Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation in visualization: some issues and best practices

The first data and information visualization techniques and systems were developed and presented without a systematic evaluation; however, researchers have become, and are more and more, aware of the importance of evaluation (Plaisant, 2004)1. Evaluation is not only a means of improving techniques and applications, but it can also produce evidence of measurable benefits that will encourage adoption. Yet, evaluating visualization applications or techniques, is not simple. We deem visualization applications should be developed using a user-centered design approach and that evaluation should take place in several phases along the process and with different purposes. An account of what issues we consider relevant while planning an evaluation in Medical Data Visualization can be found in (Sousa Santos and Dillenseger, 2005) 2. In that work the question “how well does a visualization represent the underlying phenomenon and help the user understand it? ” is identified as fundamental, and is decomposed in two aspects: A) the evaluation of the representation of the phenomenon (first part of the question). B) the evaluation of the users’ performance in their tasks when using the visualization, which implies the understanding of the phenomenon (second part of the question). We contend that these questions transcend Medical Data Visualization and can be considered central to evaluating Data and Information Visualization applications and techniques in general. In fact, the latter part of the question is related to the question Freitas et al. (2009) 3 deem crucial to user centered visualization evaluation: “How do we know if information visualization tools are useful and usable for real users performing real visualization tasks? ” In what follows issues and methods that we have been using to tackle this latter question, are briefly addressed. This excludes equally relevant topics as algorithm optimization, and accuracy, that can be dealt with using concepts and methods well known in other disciplines and are mainly related to how well the phenomenon is represented. A list of guidelines considered as our best practices to perform evaluations is presented and some conclusions are drawn.
Active site substitution A82W improves regioselectivity of steroid hydroxylation by cytochrome P450 BM3 mutants as rationalised by spin relaxation NMR studies

Cytochrome P450 BM3 from Bacillus megaterium is a monoxygenase with great potential for biotechnological applications. In this work, we present engineered drug metabolizing P450 BM3 mutants as a novel tool for regioselective hydroxylation of steroids at position 16ß. In particular, we show that by replacing alanine at position 82 with a tryptophan in P450 BM3 mutants M01 and M11, the selectivity toward 16ß-hydroxylation for both testosterone and norethisterone was strongly increased. The A82W mutation led to a < 42-fold increase in Vmax for 16ß-hydroxylation of these steroids. Moreover, this mutation improves the coupling efficiency of the enzyme, which might be explained by a more efficient exclusion of water from the active site. The substrate affinity for testosterone increased at least 9-fold in M11 with tryptophan at position 82. A change in the orientation of testosterone in the M11 A82W mutant as compared to the orientation in M11 was observed by T1 paramagnetic relaxation nuclear magnetic resonance. Testosterone is oriented in M11 with both the Aand D-ring protons closest to the heme iron. Substituting alanine at position 82 with tryptophan results in increased A-ring proton-iron distances, consistent with the relative decrease in the level of A-ring hydroxylation at position 2. Chapter 4 Regioselective steroid hydroxylation 4.
The Validity of the Health-Relevant Personality Inventory (HP5i) and the Junior Temperament and Character Inventory (JTCI) Among Adolescents Referred for a Substance Misuse Problem

The aim was to study the validity of 2 personality instruments, the Health-Relevant Personality Inventory (HP5i) and the Junior Temperament and Character Inventory (JTCI), among adolescents with a substance use problem. Clinical interviews were completed with 180 adolescents and followed up after 12 months. Discriminant validity was demonstrated in the lack of correlation to intelligence in both instruments’ scales. Two findings were in support of convergent validity: Negative affectivity (HP5i) and harm avoidance (JTCI) were correlated to internalizing symptoms, and impulsivity (HP5i) and novelty seeking (JTCI) were correlated to externalizing symptoms. The predictive validity of JTCI was partly supported. When psychiatric symptoms at baseline were controlled for, cooperativeness predicted conduct disorder after 12 months. Summarizing, both instruments can be used in adolescent clinical samples to tailor treatment efforts, although some scales need further investigation. It is important to include personality assessment when evaluating psychiatric problems in adolescents.
Bank Competition and Collateral: Theory and Evidence

We investigate the impact of bank competition on the use of collateral in loan contracts. We analyze asymmetric information about the borrowers’ type in a Salop model in which banks choose between screening the borrower and asking for collateral. We show that the presence of collateral is more likely when bank competition is low. We then test this prediction empirically on a sample of bank loans from 70 countries. We perform logit regressions of the presence of collateral on bank competition, measured by the Lerner index. Our empirical tests corroborate the theoretical predictions that bank competition reduces the presence of collateral. These findings survive several robustness checks.
Optical second-harmonic generation by quasi-phase matching in channel waveguide structure using organic molecular crystal

