Relationship duration did not significantly impact the association between partnership status and health, nor did gender. The importance of culturally sensitive clinical practice and policies that recognize the role that same-sex partnerships may play in older adult health are discussed along with implications for future research. The second paper further examines how identifying as married is associated with significantly fewer depressive symptoms and greater life satisfaction compared to those identifying as unmarried partners, but not significantly less perceived stress. Social integration, as reflected in increasing access to and identification with marriage by LGB older adults, is an important area for future research to examine in order to study how changing social acceptance of sexual minorities may impact older adult health. The final paper reviews the theoretical frameworks that have been employed to study lesbian, gay, and bisexual older adult health. Social determinants of health models are contrasted with social constructionist and post-structural critiques of gender, sexuality, age and health. Future research needs to envision both structural sources of health disparities as well as account for individual agency and the resilient subject as important elements for theorizing the source and meaning of health disparities for lesbian, gay and bisexual older adults.
Adaptação cultural de um instrumento para avaliar a satisfação no trabalho

Introduction: work plays an important role in people’s life and depending on its organization and execution it can generate satisfaction or dissatisfaction. The most widely used method to assess job satisfaction has been the application of measuring instruments. Objective: to perform the cultural adaptation of the Job Satisfaction Survey for use in the context of Brazilian’s workers. Method: the instrument cultural adaptation consisted of the following steps: (1) Translation by two independent translators; (2) Proofreading by a third translator and specialists; (3) Back-translation by two independent translators; (4) Review by a committee review; (5) Verification of the Content Validity Index; (6) Pre-test with nursing personnel; (7) Latest adjustments. Results: semantic, idiomatic, cultural and conceptual equivalence between the translated version and the original version were obtained and it was observed ease of understanding and acceptance of the items of the questionnaire in the context of the nursing personnel. Conclusion: the analysis of the experts committee and the pre-test showed the items are relevant to Brazilian culture and to assess the scale proposed by the original instrument.
Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches.

The solution structure of a 22 nt RNA hairpin and its complex with Co(NH(3))(6)(3+) bound to the GAAA tetraloop has been determined by NMR spectroscopy. Co(NH(3))(6)(3+) has a similar geometry to Mg(H(2)O)(6)(2+) and can be used as a probe for binding sites of completely solvated magnesium ions. The hairpin contains tandem G.A mismatches, similar to the P5abc region of a group I intron, and is closed by a GAAA tetraloop. The tandem G.A mismatches are imino hydrogen bonded in contrast with the sheared G.A mismatches found in a different context in the crystal structure of the P4-P6 domain. Chemical shift changes of the imino protons upon titration of the RNA hairpin with Mg(2+) and with Co(NH(3))(6)(3+) were used to identify ion-binding sites. Paramagnetic resonance broadening upon titration with Mn(2+) was also used. The titration curves gave dissociation binding constants for the magnesium ions in the millimolar range, similar to the binding in the major groove of RNA at tandem G.U base-pairs. Although the largest chemical shift change occurred at an imino proton of one of the G.A base-pairs, no nuclear Overhauser enhancement cross-peaks between the cobalt ligand and neighboring RNA protons were seen, presumably due to the high mobility of the Co(NH(3))(6)(3+) at this site. Nuclear Overhauser enhancement cross-peaks between Co(NH(3))(6)(3+) and the GAAA tetraloop were observed, which allowed the determination of the structure of the tetraloop binding site. The Co(NH(3))(6)(3+) is bound in the major groove of the GAAA tetraloop with hydrogen bonds to guanine base N7 and to phosphate oxygen atoms of the tetraloop.
Graphical Display of Search Trees for Transparent Robot Programming

Search algorithms such as Rapidly-exploring Random Trees (RRTs) are common in robot programming. Including graphical representations of the output of these algorithms in a robotics framework can make the algorithms more accessible to students, and can also help programmers analyze and account for unexpected results. For this project, we used the Tekkotsu open source robot programming framework, available at Tekkotsu.org. We extended Tekkotsu’s graphical user interface for displaying vision data and maps to also display the output of an RRT search. We created several demos using two types of searches: one from a navigation path planner, and one from an arm path planner. In some cases the search had no solution, and the graphical output helped to illustrate why. This confirms the utility of the RRT visualization for explaining unexpected search results. We expect that this tool will also contribute to improved student understanding of the search algorithm.
Evaluating Fisher Information From Data for Task-Driven Data Compression

Sensor networks and other multi-sensor systems collect data upon which estimations are based. How a particular sensor's data is to be used within the sensor system depends on the quality of that sensor's data relative to the other sensor's data. Because Fisher information (FI) is a natural way to assess the quality of a sensor's data, it is desirable to be able to numerically compute the FI for a collected set of data for a specific estimation task. We explore this issue for the specific scenario of FI-driven data compression for a sensor system tasked with estimating an RF emitter's location. The data compression scheme uses sub-band coding and therefore for FI-driven data compression it is important to numerically assess the FI of each filter bank output sample. However, as we demonstrate, an orthogonal filter bank well-suited to the compression task seems ill-suited to the FI-assessment task. Alternatively we demonstrate that the STFT is well-suited to FI-assessment but-as is well known-is ill-suited to the compression task. This leads to a hybrid structure for the sub-band coding scheme that uses the STFT for time-frequency domain assessment of the FI but retains the orthogonal filter bank for the compression processing.
Machine “ Gaydar ” : Using Facebook Profiles to Predict Sexual Orientation

