Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovering Clinical Biomarkers of Chronic Hepatitis B by Mining Mutation Hotspots

Hepatitis B virus (HBV) is the most common DNA virus that may cause hepatitis, cirrhosis and hepatocellular carcinoma. Although many people are persistently infected with HBV, the serum viral load and host immune response varies from person to person. Because the high rate of mutations in HBV protein sequences will alter the protein expressions and even their functions, in this paper, we explore to discover clinical biomarkers of chronic hepatitis B by mining mutation hotspots. A one year follow-up study was conducted with a total number of 1,694 clones from 23 patients with HBeAg-positive chronic hepatitis B. Serum alanine aminotransferase, HBV DNA and HBeAg levels were monthly measured and used as the criteria for clustering the patients into different subgroups. Using monthly derived HBV precore/core protein sequences, we analyzed amino acid mutations responsible for serologic and clinical outcome of each patient subgroup. Using an integration of covariance network and point mutation rule methods, we identified several representative covariance networks of each patient subgroup. Validation with literature-curated mutation hotspots showed that the identified mutations were strongly associated with the viral loads, presence of HBeAg-seroconversion in sera, HBV genotypes and amino acid properties. We further used these identified networks containing mutation hotspots to develop a feature tree, which is applicable for clinicians to prescribe patients a suitable treatment at early stage of HBV infection even though the patients exhibit no obvious symptoms.
Psychology and the Geography of Innovation

abstract Intangibles, such as tolerance, creativity and trust, are increasingly seen as important for the geography of innovation. Yet these factors have often been poorly approximated in empirical research that has used generalized proxy measures to account for subtle personal differences. This article argues that the psychological literature on personality traits can help address this issue and provide important insights into the socioinstitutional determinants of innovation. It uses a unique, large-scale psychological survey to investigate the relationship between the Big Five personality traits commonly used in psychology—openness to experience, neuroticism, extraversion, agreeableness, and conscientiousness—and patenting in travel-to-work areas in England and Wales. The main personality trait associated with innovation is conscientiousness, a trait defined by organization, hard work, and task completion. Instrumental variable analysis using religious observance in 1851 suggests that this is a causal relationship. Research on the role of intangibles in innovation has been preoccupied by factors, such as creativity and trust, but the results of this article suggest that a new focus—on hard work and organizational ability—is needed.
Learning through culture: seeking “critical case studies of possibilities” in the history of education

Abstract In Radical Education and the Common School (2011), Michael Field and Peter Moss argue for a radical alternative to the failed and dysfunctional contemporary discourse about education and the school with its focus on markets, competition, instrumentality, standardisation, and managerialism. They argue that it is necessary, if we are to progress “social alternatives” in education, to construct micro-histories of schools that have developed as “real utopias” through radically revising their practice. They call these micro-histories “critical case studies of possibilities”. In To Hell with Culture (1963), the art educator and anarchist Herbert Read returned to a theme he had been exploring since the early 1930s – the purpose of education. For him, “education” implied many things, but he saw modern practice as “socially disintegrating”. Instead, Read offered an alternative to the dominant discourse about education under capitalism in the 1960s which would create “that collective consciousness which is the spiritual energy of a people and the only source of its art and culture”. To what extent was Read’s conception of education an ideal, a dream unfulfilled? Following Fielding and Moss this paper will seek to trace “critical case studies of possibilities” drawn from the past which reflect the fundamental connection identified by Read between school learning, “collective consciousness”, art, and culture.
Status of MISR cloud-motion wind product

Near-simultaneous multi-angle imagery from the Multi-angle Imaging SpectroRadiometer (MISR) forms the basis of a unique method able to simultaneously retrieve cloud motion and height from a polar orbiter platform. The method is fully automated and determines the characteristic horizontal wind for a mesoscale domain of 70.4×70.4 km. Provided the co-registration of the multiangle views is accurate to a pixel, the theoretical retrieval uncertainty can be as small as ±3 ms for wind and ±400 m for height. In this paper, we give a brief summary of the retrieval scheme, demonstrating its capabilities with two examples. In addition, we discuss product validation efforts and suggest two possible improvements: (1) providing quality indicators for wind vectors, and, (2) increasing the spatial coverage of the retrievals.
Airway dimensions measured from micro-computed tomography and high-resolution computed tomography