Waveguide quasi-phase matching second-harmonic generation (QPM-SHG) using an organic molecular crystal as a nonlinear material was demonstrated for the first time. The device is constructed with an array of SiN channel guides with grooves of a fan-out grating pattern and mNA single crystal grown over the waveguides. A normalized efficiency of 0.04%/W was obtained in an experiment involving frequency doubling of CW Nd:YAG laser light. <<ETX>>
Ectopic expression of an endoparasitic wasp venom protein in Drosophila melanogaster affects immune function, larval development and oviposition

Endoparasitic hymenoptera inject maternal factors into the host, along with their eggs, to subvert the host immune system. The venom protein, Vn50, previously characterized from the wasp Cotesia rubecula inhibits prophenoloxidase activation in its host Pieris rapae and in another lepidopteran, Manduca sexta. We generated a stable line in the model insect, Drosophila melanogaster, which ectopically expresses Vn50. Results indicated that Vn50 expression accelerates larval development, increases oviposition and reduces melanization in the haemolymph of the transgenic flies. Since melanization is known to be an important facet of the insect immune response, we examined the impact of Vn50 expression on susceptibility to pathogens. Transgenic Vn50 flies challenged with the fungus Beauveria bassiana had increased mortality compared with control flies, but there was no significant change in survival in flies challenged with the pathogenic bacteria, Serratia marcescens. Interestingly, mortality induced by the natural pathogen Drosophila C virus was significantly delayed in Vn50 expressing flies. This indicates a wider range of potential hosts that may be affected by Vn50 and its potential for manipulation of immune system in insects.
Plasma Vasopressin in Uncontrolled Diabetes Mellitus

Concentrations of the antidiuretic hormone, arginine vasopressin, were measured in 28 patients with severe hyperglycemia to determine if abnormalities in hormonal regulation of water excretion could contribute to the extreme dehydration of uncontrolled diabetes mellitus. Vasopressin levels were markedly elevated in both nonketotic and ketotic patients, indicating that vasopressin deficiency plays no role in the polyuria that accompanies hyperglycemia. Instead, the observed increases in vasopressin represent an ineffective effort to conserve water in the face of an overwhelming solute diuresis caused by the glucosuria. The reasons for such marked elevations in plasma vasopressin in these diabetic patients are multifactorial. Both groups of diabetic patients had evidence of hypovolemia, which was sufficient in magnitude to stimulate vasopressin release. Furthermore, nausea provided an independent stimulus to vasopressin secretion in many patients. Osmotic stimulation might have resulted from the large fraction of unidentified plasma solutes, but this factor alone was not sufficient to explain the markedly increased concentrations of vasopressin. Whether such elevations in vasopressin could have metabolic and/or hemodynamic effects in uncontrolled diabetes remains to be established.
Al-Ghazali's concept of causality : with reference to his interpretations of reality and knowledge

The fundamental thesis upon which this book embarks is that al-Ghazali did not deny causality. However, to affirm causality, for al-Ghazali, is not necessarily to adhere categorically to the conceptual edifice of the kalam and the falasifah. He establishes the concept on his own, based on his understanding of the fundamental tenets in the worldview of Islam, without abandoning the philosophical essence of his predecessors as well as his adversaries. He concurs with the doctrine of atomism in the kalam tradition, which was constructed to prove the direct God-world relation as the explanation of the concept of God’s omnipotence, but he creatively construes the doctrine to be in accord with the general principle laid down in the Qur’an, the source of the worldview of Islam. He also agrees with the falEsifah in positing that there is uniformity in nature, that one event follows from another, or there are laws of causation in natural events, yet he jettisons their postulate that the causation is one of necessary concomitance. Al-Ghazali’s concept of causality, presented in this book, reflected his integrative thought that reconciles the discourses in the falEsifah and the kalam, reason and revelation, as well as the physical and the metaphysical realms. This book, therefore, could be instrumental for preliminary discussions on the development of the Islamic sciences.
Advances in Proteomic Technologies and Its Contribution to the Field of Cancer

Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.
Novel Function of the Fanconi Anemia Group J or RECQ1 Helicase to Disrupt Protein-DNA Complexes in a Replication Protein A-stimulated Manner*