The rise of social media and the large, rich datasets they make accessible have allowed us to learn about people not only through information shared explicitly, but also through information shared implicitly in the form of trends and patterns. Here, we emphasize the value of implicit data by creating a machinelearning algorithm that uses basic information, photos, and published text on Facebook profiles to predict sexual orientation in males. We constructed a model with Naïve Bayes classifiers and a Support Vector Machine, performing on different types of data. We used 10-fold stratified cross-validation on our dataset as a measure of generalization error. Currently, we have created a model with an accuracy of 91.02%.
SELFGUESSING FUZZY CLASSIFIERS

The problem of construction of the fuzzy classification models (fuzzy classifiers) with high generalization ability is discussed. The strong self guessing property of fuzzy classificational models is introduced and examined. It is proved that this characteristic doesn't fonn a full system of restrictions, i.e., for the unambiguous detection of the most valid fuzzy classifier (among the set of fuzzy classifiers agreed with arbitrary learning set) it is necessary to use additional "regularizing" restrictions.
PLIB ontology integration to networked manufacturing information system

Nowadays the need for sharing and exchanging information is becoming more and more important. Semantic conflicting is one of main problems that face integration of manufacturing systems based on different dada sources and structure. Based on ontology, this paper proposes an integration framework for manufacturing systems. In this paper, we mainly discuss the realization of the PLIBEI platform. Firstly, the requirement of the integration of this platform is discussed. Then the two core parts (web-based parts library and part search engine) of this platform are pointed out and analyzed. Through requirement analysis, we think PLIB ontology is fit for the solution of these requirements (unambiguous description, integration automatically, variant design in real time etc). At last, the realization method and farther work are introduced. The small and medium-sized enterprises (SMEs) can solve their complex project tasks and participate in projects far exceeding their individual capabilities.
Recurrent Scale Approximation for Object Detection in CNN

Since convolutional neural network (CNN) lacks an inherent mechanism to handle large scale variations, we always need to compute feature maps multiple times for multiscale object detection, which has the bottleneck of computational cost in practice. To address this, we devise a recurrent scale approximation (RSA) to compute feature map once only, and only through this map can we approximate the rest maps on other levels. At the core of RSA is the recursive rolling out mechanism: given an initial map on a particular scale, it generates the prediction on a smaller scale that is half the size of input. To further increase efficiency and accuracy, we (a): design a scale-forecast network to globally predict potential scales in the image since there is no need to compute maps on all levels of the pyramid. (b): propose a landmark retracing network (LRN) to retrace back locations of the regressed landmarks and generate a confidence score for each landmark; LRN can effectively alleviate false positives due to the accumulated error in RSA. The whole system could be trained end-to-end in a unified CNN framework. Experiments demonstrate that our proposed algorithm is superior against state-of-the-arts on face detection benchmarks and achieves comparable results for generic proposal generation. The source code of our system is available.
Mutation of a Dibasic Amino Acid Motif Within the C Terminus of the P2X7 Nucleotide Receptor Results in Trafficking Defects and Impaired Function 1

Activation of the P2X7 receptor by extracellular nucleotides modulates multiple immune functions, including inflammatory mediator production, membrane fusion events, and apoptosis. Previous studies have revealed that the C terminus of this multimeric cation channel possesses a lipid-interaction motif that has been proposed to regulate receptor function. This domain is homologous to the LPS binding region of the LPS binding protein, and we demonstrated that two basic residues (Arg578, Lys579) within this motif are essential for LPS binding to P2X7 in vitro. Because P2X7 can influence LPS action, and because lipid interaction motifs modulate the trafficking of other ion channel-linked receptors, we hypothesized that this motif of P2X7 is critical for receptor function and trafficking. In these studies we mutated Arg578 and Lys579 of P2X7, and the expression profile, channel activity, and pore formation of the mutant were characterized in transfected human embryonic kidney 293 cells. In contrast with the wild-type receptor, the P2X7-R578E/K579E mutant fails to demonstrate surface immunoreactivity despite normal levels of total protein expression. This effect on the mutant receptor is unlikely to result from widespread defects in protein folding, because surface localization, determined using conformation-specific Abs, can be restored by growing the cells at 25°C, conditions that slow receptor recycling. Despite surface expression at reduced temperatures, at 25°C the P2X7-R578E/K579E mutant still exhibits greatly reduced sodium, potassium, and calcium channel activity when compared with the wild-type receptor, and cannot induce pore formation. These data suggest that the lipid interaction motif of the P2X7 C terminus controls receptor trafficking and modulates channel activity.
Evaluation of Antioxidant Activity of Tetracarpidium conophorum (Müll. Arg) Hutch & Dalziel Leaves