Volume averaging results in both over- and underestimation of airway dimensions when they are measured by high-resolution computed tomography (HRCT). The current authors calibrated computerised measurements of airway dimensions from HRCT against a novel three-dimensional micro-computed tomography (CT) standard, which has a 50-fold greater resolution, as well as against traditional morphometry. Inflation-fixed porcine lung cubes were scanned by HRCT and micro-CT. A total of 59 lumen area (Ai), 30 wall area (Aaw) and 11 lumen volume (Vi) measurements were made. Ai was measured from the cut surface of 11 airways by morphometry. Airways in scanned images were matched using branching points. After calibration, the errors of Ai, Aaw and Vi HRCT measurements were determined. The current authors found a systematic, size-dependent underestimation of Ai and overestimation of Aaw from HRCT measurements. This was used to calibrate an HRCT measurement algorithm. The 95% limits of agreement of subsequent measurements were ±3.2 mm2 for Ai, ±4.3 mm2 for Aaw, and ±11.2 mm3 for Vi with no systematic error. Morphometric measurements agreed with micro-CT (±2.5 mm2) without systematic error. In conclusion, micro-computed tomography image data from inflation-fixed airways can be used as calibration standards for three-dimensional lumen volume measurements from high-resolution computed tomography, while morphometry is acceptable for two-dimensional measurements. The image dataset could be used to validate other developmental three-dimensional segmentation algorithms.
Local Gene Expression Changes after UV-Irradiation of Human Skin

UV-irradiation is a well-known translational pain model inducing local inflammation and primary hyperalgesia. The mediators and receptor proteins specifically contributing to mechanical or heat hyperalgesia are still unclear. Therefore, we irradiated buttock skin of humans (n = 16) with 5-fold MED of UV-C and assessed the time course of hyperalgesia and axon reflex erythema. In parallel, we took skin biopsies at 3, 6 and 24 h after UVC irradiation and assessed gene expression levels (RT-PCR ) of neurotrophins (e.g. NGF, BDNF, GDNF), ion channels (e.g. NaV1.7, TRPV1), inflammatory mediators (e.g. CCL-2, CCL-3) and enzymes (e.g. PGES, COX2). Hyperalgesia to mechanical impact (12 m/s) and heat (48°C) stimuli was significant at 6 h (p<0.05 and p<0.01) and 24 h (p<0.005 and p<0.01) after irradiation. Axon reflex erythema upon mechanical and thermal stimuli was significantly increased 3 h after irradiation and particularly strong at 6 h. A significant modulation of 9 genes was found post UV-C irradiation, including NGF (3, 6, 24 h), TrkA (6, 24 h), artemin, bradykinin-1 receptor, COX-2, CCL-2 and CCL-3 (3 and 6 h each). A significant down-regulation was observed for TRPV1 and iNOS (6, 24 h). Individual one-to-one correlation analysis of hyperalgesia and gene expression revealed that changes of Nav1.7 (SCN9A) mRNA levels at 6 and 24 h correlated to the intensity of mechanical hyperalgesia recorded at 24 h post UV-irradiation (Pearson r: 0.57, p<0.04 and r: 0.82, p<0.001). Expression of COX-2 and mPGES at 6 h correlated to the intensity of heat-induced erythema 24 h post UV (r: 0.57, p<0.05 for COX-2 and r: 0.83, p<0.001 for PGES). The individual correlation analyses of functional readouts (erythema and pain response) with local expression changes provided evidence for a potential role of Nav1.7 in mechanical hyperalgesia.
Evoked responses in anaesthesia.

Evoked responses are derived from the electroencephalogram (EEG) in response to auditory, somatosensory, nociceptive and visual stimuli. These evoked responses are obvious candidates for investigation as they reflect the functional integrity of specific peripheral and central nervous system (CNS) regions in humans. The changes that occur in the evoked responses allow anaesthetists to assess the effects of the drugs that they are administering on the target site, namely the brain, in vivo. Consequently, interest in evoked response monitoring in the three speciality areas of clinical anaesthesia (general anaesthesia, intensive care and pain assessment), has increased considerably in the past 10–15 yr. This review explores the potential usefulness of evoked responses in fulfilling these aims, based on an understanding of the research in these areas.
SEKS PRANIKAH BAGI REMAJA: Studi Fenomenologis pada Remaja yang Melakukan Hubungan Seksual Pranikah

Intimacy relationship pada remaja memiliki kecenderungan untuk melakukan seks pranikah. Berdasarkan data yang diperoleh dari BKKBN (2014), terdapat 46% remaja berusia 15-19 tahun sudah berani melakukan hubungan seksual pranikah. Penelitian ini dilakukan untuk mendeskripsikan pengalaman remaja yang melakukan hubungan seksual pranikah, serta mengetahui faktor-faktor dan dampak yang dialami remaja yang melakukan hubungan seksual pranikah. Metode yang digunakan dalam penelitian ini adalah metode kualitatif dengan pendekatan fenomenologis. Data diperoleh melalui wawancara dengan subjek penelitian. Karakteristik subjek penelitian adalah remaja berusia 18-21 tahun dan sudah pernah melakukan hubungan seksual pranikah. Berdasarkan hasil penelitian, kedua subjek memiliki latar belakang keluarga yang hampir sama, yaitu kurang terjalin kelekatan dengan orang tua. Kedua subjek merasa nyaman dan lebih terbuka dengan pacar, sehingga pacar dijadikan sebagai objek lekat. Faktor-faktor yang menyebabkan terjadinya hubungan seksual pranikah adalah kurang terbukanya orang tua mengenai masalah seksual, adanya kesempatan untuk melakukan hubungan seksual pranikah, sumber informasi yang salah mengenai seksualitas, rasa ingin tahu yang tinggi, kebutuhan biologis, rangsangan seksual, dan pengaruh lingkungan pertemanan. Dampak dari berhubungan seksual dengan pacar membuat Subjek 1 ketagihan dan mengganggu pikirannya, sedangkan intensitas beribadah Subjek 2 menjadi kurang akibat berhubungan seksual dengan pacar.
Dynamic level of detail for large scale agent-based urban simulations