Background: DNA unwinding by helicases is blocked by proteins bound to duplex DNA. Results: The single-stranded DNA-binding protein RPA stimulates FANCJ or RECQ1 helicase to disrupt protein-DNA complexes. Conclusion: Helicases partner with RPA to dislodge proteins bound to duplex DNA. Significance: Regulation of helicase-catalyzed protein displacement is highly relevant in cellular nucleic acid metabolic processes that require remodeling of chromatinized genomic DNA. Understanding how cellular machinery deals with chromosomal genome complexity is an important question because protein bound to DNA may affect various cellular processes of nucleic acid metabolism. DNA helicases are at the forefront of such processes, yet there is only limited knowledge how they remodel protein-DNA complexes and how these mechanisms are regulated. We have determined that representative human RecQ and Fe-S cluster DNA helicases are potently blocked by a protein-DNA interaction. The Fanconi anemia group J (FANCJ) helicase partners with the single-stranded DNA-binding protein replication protein A (RPA) to displace BamHI-E111A bound to duplex DNA in a specific manner. Protein displacement was dependent on the ATPase-driven function of the helicase and unique properties of RPA. Further biochemical studies demonstrated that the shelterin proteins TRF1 and TRF2, which preferentially bind the telomeric repeat found at chromosome ends, effectively block FANCJ from unwinding the forked duplex telomeric substrate. RPA, but not the Escherichia coli single-stranded DNA-binding protein or shelterin factor Pot1, stimulated FANCJ ejection of TRF1 from the telomeric DNA substrate. FANCJ was also able to displace TRF2 from the telomeric substrate in an RPA-dependent manner. The stimulation of helicase-catalyzed protein displacement is also observed with the DNA helicase RECQ1, suggesting a conserved functional interaction of RPA-interacting helicases. These findings suggest that partnerships between RPA and interacting human DNA helicases may greatly enhance their ability to dislodge proteins bound to duplex DNA, an activity that is likely to be highly relevant to their biological roles in DNA metabolism.
Toward Argumentation-Based Cyber Attribution

A major challenge in cyber-threat analysis is combining information from different sources to ﬁnd the person or the group responsible for the cyber-attack. It is one of the most important technical and policy challenges in cyber-security. The lack of ground truth for an individual responsible for an attack has limited previous studies. In this paper, we overcome this limitation by building a dataset from the capture-the-ﬂag event held at DEFCON, and propose an argumentation model based on a formal reasoning framework called DeLP (Defeasible Logic Programming) designed to aid an analyst in attributing a cyber-attack to an attacker. We build argumentation-based models from latent variables computed from the dataset to reduce the search space of culprits (attackers) that an analyst can use to identify the attacker. We show that reducing the search space in this manner signiﬁcantly improves the performance of classiﬁcation-based approaches to cyber-attribution.
Improving Statistical Linguistic Algorithms for Parsing Mathematics

In this paper we describe our combined statistical/semantic parsing method based on the CYK chart-parsing algorithm augmented with limited internal typechecking and external ATP filtering. This method was previously evaluated on parsing ambiguous mathematical expressions over the informalized Flyspeck corpus of 20000 theorems. We first discuss the motivation and drawbacks of the first version of the CYK-based component of the algorithm, and then we propose and implement a more sophisticated approach based on better statistical model of mathematical data structures.
Design and Experiments of the 600 kV Coaxial-Type Matched Divider for High-Power Microwave Source Array

A coaxial-type high-voltage matched divider transmitting the identical quasi-square wave pulse to the high-power microwave array sources is first proposed. To identically divide the quasi-square wave short pulse with an amplitude of above 500 kV, a pulse duration of above 20 ns, and rise time of 20-30 ns without electrical breakdown and pulse distortion, it employs a simple matched two-way coaxial divider, a coaxial-type solid dielectric spacer with the positive angle of 45° to support the inner and outer conductors for a coaxial geometry and also the improved field shaper to reduce significantly the electric field strength to near zero at the cathode triple junction. This type of divider provides an alternative way to generate the same quasi-square pulse at the same time from a single-pulse power generator under nanosecond pulse and high holdoff voltage capability. The transmission of the quasi-square wave pulse with an amplitude lager than 500 kV in the coaxial-type matched divider has been successfully demonstrated.
Toll-like receptors, inflammation, metabolism and obesity

Obesity is a highly prevalent health problem in Western countries that leads to many important diseases such as type 2 diabetes and metabolic syndrome being now considered an inflammatory chronic disease. Adipocytes are no longer considered passive cells storing fat since they are major producers of inflammatory cytokines during obesity. Adipocytes and macrophages share many biological properties including the synthesis of similar molecules regulating inflammation. Fatty acid levels are elevated in obesity and induce inflammatory pathways by yet a mostly unknown mechanism, leading to the development of insulin and leptin resistance. Recent studies suggest that these effects could be mediated through the activation of toll-like receptors (TLR). TLR signalling pathways might contribute to the development of obesity-associated insulin resistance, thus representing a connection between innate immunity and metabolism. Here, we summarize the recent evidence for the important role that TLRs play in adipose tissue, obesity and insulin resistance.
Final-State Control Using a Time-Symmetric Polynomial Input