This study evaluated the antioxidant activity as well as bioflavonoid content of the methanol and ethanol-water extracts of the fresh and dried leaves of Tetracarpidium conophorum. Antioxidant activity was determined by spectrophotometric methods using DPPH free radical, nitric oxide radical inhibition and ferric reducing antioxidant power assays. In addition, total phenolics, flavonoids and proanthocyanidin content were also determined. The ethanol: water extract of the dried leaves had the highest antioxidant activity with a 50% inhibition of DPPH at a concentration of 0.017 mg/mL compared to the standards, Vitamin C and Vitamin E with inhibition of 0.019 and 0.011 mg/mL, respectively. This extract also showed nitric oxide radical inhibition activity comparable to that of rutin, 54.45% and 55.03% for extract and rutin, respectively, at 0.1 mg/mL. Ferric reducing power was also comparable to that of ascorbic acid (281 and 287 μM Fe (11)/g, resp. ) at a concentration of 1 mg/mL. The methanol extract of both the dried and the fresh leaves had higher phenolic, flavonoids and proanthocyanidin content than the ethanol : water extract. The study reveals that T. conophorum can be an interesting source of antioxidants with their potential use in different fields namely food, cosmetics and pharmaceuticals.
The Comprehensive Assessment of Rational Thinking

The Nobel Prize in Economics was awarded in 2002 for work on judgment and decision-making tasks that are the operational measures of rational thought in cognitive science. Because assessments of intelligence (and similar tests of cognitive ability) are taken to be the quintessence of good thinking, it might be thought that such measures would serve as proxies for the assessment of rational thought. It is important to understand why such an assumption would be misplaced. It is often not recognized that rationality and intelligence (as traditionally defined) are two different things conceptually and empirically. Distinguishing between rationality and intelligence helps explain how people can be, at the same time, intelligent and irrational. Thus, individual differences in the cognitive skills that underlie rational thinking must be studied in their own right because intelligence tests do not explicitly assess rational thinking. In this article, I describe how my research group has worked to develop the first prototype of a comprehensive test of rational thought (the Comprehensive Assessment of Rational Thinking).
State-Dependent Scaling Problems and Stability of Interconnected iISS and ISS Systems

This paper addresses the problem of establishing stability of nonlinear interconnected systems. This paper introduces a mathematical formulation of the state-dependent scaling problems whose solutions directly provide Lyapunov functions proving stability properties of interconnected dissipative systems in a unified manner. Stability criteria are interpreted as sufficient conditions for the existence of solutions to the state-dependent scaling problems. Computing solutions to the problems is straightforward for systems covered by classical stability criteria. It, however, could be too difficult for systems with strong nonlinearity. The main purpose of this paper is to demonstrate the effectiveness beyond formal applicability by focusing on interconnected integral input-to-state stable (iISS) systems and input-to-state stable (ISS) systems. This paper derives small-gain-type theorems for interconnected systems involving iISS systems from the state-dependent scaling formulation. This paper provides solutions and Lyapunov functions explicitly. The new framework seamlessly generalizes the ISS small-gain theorem and classical stability criteria such as the Lp small-gain theorem, the passivity theorems, the circle, and Popov criteria. State-dependence of the scaling is crucial for effective treatment of essential nonlinearities, while constants are sufficient for classical nonlinearities
Restriction and Modification of Bacteriophage S2 in Haemophilus influenzae

The major conclusion from these studies is that variants of Haemophilus influenzae Rd which restrict and modify phage S2 are metastable and capable of giving rise to one another with high frequency. Nonrestrictive RdS cells segregate spontaneously to the restricting, modifying phenotype in about 5% of the progeny of a single clone. The restrictive cells derived from RdS revert to the nonrestrictive phenotype in 15 to 25% of the progeny of a single clone. These frequencies are not appreciably affected by treatment with acriflavine or ethidium bromide, compounds which affect plasmid stability, or by nitrosoguanidine, a powerful mutagen. The genetic locus for restriction and modification of bacteriophage S2 is found to have a chromosomal position between the biotin and proline loci. Restriction-modification of phage S2 has been shown to be a function of its deoxyribonucleic acid (DNA) in that transfection with S2 phage DNA or prophage DNA is subject to host restriction and modification. An enzyme preparation, which contains endodeoxyribonuclease but no appreciable exonuclease activity, from mutant H. influenzae com−10 did not restrict phage S2·RdS DNA or prophage DNA transfecting activity, indicating that this endodeoxyribonuclease is not responsible for phage restriction. A new restriction enzyme isolated from H. influenzae Rd was found to be the major enzyme involved in the restriction of bacteriophage S2. The enzyme inactivated the transfecting activity of unmodified phage DNA but did not attack modified phage DNA. Unlike endodeoxyribonuclease R, this enzyme requires adenosine triphosphate and S-adenosylmethionine.