Large scale agent-based simulations typically face a trade-off between the level of detail in the representation of each agent and the scalability seen as the number of agents that can be simulated with the computing resources available. In this paper, we aim at bypassing this trade-off by considering that the level of detail is itself a parameter that can be adapted automatically and dynamically during the simulation, taking into account elements such as user focus, or specific events. We introduce a framework for such a methodology, and detail its deployment within an existing simulator dedicated to the simulation of urban infrastructures. We evaluate the approach experimentally along two criteria: (1) the impact of our methodology on the resources (CPU use), and (2) an estimate of the dissimilarity between the two modes of simulation, i.e. with and without applying our methodology. Initial experiments show that a major gain in CPU time can be obtained for a very limited loss of consistency.
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of ≈65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome.
The Economics of Labor Coercion Daron Acemoglu

The majority of labor transactions throughout much of history and a significant fraction of such transactions in many developing countries today are "coercive," in the sense that force or the threat of force plays a central role in convincing workers to accept employment or its terms. We propose a tractable principal-agent mode! of coercion, based on the idea that coercive activities by employers, or ''guns," affect the participation constraint of workers. We show that coercion and effort are complements, so that coercion increases effort. Nevertheless, coercion is always "inefficient," in the sense of reducing utilitarian social welfare. Better outside options for workers reduce coercion, because of the complementarity between coercion and effort: workers with better outside option exert lower effort in equilibrium and thus are coerced less. Greater demand for labor increases coercion because it increases equilibrium effort. We investigate the interaction between outside options, market prices, and other economic variables by embedding the (coercive) principal-agent relationship in a general equilibrium setup, and study when and how labor scarcity encourages coercion. We show that general (market) equilibrium interactions working through prices lead to a positive relationship between labor scarcity and coercion along the lines of ideas suggested by Domar, while those working through outside options lead to a negative relationship similar to ideas advanced in neo-Malthusian historical analyses of the decline of feudalism. A third effect, which is present when investment in guns must be made before the realization of contracting opportunities, also leads to a negative relationship between labor scarcity and coercion. Our model also predicts that the slave trade makes slaves worse off, conditional on enslavement, and that coercion is more viable in industries that do not require relationship-specific investment by workers.
Irrelevant stimulus processing in ADHD: catecholamine dynamics and attentional networks

A cardinal symptom of attention deficit and hyperactivity disorder (ADHD) is a general distractibility where children and adults shift their attentional focus to stimuli that are irrelevant to the ongoing behavior. This has been attributed to a deficit in dopaminergic signaling in cortico-striatal networks that regulate goal-directed behavior. Furthermore, recent imaging evidence points to an impairment of large scale, antagonistic brain networks that normally contribute to attentional engagement and disengagement, such as the task-positive networks and the default mode network (DMN). Related networks are the ventral attentional network (VAN) involved in attentional shifting, and the salience network (SN) related to task expectancy. Here we discuss the tonic–phasic dynamics of catecholaminergic signaling in the brain, and attempt to provide a link between this and the activities of the large-scale cortical networks that regulate behavior. More specifically, we propose that a disbalance of tonic catecholamine levels during task performance produces an emphasis of phasic signaling and increased excitability of the VAN, yielding distractibility symptoms. Likewise, immaturity of the SN may relate to abnormal tonic signaling and an incapacity to build up a proper executive system during task performance. We discuss different lines of evidence including pharmacology, brain imaging and electrophysiology, that are consistent with our proposal. Finally, restoring the pharmacodynamics of catecholaminergic signaling seems crucial to alleviate ADHD symptoms; however, the possibility is open to explore cognitive rehabilitation strategies to top-down modulate network dynamics compensating the pharmacological deficits.
Optimal strategies to track and capture a predictable target