For information devices such as hard disk drives, actuators must be controlled as quickly and precisely as possible. The design of the feedforward input is very important in satisfying these requirements. Therefore, we have proposed design methods based on final-state control so as to reduce its spectrum at the desired frequency points. Furthermore, the final-state control method has been extended to generate the feedforward input using a polynomial. By using a polynomial, the required memory size can be drastically reduced because only the coefficients of the polynomial must be stored. However, when the step number of the input increases, the method may not produce a correct solution because of a numerically ill-posed problem. In this paper, we propose a design method for the final-state control based on a time-symmetric polynomial input. The simulation results show that the proposed method contributes to the improvement of not only the numerically ill-posed problem but also the performance.
Of Trophies and Pillars: Exploring the Terror Management Functions of Short-Term and Long-Term Relationship Partners

Prior terror management research shows that mortality salience (MS) motivates both self-esteem striving and worldview bolstering. The present research examined these processes in the context of dating preferences. It was hypothesized that in short-term romantic contexts, MS-induced self-esteem striving motivates interest in dating a physically attractive other, whereas in long-term romantic contexts, MS-induced motives for worldview validation heighten interest in dating a same-religion other. Study 1 showed that in a short-term dating context, MS increased preference for an attractive but religiously dissimilar person, whereas in a long-term dating context, MS increased preference for a religiously similar, less attractive person. Study 2 clarified that MS motivates preference for attractive short-term partners for their self-enhancing properties rather than their potential sexual availability. Study 3 supported the theorized processes, showing that under MS, self-esteem-relevant constructs became spontaneously accessible in short-term dating contexts, whereas worldview-relevant constructs became spontaneously accessible in long-term dating contexts.
Twenty-five years of breast cancer risk models and their applications.

I would like to thank the editors for the invitation to comment on “Projecting Individualized Probabilities of Developing Breast Cancer for White Females Who Are Being Examined Annually” (1) and to recognize coauthors of that article, Louise A. Brinton, David P. Byar, Donald K. Corle, Sylvan B. Green, Catherine Schairer, and John J. Mulvihill, who contributed key insights and analyses. Several features may explain the frequent citations to this paper. 1) It focused on a clinically crucial quantity, absolute risk, namely the probability that a woman with specific risk factors will develop breast cancer over a defined age interval, with allowance for competing risks. 2) Breast cancer is a common cancer for which preventive interventions have been developed. Risk models are most useful in connection with interventions because the absolute risk of breast cancer can be compared with that of other health outcomes in the presence and absence of intervention. 3) The model is simple: only age and answers to five questions about reproductive, family, and medical history are needed. 4) The model (sometimes called the “Gail model”) has been taken up by practitioners and is available at http://www.cancer. gov/bcrisktool/ as the National Cancer Institute’s (NCI’s) Breast Cancer Risk Assessment Tool (BCRAT). Currently this site is visited over three million times a year. I shall elaborate on the first two points, mention alternative models, and discuss prospects for improving risk models and other applications of absolute risk.
Neural Network Classifiers Estimate Bayesian a posteriori Probabilities

Many neural network classifiers provide outputs which estimate Bayesian a posteriori probabilities. When the estimation is accurate, network outputs can be treated as probabilities and sum to one. Simple proofs show that Bayesian probabilities are estimated when desired network outputs are 1 of M (one output unity, all others zero) and a squared-error or cross-entropy cost function is used. Results of Monte Carlo simulations performed using multilayer perceptron (MLP) networks trained with backpropagation, radial basis function (RBF) networks, and high-order polynomial networks graphically demonstrate that network outputs provide good estimates of Bayesian probabilities. Estimation accuracy depends on network complexity, the amount of training data, and the degree to which training data reflect true likelihood distributions and a priori class probabilities. Interpretation of network outputs as Bayesian probabilities allows outputs from multiple networks to be combined for higher level decision making, simplifies creation of rejection thresholds, makes it possible to compensate for differences between pattern class probabilities in training and test data, allows outputs to be used to minimize alternative risk functions, and suggests alternative measures of network performance.
Green IS: Steps Towards a Research Agenda

In this chapter, we investigate the role of ICT in dealing with environmental challenges facing contemporary industrial organizations. Green IS research can essentially be divided into two groups, focusing on technology per se or on providing tools that decreases environmental impact. Building on a planned research project we propose innovation of ICT-based services, and especially collaborative services, as useful strategies for providing firms with sense and respond capabilities in relation to environmental challenges. We also argue research that research relevance and multi-disciplinary competencies are key themes that IS researcher needs to acknowledge in order to contribute to practitioners efforts.