We present an O(nlog/sup 1+/spl epsiv// n)-time algorithm for computing the optimal robot motion that maintains line-of-sight visibility between a target moving inside a polygon with n vertices which may contain holes. The motion is optimal for the tracking robot (the observer) in the sense that the target either remains visible for the longest possible time, or it is captured by the observer in the minimum time when feasible. Thus, the algorithm maximizes the minimum time-to-escape. Our algorithm assumes that the target moves along a known path. Thus, it is an off-line algorithm. Our theoretical results for the algorithm's runtime assume that the target is moving along a shortest path from its source to its destination. This assumption, however is not required to prove the optimality of the computed solution, hence the algorithm remains correct for the general case.
Object categorization using Cartesian Genetic Programming (CGP) and CGP-Evolved Artificial Neural Network

In this paper, we address the problem of recognizing object categories by proposing a learning model based on evolutionary algorithm that takes unsegmented, complex images which is tolerant to 2D affine transformations such as scaling and translation in the image plane and 3D transformations of an object such as illumination changes and rotation in depth. To achieve this, first object features are extracted from an image using modified Bag of Keypoints model and then learning and classification is performed through evolutionary network classifiers i.e. Cartesian Genetic Programming (CGP) and Cartesian Genetic Programming Evolved Artificial Neural Network (CG-PANN). Our empirical evaluations show that proposed network classifiers exhibit outstanding ability of learning from fewer training examples with good accuracy. Results are compared with NEAT-Evolved Artificial Neural Network classifier which shows clearly that our network classifiers outperform and generalize better than NEAT.
Exploring the value of trust between teams of special education teachers and paraprofessionals

This phenomenological study explores the value of trust between teams of special education teachers and paraprofessionals. The study delves into their lived experiences, focusing on characteristics and behaviors that build, sustain, destroy and restore trust between them. There are multiple studies on trust in education, however, there is relatively little literature published on the value of trust among individuals committed to providing support for transition-aged students within various Los Angeles County school districts. Existing theories and models on trust have similar characteristics that span across diverse industries. As a result, clear-cut guidelines have enabled members of a team to be aware of how trust impacts their working environment. Purposive sampling provided teams of special education professionals who possessed a depth of knowledge of the subject matter and experience in the classroom. Individual face-to-face, semi-structured interviews were conducted with 12 participants focusing on how they make meaning of the role and value of trust with their special education colleagues. As a result, 165 coded passages were grouped into the following eight themes: (a) characteristics of a trustworthy colleague, (b) importance of trust, (c) outcome of trust, (d) outcome of a lack of trust, (e) building trust, (f) sustaining trust, (g) destroying trust, and (h) restoring trust. Two study conclusions emerged. Conclusion one, trust increases communication, respect and collaboration between special education colleagues, as well as enhances student success. Conclusion two, a lack of trust negatively impacts the special education environment, as well as relevant stakeholders, which include: students, parents, special education teachers, paraprofessionals and administrators. Recommendations include participation in team development trainings, as well as personal and professional development that focus on acquiring the characteristics of a
Privacy in the Information and Communications Technologies

Information and communications technologies (ICT) are fostering the appearance of a plethora of new services and applications. On the one hand, ICT will improve the efficiency of a variety of processes (e.g. supply chains, e-commerce, etc.) and they will make easy the development of new services. On the other hand, the massive deployment of these new technologies may lead to the invasion of users privacy. In this article, we analyse four of the main technologies which can put the privacy of their users in jeopardy: Internet browsing, location-based services, RFID technology and statistical databases.
Education and research: evidence of a dual life

To study the differences of the CS Education and Research communities we have studied the collaboration networks of 6 CS Education conferences and 7 CS Research conferences. Results show that both communities behave differently when collaborating to create technical papers. It could be said that the CS Education community has introversion traits: there is a higher tendency to only collaborate with nearby colleagues.
On Quasar Masses and Quasar Host Galaxies

The mass of massive black holes in quasar cores can be deduced by using the typical velocities of Hβ-emitting clouds in the broad-line region and by the size of this region. However, this estimate depends on various assumptions and is susceptible to large systematic errors. The Hβ-deduced black hole mass in a sample of 14 bright quasars is found here to correlate with the quasar host galaxy luminosity, as determined with the Hubble Space Telescope (HST). This correlation is similar to the black hole mass versus bulge luminosity correlation found by Magorrian et al. in a sample of 32 nearby normal galaxies. The similarity of the two correlations is remarkable since the two samples involve apparently different types of objects and since the black hole mass estimates in quasars and in nearby galaxies are based on very different methods. This similarity provides a "calibration" of the Hβ-deduced black hole mass estimate, suggesting that it is accurate to ±0.5 on a log scale. The similarity of the two correlations also suggests that quasars reside in otherwise normal galaxies and that the luminosity of quasar hosts can be estimated to ±0.5 mag based on the quasar continuum luminosity and the Hβ line width. Future imaging observations of additional broad-line active galaxies with the HST are required in order to explore the extent, slope, and scatter of the black hole mass versus host bulge luminosity correlation in active galaxies.